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| 59 |
|
| 60 | (define-module (gnu packages python-science)
|
| 61 | #:use-module ((guix licenses) #:prefix license:)
|
| 62 | #:use-module (gnu packages)
|
| 63 | #:use-module (gnu packages algebra)
|
| 64 | #:use-module (gnu packages base)
|
| 65 | #:use-module (gnu packages bioinformatics)
|
| 66 | #:use-module (gnu packages boost)
|
| 67 | #:use-module (gnu packages build-tools)
|
| 68 | #:use-module (gnu packages check)
|
| 69 | #:use-module (gnu packages chemistry)
|
| 70 | #:use-module (gnu packages cmake)
|
| 71 | #:use-module (gnu packages compression)
|
| 72 | #:use-module (gnu packages cpp)
|
| 73 | #:use-module (gnu packages cross-base)
|
| 74 | #:use-module (gnu packages crypto)
|
| 75 | #:use-module (gnu packages databases)
|
| 76 | #:use-module (gnu packages digest)
|
| 77 | #:use-module (gnu packages duckdb)
|
| 78 | #:use-module (gnu packages elf)
|
| 79 | #:use-module (gnu packages gcc)
|
| 80 | #:use-module (gnu packages geo)
|
| 81 | #:use-module (gnu packages gl)
|
| 82 | #:use-module (gnu packages graphviz)
|
| 83 | #:use-module (gnu packages image)
|
| 84 | #:use-module (gnu packages image-processing)
|
| 85 | #:use-module (gnu packages jemalloc)
|
| 86 | #:use-module (gnu packages jupyter)
|
| 87 | #:use-module (gnu packages machine-learning)
|
| 88 | #:use-module (gnu packages maths)
|
| 89 | #:use-module (gnu packages mpi)
|
| 90 | #:use-module (gnu packages networking)
|
| 91 | #:use-module (gnu packages nss)
|
| 92 | #:use-module (gnu packages pcre)
|
| 93 | #:use-module (gnu packages perl)
|
| 94 | #:use-module (gnu packages physics)
|
| 95 | #:use-module (gnu packages pkg-config)
|
| 96 | #:use-module (gnu packages python)
|
| 97 | #:use-module (gnu packages python-build)
|
| 98 | #:use-module (gnu packages python-check)
|
| 99 | #:use-module (gnu packages python-compression)
|
| 100 | #:use-module (gnu packages python-crypto)
|
| 101 | #:use-module (gnu packages python-graphics)
|
| 102 | #:use-module (gnu packages python-web)
|
| 103 | #:use-module (gnu packages python-xyz)
|
| 104 | #:use-module (gnu packages qt)
|
| 105 | #:use-module (gnu packages rust)
|
| 106 | #:use-module (gnu packages rust-apps)
|
| 107 | #:use-module (gnu packages serialization)
|
| 108 | #:use-module (gnu packages simulation)
|
| 109 | #:use-module (gnu packages sphinx)
|
| 110 | #:use-module (gnu packages ssh)
|
| 111 | #:use-module (gnu packages statistics)
|
| 112 | #:use-module (gnu packages tbb)
|
| 113 | #:use-module (gnu packages time)
|
| 114 | #:use-module (gnu packages tls)
|
| 115 | #:use-module (gnu packages version-control)
|
| 116 | #:use-module (gnu packages xdisorg)
|
| 117 | #:use-module (gnu packages xml)
|
| 118 | #:use-module (gnu packages xorg)
|
| 119 | #:use-module (guix packages)
|
| 120 | #:use-module (guix gexp)
|
| 121 | #:use-module (guix deprecation)
|
| 122 | #:use-module (guix download)
|
| 123 | #:use-module (guix git-download)
|
| 124 | #:use-module (guix utils)
|
| 125 | #:use-module (guix build-system cargo)
|
| 126 | #:use-module (guix build-system cmake)
|
| 127 | #:use-module (guix build-system meson)
|
| 128 | #:use-module (guix build-system pyproject))
|
| 129 |
|
| 130 | (define-public pyre
|
| 131 | (package
|
| 132 | (name "pyre")
|
| 133 | (version "1.12.5")
|
| 134 | (source
|
| 135 | (origin
|
| 136 | (method git-fetch)
|
| 137 | (uri (git-reference
|
| 138 | (url "https://github.com/pyre/pyre")
|
| 139 | (commit (string-append "v" version))))
|
| 140 | (file-name (git-file-name name version))
|
| 141 | (sha256
|
| 142 | (base32
|
| 143 | "0crmssga481q2ggwcmj40nj5n9975wri14p609jdr9hwg4vdyvj2"))))
|
| 144 | (build-system cmake-build-system)
|
| 145 | (arguments
|
| 146 | (list
|
| 147 | #:imported-modules (append %cmake-build-system-modules
|
| 148 | %pyproject-build-system-modules)
|
| 149 | #:modules '((guix build cmake-build-system)
|
| 150 | ((guix build pyproject-build-system) #:prefix py:)
|
| 151 | (guix build utils))
|
| 152 | #:configure-flags
|
| 153 | #~(list (string-append "-DPYRE_VERSION=" #$version)
|
| 154 | (string-append "-DPYRE_DEST_PACKAGES="
|
| 155 | (py:site-packages %build-inputs %outputs)))
|
| 156 | #:phases
|
| 157 | #~(modify-phases %standard-phases
|
| 158 | (add-after 'unpack 'enable-bytecode-determinism
|
| 159 | (assoc-ref py:%standard-phases 'enable-bytecode-determinism))
|
| 160 | |
| 161 | |
| 162 | (delete 'check)
|
| 163 | (add-after 'install 'add-to-pythonpath
|
| 164 | (lambda* (#:key inputs outputs #:allow-other-keys)
|
| 165 | (py:add-installed-pythonpath inputs outputs)))
|
| 166 | (add-after 'add-to-pythonpath 'wrap
|
| 167 | (assoc-ref py:%standard-phases 'wrap))
|
| 168 | (add-after 'add-to-pythonpath 'check
|
| 169 | (lambda* (#:key tests? parallel-tests? #:allow-other-keys)
|
| 170 | (when tests?
|
| 171 | (setenv "CTEST_OUTPUT_ON_FAILURE" "1")
|
| 172 | (let ((ignored-tests
|
| 173 | (list
|
| 174 | |
| 175 | |
| 176 | "tests.mpi"
|
| 177 | |
| 178 | |
| 179 | |
| 180 | "tests.pyre.lib.viz.flow"
|
| 181 | |
| 182 | "tests.pyre.pkg.ipc.tcp.py"
|
| 183 | |
| 184 | |
| 185 | "tests.postgres.ext"
|
| 186 | |
| 187 | |
| 188 | "tests.pyre.pkg.filesystem.zip_open.py"
|
| 189 | |
| 190 | "tests.pyre.pkg.filesystem.local_open.py")))
|
| 191 | (invoke "ctest"
|
| 192 | "-j" (if parallel-tests?
|
| 193 | (number->string (parallel-job-count))
|
| 194 | "1")
|
| 195 | "-E" (string-join ignored-tests "|")))))))))
|
| 196 | (native-inputs (list openssh-sans-x python python-numpy pybind11-2 zip))
|
| 197 | (inputs (list gsl hdf5 openmpi postgresql))
|
| 198 | (propagated-inputs (list python-pyyaml)) |
| 199 | (home-page "http://pyre.orthologue.com/")
|
| 200 | (synopsis "Framework for building Scientific applications")
|
| 201 | (description
|
| 202 | "This package provides a framework for building scientific applications.
|
| 203 | It aims to bring state of the art software design practices to scientific
|
| 204 | computing, with the goal of providing a strong skeleton on which to build
|
| 205 | scientific codes by steering the implementation towards usability and
|
| 206 | maintainability.")
|
| 207 | (license license:bsd-3)))
|
| 208 |
|
| 209 | (define-public python-adjusttext
|
| 210 | (package
|
| 211 | (name "python-adjusttext")
|
| 212 | (version "1.3.0")
|
| 213 | (source
|
| 214 | (origin
|
| 215 | (method url-fetch)
|
| 216 | (uri (pypi-uri "adjusttext" version))
|
| 217 | (sha256
|
| 218 | (base32 "18dw5kqxan4m8kvw3w1lm0p69gj95i7rcgmcfs485x1s8pa5rdsa"))))
|
| 219 | (build-system pyproject-build-system)
|
| 220 | (arguments
|
| 221 | (list #:tests? #false)) |
| 222 | (native-inputs
|
| 223 | (list python-setuptools
|
| 224 | python-wheel))
|
| 225 | (propagated-inputs
|
| 226 | (list python-matplotlib
|
| 227 | python-numpy
|
| 228 | python-scipy))
|
| 229 | (home-page "https://github.com/Phlya/adjustText")
|
| 230 | (synopsis "Adjust text position in matplotlib plots to minimize overlaps")
|
| 231 | (description
|
| 232 | "Often when we want to label multiple points on a graph the text will
|
| 233 | start heavily overlapping with both other labels and data points. This can be
|
| 234 | a major problem requiring manual solution. However this can be largely
|
| 235 | automated by smart placing of the labels (difficult) or iterative adjustment
|
| 236 | of their positions to minimize overlaps (relatively easy). This library
|
| 237 | implements the latter option to help with matplotlib graphs.")
|
| 238 | (license license:expat)))
|
| 239 |
|
| 240 | (define-public python-algopy
|
| 241 | (package
|
| 242 | (name "python-algopy")
|
| 243 | (version "0.7.2")
|
| 244 | (source
|
| 245 | (origin
|
| 246 | (method url-fetch)
|
| 247 | (uri (pypi-uri "algopy" version))
|
| 248 | (sha256
|
| 249 | (base32 "0l9d4pkbal6m6q8v6w5zr9wlij4sfycc8i2w7irk0i4n8hyvm0ja"))))
|
| 250 | (build-system pyproject-build-system)
|
| 251 | (native-inputs
|
| 252 | (list python-pytest
|
| 253 | python-setuptools))
|
| 254 | (propagated-inputs
|
| 255 | (list python-numpy
|
| 256 | python-scipy))
|
| 257 | (home-page "https://pythonhosted.org/algopy")
|
| 258 | (synopsis "Algorithmic Differentation in Python")
|
| 259 | (description
|
| 260 | "AlgoPy provides a functionality to differentiate functions implemented
|
| 261 | as computer programs by using Algorithmic Differentiation (AD) techniques in
|
| 262 | the forward and reverse mode.
|
| 263 |
|
| 264 | The forward mode propagates univariate Taylor polynomials of arbitrary order.
|
| 265 | Hence it is also possible to use AlgoPy to evaluate higher-order derivative
|
| 266 | tensors. The reverse mode is also known as backpropagation and can be found
|
| 267 | in similar form in tools like PyTorch. Speciality of AlgoPy is the
|
| 268 | possibility to differentiate functions that contain matrix functions as
|
| 269 | +,-,*,/, dot, solve, qr, eigh, cholesky.")
|
| 270 | (license license:bsd-3)))
|
| 271 |
|
| 272 | (define-public python-anndata
|
| 273 | (package
|
| 274 | (name "python-anndata")
|
| 275 | (version "0.12.7")
|
| 276 | (source
|
| 277 | (origin
|
| 278 | (method git-fetch)
|
| 279 | (uri (git-reference
|
| 280 | (url "https://github.com/theislab/anndata")
|
| 281 | (commit version)))
|
| 282 | (file-name (git-file-name name version))
|
| 283 | (sha256
|
| 284 | (base32 "1404x0z37z7xfdzkkafh62amchikrz0ssyc83rn6pv3dd4nn8nid"))))
|
| 285 | (build-system pyproject-build-system)
|
| 286 | (arguments
|
| 287 | (list
|
| 288 | |
| 289 | #:test-flags
|
| 290 | #~(list "--numprocesses" (number->string (min 8 (parallel-job-count)))
|
| 291 | |
| 292 | |
| 293 | "--ignore=tests/test_awkward.py"
|
| 294 | |
| 295 | |
| 296 | "--deselect=sts/test_views.py::test_view_of_view"
|
| 297 | #$@(map (lambda (test) (string-append "--deselect="
|
| 298 | "tests/"
|
| 299 | test))
|
| 300 | (list "test_concatenate.py::test_concatenate_layers"
|
| 301 | "test_concatenate.py::test_concat_different_types_dask"
|
| 302 | "test_concatenate.py::test_concat_on_var_outer_join"
|
| 303 | "test_concatenate.py::test_concatenate_layers_misaligned"
|
| 304 | "test_concatenate.py::test_concatenate_layers_outer"
|
| 305 | "test_concatenate.py::test_concatenate_roundtrip"
|
| 306 | "test_concatenate.py::test_error_on_mixed_device"
|
| 307 | "test_concatenate.py::test_nan_merge"
|
| 308 | "test_concatenate.py::test_pairwise_concat"
|
| 309 | "test_concatenate.py::test_transposed_concat"
|
| 310 | "test_dask.py::test_dask_to_disk_view"
|
| 311 | "test_dask.py::test_dask_to_memory_unbacked"
|
| 312 | "test_gpu.py::test_adata_raw_gpu"
|
| 313 | "test_gpu.py::test_gpu"
|
| 314 | "test_gpu.py::test_raw_gpu"
|
| 315 | "test_helpers.py::test_as_cupy_dask"
|
| 316 | "test_helpers.py::test_as_dask_functions"
|
| 317 | "test_io_elementwise.py::test_io_spec_cupy"
|
| 318 | "test_obsmvarm.py::test_1d_declaration"
|
| 319 | "test_obsmvarm.py::test_1d_set"
|
| 320 | "test_views.py::test_ellipsis_index"
|
| 321 | "test_views.py::test_modify_view_component"
|
| 322 | "test_views.py::test_set_scalar_subset_X"
|
| 323 | "test_views.py::test_view_different_type_indices"
|
| 324 | "test_views.py::test_view_of_view"))
|
| 325 | "-k" (string-join
|
| 326 | |
| 327 | |
| 328 | (list "not test_hints"
|
| 329 | |
| 330 | |
| 331 | "test_backed_modification_sparse[csc_matrix]"
|
| 332 | |
| 333 | |
| 334 | "test_old_format_warning_thrown")
|
| 335 | " and not "))
|
| 336 | #:phases
|
| 337 | #~(modify-phases %standard-phases
|
| 338 | |
| 339 | (add-after 'unpack 'disable-doctests
|
| 340 | (lambda _
|
| 341 | (substitute* "pyproject.toml"
|
| 342 | (("--doctest-modules") ""))))
|
| 343 | |
| 344 | (add-before 'check 'set-numba-cache-dir
|
| 345 | (lambda _
|
| 346 | (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
|
| 347 | (native-inputs
|
| 348 | (list hdf5 |
| 349 | python-awkward
|
| 350 | python-boltons
|
| 351 | python-dask
|
| 352 | python-distributed
|
| 353 | python-filelock
|
| 354 | python-hatch-vcs
|
| 355 | python-hatchling
|
| 356 | python-joblib
|
| 357 | python-loompy
|
| 358 | python-matplotlib
|
| 359 | python-openpyxl
|
| 360 | python-pyarrow
|
| 361 | python-pytest
|
| 362 | python-pytest-mock
|
| 363 | python-pytest-randomly
|
| 364 | python-pytest-xdist
|
| 365 | python-scikit-learn
|
| 366 | python-setuptools-scm))
|
| 367 | (propagated-inputs
|
| 368 | (list python-array-api-compat
|
| 369 | python-h5py
|
| 370 | python-legacy-api-wrap
|
| 371 | python-natsort
|
| 372 | python-numpy
|
| 373 | python-packaging
|
| 374 | python-pandas
|
| 375 | python-scipy
|
| 376 | python-zarr))
|
| 377 | (home-page "https://github.com/theislab/anndata")
|
| 378 | (synopsis "Annotated data for data analysis pipelines")
|
| 379 | (description "Anndata is a package for simple (functional) high-level APIs
|
| 380 | for data analysis pipelines. In this context, it provides an efficient,
|
| 381 | scalable way of keeping track of data together with learned annotations and
|
| 382 | reduces the code overhead typically encountered when using a mostly
|
| 383 | object-oriented library such as @code{scikit-learn}.")
|
| 384 | (license license:bsd-3)))
|
| 385 |
|
| 386 | |
| 387 | |
| 388 | (define-public python-anndata-minimal
|
| 389 | (package/inherit python-anndata
|
| 390 | (name "python-anndata-minimal")
|
| 391 | (arguments
|
| 392 | (substitute-keyword-arguments arguments
|
| 393 | ((#:tests? _ #t) #f)))
|
| 394 | (native-inputs
|
| 395 | (list python-hatch-vcs
|
| 396 | python-hatchling
|
| 397 | python-setuptools-scm))))
|
| 398 |
|
| 399 | |
| 400 | (define-public python-aplus
|
| 401 | |
| 402 | (let ((commit "1ab8ebec987fb7213766784aad02cbf4410d9036")
|
| 403 | (revision "0"))
|
| 404 | (package
|
| 405 | (name "python-aplus")
|
| 406 | (version (git-version "0.11.1" revision commit))
|
| 407 | (source
|
| 408 | (origin
|
| 409 | (method git-fetch)
|
| 410 | (uri (git-reference
|
| 411 | (url "https://github.com/xogeny/aplus")
|
| 412 | (commit commit)))
|
| 413 | (file-name (git-file-name name version))
|
| 414 | (sha256
|
| 415 | (base32 "02jcfj7dywvs0sd60c85pxwh0mwsj9p1q27445pba6j489x3dffj"))))
|
| 416 | (build-system pyproject-build-system)
|
| 417 | (arguments
|
| 418 | (list #:tests? #f)) |
| 419 | (native-inputs
|
| 420 | (list python-setuptools))
|
| 421 | (home-page "https://github.com/xogeny/aplus")
|
| 422 | (synopsis "Promises/A+ for Python")
|
| 423 | (description
|
| 424 | "This package is an implementation of the Promises/A+ specification and
|
| 425 | test suite in Python.")
|
| 426 | (license license:expat))))
|
| 427 |
|
| 428 | (define-public python-apted
|
| 429 | |
| 430 | (let ((commit "828b3e3f4c053f7d35f0b55b0d5597e8041719ac")
|
| 431 | (revision "0"))
|
| 432 | (package
|
| 433 | (name "python-apted")
|
| 434 | (version (git-version "1.0.3" revision commit))
|
| 435 | (source
|
| 436 | (origin
|
| 437 | (method git-fetch)
|
| 438 | (uri (git-reference
|
| 439 | (url "https://github.com/JoaoFelipe/apted")
|
| 440 | (commit commit)))
|
| 441 | (file-name (git-file-name name version))
|
| 442 | (sha256
|
| 443 | (base32 "1vw1sbn41cysmhr4ib58cw3hzs1xjxwb1d8r1yhrqgjk5q6ckjw7"))))
|
| 444 | (build-system pyproject-build-system)
|
| 445 | (arguments
|
| 446 | (list
|
| 447 | #:test-flags
|
| 448 | #~(list "--deselect=apted/tests/test_chained.py::test_factory"
|
| 449 | "--deselect=apted/tests/test_correctness.py::test_factory"
|
| 450 | "--deselect=apted/tests/test_per_edit_operation_correctness.py::test_factory")))
|
| 451 | (native-inputs
|
| 452 | (list python-pytest
|
| 453 | python-setuptools
|
| 454 | python-wheel))
|
| 455 | (home-page "https://github.com/JoaoFelipe/apted")
|
| 456 | (synopsis "Algorithm for the tree edit distance")
|
| 457 | (description
|
| 458 | "This is a Python implementation of the APTED algorithm,which
|
| 459 | supersedes the RTED algorithm for computing the tree edit distance.")
|
| 460 | (license license:expat))))
|
| 461 |
|
| 462 | (define-public python-asap3
|
| 463 | (package
|
| 464 | (name "python-asap3")
|
| 465 | (version "3.13.10")
|
| 466 | (source
|
| 467 | (origin
|
| 468 | (method url-fetch)
|
| 469 | (uri (pypi-uri "asap3" version))
|
| 470 | (sha256
|
| 471 | (base32 "1qpy9nnwv692hd3cg70n2zwjank25mlsfvvirklijwis3m4lfqg4"))))
|
| 472 | (build-system pyproject-build-system)
|
| 473 | (native-inputs
|
| 474 | (list python-pytest
|
| 475 | python-setuptools
|
| 476 | which)) |
| 477 | (propagated-inputs
|
| 478 | (list python-ase
|
| 479 | python-numpy))
|
| 480 | (home-page "https://wiki.fysik.dtu.dk/asap")
|
| 481 | (synopsis "ASAP - classical potentials for Molecular Dynamics with ASE.")
|
| 482 | (description "This package provides accelerated simulations and potentials
|
| 483 | of solids.")
|
| 484 | (license license:lgpl3)))
|
| 485 |
|
| 486 | (define-public python-ase
|
| 487 | (package
|
| 488 | (name "python-ase")
|
| 489 | (version "3.26.0")
|
| 490 | (source
|
| 491 | (origin
|
| 492 | (method url-fetch)
|
| 493 | (uri (pypi-uri "ase" version))
|
| 494 | (sha256
|
| 495 | (base32 "0xahqqyxkxrjh1g23icydngrvc8iv3lnd4iys9i802jvfxas6wd0"))))
|
| 496 | (build-system pyproject-build-system)
|
| 497 | (arguments
|
| 498 | (list
|
| 499 | |
| 500 | #:test-flags
|
| 501 | #~(list "--numprocesses" (number->string (min 8 (parallel-job-count)))
|
| 502 | |
| 503 | "--deselect"
|
| 504 | "ase/test/fio/test_espresso.py::test_pw_input_write_nested_flat"
|
| 505 | |
| 506 | "--deselect"
|
| 507 | "ase/test/fio/test_espresso.py::TestConstraints::test_fix_scaled")))
|
| 508 | (native-inputs
|
| 509 | (list python-pytest
|
| 510 | python-pytest-xdist
|
| 511 | python-setuptools))
|
| 512 | (inputs (list spglib))
|
| 513 | (propagated-inputs
|
| 514 | (list python-matplotlib
|
| 515 | python-numpy
|
| 516 | python-scipy))
|
| 517 | (home-page "https://wiki.fysik.dtu.dk/ase/")
|
| 518 | (synopsis "Atomic Simulation Environment")
|
| 519 | (description "This package provides a set of tools and Python modules for
|
| 520 | setting up, manipulating, running, visualizing and analyzing atomistic
|
| 521 | simulations.")
|
| 522 | (license license:lgpl2.1+)))
|
| 523 |
|
| 524 | (define-public python-autoray
|
| 525 | (package
|
| 526 | (name "python-autoray")
|
| 527 | (version "0.8.10")
|
| 528 | (source
|
| 529 | (origin
|
| 530 | (method git-fetch)
|
| 531 | (uri (git-reference
|
| 532 | (url "https://github.com/jcmgray/autoray")
|
| 533 | (commit (string-append "v" version))))
|
| 534 | (file-name (git-file-name name version))
|
| 535 | (sha256
|
| 536 | (base32 "1gqfkpdng09l804xm9r1r098w10gr1bc5ax2xmhrpz9niybv71f5"))))
|
| 537 | (build-system pyproject-build-system)
|
| 538 | |
| 539 | (native-inputs
|
| 540 | (list python-hatch-vcs
|
| 541 | python-hatchling
|
| 542 | python-pytest))
|
| 543 | (propagated-inputs
|
| 544 | (list python-dask
|
| 545 | python-matplotlib
|
| 546 | python-networkx
|
| 547 | python-numpy
|
| 548 | python-opt-einsum
|
| 549 | python-scipy
|
| 550 | python-sparse))
|
| 551 | (home-page "https://github.com/jcmgray/autoray")
|
| 552 | (synopsis "Library for abstracting tensor operations")
|
| 553 | (description
|
| 554 | "This package provides a lightweight Python library for
|
| 555 | abstracting tensor operations. It provides an automatic dispatch mechanism
|
| 556 | that means you can write backend agnostic code that works for any library
|
| 557 | that provides a @code{numpy} compatible API.")
|
| 558 | (license license:asl2.0)))
|
| 559 |
|
| 560 | (define-public python-baycomp
|
| 561 | (package
|
| 562 | (name "python-baycomp")
|
| 563 | (version "1.0.3")
|
| 564 | (source
|
| 565 | (origin
|
| 566 | (method url-fetch)
|
| 567 | (uri (pypi-uri "baycomp" version))
|
| 568 | (sha256
|
| 569 | (base32 "1v6s4mfr6xzjbv9a2v89hywm6fbv5nii0qczvcfjanvdn7bmmcij"))))
|
| 570 | (build-system pyproject-build-system)
|
| 571 | (native-inputs
|
| 572 | (list python-pytest python-setuptools python-wheel))
|
| 573 | (propagated-inputs
|
| 574 | (list python-matplotlib python-numpy python-scipy))
|
| 575 | (home-page "https://github.com/janezd/baycomp")
|
| 576 | (synopsis "Library for comparison of Bayesian classifiers")
|
| 577 | (description
|
| 578 | "Baycomp is a library for Bayesian comparison of classifiers. Functions
|
| 579 | in the library compare two classifiers on one or on multiple data sets. They
|
| 580 | compute three probabilities: the probability that the first classifier has
|
| 581 | higher scores than the second, the probability that differences are within the
|
| 582 | region of practical equivalence (rope), or that the second classifier has
|
| 583 | higher scores.")
|
| 584 | (license license:expat)))
|
| 585 |
|
| 586 | (define-public python-boost-histogram
|
| 587 | (package
|
| 588 | (name "python-boost-histogram")
|
| 589 | (version "1.7.1")
|
| 590 | (source
|
| 591 | (origin
|
| 592 | (method url-fetch)
|
| 593 | (uri (pypi-uri "boost_histogram" version))
|
| 594 | (sha256
|
| 595 | (base32 "06av8lxvvfafn4xbqakx2fbdcq0djbs7w6j4vn4ji8wgd39dglvf"))))
|
| 596 | (build-system pyproject-build-system)
|
| 597 | |
| 598 | |
| 599 | (propagated-inputs (list python-numpy))
|
| 600 | (native-inputs (list cmake-minimal
|
| 601 | pybind11-2
|
| 602 | python-pytest
|
| 603 | python-pytest-benchmark
|
| 604 | python-scikit-build-core
|
| 605 | python-setuptools-scm))
|
| 606 | (home-page "https://boost-histogram.readthedocs.io/en/latest/")
|
| 607 | (synopsis "Python bindings for the Boost::Histogram library")
|
| 608 | (description
|
| 609 | "This package provides Python bindings for the Boost::Histogram library,
|
| 610 | one of the fastest libraries for histogramming.")
|
| 611 | (license license:bsd-3)))
|
| 612 |
|
| 613 | (define-public python-bottleneck
|
| 614 | (package
|
| 615 | (name "python-bottleneck")
|
| 616 | (version "1.4.2")
|
| 617 | (source
|
| 618 | (origin
|
| 619 | (method url-fetch)
|
| 620 | (uri (pypi-uri "bottleneck" version))
|
| 621 | (sha256
|
| 622 | (base32 "1x29yj4yr12v646si63gkxj9b6lx1xk65536wqy4i9fyk4bqx3ps"))))
|
| 623 | (build-system pyproject-build-system)
|
| 624 | (arguments
|
| 625 | (list
|
| 626 | #:phases
|
| 627 | #~(modify-phases %standard-phases
|
| 628 | (add-before 'check 'rebuild-ext
|
| 629 | (lambda _
|
| 630 | (invoke "python" "setup.py" "build_ext" "--inplace"))))))
|
| 631 | (native-inputs (list python-pytest
|
| 632 | python-setuptools
|
| 633 | python-wheel))
|
| 634 | (propagated-inputs (list python-numpy))
|
| 635 | (home-page "https://github.com/pydata/bottleneck")
|
| 636 | (synopsis "Fast NumPy array functions written in C")
|
| 637 | (description
|
| 638 | "Bottleneck is a collection of fast, NaN-aware NumPy array functions
|
| 639 | written in C.")
|
| 640 | (license license:bsd-2)))
|
| 641 |
|
| 642 | (define-public python-clarabel
|
| 643 | (package
|
| 644 | (name "python-clarabel")
|
| 645 | (version "0.7.1")
|
| 646 | (source
|
| 647 | (origin
|
| 648 | (method url-fetch)
|
| 649 | (uri (pypi-uri "clarabel" version))
|
| 650 | (sha256
|
| 651 | (base32 "15k32ynvh45n9q905bxwamh5w5cia9bxzmwz69wbribmyhsv22m3"))
|
| 652 | (patches
|
| 653 | (search-patches "python-clarabel-blas.patch"))))
|
| 654 | (build-system cargo-build-system)
|
| 655 | (arguments
|
| 656 | (list
|
| 657 | #:imported-modules `(,@%cargo-build-system-modules
|
| 658 | ,@%pyproject-build-system-modules)
|
| 659 | #:modules '((guix build cargo-build-system)
|
| 660 | ((guix build pyproject-build-system) #:prefix py:)
|
| 661 | (guix build utils))
|
| 662 | #:phases
|
| 663 | #~(modify-phases %standard-phases
|
| 664 | (add-after 'build 'build-python-module
|
| 665 | (assoc-ref py:%standard-phases 'build))
|
| 666 | (add-after 'build-python-module 'install-python-module
|
| 667 | (assoc-ref py:%standard-phases 'install)))
|
| 668 | #:features '(list "python")
|
| 669 | #:install-source? #false))
|
| 670 | (inputs
|
| 671 | (cons maturin (cargo-inputs 'python-clarabel)))
|
| 672 | (native-inputs
|
| 673 | (list python-wrapper))
|
| 674 | (propagated-inputs (list python-numpy python-scipy))
|
| 675 | (home-page "https://github.com/oxfordcontrol/Clarabel.rs")
|
| 676 | (synopsis "Interior-point solver for convex conic optimisation problems")
|
| 677 | (description "Clarabel.rs is a Rust implementation of an interior point
|
| 678 | numerical solver for convex optimization problems using a novel homogeneous
|
| 679 | embedding.")
|
| 680 | (license license:asl2.0)))
|
| 681 |
|
| 682 | (define-public python-cmasher
|
| 683 | (package
|
| 684 | (name "python-cmasher")
|
| 685 | (version "1.9.2")
|
| 686 | (source
|
| 687 | (origin
|
| 688 | (method url-fetch)
|
| 689 | (uri (pypi-uri "cmasher" version))
|
| 690 | (sha256
|
| 691 | (base32 "1xbzyla0l5i5vv86q4vwv33qmqzfzhhj6zry1lhy6ikir37c543c"))))
|
| 692 | (build-system pyproject-build-system)
|
| 693 | |
| 694 | (native-inputs
|
| 695 | (list python-pytest
|
| 696 | python-hatchling))
|
| 697 | (propagated-inputs
|
| 698 | (list python-colorspacious
|
| 699 | python-matplotlib
|
| 700 | python-numpy))
|
| 701 | (home-page "https://cmasher.readthedocs.io")
|
| 702 | (synopsis "Scientific colormaps utilities")
|
| 703 | (description
|
| 704 | "The CMasher package provides a collection of scientific colormaps and utility
|
| 705 | functions to be used by different Python packages and projects, mainly in
|
| 706 | combination with Matplotlib. It offers several alternatives to commonly used
|
| 707 | colormaps, like chroma and rainforest for jet; sunburst for hot; neutral for
|
| 708 | binary; and fusion and redshift for coolwarm.")
|
| 709 | (license license:bsd-3)))
|
| 710 |
|
| 711 | (define-public python-cmcrameri
|
| 712 | (package
|
| 713 | (name "python-cmcrameri")
|
| 714 | (version "1.9")
|
| 715 | (source
|
| 716 | (origin
|
| 717 | (method git-fetch)
|
| 718 | (uri (git-reference
|
| 719 | (url "https://github.com/callumrollo/cmcrameri")
|
| 720 | (commit (string-append "v" version))))
|
| 721 | (file-name (git-file-name name version))
|
| 722 | (sha256
|
| 723 | (base32 "0wvqld65c1p3iqxmidfsavpp1nkjc1f4z6riqv0lmafpxrz2snbi"))))
|
| 724 | (build-system pyproject-build-system)
|
| 725 | (propagated-inputs (list python-matplotlib python-numpy python-packaging))
|
| 726 | (native-inputs (list python-pytest python-setuptools python-setuptools-scm))
|
| 727 | (home-page "https://github.com/callumrollo/cmcrameri")
|
| 728 | (synopsis "Perceptually uniform colormaps by Fabio Crameri")
|
| 729 | (description "This package provides a Python wrapper around Fabio
|
| 730 | Crameri's perceptually uniform colormaps for scientific data visualization.")
|
| 731 | (license license:expat)))
|
| 732 |
|
| 733 | (define-public python-cmocean
|
| 734 | (package
|
| 735 | (name "python-cmocean")
|
| 736 | (version "4.0.3")
|
| 737 | (source
|
| 738 | (origin
|
| 739 | (method url-fetch)
|
| 740 | (uri (pypi-uri "cmocean" version))
|
| 741 | (sha256
|
| 742 | (base32 "0z0d4ma6i228gwpgnkai8scs9bmzz41rirlnqpmb8hazzfcq71ip"))))
|
| 743 | (build-system pyproject-build-system)
|
| 744 | (native-inputs
|
| 745 | (list python-pytest
|
| 746 | python-setuptools
|
| 747 | python-wheel))
|
| 748 | (propagated-inputs
|
| 749 | (list python-matplotlib
|
| 750 | python-numpy
|
| 751 | python-packaging))
|
| 752 | (home-page "https://github.com/matplotlib/cmocean")
|
| 753 | (synopsis "Colormaps for Oceanography")
|
| 754 | (description
|
| 755 | "This package contains colormaps for commonly-used oceanographic
|
| 756 | variables. Most of the colormaps started from @code{matplotlib} colormaps,
|
| 757 | but have now been adjusted using the viscm tool to be perceptually uniform.")
|
| 758 | (license license:expat)))
|
| 759 |
|
| 760 | (define-public python-corner
|
| 761 | (package
|
| 762 | (name "python-corner")
|
| 763 | (version "2.2.2")
|
| 764 | (source
|
| 765 | (origin
|
| 766 | (method git-fetch) |
| 767 | (uri (git-reference
|
| 768 | (url "https://github.com/dfm/corner.py")
|
| 769 | (commit (string-append "v" version))))
|
| 770 | (file-name (git-file-name name version))
|
| 771 | (sha256
|
| 772 | (base32 "1i4dk4jxh0saysya2cnsfwlxwpldbdl174i9pwi4qj82av9jr2ii"))))
|
| 773 | (build-system pyproject-build-system)
|
| 774 | (arguments
|
| 775 | (list
|
| 776 | #:test-flags
|
| 777 | #~(list
|
| 778 | |
| 779 | "-k" (string-append "not test_labels[png]"
|
| 780 | " and not test_title_quantiles[png]"
|
| 781 | " and not test_title_quantiles_default[png]"
|
| 782 | " and not test_title_quantiles_raises[png]"
|
| 783 | " and not test_bins[png]"
|
| 784 | " and not test_bins_log[png]"
|
| 785 | " and not test_titles1[png]"
|
| 786 | " and not test_titles2[png]"
|
| 787 | " and not test_pandas[png]"
|
| 788 | " and not test_tight[png]"
|
| 789 | " and not test_extended_overplotting[png]"
|
| 790 | " and not test_reverse_overplotting[png]"
|
| 791 | " and not test_arviz[png]"
|
| 792 | " and not test_range_fig_arg[png]"))))
|
| 793 | (propagated-inputs
|
| 794 | (list python-matplotlib))
|
| 795 | (native-inputs
|
| 796 | (list python-arviz python-pytest python-scipy python-setuptools-scm))
|
| 797 | (home-page "http://corner.readthedocs.io/")
|
| 798 | (synopsis "Make some beautiful corner plots")
|
| 799 | (description
|
| 800 | "This Python module uses @code{matplotlib} to visualize multidimensional
|
| 801 | samples using a scatterplot matrix. In these visualizations, each one- and
|
| 802 | two-dimensional projection of the sample is plotted to reveal covariances.
|
| 803 | corner was originally conceived to display the results of Markov Chain Monte
|
| 804 | Carlo simulations and the defaults are chosen with this application in mind but
|
| 805 | it can be used for displaying many qualitatively different samples.")
|
| 806 | (license license:bsd-2)))
|
| 807 |
|
| 808 | (define-public python-cotengra
|
| 809 | (package
|
| 810 | (name "python-cotengra")
|
| 811 | (version "0.8.0")
|
| 812 | (source
|
| 813 | (origin
|
| 814 | (method git-fetch)
|
| 815 | (uri (git-reference
|
| 816 | (url "https://github.com/jcmgray/cotengra")
|
| 817 | (commit (string-append "v" version))))
|
| 818 | (file-name (git-file-name name version))
|
| 819 | (sha256
|
| 820 | (base32 "000z233s6nr2qmpjyn4sl1gym8a980xh2vf1jkvfjxfnrv40zl73"))))
|
| 821 | (build-system pyproject-build-system)
|
| 822 | (native-inputs
|
| 823 | (list python-hatch-vcs
|
| 824 | python-hatchling
|
| 825 | python-pytest))
|
| 826 | (propagated-inputs
|
| 827 | (list python-autoray
|
| 828 | python-matplotlib
|
| 829 | python-seaborn))
|
| 830 | (home-page "https://cotengra.readthedocs.io")
|
| 831 | (synopsis
|
| 832 | "Hyper optimized contraction trees")
|
| 833 | (description
|
| 834 | "This library allows for contracting tensor networks or einsum expressions
|
| 835 | involving large numbers of tensors. It includes drop-in replacements for
|
| 836 | @code{einsum} and @code{ncon}, an explicit contraction tree object, a hyper
|
| 837 | optimizer that samples trees while tuning the generating meta-parameters,
|
| 838 | dynamic slicing for massive memory savings and parallelism, simulated annealing
|
| 839 | as an alternative strategy for optimizing and slicing, and integrations with
|
| 840 | other libraries such as @code{numpy}, @code{opt_einsum}, @code{quimb}, and
|
| 841 | others.")
|
| 842 | (license license:asl2.0)))
|
| 843 |
|
| 844 | (define-public python-cvxpy
|
| 845 | (package
|
| 846 | (name "python-cvxpy")
|
| 847 | (version "1.7.5")
|
| 848 | (source
|
| 849 | (origin
|
| 850 | (method url-fetch)
|
| 851 | (uri (pypi-uri "cvxpy" version))
|
| 852 | (sha256
|
| 853 | (base32 "0p9zp2ci1zw56hy2q0w18s3kb1h3j0j4m4gw2sg6a9qw00c24lab"))))
|
| 854 | (build-system pyproject-build-system)
|
| 855 | (arguments
|
| 856 | (list
|
| 857 | |
| 858 | #:test-flags
|
| 859 | #~(list #$@(map (lambda (test) (string-append "--deselect="
|
| 860 | "cvxpy/tests/"
|
| 861 | "test_cone2cone.py::"
|
| 862 | test))
|
| 863 | |
| 864 | |
| 865 | |
| 866 | |
| 867 | (list "TestSlacks::test_mi_socp_2"
|
| 868 | |
| 869 | |
| 870 | |
| 871 | "TestOpRelConeQuad::test_oprelcone_1_m1_k3_complex"
|
| 872 | "TestOpRelConeQuad::test_oprelcone_1_m3_k1_complex"
|
| 873 | |
| 874 | |
| 875 | |
| 876 | "TestOpRelConeQuad::test_oprelcone_2")))
|
| 877 | #:phases
|
| 878 | #~(modify-phases %standard-phases
|
| 879 | (add-before 'check 'set-ci-environment
|
| 880 | (lambda _
|
| 881 | |
| 882 | |
| 883 | (setenv "CI" "1"))))))
|
| 884 | (native-inputs
|
| 885 | (list pybind11-2
|
| 886 | python-pytest
|
| 887 | python-setuptools))
|
| 888 | (propagated-inputs
|
| 889 | (list python-clarabel
|
| 890 | python-numpy
|
| 891 | python-osqp
|
| 892 | python-scipy
|
| 893 | python-scs
|
| 894 | |
| 895 | |
| 896 | python-cvxopt
|
| 897 | |
| 898 | |
| 899 | |
| 900 | python-ecos
|
| 901 | |
| 902 | |
| 903 | |
| 904 | |
| 905 | |
| 906 | |
| 907 | |
| 908 | |
| 909 | |
| 910 | #;python-xpress))
|
| 911 | (home-page "https://github.com/cvxpy/cvxpy")
|
| 912 | (synopsis "DSL for modeling convex optimization problems")
|
| 913 | (description
|
| 914 | "This package provides a domain-specific language for modeling convex
|
| 915 | optimization problems in Python.")
|
| 916 | (license license:asl2.0)))
|
| 917 |
|
| 918 | |
| 919 | (define-public python-dask
|
| 920 | (package
|
| 921 | (name "python-dask")
|
| 922 | (version "2025.11.0")
|
| 923 | (source
|
| 924 | (origin
|
| 925 | (method git-fetch)
|
| 926 | (uri (git-reference
|
| 927 | (url "https://github.com/dask/dask/")
|
| 928 | (commit version)))
|
| 929 | (file-name (git-file-name name version))
|
| 930 | (sha256
|
| 931 | (base32 "12m4p4zfm96fjsm45wppdrylsi71vjr0ywplz6q7fhw9vbhk0kki"))))
|
| 932 | (build-system pyproject-build-system)
|
| 933 | (arguments
|
| 934 | (list
|
| 935 | |
| 936 | #:test-flags
|
| 937 | #~(list "-m" "not gpu and not slow and not network"
|
| 938 | "--pyargs" "dask"
|
| 939 | "--numprocesses" (number->string (min 4 (parallel-job-count)))
|
| 940 | "--reruns=3"
|
| 941 | "-k" (string-join
|
| 942 | |
| 943 | (list "not test_interrupt"
|
| 944 | |
| 945 | |
| 946 | "test_blockwise"
|
| 947 | "test_is_dask_collection_doesnt_materialize")
|
| 948 | " and not "))
|
| 949 | #:phases
|
| 950 | #~(modify-phases %standard-phases
|
| 951 | (add-before 'check 'remove-local-source
|
| 952 | (lambda _
|
| 953 | (delete-file-recursively "dask"))))))
|
| 954 | (native-inputs
|
| 955 | (list python-pytest
|
| 956 | python-pytest-asyncio
|
| 957 | python-pytest-mock
|
| 958 | python-pytest-rerunfailures
|
| 959 | python-pytest-timeout
|
| 960 | python-pytest-xdist
|
| 961 | python-setuptools
|
| 962 | python-setuptools-scm-next
|
| 963 | tzdata-for-tests))
|
| 964 | (propagated-inputs
|
| 965 | (list python-click
|
| 966 | python-cloudpickle
|
| 967 | python-fsspec
|
| 968 | python-importlib-metadata
|
| 969 | python-packaging
|
| 970 | python-partd
|
| 971 | python-pyyaml
|
| 972 | python-toolz
|
| 973 | |
| 974 | python-lz4
|
| 975 | python-numpy
|
| 976 | python-pandas
|
| 977 | python-pyarrow))
|
| 978 | (home-page "https://github.com/dask/dask/")
|
| 979 | (synopsis "Parallel computing with task scheduling")
|
| 980 | (description
|
| 981 | "Dask is a flexible parallel computing library for analytics. It
|
| 982 | consists of two components: dynamic task scheduling optimized for computation,
|
| 983 | and large data collections like parallel arrays, dataframes, and lists that
|
| 984 | extend common interfaces like NumPy, Pandas, or Python iterators to
|
| 985 | larger-than-memory or distributed environments. These parallel collections
|
| 986 | run on top of the dynamic task schedulers.")
|
| 987 | (license license:bsd-3)))
|
| 988 |
|
| 989 | (define-public python-dask-image
|
| 990 | (package
|
| 991 | (name "python-dask-image")
|
| 992 | (version "2025.11.0")
|
| 993 | (source
|
| 994 | (origin
|
| 995 | (method url-fetch)
|
| 996 | (uri (pypi-uri "dask_image" version))
|
| 997 | (sha256
|
| 998 | (base32 "1cx07dh09yqq6swyziiy9mb2f27ywja18gylfly1874a7af1mks5"))))
|
| 999 | (build-system pyproject-build-system)
|
| 1000 | (arguments
|
| 1001 | (list
|
| 1002 | |
| 1003 | #:phases
|
| 1004 | #~(modify-phases %standard-phases
|
| 1005 | (add-after 'unpack 'fix-pytest-config
|
| 1006 | (lambda _
|
| 1007 | (substitute* "pyproject.toml"
|
| 1008 | (("--flake8") "")))))))
|
| 1009 | (native-inputs
|
| 1010 | (list python-pytest
|
| 1011 | python-pytest-timeout
|
| 1012 | python-setuptools
|
| 1013 | python-setuptools-scm-next))
|
| 1014 | (propagated-inputs
|
| 1015 | (list python-dask
|
| 1016 | python-numpy
|
| 1017 | python-pandas
|
| 1018 | python-pims
|
| 1019 | python-scipy
|
| 1020 | python-tifffile))
|
| 1021 | (home-page "https://github.com/dask/dask-image")
|
| 1022 | (synopsis "Distributed image processing")
|
| 1023 | (description "This is a package for image processing with Dask arrays.
|
| 1024 | Features:
|
| 1025 |
|
| 1026 | @itemize
|
| 1027 | @item Provides support for loading image files.
|
| 1028 | @item Implements commonly used N-D filters.
|
| 1029 | @item Includes a few N-D Fourier filters.
|
| 1030 | @item Provides some functions for working with N-D label images.
|
| 1031 | @item Supports a few N-D morphological operators.
|
| 1032 | @end itemize")
|
| 1033 | (license license:bsd-3)))
|
| 1034 |
|
| 1035 | |
| 1036 | |
| 1037 | |
| 1038 | (define-public python-dask-minimal
|
| 1039 | (package/inherit python-dask
|
| 1040 | (name "python-dask-minimal")
|
| 1041 | (arguments
|
| 1042 | (substitute-keyword-arguments arguments
|
| 1043 | ((#:tests? _ #t) #f)))
|
| 1044 | (native-inputs
|
| 1045 | (list python-setuptools
|
| 1046 | python-setuptools-scm-next))
|
| 1047 | (propagated-inputs
|
| 1048 | (list python-click
|
| 1049 | python-cloudpickle
|
| 1050 | python-fsspec
|
| 1051 | python-packaging
|
| 1052 | python-partd
|
| 1053 | python-pyyaml
|
| 1054 | python-toolz))))
|
| 1055 |
|
| 1056 | (define-public python-decaylanguage
|
| 1057 | (package
|
| 1058 | (name "python-decaylanguage")
|
| 1059 | (version "0.20.2")
|
| 1060 | (source
|
| 1061 | (origin
|
| 1062 | (method url-fetch)
|
| 1063 | (uri (pypi-uri "decaylanguage" version))
|
| 1064 | (sha256
|
| 1065 | (base32 "1l867w7srvx0hwfys56469lzdkcs2awbwjpj573bjqv2ngdycmwb"))))
|
| 1066 | (build-system pyproject-build-system)
|
| 1067 | (arguments
|
| 1068 | (list
|
| 1069 | |
| 1070 | |
| 1071 | #:test-flags #~(list "--ignore" "tests/test_convert.py")))
|
| 1072 | (propagated-inputs (list python-attrs
|
| 1073 | python-graphviz
|
| 1074 | python-hepunits
|
| 1075 | python-lark
|
| 1076 | python-numpy
|
| 1077 | python-pandas
|
| 1078 | python-particle
|
| 1079 | python-plumbum))
|
| 1080 | (native-inputs (list python-hatch-vcs
|
| 1081 | python-hatchling
|
| 1082 | python-pytest))
|
| 1083 | (home-page "https://decaylanguage.readthedocs.io/en/latest/")
|
| 1084 | (synopsis "Language to describe, manipulate and convert particle decays")
|
| 1085 | (description "DecayLanguage implements a language to describe and convert
|
| 1086 | particle decays between digital representations, effectively making it
|
| 1087 | possible to interoperate several fitting programs. Particular interest is
|
| 1088 | given to programs dedicated to amplitude analyses.")
|
| 1089 | (license license:bsd-3)))
|
| 1090 |
|
| 1091 | (define-public python-distributed
|
| 1092 | (package
|
| 1093 | (name "python-distributed")
|
| 1094 | (version "2025.11.0")
|
| 1095 | (source
|
| 1096 | (origin
|
| 1097 | (method git-fetch)
|
| 1098 | (uri (git-reference
|
| 1099 | (url "https://github.com/dask/distributed")
|
| 1100 | (commit version)))
|
| 1101 | (file-name (git-file-name name version))
|
| 1102 | (sha256
|
| 1103 | (base32 "1ljzgbbs61si8b3qvxf7fb74wdhnj2mfg9a5nfngqv662fnibabg"))))
|
| 1104 | (build-system pyproject-build-system)
|
| 1105 | (arguments
|
| 1106 | (list
|
| 1107 | |
| 1108 | |
| 1109 | |
| 1110 | #:tests? #f))
|
| 1111 | (native-inputs
|
| 1112 | (list python-setuptools
|
| 1113 | python-setuptools-scm-next))
|
| 1114 | (propagated-inputs
|
| 1115 | (list python-click
|
| 1116 | python-cloudpickle
|
| 1117 | python-dask
|
| 1118 | python-jinja2
|
| 1119 | python-locket
|
| 1120 | python-msgpack
|
| 1121 | python-packaging
|
| 1122 | python-psutil
|
| 1123 | python-pyyaml
|
| 1124 | python-sortedcontainers
|
| 1125 | python-tblib
|
| 1126 | python-toolz
|
| 1127 | python-tornado
|
| 1128 | python-urllib3
|
| 1129 | python-zict))
|
| 1130 | (home-page "https://distributed.dask.org")
|
| 1131 | (synopsis "Distributed scheduler for Dask")
|
| 1132 | (description "Dask.distributed is a lightweight library for distributed
|
| 1133 | computing in Python. It extends both the @code{concurrent.futures} and
|
| 1134 | @code{dask} APIs to moderate sized clusters.")
|
| 1135 | (license license:bsd-3)))
|
| 1136 |
|
| 1137 | (define-public python-dvc-data
|
| 1138 | (package
|
| 1139 | (name "python-dvc-data")
|
| 1140 | (version "3.16.12")
|
| 1141 | (home-page "https://github.com/iterative/dvc-data")
|
| 1142 | (source (origin
|
| 1143 | (method url-fetch)
|
| 1144 | (uri (pypi-uri "dvc_data" version))
|
| 1145 | (sha256
|
| 1146 | (base32
|
| 1147 | "156iwdn7v5jhwbpwz92n28qiasgcbmcqv9vxg8xbvdfxzlzw0b7r"))))
|
| 1148 | (build-system pyproject-build-system)
|
| 1149 | (propagated-inputs
|
| 1150 | (list python-attrs
|
| 1151 | python-dictdiffer
|
| 1152 | python-diskcache
|
| 1153 | python-dvc-objects
|
| 1154 | python-fsspec
|
| 1155 | python-funcy-1.14
|
| 1156 | python-orjson
|
| 1157 | python-pygtrie
|
| 1158 | python-sqltrie
|
| 1159 | python-tqdm))
|
| 1160 | (native-inputs
|
| 1161 | (list python-click
|
| 1162 | python-pytest
|
| 1163 | python-pytest-benchmark
|
| 1164 | python-pytest-mock
|
| 1165 | |
| 1166 | python-setuptools
|
| 1167 | python-setuptools-scm
|
| 1168 | python-typer
|
| 1169 | python-wheel))
|
| 1170 | (arguments
|
| 1171 | (list
|
| 1172 | #:test-flags
|
| 1173 | |
| 1174 | #~(list "--ignore=tests/hashfile/test_db.py"
|
| 1175 | "--ignore=tests/hashfile/test_db_index.py"
|
| 1176 | "--ignore=tests/hashfile/test_obj.py"
|
| 1177 | "--ignore=tests/index/test_build.py"
|
| 1178 | "--ignore=tests/index/test_checkout.py"
|
| 1179 | "--ignore=tests/index/test_fs.py"
|
| 1180 | "--ignore=tests/index/test_index.py"
|
| 1181 | "--ignore=tests/index/test_storage.py")
|
| 1182 | #:phases
|
| 1183 | #~(modify-phases %standard-phases
|
| 1184 | (add-after 'unpack 'patch-pyproject
|
| 1185 | (lambda _
|
| 1186 | |
| 1187 | (substitute* "pyproject.toml"
|
| 1188 | (("^license = .*") "license = {text = \"Apache-2.0\"}\n")
|
| 1189 | (("^license-files = .*") "")))))))
|
| 1190 | (synopsis "DVC's data management subsystem")
|
| 1191 | (description "Dvc data is DVC's data management subsystem.")
|
| 1192 | (license license:asl2.0)))
|
| 1193 |
|
| 1194 | (define-public python-dvc-objects
|
| 1195 | (package
|
| 1196 | (name "python-dvc-objects")
|
| 1197 | (version "5.1.1")
|
| 1198 | (home-page "https://github.com/iterative/dvc-objects")
|
| 1199 | (source
|
| 1200 | (origin
|
| 1201 | (method url-fetch)
|
| 1202 | (uri (pypi-uri "dvc_objects" version))
|
| 1203 | (sha256
|
| 1204 | (base32 "1amx5z8k2v2hbsajg0dcd5dxmmlv9bnbchpas95s8sj86cm8yc4y"))))
|
| 1205 | (build-system pyproject-build-system)
|
| 1206 | (propagated-inputs (list python-fsspec
|
| 1207 | python-funcy-1.14))
|
| 1208 | (native-inputs
|
| 1209 | (list python-mypy
|
| 1210 | python-pytest
|
| 1211 | python-pytest-asyncio
|
| 1212 | python-pytest-benchmark
|
| 1213 | python-pytest-mock
|
| 1214 | python-pytest-sugar
|
| 1215 | python-reflink
|
| 1216 | python-setuptools
|
| 1217 | python-setuptools-scm
|
| 1218 | python-wheel))
|
| 1219 | (synopsis "Filesystem and object-db level abstractions for DVC")
|
| 1220 | (description "Dvc objects provides a filesystem and object-db level
|
| 1221 | abstractions to use in dvc and dvc-data.")
|
| 1222 | (license license:asl2.0)))
|
| 1223 |
|
| 1224 | (define-public python-ecos
|
| 1225 | (package
|
| 1226 | (name "python-ecos")
|
| 1227 | (version "2.0.13")
|
| 1228 | (source
|
| 1229 | (origin
|
| 1230 | (method git-fetch)
|
| 1231 | (uri (git-reference
|
| 1232 | (url "https://github.com/embotech/ecos-python")
|
| 1233 | (commit (string-append "v" version))
|
| 1234 | (recursive? #true)))
|
| 1235 | (file-name (git-file-name name version))
|
| 1236 | (sha256
|
| 1237 | (base32 "16ljq8maflfkgbw16rldg6cy14vgz2pb3b2iga60i7yzkq2ikmyw"))))
|
| 1238 | (build-system pyproject-build-system)
|
| 1239 | (propagated-inputs (list python-numpy python-scipy))
|
| 1240 | (native-inputs (list python-pytest python-setuptools python-wheel))
|
| 1241 | (home-page "https://github.com/embotech/ecos")
|
| 1242 | (synopsis "Embedded Cone Solver")
|
| 1243 | (description
|
| 1244 | "This is the Python package for ECOS: Embedded Cone Solver. ECOS is
|
| 1245 | numerical software for solving convex second-order cone programs (SOCPs).")
|
| 1246 | (license license:gpl3)))
|
| 1247 |
|
| 1248 | (define-public python-efficient-apriori
|
| 1249 | (package
|
| 1250 | (name "python-efficient-apriori")
|
| 1251 | (version "2.0.6")
|
| 1252 | (source
|
| 1253 | (origin
|
| 1254 | (method url-fetch)
|
| 1255 | (uri (pypi-uri "efficient_apriori" version))
|
| 1256 | (sha256
|
| 1257 | (base32 "0vmdp8qkir7jrmwgpzajssyxh6q78m0q16pr1v657vla9x5wxn2s"))))
|
| 1258 | (build-system pyproject-build-system)
|
| 1259 | (arguments
|
| 1260 | (list
|
| 1261 | #:test-flags
|
| 1262 | #~(list "--doctest-modules" "-vv" "efficient_apriori")))
|
| 1263 | (native-inputs (list python-setuptools python-pytest))
|
| 1264 | (home-page "https://github.com/tommyod/Efficient-Apriori")
|
| 1265 | (synopsis "An efficient Python implementation of the Apriori algorithm.")
|
| 1266 | (description "An efficient Python implementation of the Apriori algorithm,
|
| 1267 | which uncovers hidden structures in categorical data")
|
| 1268 | (license license:expat)))
|
| 1269 |
|
| 1270 | (define-public python-einops
|
| 1271 | (package
|
| 1272 | (name "python-einops")
|
| 1273 | (version "0.8.1")
|
| 1274 | (source
|
| 1275 | (origin
|
| 1276 | (method git-fetch) |
| 1277 | (uri (git-reference
|
| 1278 | (url "https://github.com/arogozhnikov/einops")
|
| 1279 | (commit (string-append "v" version))))
|
| 1280 | (file-name (git-file-name name version))
|
| 1281 | (sha256
|
| 1282 | (base32 "07xd5a4sya3mr003f17hxykcbq3zf3mnr51qagv7fy55qcnbkn97"))))
|
| 1283 | (build-system pyproject-build-system)
|
| 1284 | (arguments
|
| 1285 | (list
|
| 1286 | #:test-flags
|
| 1287 | |
| 1288 | #~(list "--ignore=scripts/test_notebooks.py")
|
| 1289 | #:phases
|
| 1290 | #~(modify-phases %standard-phases
|
| 1291 | (add-after 'unpack 'set-backend
|
| 1292 | (lambda _
|
| 1293 | |
| 1294 | |
| 1295 | (setenv "EINOPS_TEST_BACKENDS" "numpy"))))))
|
| 1296 | (native-inputs
|
| 1297 | (list python-hatchling
|
| 1298 | python-nbconvert
|
| 1299 | python-nbformat
|
| 1300 | python-parameterized
|
| 1301 | python-pytest))
|
| 1302 | (propagated-inputs
|
| 1303 | (list python-numpy))
|
| 1304 | (home-page "https://einops.rocks/")
|
| 1305 | (synopsis "Tensor operations for different backends")
|
| 1306 | (description
|
| 1307 | "Einops provides a set of tensor operations for NumPy and multiple deep
|
| 1308 | learning frameworks.")
|
| 1309 | (license license:expat)))
|
| 1310 |
|
| 1311 | (define-public python-fast-array-utils
|
| 1312 | (package
|
| 1313 | (name "python-fast-array-utils")
|
| 1314 | (version "1.4.1")
|
| 1315 | (source
|
| 1316 | (origin
|
| 1317 | (method git-fetch)
|
| 1318 | (uri (git-reference
|
| 1319 | (url "https://github.com/scverse/fast-array-utils")
|
| 1320 | (commit (string-append "v" version))))
|
| 1321 | (file-name (git-file-name name version))
|
| 1322 | (sha256
|
| 1323 | (base32 "07qbsbsmzycxa5nib39zp7rfwcj3cvqyg4mpfkdn7xg2bmqprl7n"))))
|
| 1324 | (build-system pyproject-build-system)
|
| 1325 | (arguments
|
| 1326 | |
| 1327 | (list #:test-flags #~(list "-m" "not benchmark")))
|
| 1328 | (native-inputs
|
| 1329 | (list python-dask-minimal
|
| 1330 | python-hatch-docstring-description
|
| 1331 | python-hatch-fancy-pypi-readme
|
| 1332 | python-hatch-vcs
|
| 1333 | python-hatchling
|
| 1334 | python-numba
|
| 1335 | python-packaging
|
| 1336 | python-pytest
|
| 1337 | python-pytest-doctestplus
|
| 1338 | python-scipy-minimal))
|
| 1339 | (propagated-inputs
|
| 1340 | (list python-numpy))
|
| 1341 | (home-page "https://fast-array-utils.scverse.org/")
|
| 1342 | (synopsis "Fast array utilities")
|
| 1343 | (description
|
| 1344 | "This package provides fast array utilities with minimal dependencies.")
|
| 1345 | (license license:mpl2.0)))
|
| 1346 |
|
| 1347 | (define-public python-fast-histogram
|
| 1348 | (package
|
| 1349 | (name "python-fast-histogram")
|
| 1350 | (properties '((commit . "92ed2049a2e24b15993bb770e96a5d21f4736be3")
|
| 1351 | (revision . "0")))
|
| 1352 | (version (git-version "0.14"
|
| 1353 | (assoc-ref properties 'revision)
|
| 1354 | (assoc-ref properties 'commit)))
|
| 1355 | (source
|
| 1356 | (origin
|
| 1357 | (method git-fetch)
|
| 1358 | (uri (git-reference
|
| 1359 | (url "https://github.com/astrofrog/fast-histogram")
|
| 1360 | (commit (assoc-ref properties 'commit))))
|
| 1361 | (file-name (git-file-name name version))
|
| 1362 | (sha256
|
| 1363 | (base32 "0iqgrnzs2w0v36iyp9782lxc8nji2v7fvs1k90pnrrf6r3w98p0v"))))
|
| 1364 | (build-system pyproject-build-system)
|
| 1365 | (arguments
|
| 1366 | (list
|
| 1367 | #:test-flags
|
| 1368 | |
| 1369 | #~(list "-k" "not test_1d_compare_with_numpy")
|
| 1370 | #:phases
|
| 1371 | #~(modify-phases %standard-phases
|
| 1372 | (add-before 'check 'build-extensions
|
| 1373 | (lambda _
|
| 1374 | (invoke "python" "setup.py" "build_ext" "--inplace"))))))
|
| 1375 | (native-inputs
|
| 1376 | (list python-hypothesis
|
| 1377 | python-pytest
|
| 1378 | python-setuptools
|
| 1379 | python-setuptools-scm
|
| 1380 | python-wheel))
|
| 1381 | (propagated-inputs
|
| 1382 | (list python-numpy))
|
| 1383 | (home-page "https://github.com/astrofrog/fast-histogram")
|
| 1384 | (synopsis "Fast simple 1D and 2D histograms")
|
| 1385 | (description
|
| 1386 | "The fast-histogram mini-package aims to provide simple and fast
|
| 1387 | histogram functions for regular bins that don't compromise on performance. It
|
| 1388 | doesn't do anything complicated - it just implements a simple histogram
|
| 1389 | algorithm in C and keeps it simple. The aim is to have functions that are
|
| 1390 | fast but also robust and reliable. The result is a 1D histogram function here
|
| 1391 | that is 7-15x faster than @code{numpy.histogram}, and a 2D histogram function
|
| 1392 | that is 20-25x faster than @code{numpy.histogram2d}.")
|
| 1393 | (license license:bsd-3)))
|
| 1394 |
|
| 1395 | (define-public python-fastcluster
|
| 1396 | (package
|
| 1397 | (name "python-fastcluster")
|
| 1398 | (version "1.3.0")
|
| 1399 | (source
|
| 1400 | (origin
|
| 1401 | (method url-fetch)
|
| 1402 | (uri (pypi-uri "fastcluster" version))
|
| 1403 | (sha256
|
| 1404 | (base32 "00nzjrk8cp3kwm0qax5xxg61dxq9b8s3jspsqx4skyn3lpmkl8ym"))))
|
| 1405 | (build-system pyproject-build-system)
|
| 1406 | (native-inputs
|
| 1407 | (list python-pytest
|
| 1408 | python-scipy
|
| 1409 | python-setuptools))
|
| 1410 | (propagated-inputs
|
| 1411 | (list python-numpy))
|
| 1412 | (home-page "https://danifold.net/fastcluster.html")
|
| 1413 | (synopsis "Fast hierarchical clustering routines for R and Python")
|
| 1414 | (description "The fastcluster package implements seven common hierarchical
|
| 1415 | clustering schemes efficiently. The package is made with two interfaces to
|
| 1416 | standard software: R and Python.")
|
| 1417 | (license license:bsd-2)))
|
| 1418 |
|
| 1419 | |
| 1420 | |
| 1421 | (define-public python-fbpca
|
| 1422 | (package
|
| 1423 | (name "python-fbpca")
|
| 1424 | (version "1.0")
|
| 1425 | (source (origin
|
| 1426 | (method url-fetch)
|
| 1427 | (uri (pypi-uri "fbpca" version))
|
| 1428 | (sha256
|
| 1429 | (base32
|
| 1430 | "1lbjqhqsdmqk86lb86q3ywf7561zmdny1dfvgwqkyrkr4ij7f1hm"))))
|
| 1431 | (build-system pyproject-build-system)
|
| 1432 | (arguments
|
| 1433 | (list
|
| 1434 | #:test-flags
|
| 1435 | |
| 1436 | #~(list "--deselect=fbpca.py::TestPCA::test_sparse"
|
| 1437 | "fbpca.py")))
|
| 1438 | (native-inputs (list python-pytest python-setuptools))
|
| 1439 | (propagated-inputs
|
| 1440 | (list python-numpy python-scipy))
|
| 1441 | (home-page "https://fbpca.readthedocs.io/")
|
| 1442 | (synopsis "Functions for principal component analysis and accuracy checks")
|
| 1443 | (description
|
| 1444 | "This package provides fast computations for @dfn{principal component
|
| 1445 | analysis} (PCA), SVD, and eigendecompositions via randomized methods")
|
| 1446 | (license license:bsd-3)))
|
| 1447 |
|
| 1448 | (define-public python-fgivenx
|
| 1449 | (package
|
| 1450 | (name "python-fgivenx")
|
| 1451 | |
| 1452 | (properties '((commit . "cf51dbf8b7efdd8d84f055740a069a5b882dcf77")
|
| 1453 | (revision . "0")))
|
| 1454 | (version (git-version "2.4.2"
|
| 1455 | (assoc-ref properties 'revision)
|
| 1456 | (assoc-ref properties 'commit)))
|
| 1457 | (source
|
| 1458 | (origin
|
| 1459 | (method git-fetch)
|
| 1460 | (uri (git-reference
|
| 1461 | (url "https://github.com/handley-lab/fgivenx")
|
| 1462 | (commit (assoc-ref properties 'commit))))
|
| 1463 | (file-name (git-file-name name version))
|
| 1464 | (sha256
|
| 1465 | (base32 "1z9lwrjvz977gk6z7zqj8d21yi0xcz67mj1737yzzdc8c03nzg9w"))))
|
| 1466 | (build-system pyproject-build-system)
|
| 1467 | |
| 1468 | (native-inputs
|
| 1469 | (list python-pytest
|
| 1470 | python-pytest-mpl
|
| 1471 | python-setuptools))
|
| 1472 | (propagated-inputs
|
| 1473 | (list python-matplotlib
|
| 1474 | python-numpy
|
| 1475 | python-scipy
|
| 1476 | |
| 1477 | python-getdist
|
| 1478 | python-joblib
|
| 1479 | python-tqdm))
|
| 1480 | (home-page "https://github.com/handley-lab/fgivenx")
|
| 1481 | (synopsis "Functional Posterior Plotter")
|
| 1482 | (description
|
| 1483 | "@code{fgivenx} is a Python package for plotting posteriors of functions.
|
| 1484 | It is currently used in astronomy, but will be of use to any scientists
|
| 1485 | performing Bayesian analyses which have predictive posteriors that are
|
| 1486 | functions.
|
| 1487 |
|
| 1488 | This package allows one to plot a predictive posterior of a function,
|
| 1489 | dependent on sampled parameters. It assumes one has a Bayesian posterior
|
| 1490 | @code{Post(theta|D,M)} described by a set of posterior samples
|
| 1491 | @code{{theta_i}~Post}. If there is a function parameterised by theta
|
| 1492 | @code{y=f(x;theta)}, then this script will produce a contour plot of the
|
| 1493 | conditional posterior @code{P(y|x,D,M)} in the @code{(x,y)} plane.")
|
| 1494 | (license license:expat)))
|
| 1495 |
|
| 1496 | (define-public python-flox
|
| 1497 | (package
|
| 1498 | (name "python-flox")
|
| 1499 | (version "0.11.2")
|
| 1500 | (source
|
| 1501 | (origin
|
| 1502 | (method git-fetch)
|
| 1503 | (uri (git-reference
|
| 1504 | (url "https://github.com/xarray-contrib/flox")
|
| 1505 | (commit (string-append "v" version))))
|
| 1506 | (file-name (git-file-name name version))
|
| 1507 | (sha256
|
| 1508 | (base32 "0jy1kxk9r0az39zmbmf6md55c35ldkk9q6pcfg8jb4chwi4i34iw"))))
|
| 1509 | (build-system pyproject-build-system)
|
| 1510 | (arguments
|
| 1511 | (list
|
| 1512 | #:test-flags
|
| 1513 | #~(list "--ignore" "tests/test_asv.py" |
| 1514 | |
| 1515 | "--ignore" "tests/test_cohorts.py")))
|
| 1516 | (propagated-inputs (list python-numpy
|
| 1517 | python-numpy-groupies
|
| 1518 | python-packaging
|
| 1519 | python-pandas
|
| 1520 | python-scipy
|
| 1521 | python-toolz))
|
| 1522 | (native-inputs (list |
| 1523 | python-dask
|
| 1524 | python-netcdf4
|
| 1525 | python-numbagg
|
| 1526 | python-pytest
|
| 1527 | python-pytest-snapshot
|
| 1528 | python-pytest-xdist
|
| 1529 | python-setuptools
|
| 1530 | python-setuptools-scm
|
| 1531 | python-sparse
|
| 1532 | python-xarray))
|
| 1533 | (home-page "https://github.com/xarray-contrib/flox")
|
| 1534 | (synopsis "GroupBy operations for @code{dask.array}")
|
| 1535 | (description "@code{flox} mainly provides strategies for fast GroupBy
|
| 1536 | reductions with @code{dask.array}. It uses the MapReduce paradigm (or a
|
| 1537 | \"tree reduction\") to run the GroupBy operation in a parallel-native way
|
| 1538 | totally avoiding a sort or shuffle operation. @code{flox} can use either
|
| 1539 | @code{dask} or @code{cubed} as its backend.")
|
| 1540 | (license license:asl2.0)))
|
| 1541 |
|
| 1542 | (define-public python-formulaic
|
| 1543 | (package
|
| 1544 | (name "python-formulaic")
|
| 1545 | (version "1.0.1")
|
| 1546 | (source
|
| 1547 | (origin
|
| 1548 | (method url-fetch)
|
| 1549 | (uri (pypi-uri "formulaic" version))
|
| 1550 | (sha256
|
| 1551 | (base32 "18gvd3f2x358jj0df8vx5fhhnvzw047rsrs03vmvqnxaly97kpb4"))))
|
| 1552 | (build-system pyproject-build-system)
|
| 1553 | (propagated-inputs (list python-astor
|
| 1554 | python-cached-property
|
| 1555 | python-interface-meta
|
| 1556 | python-numpy
|
| 1557 | python-pandas
|
| 1558 | python-scipy
|
| 1559 | python-typing-extensions
|
| 1560 | python-wrapt))
|
| 1561 | (native-inputs (list python-hatchling python-hatch-vcs python-pytest))
|
| 1562 | (home-page "https://github.com/matthewwardrop/formulaic")
|
| 1563 | (synopsis "Implementation of Wilkinson formulas")
|
| 1564 | (description "Formulaic is a high-performance implementation of Wilkinson
|
| 1565 | formulas for Python.")
|
| 1566 | (license license:expat)))
|
| 1567 |
|
| 1568 | (define-public python-geosketch
|
| 1569 | (package
|
| 1570 | (name "python-geosketch")
|
| 1571 | (version "1.3")
|
| 1572 | (source
|
| 1573 | (origin
|
| 1574 | (method git-fetch)
|
| 1575 | (uri (git-reference
|
| 1576 | (url "https://github.com/brianhie/geosketch")
|
| 1577 | (commit (string-append "v" version))))
|
| 1578 | (file-name (git-file-name name version))
|
| 1579 | (sha256
|
| 1580 | (base32 "0lnynk4r87zqck5mmj33axmly34hh7lrlmfy1qidrw7xihy28g5a"))))
|
| 1581 | (build-system pyproject-build-system)
|
| 1582 | |
| 1583 | (arguments (list #:tests? #f))
|
| 1584 | (native-inputs (list python-setuptools))
|
| 1585 | (propagated-inputs (list python-fbpca python-numpy python-scikit-learn))
|
| 1586 | (home-page "https://github.com/brianhie/geosketch")
|
| 1587 | (synopsis "Geometry-preserving random sampling")
|
| 1588 | (description "geosketch is a Python package that implements the geometric
|
| 1589 | sketching algorithm described by Brian Hie, Hyunghoon Cho, Benjamin DeMeo,
|
| 1590 | Bryan Bryson, and Bonnie Berger in \"Geometric sketching compactly summarizes
|
| 1591 | the single-cell transcriptomic landscape\", Cell Systems (2019). This package
|
| 1592 | provides an example implementation of the algorithm as well as scripts
|
| 1593 | necessary for reproducing the experiments in the paper.")
|
| 1594 | (license license:expat)))
|
| 1595 |
|
| 1596 | (define-public python-hepunits
|
| 1597 | (package
|
| 1598 | (name "python-hepunits")
|
| 1599 | (version "2.4.4")
|
| 1600 | (source
|
| 1601 | (origin
|
| 1602 | (method url-fetch)
|
| 1603 | (uri (pypi-uri "hepunits" version))
|
| 1604 | (sha256
|
| 1605 | (base32 "1sq597amy82wnw7q61i9q2ylmp1cpnwdg7jrzxmv6kryz8lyfihq"))))
|
| 1606 | (build-system pyproject-build-system)
|
| 1607 | (native-inputs (list python-hatch-vcs
|
| 1608 | python-hatchling
|
| 1609 | python-pint
|
| 1610 | python-pytest))
|
| 1611 | (home-page "https://github.com/scikit-hep/hepunits")
|
| 1612 | (synopsis "Units and constants in the HEP system of units")
|
| 1613 | (description "@code{hepunits} collects the most commonly used units and
|
| 1614 | constants in the HEP System of Units, as derived from the basic units
|
| 1615 | originally defined by the CLHEP project.")
|
| 1616 | (license license:bsd-3)))
|
| 1617 |
|
| 1618 | (define-public python-hist
|
| 1619 | (package
|
| 1620 | (name "python-hist")
|
| 1621 | (version "2.10.1")
|
| 1622 | (source
|
| 1623 | (origin
|
| 1624 | (method url-fetch)
|
| 1625 | (uri (pypi-uri "hist" version))
|
| 1626 | (sha256
|
| 1627 | (base32 "0bhv8bf7zizxf7nsps5hyfppjk1ry0z6pwrwhz44xmm6g6nfdj6y"))))
|
| 1628 | (build-system pyproject-build-system)
|
| 1629 | (propagated-inputs (list python-boost-histogram
|
| 1630 | python-histoprint
|
| 1631 | python-numpy
|
| 1632 | python-typing-extensions))
|
| 1633 | (native-inputs (list python-hatch-vcs
|
| 1634 | python-hatchling
|
| 1635 | python-pytest
|
| 1636 | python-pytest-mpl))
|
| 1637 | (home-page "https://hist.readthedocs.io/en/latest/")
|
| 1638 | (synopsis "Hist classes and utilities")
|
| 1639 | (description
|
| 1640 | "Hist is an analyst-friendly front-end for @code{boost-histogram}.")
|
| 1641 | (license license:bsd-3)))
|
| 1642 |
|
| 1643 | (define-public python-histoprint
|
| 1644 | (package
|
| 1645 | (name "python-histoprint")
|
| 1646 | (version "2.6.0")
|
| 1647 | (source
|
| 1648 | (origin
|
| 1649 | (method url-fetch)
|
| 1650 | (uri (pypi-uri "histoprint" version))
|
| 1651 | (sha256
|
| 1652 | (base32 "07d2lk64gwhjvw4wccvwks3j4ig7g99q627jjxz4ans5a29p5pz1"))))
|
| 1653 | (build-system pyproject-build-system)
|
| 1654 | (propagated-inputs (list python-click python-numpy python-uhi))
|
| 1655 | (native-inputs (list python-awkward
|
| 1656 | python-boost-histogram
|
| 1657 | python-hatch-vcs
|
| 1658 | python-hatchling
|
| 1659 | python-pytest
|
| 1660 | python-rich))
|
| 1661 | (home-page "https://github.com/scikit-hep/histoprint")
|
| 1662 | (synopsis "Pretty print histograms to the console")
|
| 1663 | (description "Histoprint uses a mix of terminal color codes and Unicode
|
| 1664 | trickery (i.e. combining characters) to plot overlaying histograms.")
|
| 1665 | (license license:expat)))
|
| 1666 |
|
| 1667 | (define-public python-imagehash
|
| 1668 | (package
|
| 1669 | (name "python-imagehash")
|
| 1670 | (version "4.3.2")
|
| 1671 | (source
|
| 1672 | (origin
|
| 1673 | (method git-fetch) |
| 1674 | (uri (git-reference
|
| 1675 | |
| 1676 | |
| 1677 | |
| 1678 | (url "https://github.com/JohannesBuchner/imagehash")
|
| 1679 | (commit (string-append "v" version))))
|
| 1680 | (file-name (git-file-name name version))
|
| 1681 | (sha256
|
| 1682 | (base32 "1rz1fpwhcx0cbln189bcs61wlwgngcjcn77jvm0yji5s7lshhipy"))))
|
| 1683 | (build-system pyproject-build-system)
|
| 1684 | (arguments
|
| 1685 | (list
|
| 1686 | #:phases
|
| 1687 | #~(modify-phases %standard-phases
|
| 1688 | |
| 1689 | |
| 1690 | (add-after 'unpack 'remove-six
|
| 1691 | (lambda _
|
| 1692 | (substitute* (find-files "." ".py$")
|
| 1693 | (("import six") "")
|
| 1694 | (("six\\.assertRaisesRegex\\(self, ")
|
| 1695 | "self.assertRaisesRegex(")
|
| 1696 | (("six\\.exec_") "")))))))
|
| 1697 | (native-inputs
|
| 1698 | (list python-pytest
|
| 1699 | python-setuptools
|
| 1700 | python-wheel))
|
| 1701 | (propagated-inputs
|
| 1702 | (list python-numpy
|
| 1703 | python-pillow
|
| 1704 | python-pywavelets
|
| 1705 | python-scipy))
|
| 1706 | (home-page "https://github.com/JohannesBuchner/imagehash")
|
| 1707 | (synopsis "Perceptual Image Hashing library")
|
| 1708 | (description
|
| 1709 | "This package implements a functionality to tell whether two images look
|
| 1710 | nearly identical. The image hash algorithms (average, perceptual, difference,
|
| 1711 | wavelet) analyse the image structure on luminance (without color information).
|
| 1712 | The color hash algorithm analyses the color distribution and black & gray
|
| 1713 | fractions (without position information).
|
| 1714 |
|
| 1715 | Features:
|
| 1716 | @itemize
|
| 1717 | @item average hashing
|
| 1718 | @item perceptual hashing
|
| 1719 | @item difference hashing
|
| 1720 | @item wavelet hashing
|
| 1721 | @item HSV color hashing (colorhash)
|
| 1722 | @item crop-resistant hashing
|
| 1723 | @end itemize")
|
| 1724 | (license license:bsd-2)))
|
| 1725 |
|
| 1726 | (define-public python-iminuit
|
| 1727 | (package
|
| 1728 | (name "python-iminuit")
|
| 1729 | (version "2.32.0")
|
| 1730 | (source
|
| 1731 | (origin
|
| 1732 | (method url-fetch)
|
| 1733 | (uri (pypi-uri "iminuit" version))
|
| 1734 | (sha256
|
| 1735 | (base32 "1lpprnn6h1f065b4aay6cr2bk6s5h3fv3gfnbbkrp5b5hv8k8ax3"))))
|
| 1736 | (build-system pyproject-build-system)
|
| 1737 | (arguments
|
| 1738 | (list #:test-flags #~(list "-k" "not test_interactive_pyside6")))
|
| 1739 | (native-inputs
|
| 1740 | (list cmake-minimal
|
| 1741 | pybind11-2
|
| 1742 | python-annotated-types
|
| 1743 | python-boost-histogram
|
| 1744 | python-ipykernel
|
| 1745 | python-jacobi
|
| 1746 | python-joblib
|
| 1747 | python-pydantic
|
| 1748 | python-pytest
|
| 1749 | python-resample
|
| 1750 | python-scikit-build-core
|
| 1751 | python-tabulate))
|
| 1752 | |
| 1753 | |
| 1754 | |
| 1755 | (propagated-inputs
|
| 1756 | (list python-ipywidgets
|
| 1757 | python-matplotlib
|
| 1758 | |
| 1759 | |
| 1760 | python-numpy
|
| 1761 | python-scipy
|
| 1762 | python-unicodeitplus))
|
| 1763 | (home-page "https://github.com/scikit-hep/iminuit")
|
| 1764 | (synopsis "Python interface for MINUIT2")
|
| 1765 | (description
|
| 1766 | "@code{iminuit} is a Jupyter-friendly Python interface for the @code{Minuit2}
|
| 1767 | C++ library maintained by CERN's ROOT team.
|
| 1768 |
|
| 1769 | Minuit was designed to optimize statistical cost functions, for
|
| 1770 | maximum-likelihood and least-squares fits. It provides the best-fit
|
| 1771 | parameters and error estimates from likelihood profile analysis.
|
| 1772 |
|
| 1773 | Optionally, Iminuit supports SciPy minimizers as alternatives to Minuit's
|
| 1774 | MIGRAD algorithm and Numba accelerated functions.")
|
| 1775 | |
| 1776 | (license (list license:expat license:lgpl2.1+))))
|
| 1777 |
|
| 1778 | (define-public python-jacobi
|
| 1779 | (package
|
| 1780 | (name "python-jacobi")
|
| 1781 | (version "0.9.2")
|
| 1782 | (source
|
| 1783 | (origin
|
| 1784 | (method url-fetch)
|
| 1785 | (uri (pypi-uri "jacobi" version))
|
| 1786 | (sha256
|
| 1787 | (base32 "0a08680q6rnl6b1azq0lzd8r08pgnjd9ynwivb1g2vi4ccb4h7y1"))))
|
| 1788 | (build-system pyproject-build-system)
|
| 1789 | (arguments
|
| 1790 | (list
|
| 1791 | #:phases
|
| 1792 | #~(modify-phases %standard-phases
|
| 1793 | (add-after 'unpack 'fix-pytest-config
|
| 1794 | (lambda _
|
| 1795 | (substitute* "pyproject.toml"
|
| 1796 | |
| 1797 | |
| 1798 | ((".*error::numpy.VisibleDeprecationWarning.*") "")))))))
|
| 1799 | (native-inputs
|
| 1800 | (list python-pytest
|
| 1801 | python-pytest-benchmark
|
| 1802 | python-setuptools
|
| 1803 | python-setuptools-scm))
|
| 1804 | (propagated-inputs
|
| 1805 | (list python-numpy))
|
| 1806 | (home-page "https://github.com/hdembinski/jacobi")
|
| 1807 | (synopsis "Compute numerical derivatives")
|
| 1808 | (description
|
| 1809 | "This package provides fast numerical derivatives for analytic
|
| 1810 | functions with arbitrary round-off error and error propagation.")
|
| 1811 | (license license:expat)))
|
| 1812 |
|
| 1813 | (define-public python-legendkit
|
| 1814 | (package
|
| 1815 | (name "python-legendkit")
|
| 1816 | (version "0.3.6")
|
| 1817 | (source
|
| 1818 | (origin
|
| 1819 | (method git-fetch) |
| 1820 | (uri (git-reference
|
| 1821 | (url "https://github.com/Marsilea-viz/legendkit")
|
| 1822 | (commit (string-append "v" version))))
|
| 1823 | (file-name (git-file-name name version))
|
| 1824 | (sha256
|
| 1825 | (base32 "03xdhh95w4zydwa4ahp3gyfa6i60c9s5arfcj366knckb1bnpnn9"))))
|
| 1826 | (build-system pyproject-build-system)
|
| 1827 | (native-inputs
|
| 1828 | (list python-hatchling
|
| 1829 | python-pytest))
|
| 1830 | (propagated-inputs
|
| 1831 | (list python-matplotlib))
|
| 1832 | (home-page "https://github.com/Marsilea-viz/legendki")
|
| 1833 | (synopsis "Legend creation and manipulation for matplotlib")
|
| 1834 | (description
|
| 1835 | "This package implements a functionality to create and manipulate plot
|
| 1836 | legends for @code{matplotlib}.")
|
| 1837 | (license license:expat)))
|
| 1838 |
|
| 1839 | (define-public python-libneuroml
|
| 1840 | (package
|
| 1841 | (name "python-libneuroml")
|
| 1842 | (version "0.6.7")
|
| 1843 | (source
|
| 1844 | (origin
|
| 1845 | (method git-fetch)
|
| 1846 | (uri (git-reference
|
| 1847 | (url "https://github.com/NeuralEnsemble/libNeuroML.git")
|
| 1848 | (commit (string-append "v" version))))
|
| 1849 | (file-name (git-file-name name version))
|
| 1850 | (sha256
|
| 1851 | (base32 "1x5sgm0250zdfnw16cbmgl45hz2kfmww5lghpyhlcadgnbzyq3dx"))))
|
| 1852 | (build-system pyproject-build-system)
|
| 1853 | |
| 1854 | (native-inputs
|
| 1855 | (list python-pytest
|
| 1856 | python-numpy
|
| 1857 | python-setuptools
|
| 1858 | python-tables))
|
| 1859 | (propagated-inputs
|
| 1860 | (list python-lxml
|
| 1861 | python-natsort
|
| 1862 | python-networkx))
|
| 1863 | (home-page "https://libneuroml.readthedocs.org/en/latest/")
|
| 1864 | (synopsis
|
| 1865 | "Python library for working with NeuroML descriptions of neuronal models")
|
| 1866 | (description
|
| 1867 | "This package provides a Python library for working with NeuroML descriptions of
|
| 1868 | neuronal models")
|
| 1869 | (license license:bsd-3)))
|
| 1870 |
|
| 1871 | (define-public python-marsilea
|
| 1872 | (package
|
| 1873 | (name "python-marsilea")
|
| 1874 | (version "0.6.2")
|
| 1875 | (source
|
| 1876 | (origin
|
| 1877 | (method git-fetch)
|
| 1878 | (uri (git-reference
|
| 1879 | (url "https://github.com/Marsilea-viz/marsilea")
|
| 1880 | (commit (string-append "v" version))))
|
| 1881 | (file-name (git-file-name name version))
|
| 1882 | (sha256
|
| 1883 | (base32 "0i7n44fzy8qibdk8jc6f1g356xa10cc7fr64dhpqkrsp9sz6kx70"))))
|
| 1884 | (build-system pyproject-build-system)
|
| 1885 | (arguments
|
| 1886 | (list
|
| 1887 | #:phases
|
| 1888 | #~(modify-phases %standard-phases
|
| 1889 | (add-before 'build 'set-version
|
| 1890 | (lambda _
|
| 1891 | (substitute* "pyproject.toml"
|
| 1892 | ((".*uv-dynamic-versioning>.*") "")
|
| 1893 | (("source.*uv-dynamic-versioning.*") "source = 'vcs'")))))))
|
| 1894 | (native-inputs
|
| 1895 | (list python-hatch-vcs
|
| 1896 | python-hatchling
|
| 1897 | python-pytest))
|
| 1898 | (propagated-inputs
|
| 1899 | (list python-legendkit
|
| 1900 | python-matplotlib
|
| 1901 | python-numpy
|
| 1902 | python-pandas
|
| 1903 | python-platformdirs
|
| 1904 | python-scipy
|
| 1905 | python-seaborn
|
| 1906 | |
| 1907 | python-fastcluster
|
| 1908 | python-pyarrow)) |
| 1909 | (home-page "https://github.com/Marsilea-viz/marsilea")
|
| 1910 | (synopsis "Declarative creation of composable visualizations")
|
| 1911 | (description
|
| 1912 | "Marsilea is a Python library for creating composable visualizations in a
|
| 1913 | declarative way. It is built on top of Matplotlib and provides a high-level
|
| 1914 | API for you to puzzle different visualizations together like logo.")
|
| 1915 | (license license:expat)))
|
| 1916 |
|
| 1917 | (define-public python-maxent-disaggregation
|
| 1918 | (package
|
| 1919 | (name "python-maxent-disaggregation")
|
| 1920 | (version "1.3.1")
|
| 1921 | (source
|
| 1922 | (origin
|
| 1923 | (method git-fetch)
|
| 1924 | (uri (git-reference
|
| 1925 | (url "https://github.com/jakobsarthur/maxent_disaggregation")
|
| 1926 | (commit (string-append "v" version))))
|
| 1927 | (file-name (git-file-name name version))
|
| 1928 | (sha256
|
| 1929 | (base32 "0iqvgm5vcaj34wgbiyq6f7kqqyyvvj8wlc2fjanrsgnyp7imnvjd"))))
|
| 1930 | (build-system pyproject-build-system)
|
| 1931 | (native-inputs
|
| 1932 | (list python-corner
|
| 1933 | python-matplotlib
|
| 1934 | python-pytest
|
| 1935 | python-setuptools))
|
| 1936 | (propagated-inputs
|
| 1937 | (list nlopt python-numpy
|
| 1938 | python-scipy))
|
| 1939 | (home-page "https://github.com/jakobsarthur/maxent_disaggregation")
|
| 1940 | (synopsis "Propagate uncertainty when disaggregating data")
|
| 1941 | (description
|
| 1942 | "This package provides tooling to help with the propagation of
|
| 1943 | uncertainty when disaggregating data, using the maximum entropy principle.")
|
| 1944 | (license license:expat)))
|
| 1945 |
|
| 1946 | (define-public python-meshzoo
|
| 1947 | (package
|
| 1948 | (name "python-meshzoo")
|
| 1949 | (version "0.9.4")
|
| 1950 | (source
|
| 1951 | (origin
|
| 1952 | (method git-fetch)
|
| 1953 | (uri (git-reference
|
| 1954 | (url "https://github.com/diego-hayashi/meshzoo")
|
| 1955 | (commit (string-append "v" version))))
|
| 1956 | (file-name (git-file-name name version))
|
| 1957 | (sha256
|
| 1958 | (base32 "107byfppbq16fqyp2hw7ydcvvahspzq0hzvlvzqg2zxi1aigbr68"))))
|
| 1959 | (build-system pyproject-build-system)
|
| 1960 | (propagated-inputs
|
| 1961 | (list python-numpy))
|
| 1962 | (native-inputs (list python-flit-core python-matplotlib python-pytest))
|
| 1963 | (home-page "https://github.com/diego-hayashi/meshzoo")
|
| 1964 | (synopsis "Mesh generator for simple geometries")
|
| 1965 | (description
|
| 1966 | "@code{meshzoo} is a mesh generator for finite element or finite
|
| 1967 | volume computations for simple domains like regular polygons, disks,
|
| 1968 | spheres, cubes, etc.")
|
| 1969 | (license license:gpl3+)))
|
| 1970 |
|
| 1971 | (define-public python-modin
|
| 1972 | (package
|
| 1973 | (name "python-modin")
|
| 1974 | (version "0.37.1")
|
| 1975 | (source
|
| 1976 | (origin
|
| 1977 | (method git-fetch)
|
| 1978 | (uri (git-reference
|
| 1979 | (url "https://github.com/modin-project/modin")
|
| 1980 | (commit version)))
|
| 1981 | (file-name (git-file-name name version))
|
| 1982 | (sha256
|
| 1983 | (base32 "1kqdx3b7sb3895ynypb6swf2jly26xvdghqqrm9ahqps16cn9dx9"))))
|
| 1984 | (build-system pyproject-build-system)
|
| 1985 | (arguments
|
| 1986 | (list
|
| 1987 | |
| 1988 | |
| 1989 | |
| 1990 | |
| 1991 | #:test-flags
|
| 1992 | #~(list "--numprocesses" (number->string (min 8 (parallel-job-count)))
|
| 1993 | |
| 1994 | "-k" (string-join
|
| 1995 | (list "not test_repr[100]"
|
| 1996 | "test_repr[size1]"
|
| 1997 | "test_repr[size2]"
|
| 1998 | "test_repr[size3]"
|
| 1999 | "test_repr[size4]"
|
| 2000 | "test_repr[size5]"
|
| 2001 | "test_repr[size6]"
|
| 2002 | "test_repr[size7]"
|
| 2003 | "test_repr[size8]"
|
| 2004 | "test_repr[size9]")
|
| 2005 | " and not ")
|
| 2006 | "modin/tests/numpy")
|
| 2007 | #:phases
|
| 2008 | #~(modify-phases %standard-phases
|
| 2009 | (add-after 'unpack 'fix-pytest-config
|
| 2010 | (lambda _
|
| 2011 | (substitute* "setup.cfg"
|
| 2012 | ((" --cov-.*--cov-report=") ""))))
|
| 2013 | (replace 'check
|
| 2014 | (lambda* (#:key tests? test-flags #:allow-other-keys)
|
| 2015 | (when tests?
|
| 2016 | |
| 2017 | (invoke "pytest" "-vv"
|
| 2018 | "modin/tests/test_executions_api.py"
|
| 2019 | "modin/tests/test_headers.py"
|
| 2020 | "modin/tests/core/test_dispatcher.py::test_add_option")
|
| 2021 | |
| 2022 | |
| 2023 | |
| 2024 | (setenv "MODIN_ENGINE" "dask")
|
| 2025 | (apply invoke "pytest" "-vv" test-flags)
|
| 2026 | (setenv "MODIN_ENGINE" "python")
|
| 2027 | (apply invoke "pytest" "-vv" test-flags)))))))
|
| 2028 | (native-inputs
|
| 2029 | (list python-boto3
|
| 2030 | python-pytest
|
| 2031 | python-pytest-xdist
|
| 2032 | python-s3fs
|
| 2033 | python-setuptools
|
| 2034 | python-versioneer))
|
| 2035 | (propagated-inputs
|
| 2036 | (list python-fsspec
|
| 2037 | python-numpy
|
| 2038 | python-packaging
|
| 2039 | python-pandas
|
| 2040 | python-psutil
|
| 2041 | python-typing-extensions
|
| 2042 | |
| 2043 | python-dask
|
| 2044 | python-distributed))
|
| 2045 | (home-page "https://github.com/modin-project/modin")
|
| 2046 | (synopsis "Make your pandas code run faster")
|
| 2047 | (description
|
| 2048 | "Modin uses Ray or Dask to provide an effortless way to speed up your
|
| 2049 | pandas notebooks, scripts, and libraries. Unlike other distributed DataFrame
|
| 2050 | libraries, Modin provides seamless integration and compatibility with existing
|
| 2051 | pandas code.")
|
| 2052 | (license license:asl2.0)))
|
| 2053 |
|
| 2054 | (define-public python-mpl-scatter-density
|
| 2055 | (package
|
| 2056 | (name "python-mpl-scatter-density")
|
| 2057 | (version "0.8")
|
| 2058 | (source
|
| 2059 | (origin
|
| 2060 | (method url-fetch)
|
| 2061 | (uri (pypi-uri "mpl_scatter_density" version))
|
| 2062 | (sha256
|
| 2063 | (base32 "0cynk1rk6k2xklgv69difphrz6id77x3xb58kbs4mc4q7z6bvfid"))))
|
| 2064 | (build-system pyproject-build-system)
|
| 2065 | (arguments
|
| 2066 | (list
|
| 2067 | |
| 2068 | #:test-flags #~(list "-k" "not test_default_dpi")))
|
| 2069 | (native-inputs
|
| 2070 | (list python-pytest
|
| 2071 | python-pytest-mpl
|
| 2072 | python-setuptools
|
| 2073 | python-setuptools-scm
|
| 2074 | python-wheel))
|
| 2075 | (propagated-inputs
|
| 2076 | (list python-fast-histogram
|
| 2077 | python-matplotlib
|
| 2078 | python-numpy))
|
| 2079 | (home-page "https://github.com/astrofrog/mpl-scatter-density")
|
| 2080 | (synopsis "Matplotlib helpers to make density scatter plots")
|
| 2081 | (description
|
| 2082 | "This package provides functionality to make it easy to make scatter
|
| 2083 | density maps, both for interactive and non-interactive use.")
|
| 2084 | (license license:bsd-2)))
|
| 2085 |
|
| 2086 | (define-public python-mpsplines
|
| 2087 | |
| 2088 | (let ((commit "4967655fca8f4d0fc0685486c8ec2f1fe2f199d2")
|
| 2089 | (revision "0"))
|
| 2090 | (package
|
| 2091 | (name "python-mpsplines")
|
| 2092 | (version (git-version "0.0.0" revision commit))
|
| 2093 | (source
|
| 2094 | (origin
|
| 2095 | (method git-fetch)
|
| 2096 | (uri (git-reference
|
| 2097 | (url "https://github.com/jararias/mpsplines")
|
| 2098 | (commit commit)))
|
| 2099 | (file-name (git-file-name name version))
|
| 2100 | (sha256
|
| 2101 | (base32 "1wqfvjp1d6xzb07qnq72h76f0mx7za9pasgw3qp3ciaycmlkvdr3"))))
|
| 2102 | (build-system pyproject-build-system)
|
| 2103 | (arguments
|
| 2104 | (list #:tests? #f)) |
| 2105 | (native-inputs
|
| 2106 | (list python-setuptools
|
| 2107 | python-wheel))
|
| 2108 | (propagated-inputs
|
| 2109 | (list python-scipy
|
| 2110 | python-numpy
|
| 2111 | python-loguru))
|
| 2112 | (home-page "https://github.com/jararias/mpsplines")
|
| 2113 | (synopsis "Mean preserving interpolation with splines")
|
| 2114 | (description
|
| 2115 | "This package implements a functionality for mean-preserving
|
| 2116 | interpolation of 1D data (for example, time series) with splines.")
|
| 2117 | (license license:bsd-3))))
|
| 2118 |
|
| 2119 | (define-public python-msgpack-numpy
|
| 2120 | (package
|
| 2121 | (name "python-msgpack-numpy")
|
| 2122 | (version "0.4.8")
|
| 2123 | (source
|
| 2124 | (origin
|
| 2125 | (method url-fetch)
|
| 2126 | (uri (pypi-uri "msgpack-numpy" version))
|
| 2127 | (sha256
|
| 2128 | (base32
|
| 2129 | "0sbfanbkfs6c77np4vz0ayrwnv99bpn5xgj5fnf2yhhk0lcd6ry6"))))
|
| 2130 | (build-system pyproject-build-system)
|
| 2131 | (arguments
|
| 2132 | (list #:test-backend #~'unittest))
|
| 2133 | (native-inputs
|
| 2134 | (list python-setuptools))
|
| 2135 | (propagated-inputs
|
| 2136 | (list python-msgpack python-numpy))
|
| 2137 | (home-page "https://github.com/lebedov/msgpack-numpy")
|
| 2138 | (synopsis
|
| 2139 | "Numpy data serialization using msgpack")
|
| 2140 | (description
|
| 2141 | "This package provides encoding and decoding routines that enable the
|
| 2142 | serialization and deserialization of numerical and array data types provided
|
| 2143 | by numpy using the highly efficient @code{msgpack} format. Serialization of
|
| 2144 | Python's native complex data types is also supported.")
|
| 2145 | (license license:bsd-3)))
|
| 2146 |
|
| 2147 | (define-public python-multiscale-spatial-image
|
| 2148 | (package
|
| 2149 | (name "python-multiscale-spatial-image")
|
| 2150 | (version "2.0.3")
|
| 2151 | (source
|
| 2152 | (origin
|
| 2153 | (method url-fetch)
|
| 2154 | (uri (pypi-uri "multiscale_spatial_image" version))
|
| 2155 | (sha256
|
| 2156 | (base32 "1avcc7hrgyza793i02vjfvyn2bg0ag50h1pagapbpj65hl3v4whb"))))
|
| 2157 | (build-system pyproject-build-system)
|
| 2158 | |
| 2159 | (arguments (list #:tests? #false))
|
| 2160 | (propagated-inputs
|
| 2161 | (list python-dask
|
| 2162 | python-numpy
|
| 2163 | python-dateutil
|
| 2164 | python-spatial-image
|
| 2165 | python-xarray
|
| 2166 | python-xarray-dataclass
|
| 2167 | python-zarr))
|
| 2168 | (native-inputs
|
| 2169 | (list python-hatchling))
|
| 2170 | (home-page "https://github.com/spatial-image/multiscale-spatial-image")
|
| 2171 | (synopsis "Multi-dimensional spatial image data structure")
|
| 2172 | (description
|
| 2173 | "This package lets you generate a multiscale, chunked, multi-dimensional
|
| 2174 | spatial image data structure that can serialized to OME-NGFF. Each scale is a
|
| 2175 | scientific Python Xarray spatial-image Dataset, organized into nodes of an
|
| 2176 | Xarray Datatree.")
|
| 2177 | (license license:asl2.0)))
|
| 2178 |
|
| 2179 | (define-public python-narwhals
|
| 2180 | (package
|
| 2181 | (name "python-narwhals")
|
| 2182 | (version "2.22.1")
|
| 2183 | (source
|
| 2184 | (origin
|
| 2185 | (method git-fetch)
|
| 2186 | (uri (git-reference
|
| 2187 | (url "https://github.com/narwhals-dev/narwhals")
|
| 2188 | (commit (string-append "v" version))))
|
| 2189 | (file-name (git-file-name name version))
|
| 2190 | (sha256
|
| 2191 | (base32 "0rq7asql365iv40jdbdnp05jja3y304pr2xd85ng83ly24h2bidx"))))
|
| 2192 | (build-system pyproject-build-system)
|
| 2193 | (arguments
|
| 2194 | (list
|
| 2195 | #:build-backend "hatchling.build" |
| 2196 | |
| 2197 | #:test-flags
|
| 2198 | #~(list "--numprocesses" (number->string (min 8 (parallel-job-count)))
|
| 2199 | |
| 2200 | |
| 2201 | "--constructors=pandas")))
|
| 2202 | (native-inputs
|
| 2203 | (list python-hatchling
|
| 2204 | python-pytest
|
| 2205 | python-pytest-env
|
| 2206 | python-pytest-xdist))
|
| 2207 | (propagated-inputs
|
| 2208 | |
| 2209 | (list python-duckdb
|
| 2210 | python-pandas
|
| 2211 | python-polars
|
| 2212 | python-pyarrow
|
| 2213 | |
| 2214 | |
| 2215 | |
| 2216 | python-dask
|
| 2217 | |
| 2218 | python-modin
|
| 2219 | python-packaging
|
| 2220 | |
| 2221 | |
| 2222 | python-rich))
|
| 2223 | (home-page "https://narwhals-dev.github.io/narwhals/")
|
| 2224 | (synopsis "Compatibility layer between dataframe libraries")
|
| 2225 | (description
|
| 2226 | "This package provides an extremely lightweight compatibility layer
|
| 2227 | between dataframe libraries.
|
| 2228 | @itemize
|
| 2229 | @item full API support: cuDF, Modin, pandas, Polars, PyArrow
|
| 2230 | @item lazy-only support: Dask, DuckDB, Ibis, PySpark, SQLFrame
|
| 2231 | @end itemize")
|
| 2232 | (license license:expat)))
|
| 2233 |
|
| 2234 | |
| 2235 | |
| 2236 | (define-public python-narwhals-minimal
|
| 2237 | (package/inherit python-narwhals
|
| 2238 | (name "python-narwhals-minimal")
|
| 2239 | (arguments
|
| 2240 | (substitute-keyword-arguments arguments
|
| 2241 | ((#:tests? _ #t) #f)))
|
| 2242 | (native-inputs
|
| 2243 | (list python-hatchling))
|
| 2244 | |
| 2245 | (propagated-inputs '())))
|
| 2246 |
|
| 2247 | (define-public python-ndindex
|
| 2248 | (package
|
| 2249 | (name "python-ndindex")
|
| 2250 | (version "1.10.1")
|
| 2251 | (source
|
| 2252 | (origin
|
| 2253 | (method url-fetch)
|
| 2254 | (uri (pypi-uri "ndindex" version))
|
| 2255 | (sha256
|
| 2256 | (base32 "048gc4pwvsyxkz7brph1fwmlgjd35alimvnb3248y91iy30i6q8g"))))
|
| 2257 | (build-system pyproject-build-system)
|
| 2258 | (arguments
|
| 2259 | (list
|
| 2260 | |
| 2261 | #:test-flags
|
| 2262 | #~(list "--pyargs" "ndindex"
|
| 2263 | "--numprocesses" (number->string (min 8 (parallel-job-count)))
|
| 2264 | "-p" "no:cov"
|
| 2265 | "-W" "ignore:Unknown pytest.mark.no_cover:pytest.PytestUnknownMarkWarning"
|
| 2266 | "-k" "not test_iter_indices_matmul") |
| 2267 | #:phases
|
| 2268 | #~(modify-phases %standard-phases
|
| 2269 | (add-before 'check 'remove-local-source
|
| 2270 | (lambda _
|
| 2271 | (delete-file-recursively "ndindex"))))))
|
| 2272 | (native-inputs
|
| 2273 | (list python-cython
|
| 2274 | python-numpy
|
| 2275 | python-pytest
|
| 2276 | python-pytest-xdist
|
| 2277 | python-setuptools
|
| 2278 | python-sympy))
|
| 2279 | (home-page "https://quansight-labs.github.io/ndindex/")
|
| 2280 | (synopsis "Python library for manipulating indices of ndarrays")
|
| 2281 | (description "This package provides a Python library for manipulating
|
| 2282 | indices of @code{ndarrays}.")
|
| 2283 | (license license:expat)))
|
| 2284 |
|
| 2285 | (define-public python-nestcheck
|
| 2286 | (package
|
| 2287 | (name "python-nestcheck")
|
| 2288 | |
| 2289 | |
| 2290 | |
| 2291 | (properties '((commit . "513ef962ef7b0d66377686f9fe0a9e354dad48b3")
|
| 2292 | (revision . "0")))
|
| 2293 | (version (git-version "0.2.1"
|
| 2294 | (assoc-ref properties 'revision)
|
| 2295 | (assoc-ref properties 'commit)))
|
| 2296 | (source
|
| 2297 | (origin
|
| 2298 | (method git-fetch)
|
| 2299 | (uri (git-reference
|
| 2300 | (url "https://github.com/ejhigson/nestcheck")
|
| 2301 | (commit (assoc-ref properties 'commit))))
|
| 2302 | (file-name (git-file-name name version))
|
| 2303 | (sha256
|
| 2304 | (base32 "0zzms2jkiapawnjyr5i7c61m7pmg6yd3nmpv23bdx51glz2fmglc"))))
|
| 2305 | (build-system pyproject-build-system)
|
| 2306 | (arguments
|
| 2307 | (list
|
| 2308 | |
| 2309 | #:test-flags
|
| 2310 | |
| 2311 | |
| 2312 | #~(list "-k" (string-append "not test_run_list_error_summary"
|
| 2313 | |
| 2314 | |
| 2315 | " and not test_kde_plot_df"
|
| 2316 | |
| 2317 | |
| 2318 | " and not test_summary_df"))
|
| 2319 | #:phases
|
| 2320 | #~(modify-phases %standard-phases
|
| 2321 | (add-after 'unpack 'use-pytest
|
| 2322 | (lambda _
|
| 2323 | (substitute* "tests/test_core.py"
|
| 2324 | (("'nose'") "'pytest'")))))))
|
| 2325 | (native-inputs
|
| 2326 | (list python-pytest
|
| 2327 | python-setuptools))
|
| 2328 | (propagated-inputs
|
| 2329 | (list python-fgivenx
|
| 2330 | python-matplotlib
|
| 2331 | python-numpy
|
| 2332 | python-pandas
|
| 2333 | python-scipy
|
| 2334 | python-tqdm))
|
| 2335 | (home-page "https://github.com/ejhigson/nestcheck")
|
| 2336 | (synopsis "Nested sampling calculations utilities")
|
| 2337 | (description
|
| 2338 | "This package implements a functionality to work with
|
| 2339 | @url{https://en.wikipedia.org/wiki/Nested_sampling_algorithm, Nested
|
| 2340 | sampling}, a popular numerical method for Bayesian computation, which
|
| 2341 | simultaneously generates samples from the posterior distribution and an
|
| 2342 | estimate of the Bayesian evidence for a given likelihood and prior.
|
| 2343 | @code{nestcheck} provides Python utilities for analysing samples produced by
|
| 2344 | nested sampling, and estimating uncertainties on nested sampling
|
| 2345 | calculations (which have different statistical properties to calculations
|
| 2346 | using other numerical methods).")
|
| 2347 | (license license:expat)))
|
| 2348 |
|
| 2349 | (define-public python-nibabel
|
| 2350 | (package
|
| 2351 | (name "python-nibabel")
|
| 2352 | (version "5.3.2")
|
| 2353 | (source
|
| 2354 | (origin
|
| 2355 | (method url-fetch)
|
| 2356 | (uri (pypi-uri "nibabel" version))
|
| 2357 | (sha256
|
| 2358 | (base32 "16snprwgp7qzp51j3mx0zdn7brvx6r14ankldi24ny0w7d8adp0b"))))
|
| 2359 | (build-system pyproject-build-system)
|
| 2360 | (arguments
|
| 2361 | (list
|
| 2362 | |
| 2363 | #:test-flags #~(list "-k" "not test_first and not test_second")))
|
| 2364 | (propagated-inputs (list python-importlib-resources python-numpy
|
| 2365 | python-packaging python-typing-extensions))
|
| 2366 | (native-inputs (list python-hatch-vcs
|
| 2367 | python-hatchling
|
| 2368 | python-pytest
|
| 2369 | python-pytest-httpserver
|
| 2370 | python-pytest-xdist))
|
| 2371 | (home-page "https://nipy.org/nibabel/")
|
| 2372 | (synopsis "Read and write access to common neuroimaging file formats")
|
| 2373 | (description
|
| 2374 | "@code{nibabel} is a library that provides read and write access to
|
| 2375 | common neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2
|
| 2376 | and later), GIFTI, NIfTI1, NIfTI2, CIFTI-2, MINC1, MINC2, AFNI BRIK/HEAD,
|
| 2377 | ECAT and Philips PAR/REC. In addition, NiBabel also supports FreeSurfer’s
|
| 2378 | MGH, geometry, annotation and morphometry files, and provides some limited
|
| 2379 | support for DICOM.")
|
| 2380 | (license license:expat))) |
| 2381 |
|
| 2382 | (define-public python-numba-stats
|
| 2383 | (package
|
| 2384 | (name "python-numba-stats")
|
| 2385 | (version "1.11.0")
|
| 2386 | (source
|
| 2387 | (origin
|
| 2388 | (method url-fetch)
|
| 2389 | (uri (pypi-uri "numba_stats" version))
|
| 2390 | (sha256
|
| 2391 | (base32 "1m5gwrc3liqydpix5ckyc7s5ysvgvinbznnkcvk2xjz13lwfy2s8"))))
|
| 2392 | (build-system pyproject-build-system)
|
| 2393 | (native-inputs
|
| 2394 | (list python-pytest
|
| 2395 | python-setuptools
|
| 2396 | python-setuptools-scm))
|
| 2397 | (propagated-inputs
|
| 2398 | (list python-numba
|
| 2399 | python-numpy
|
| 2400 | python-scipy))
|
| 2401 | (home-page "https://github.com/scikit-hep/numba-stats")
|
| 2402 | (synopsis "Accelerated implementations of SciPy probability distributions")
|
| 2403 | (description
|
| 2404 | "This package provides Numba-accelerated implementations of common SciPy
|
| 2405 | probability distributions and others used in particle physics.
|
| 2406 |
|
| 2407 | The supported distributions are:
|
| 2408 |
|
| 2409 | @itemize
|
| 2410 | @item Uniform
|
| 2411 | @item (Truncated) Normal
|
| 2412 | @item Log-normal
|
| 2413 | @item Poisson
|
| 2414 | @item Binomial
|
| 2415 | @item (Truncated) Exponential
|
| 2416 | @item Student's t
|
| 2417 | @item Voigtian
|
| 2418 | @item Crystal Ball
|
| 2419 | @item Generalised double-sided Crystal Ball
|
| 2420 | @item Tsallis-Hagedorn, a model for the minimum bias pT distribution
|
| 2421 | @item Q-Gaussian
|
| 2422 | @item Bernstein density (not normalized to unity)
|
| 2423 | @item Cruijff density (not normalized to unity)
|
| 2424 | @item CMS-Shape
|
| 2425 | @item Generalized Argus
|
| 2426 | @end itemize")
|
| 2427 | (license license:expat)))
|
| 2428 |
|
| 2429 | (define-public python-numbagg
|
| 2430 | (package
|
| 2431 | (name "python-numbagg")
|
| 2432 | (version "0.9.4")
|
| 2433 | (source
|
| 2434 | (origin
|
| 2435 | (method git-fetch)
|
| 2436 | (uri (git-reference
|
| 2437 | (url "https://github.com/numbagg/numbagg")
|
| 2438 | (commit (string-append "v" version))))
|
| 2439 | (file-name (git-file-name name version))
|
| 2440 | (sha256
|
| 2441 | (base32 "1frx10rdyklp0zbd8bckl63i0vmj0z93nkx1i7dylbv99iw27215"))))
|
| 2442 | (build-system pyproject-build-system)
|
| 2443 | (propagated-inputs (list python-numba python-numpy))
|
| 2444 | (native-inputs (list python-bottleneck
|
| 2445 | python-pandas
|
| 2446 | python-pytest
|
| 2447 | python-pytest-benchmark |
| 2448 | python-setuptools
|
| 2449 | python-setuptools-scm
|
| 2450 | python-tabulate))
|
| 2451 | (home-page "https://github.com/numbagg/numbagg")
|
| 2452 | (synopsis "Fast N-dimensional aggregation functions with Numba")
|
| 2453 | (description "Numbagg provides high-performance implementations for moving
|
| 2454 | window, aggregation, and grouping functions. It leverages Numba's JIT
|
| 2455 | compilation and is especially performant on multi-core parallelism.")
|
| 2456 | (license license:bsd-3)))
|
| 2457 |
|
| 2458 | (define-public python-numdifftools
|
| 2459 | (package
|
| 2460 | (name "python-numdifftools")
|
| 2461 | (version "0.9.42")
|
| 2462 | (source
|
| 2463 | (origin
|
| 2464 | (method url-fetch)
|
| 2465 | (uri (pypi-uri "numdifftools" version))
|
| 2466 | (sha256
|
| 2467 | (base32 "1hgv3jhf4y9qrizkwfryj2b56zd0i2dvzig1y7r4ng193wbparl6"))))
|
| 2468 | (build-system pyproject-build-system)
|
| 2469 | (arguments
|
| 2470 | (list
|
| 2471 | |
| 2472 | #:test-flags
|
| 2473 | #~(list "-m" "not benchmark and not slow")))
|
| 2474 | (native-inputs
|
| 2475 | (list python-algopy
|
| 2476 | python-line-profiler
|
| 2477 | python-pdm-backend
|
| 2478 | python-pytest
|
| 2479 | python-statsmodels))
|
| 2480 | (propagated-inputs
|
| 2481 | (list python-numpy
|
| 2482 | python-scipy
|
| 2483 | |
| 2484 | python-matplotlib))
|
| 2485 | (home-page "https://github.com/pbrod/numdifftools")
|
| 2486 | (synopsis "Solves automatic numerical differentiation problems")
|
| 2487 | (description
|
| 2488 | "This package implements a functionality to solve automatic numerical
|
| 2489 | differentiation problems in one or more variables. Finite differences are
|
| 2490 | used in an adaptive manner, coupled with a Richardson extrapolation
|
| 2491 | methodology to provide a maximally accurate result. The user can configure
|
| 2492 | many options like; changing the order of the method or the extrapolation, even
|
| 2493 | allowing the user to specify whether complex-step, central, forward or
|
| 2494 | backward differences are used.")
|
| 2495 | (license license:bsd-3)))
|
| 2496 |
|
| 2497 | (define-public python-numpoly
|
| 2498 | (package
|
| 2499 | (name "python-numpoly")
|
| 2500 | (version "1.3.9")
|
| 2501 | (source
|
| 2502 | (origin
|
| 2503 | (method git-fetch)
|
| 2504 | (uri (git-reference
|
| 2505 | (url "https://github.com/jonathf/numpoly")
|
| 2506 | (commit version)))
|
| 2507 | (file-name (git-file-name name version))
|
| 2508 | (sha256
|
| 2509 | (base32 "1abz6ch2bzghbzwkvrr2yrg6zkkaz4wn7qqc5810szryrv0is3ih"))))
|
| 2510 | (build-system pyproject-build-system)
|
| 2511 | (arguments
|
| 2512 | (list
|
| 2513 | |
| 2514 | #:phases
|
| 2515 | #~(modify-phases %standard-phases
|
| 2516 | (add-after 'unpack 'set-version
|
| 2517 | |
| 2518 | (lambda _
|
| 2519 | (substitute* "pyproject.toml"
|
| 2520 | (("0.1.0")
|
| 2521 | #$version))))
|
| 2522 | (add-before 'check 'remove-local-source
|
| 2523 | (lambda _
|
| 2524 | (delete-file-recursively "numpoly"))))))
|
| 2525 | (native-inputs
|
| 2526 | (list python-cython
|
| 2527 | python-pytest
|
| 2528 | python-setuptools
|
| 2529 | python-sympy))
|
| 2530 | (propagated-inputs
|
| 2531 | (list python-importlib-metadata
|
| 2532 | python-numpy))
|
| 2533 | (home-page "https://numpoly.readthedocs.io/en/master/")
|
| 2534 | (synopsis "Polynomials as a numpy datatype")
|
| 2535 | (description "Numpoly is a generic library for creating, manipulating and
|
| 2536 | evaluating arrays of polynomials based on @code{numpy.ndarray objects}.")
|
| 2537 | |
| 2538 | |
| 2539 | (supported-systems '("x86_64-linux" "aarch64-linux" "powerpc64le-linux"))
|
| 2540 | (license license:bsd-2)))
|
| 2541 |
|
| 2542 | (define-public python-numpy-groupies
|
| 2543 | (package
|
| 2544 | (name "python-numpy-groupies")
|
| 2545 | (version "0.11.3")
|
| 2546 | (source
|
| 2547 | (origin
|
| 2548 | (method url-fetch)
|
| 2549 | (uri (pypi-uri "numpy_groupies" version))
|
| 2550 | (sha256
|
| 2551 | (base32 "1q13gi0018maifhn6dkwi0pprr3p7ikv9r3zffg6p1ayspdazm5f"))))
|
| 2552 | (build-system pyproject-build-system)
|
| 2553 | (native-inputs
|
| 2554 | (list python-numba
|
| 2555 | python-pandas
|
| 2556 | python-pytest
|
| 2557 | python-setuptools
|
| 2558 | python-setuptools-scm))
|
| 2559 | (propagated-inputs
|
| 2560 | (list python-numpy))
|
| 2561 | (home-page "https://github.com/ml31415/numpy-groupies")
|
| 2562 | (synopsis "Tools for group-indexing operations: aggregated sum and more")
|
| 2563 | (description
|
| 2564 | "This package provides optimized tools for group-indexing operations:
|
| 2565 | aggregated sum and more.")
|
| 2566 | (license license:bsd-3)))
|
| 2567 |
|
| 2568 | (define-public python-openpmd-api
|
| 2569 | (package
|
| 2570 | (name "python-openpmd-api")
|
| 2571 | |
| 2572 | (properties '((commit . "ec8251eaa80ecc7182f83de2180d020f42978046")
|
| 2573 | (revision . "0")))
|
| 2574 | (version (git-version "0.17.0"
|
| 2575 | (assoc-ref properties 'revision)
|
| 2576 | (assoc-ref properties 'commit)))
|
| 2577 | (source
|
| 2578 | (origin
|
| 2579 | (method git-fetch)
|
| 2580 | (uri (git-reference
|
| 2581 | (url "https://github.com/openPMD/openPMD-api")
|
| 2582 | (commit (assoc-ref properties 'commit))))
|
| 2583 | (file-name (git-file-name name version))
|
| 2584 | (sha256
|
| 2585 | (base32 "1y9jz1igjwcrxh5w31q0dmzb9hpizbmg4yzma14ca3pcs0na4mqc"))))
|
| 2586 | (build-system cmake-build-system)
|
| 2587 | (arguments
|
| 2588 | (list
|
| 2589 | #:configure-flags
|
| 2590 | #~(list "-DopenPMD_SUPERBUILD=OFF")))
|
| 2591 | (native-inputs
|
| 2592 | (list catch2-2
|
| 2593 | python-numpy))
|
| 2594 | (inputs
|
| 2595 | (list hdf5
|
| 2596 | nlohmann-json
|
| 2597 | openmpi
|
| 2598 | pybind11
|
| 2599 | python
|
| 2600 | toml11))
|
| 2601 | (propagated-inputs
|
| 2602 | (list python-mpi4py))
|
| 2603 | (home-page "https://openpmd-api.readthedocs.io/")
|
| 2604 | (synopsis "C++ & Python API for Scientific I/O")
|
| 2605 | (description
|
| 2606 | "openPMD is an open meta-data schema that provides meaning and
|
| 2607 | self-description for data sets in science and engineering. See the
|
| 2608 | @url{https://github.com/openPMD/openPMD-standard, openPMD standard} for
|
| 2609 | details of this schema.
|
| 2610 |
|
| 2611 | This library provides a reference API for openPMD data handling. Since
|
| 2612 | openPMD is a schema (or markup) on top of portable, hierarchical file formats,
|
| 2613 | this library implements various backends such as HDF5, ADIOS2 and JSON.
|
| 2614 | Writing & reading through those backends and their associated files are
|
| 2615 | supported for serial and @url{https://www.mpi-forum.org/docs/, MPI-parallel}
|
| 2616 | workflows.")
|
| 2617 | (license (list license:gpl3 license:lgpl3))))
|
| 2618 |
|
| 2619 | (define-public python-opt-einsum
|
| 2620 | (package
|
| 2621 | (name "python-opt-einsum")
|
| 2622 | (version "3.4.0")
|
| 2623 | (source
|
| 2624 | (origin
|
| 2625 | (method git-fetch)
|
| 2626 | (uri (git-reference
|
| 2627 | (url "https://github.com/dgasmith/opt_einsum")
|
| 2628 | (commit (string-append "v" version))))
|
| 2629 | (file-name (git-file-name name version))
|
| 2630 | (sha256
|
| 2631 | (base32 "14p8rncba295w1bfnmn27fxi6mjas31y7yawvbiwj7d7ci196kx4"))))
|
| 2632 | (build-system pyproject-build-system)
|
| 2633 | |
| 2634 | (native-inputs
|
| 2635 | (list python-hatch-fancy-pypi-readme
|
| 2636 | python-hatch-vcs
|
| 2637 | python-hatchling
|
| 2638 | python-pytest))
|
| 2639 | (propagated-inputs
|
| 2640 | (list python-dask
|
| 2641 | |
| 2642 | python-numpy
|
| 2643 | python-sparse
|
| 2644 | #;python-torch))
|
| 2645 | (home-page "https://github.com/dgasmith/opt_einsum")
|
| 2646 | (synopsis "Optimizing numpys einsum function")
|
| 2647 | (description
|
| 2648 | "Optimized einsum can significantly reduce the overall execution time of
|
| 2649 | einsum-like expressions by optimizing the expression's contraction order and
|
| 2650 | dispatching many operations to canonical BLAS, cuBLAS, or other specialized
|
| 2651 | routines. Optimized einsum is agnostic to the backend and can handle NumPy,
|
| 2652 | Dask, PyTorch, Tensorflow, CuPy, Sparse, Theano, JAX, and Autograd arrays as
|
| 2653 | well as potentially any library which conforms to a standard API. See the
|
| 2654 | documentation for more information.")
|
| 2655 | (license license:expat)))
|
| 2656 |
|
| 2657 | (define-public python-osfclient
|
| 2658 | (package
|
| 2659 | (name "python-osfclient")
|
| 2660 | (version "0.0.5")
|
| 2661 | (source
|
| 2662 | (origin
|
| 2663 | (method git-fetch)
|
| 2664 | (uri (git-reference
|
| 2665 | (url "https://github.com/osfclient/osfclient")
|
| 2666 | (commit version)))
|
| 2667 | (file-name (git-file-name name version))
|
| 2668 | (sha256
|
| 2669 | (base32 "1ympjh028xgwkzvhwqa31rack1h8nni7zzn2alp1819m4pm8hysn"))))
|
| 2670 | (build-system pyproject-build-system)
|
| 2671 | (arguments
|
| 2672 | (list
|
| 2673 | #:test-flags
|
| 2674 | |
| 2675 | |
| 2676 | |
| 2677 | #~(list "-k"
|
| 2678 | (string-append "not test_recursive_upload"
|
| 2679 | " and not nottest_recursive_upload_with_subdir"))))
|
| 2680 | (native-inputs
|
| 2681 | (list python-pytest
|
| 2682 | python-mock
|
| 2683 | python-setuptools))
|
| 2684 | (propagated-inputs
|
| 2685 | (list python-requests
|
| 2686 | python-six
|
| 2687 | python-tqdm))
|
| 2688 | (home-page "https://github.com/osfclient/osfclient")
|
| 2689 | (synopsis "Python library and command-line client for file storage on OSF")
|
| 2690 | (description
|
| 2691 | "The @code{osfclient} is a python library and a command-line client for
|
| 2692 | up- and downloading files to and from @url{https://osf.io/, Open Science
|
| 2693 | Framework} projects. The @acronym{OSF, Open Science Framework} is an open
|
| 2694 | source project which facilitates the open collaboration of researchers on the
|
| 2695 | web, by sharing data and other research outputs.")
|
| 2696 | (license license:bsd-3)))
|
| 2697 |
|
| 2698 | (define-public python-osqp
|
| 2699 | (package
|
| 2700 | (name "python-osqp")
|
| 2701 | (version "1.0.5")
|
| 2702 | (source
|
| 2703 | (origin
|
| 2704 | (method git-fetch)
|
| 2705 | (uri (git-reference
|
| 2706 | (url "https://github.com/osqp/osqp-python")
|
| 2707 | (commit (string-append "v" version))
|
| 2708 | (recursive? #true)))
|
| 2709 | (file-name (git-file-name name version))
|
| 2710 | (sha256
|
| 2711 | (base32 "0b5j0hv6dlbs3dm9xvs2ijnjr2r8xnchs4jyk3dx16qhcp85wklb"))))
|
| 2712 | (build-system pyproject-build-system)
|
| 2713 | (arguments
|
| 2714 | (list
|
| 2715 | |
| 2716 | #:test-flags
|
| 2717 | |
| 2718 | #~(list "--ignore=src/osqp/tests/codegen_vectors_test.py"
|
| 2719 | |
| 2720 | "--ignore=src/osqp/tests/codegen_matrices_test.py")
|
| 2721 | #:phases
|
| 2722 | #~(modify-phases %standard-phases
|
| 2723 | (add-after 'unpack 'fix-osqp-source-location
|
| 2724 | |
| 2725 | |
| 2726 | (lambda _
|
| 2727 | (copy-recursively #$(package-source
|
| 2728 | (this-package-native-input "osqp"))
|
| 2729 | "osqp")
|
| 2730 | (substitute* "osqp/algebra/_common/lin_sys/qdldl/qdldl.cmake"
|
| 2731 | (("Fetching/configuring QDLDL solver")
|
| 2732 | (format #f "Adding/configuring QDLDL solver from: ~a"
|
| 2733 | #$(package-source
|
| 2734 | (this-package-native-input "qdldl"))))
|
| 2735 | (("GIT_REPOSITORY https://github.com/osqp/qdldl\\.git")
|
| 2736 | (format #f "SOURCE_DIR ~a"
|
| 2737 | #$(package-source
|
| 2738 | (this-package-native-input "qdldl"))))
|
| 2739 | (("GIT_TAG v0.1.8")
|
| 2740 | ""))
|
| 2741 | (substitute* "CMakeLists.txt"
|
| 2742 | (("Fetching/configuring OSQP")
|
| 2743 | (format #f "Adding/configuring OSQP: ~a"
|
| 2744 | (string-append (getcwd) "/osqp")))
|
| 2745 | (("GIT_REPOSITORY https://github.com/osqp/osqp\\.git")
|
| 2746 | (format #f "SOURCE_DIR ~a"
|
| 2747 | (string-append (getcwd) "/osqp")))
|
| 2748 | (("GIT_TAG v1.0.0")
|
| 2749 | "")))))))
|
| 2750 | (native-inputs
|
| 2751 | (list cmake-minimal
|
| 2752 | osqp
|
| 2753 | pybind11-2
|
| 2754 | python-pytest
|
| 2755 | python-pytorch
|
| 2756 | python-scikit-build-core
|
| 2757 | python-setuptools-scm
|
| 2758 | qdldl))
|
| 2759 | (propagated-inputs
|
| 2760 | (list python-jinja2
|
| 2761 | python-joblib
|
| 2762 | python-numpy
|
| 2763 | python-scipy
|
| 2764 | python-setuptools))
|
| 2765 | (home-page "https://osqp.org/")
|
| 2766 | (synopsis "OSQP: operator splitting QP solver")
|
| 2767 | (description "The OSQP (Operator Splitting Quadratic Program) solver is a
|
| 2768 | numerical optimization package.")
|
| 2769 | (license license:asl2.0)))
|
| 2770 |
|
| 2771 | (define-public python-particle
|
| 2772 | (package
|
| 2773 | (name "python-particle")
|
| 2774 | (version "0.26.1")
|
| 2775 | (source
|
| 2776 | (origin
|
| 2777 | (method url-fetch)
|
| 2778 | (uri (pypi-uri "particle" version))
|
| 2779 | (sha256
|
| 2780 | (base32 "1iwhfljihqlxacqxx9c782hp5mp54ks6fwzrirbdcmldmp89hxhh"))))
|
| 2781 | (build-system pyproject-build-system)
|
| 2782 | (propagated-inputs (list python-attrs
|
| 2783 | python-hepunits
|
| 2784 | python-typing-extensions))
|
| 2785 | (native-inputs (list python-hatch-vcs
|
| 2786 | python-hatchling
|
| 2787 | python-pandas
|
| 2788 | python-pytest
|
| 2789 | python-pytest-benchmark
|
| 2790 | python-tabulate))
|
| 2791 | (home-page "https://github.com/scikit-hep/particle")
|
| 2792 | (synopsis "Extended PDG particle data and MC identification codes")
|
| 2793 | (description
|
| 2794 | "@code{Particle} provides a pythonic interface to the Particle Data Group
|
| 2795 | (PDG) particle data tables and particle identification codes, with extended
|
| 2796 | particle information and extra goodies.")
|
| 2797 | (license license:bsd-3)))
|
| 2798 |
|
| 2799 | (define-public python-pint
|
| 2800 | (package
|
| 2801 | (name "python-pint")
|
| 2802 | (version "0.24.4")
|
| 2803 | (source
|
| 2804 | (origin
|
| 2805 | (method url-fetch)
|
| 2806 | (uri (pypi-uri "pint" version))
|
| 2807 | (sha256
|
| 2808 | (base32 "100vp5jg2sqj5wxaflj1rqjv2pk4fd55l2h2sdn7m0vlnlwm89rm"))))
|
| 2809 | (build-system pyproject-build-system)
|
| 2810 | (arguments
|
| 2811 | (list
|
| 2812 | #:test-flags #~(list "--ignore=pint/testsuite/benchmarks")
|
| 2813 | #:phases
|
| 2814 | #~(modify-phases %standard-phases
|
| 2815 | (add-before 'check 'pre-check
|
| 2816 | (lambda _
|
| 2817 | |
| 2818 | |
| 2819 | (setenv "HOME" "/tmp"))))))
|
| 2820 | (native-inputs
|
| 2821 | (list python-pytest
|
| 2822 | python-pytest-mpl
|
| 2823 | python-pytest-subtests
|
| 2824 | python-setuptools
|
| 2825 | python-setuptools-scm
|
| 2826 | python-wheel))
|
| 2827 | (propagated-inputs
|
| 2828 | (list python-flexcache
|
| 2829 | python-flexparser
|
| 2830 | python-platformdirs
|
| 2831 | python-typing-extensions))
|
| 2832 | (home-page "https://github.com/hgrecco/pint")
|
| 2833 | (synopsis "Physical quantities module")
|
| 2834 | (description
|
| 2835 | "Pint is a Python package to define, operate and manipulate physical
|
| 2836 | quantities: the product of a numerical value and a unit of measurement. It
|
| 2837 | allows arithmetic operations between them and conversions from and to
|
| 2838 | different units.")
|
| 2839 | (license license:bsd-3)))
|
| 2840 |
|
| 2841 | (define-public python-pyamg
|
| 2842 | (package
|
| 2843 | (name "python-pyamg")
|
| 2844 | (version "5.3.0")
|
| 2845 | (source (origin
|
| 2846 | (method url-fetch)
|
| 2847 | (uri (pypi-uri "pyamg" version))
|
| 2848 | (modules '((guix build utils)))
|
| 2849 | (snippet
|
| 2850 | |
| 2851 | #~(begin
|
| 2852 | (for-each
|
| 2853 | (lambda (file)
|
| 2854 | (delete-file (string-append "pyamg/amg_core/" file)))
|
| 2855 | '("air_bind.cpp"
|
| 2856 | "evolution_strength_bind.cpp"
|
| 2857 | "graph_bind.cpp"
|
| 2858 | "krylov_bind.cpp"
|
| 2859 | "linalg_bind.cpp"
|
| 2860 | "relaxation_bind.cpp"
|
| 2861 | "ruge_stuben_bind.cpp"
|
| 2862 | "smoothed_aggregation_bind.cpp"
|
| 2863 | "tests/bind_examples_bind.cpp"))))
|
| 2864 | (sha256
|
| 2865 | (base32
|
| 2866 | "02w6xy3i0qcpsfc64zw8k15mi6qykq65h3d98vi9p6fdlkqx08sk"))))
|
| 2867 | (arguments
|
| 2868 | (list
|
| 2869 | |
| 2870 | #:phases
|
| 2871 | #~(modify-phases %standard-phases
|
| 2872 | |
| 2873 | (add-after 'unpack 'amg-core-bind-them
|
| 2874 | (lambda _
|
| 2875 | |
| 2876 | |
| 2877 | (copy-file "pyamg/amg_core/bindthem.py"
|
| 2878 | "pyamg/amg_core/tests/bindthem.py")
|
| 2879 | (with-directory-excursion "pyamg/amg_core"
|
| 2880 | (substitute* "bindthem.py"
|
| 2881 | (("/usr/bin/env python3") (which "python3")))
|
| 2882 | (invoke "sh" "generate.sh"))
|
| 2883 | (with-directory-excursion "pyamg/amg_core/tests"
|
| 2884 | (invoke "python" "bindthem.py" "bind_examples.h"))))
|
| 2885 | (add-before 'check 'pre-check
|
| 2886 | (lambda _
|
| 2887 | (copy-recursively "pyamg/tests" "tests")
|
| 2888 | (delete-file-recursively "pyamg"))))))
|
| 2889 | (build-system pyproject-build-system)
|
| 2890 | (native-inputs
|
| 2891 | (list pybind11-2
|
| 2892 | python-cppheaderparser
|
| 2893 | python-pytest
|
| 2894 | python-pyyaml
|
| 2895 | python-setuptools
|
| 2896 | python-setuptools-scm))
|
| 2897 | (propagated-inputs
|
| 2898 | (list python-numpy
|
| 2899 | python-scipy))
|
| 2900 | (home-page "https://github.com/pyamg/pyamg")
|
| 2901 | (synopsis "Algebraic Multigrid Solvers in Python")
|
| 2902 | (description "PyAMG is a Python library of Algebraic Multigrid
|
| 2903 | (AMG) solvers. It features implementations of:
|
| 2904 | @itemize
|
| 2905 | @item Ruge-Stuben (RS) or Classical AMG
|
| 2906 | @item AMG based on Smoothed Aggregation (SA)
|
| 2907 | @item Adaptive Smoothed Aggregation (αSA)
|
| 2908 | @item Compatible Relaxation (CR)
|
| 2909 | @item Krylov methods such as CG, GMRES, FGMRES, BiCGStab, MINRES, etc.
|
| 2910 | @end itemize")
|
| 2911 | (license license:expat)))
|
| 2912 |
|
| 2913 | (define-public python-pyet
|
| 2914 | (package
|
| 2915 | (name "python-pyet")
|
| 2916 | (version "1.3.1")
|
| 2917 | (source
|
| 2918 | (origin
|
| 2919 | (method url-fetch)
|
| 2920 | (uri (pypi-uri "pyet" version))
|
| 2921 | (sha256
|
| 2922 | (base32 "1dblsx0bv1g453hcx5vwij1zgankwgwvhwllqkn47k578h038xvy"))))
|
| 2923 | (build-system pyproject-build-system)
|
| 2924 | (native-inputs
|
| 2925 | (list python-mock
|
| 2926 | python-pytest
|
| 2927 | python-setuptools
|
| 2928 | python-wheel))
|
| 2929 | (propagated-inputs
|
| 2930 | (list python-pandas
|
| 2931 | python-xarray))
|
| 2932 | (home-page "https://github.com/pyet-org/pyet")
|
| 2933 | (synopsis "Python package for evapotranspiration calculation")
|
| 2934 | (description
|
| 2935 | "This package provides a Python library for calculating
|
| 2936 | Evapotranspiration using various standard methods.")
|
| 2937 | (license license:expat)))
|
| 2938 |
|
| 2939 | (define-public python-pykdtree
|
| 2940 | (package
|
| 2941 | (name "python-pykdtree")
|
| 2942 | (version "1.4.2")
|
| 2943 | (source
|
| 2944 | (origin
|
| 2945 | (method url-fetch)
|
| 2946 | (uri (pypi-uri "pykdtree" version))
|
| 2947 | (sha256
|
| 2948 | (base32 "1xb5xdp32s5ffcbbb6vlrj4i70hdknajvr9yhzx0wld52rx9caxx"))))
|
| 2949 | (build-system pyproject-build-system)
|
| 2950 | (arguments
|
| 2951 | (list
|
| 2952 | |
| 2953 | |
| 2954 | #:tests? #f
|
| 2955 | #:phases
|
| 2956 | #~(modify-phases %standard-phases
|
| 2957 | (add-after 'install 'fix-site-packages
|
| 2958 | (lambda* (#:key inputs outputs #:allow-other-keys)
|
| 2959 | (with-directory-excursion (site-packages inputs outputs)
|
| 2960 | (for-each delete-file (find-files "." "test*"))))))))
|
| 2961 | (native-inputs
|
| 2962 | (list python-cython python-pytest python-setuptools python-wheel))
|
| 2963 | (propagated-inputs
|
| 2964 | (list python-numpy))
|
| 2965 | (home-page "https://github.com/storpipfugl/pykdtree")
|
| 2966 | (synopsis "Fast kd-tree implementation with OpenMP-enabled queries")
|
| 2967 | (description
|
| 2968 | "@code{pykdtree} is a kd-tree implementation for fast nearest neighbour
|
| 2969 | search in Python.")
|
| 2970 | (license license:lgpl3+)))
|
| 2971 |
|
| 2972 | (define-public python-pynetdicom
|
| 2973 | (package
|
| 2974 | (name "python-pynetdicom")
|
| 2975 | (version "2.1.1")
|
| 2976 | (source (origin
|
| 2977 | (method url-fetch)
|
| 2978 | (uri (pypi-uri "pynetdicom" version))
|
| 2979 | (sha256
|
| 2980 | (base32
|
| 2981 | "1smzrnc93nmv8jz4np9knas74a46b1nhb3hjpf8n9vfpxypgnwcn"))))
|
| 2982 | (build-system pyproject-build-system)
|
| 2983 | (arguments
|
| 2984 | (list
|
| 2985 | #:test-flags
|
| 2986 | |
| 2987 | |
| 2988 | #~(list "-k" (string-append
|
| 2989 | " not TestFindSCP"
|
| 2990 | " and not TestQRGetServiceClass"
|
| 2991 | " and not TestQRMoveServiceClass"
|
| 2992 | " and not TestStoreSCP"
|
| 2993 | " and not test_ae.py"
|
| 2994 | " and not test_echoscp.py"
|
| 2995 | " and not test_qrscp_echo.py"
|
| 2996 | " and not test_storescp.py"
|
| 2997 | " and not test_pr_level_patient"
|
| 2998 | " and not test_pr_level_series"
|
| 2999 | " and not test_scp_cancelled"))))
|
| 3000 | (native-inputs (list python-numpydoc
|
| 3001 | python-poetry-core
|
| 3002 | python-pytest))
|
| 3003 | (propagated-inputs (list python-pydicom
|
| 3004 | python-pyfakefs
|
| 3005 | python-sqlalchemy))
|
| 3006 | (home-page "https://github.com/pydicom/pynetdicom")
|
| 3007 | (synopsis "Python implementation of the DICOM networking protocol")
|
| 3008 | (description
|
| 3009 | "@code{pynetdicom} is a Python package that implements the DICOM
|
| 3010 | networking protocol. It allows the easy creation of DICOM
|
| 3011 | @acronym{SCUs,Service Class Users} and @acronym{SCPs,Service Class
|
| 3012 | Providers}.")
|
| 3013 | (license license:expat)))
|
| 3014 |
|
| 3015 | (define-public python-pyzx
|
| 3016 | (package
|
| 3017 | (name "python-pyzx")
|
| 3018 | (version "0.9.0")
|
| 3019 | (source
|
| 3020 | (origin
|
| 3021 | (method git-fetch) |
| 3022 | (uri (git-reference
|
| 3023 | (url "https://github.com/zxcalc/pyzx")
|
| 3024 | (commit (string-append "v" version))))
|
| 3025 | (file-name (git-file-name name version))
|
| 3026 | (sha256
|
| 3027 | (base32 "1bnmz08w1bmipir1wnn1k3fw64rply7891xns22qfj6yh0j1n6rj"))))
|
| 3028 | (build-system pyproject-build-system)
|
| 3029 | (arguments (list #:test-flags
|
| 3030 | #~(list
|
| 3031 | |
| 3032 | "--ignore=tests/long_test.py"
|
| 3033 | "--ignore=tests/long_scalar_test.py")
|
| 3034 | #:phases
|
| 3035 | #~(modify-phases %standard-phases
|
| 3036 | (add-before 'check 'pre-check
|
| 3037 | (lambda* (#:key inputs outputs #:allow-other-keys)
|
| 3038 | (setenv "HOME" "/tmp")
|
| 3039 | |
| 3040 | |
| 3041 | (setenv "MPLCONFIGDIR" "/tmp"))))))
|
| 3042 | (native-inputs (list python-pytest
|
| 3043 | python-setuptools
|
| 3044 | python-wheel))
|
| 3045 | (propagated-inputs (list python-ipywidgets
|
| 3046 | python-lark
|
| 3047 | python-numpy
|
| 3048 | python-pyperclip
|
| 3049 | python-tqdm))
|
| 3050 | (home-page "https://github.com/zxcalc/pyzx")
|
| 3051 | (synopsis "Quantum circuit rewriting and optimisation using the ZX-calculus")
|
| 3052 | (description
|
| 3053 | "PyZX is a Python tool implementing the theory of ZX-calculus for the
|
| 3054 | creation, visualisation, and automated rewriting of large-scale quantum
|
| 3055 | circuits. PyZX currently allows you to:
|
| 3056 |
|
| 3057 | @itemize
|
| 3058 | @item Read in quantum circuits in the file format of QASM, Quipper or Quantomatic;
|
| 3059 | @item Rewrite circuits into a pseudo-normal form using the ZX-calculus;
|
| 3060 | @item Extract new simplified circuits from these reduced graphs;
|
| 3061 | @item Visualise the ZX-graphs and rewrites using either Matplotlib, Quantomatic
|
| 3062 | or as a TikZ file for use in LaTeX documents;
|
| 3063 | @item Output the optimised circuits in QASM, QC or QUIPPER format.
|
| 3064 | @end itemize")
|
| 3065 | (license license:asl2.0)))
|
| 3066 |
|
| 3067 | (define-public python-qdldl
|
| 3068 | (package
|
| 3069 | (name "python-qdldl")
|
| 3070 | (version "0.1.7.post5")
|
| 3071 | (source
|
| 3072 | (origin
|
| 3073 | (method url-fetch)
|
| 3074 | (uri (pypi-uri "qdldl" version))
|
| 3075 | (sha256
|
| 3076 | (base32 "0vi8dgrw32qj03z2dd3zqd0d625pibq3xmlgmidfsnwvqkhrj4qb"))))
|
| 3077 | (build-system pyproject-build-system)
|
| 3078 | (native-inputs
|
| 3079 | (list cmake-minimal
|
| 3080 | pybind11-2
|
| 3081 | python-pytest
|
| 3082 | python-setuptools))
|
| 3083 | (propagated-inputs (list python-numpy python-scipy))
|
| 3084 | (home-page "https://github.com/oxfordcontrol/qdldl-python/")
|
| 3085 | (synopsis "QDLDL LDL factorization routine")
|
| 3086 | (description "This package provides a Python interface to the QDLDL LDL
|
| 3087 | factorization routine for quasi-definite linear system.")
|
| 3088 | (license license:asl2.0)))
|
| 3089 |
|
| 3090 | (define-public python-quantities
|
| 3091 | (package
|
| 3092 | (name "python-quantities")
|
| 3093 | (version "0.16.4")
|
| 3094 | (source
|
| 3095 | (origin
|
| 3096 | (method url-fetch)
|
| 3097 | (uri (pypi-uri "quantities" version))
|
| 3098 | (sha256
|
| 3099 | (base32 "0dmzk17hd0c6lzjlipjpc52jdifknpvxq15javn19n3f9yvxxdpm"))))
|
| 3100 | (build-system pyproject-build-system)
|
| 3101 | (arguments
|
| 3102 | (list
|
| 3103 | #:phases
|
| 3104 | #~(modify-phases %standard-phases
|
| 3105 | (add-before 'check 'pre-check
|
| 3106 | (lambda _
|
| 3107 | (setenv "PY_IGNORE_IMPORTMISMATCH" "1"))))))
|
| 3108 | (native-inputs
|
| 3109 | (list python-pytest
|
| 3110 | python-setuptools
|
| 3111 | python-setuptools-scm))
|
| 3112 | (propagated-inputs
|
| 3113 | (list python-numpy))
|
| 3114 | (home-page "https://github.com/python-quantities/python-quantities")
|
| 3115 | (synopsis "Support for physical quantities with units, based on NumPy")
|
| 3116 | (description
|
| 3117 | "Quantities is designed to handle arithmetic and conversions of physical
|
| 3118 | quantities, which have a magnitude, dimensionality specified by various units,
|
| 3119 | and possibly an uncertainty. It builds on the NumPy library and is designed
|
| 3120 | to work with @code{numpy.ufuncs}, many of which are already supported.")
|
| 3121 | |
| 3122 | (license license:bsd-3)))
|
| 3123 |
|
| 3124 | |
| 3125 | (define-deprecated/public-alias hugs (@ (gnu packages physiscs) python-qutip))
|
| 3126 |
|
| 3127 | (define-public python-ruffus
|
| 3128 | (package
|
| 3129 | (name "python-ruffus")
|
| 3130 | (version "2.8.4")
|
| 3131 | (source
|
| 3132 | (origin
|
| 3133 | (method url-fetch)
|
| 3134 | (uri (pypi-uri "ruffus" version))
|
| 3135 | (sha256
|
| 3136 | (base32 "1ai673k1s94s8b6pyxai8mk17p6zvvyi87rl236fs6ls8mpdklvc"))))
|
| 3137 | (build-system pyproject-build-system)
|
| 3138 | (arguments
|
| 3139 | (list
|
| 3140 | #:phases
|
| 3141 | #~(modify-phases %standard-phases
|
| 3142 | (replace 'check
|
| 3143 | (lambda* (#:key tests? #:allow-other-keys)
|
| 3144 | (when tests?
|
| 3145 | (with-directory-excursion "ruffus/test"
|
| 3146 | (invoke "bash" "run_all_unit_tests3.cmd"))))))))
|
| 3147 | (native-inputs (list python-pytest python-setuptools))
|
| 3148 | (home-page "http://www.ruffus.org.uk")
|
| 3149 | (synopsis "Light-weight computational pipeline management")
|
| 3150 | (description
|
| 3151 | "Ruffus is designed to allow scientific and other analyses to be
|
| 3152 | automated with the minimum of fuss and the least effort.")
|
| 3153 | (license license:expat)))
|
| 3154 |
|
| 3155 | (define-public python-salib
|
| 3156 | (package
|
| 3157 | (name "python-salib")
|
| 3158 | (version "1.5.2")
|
| 3159 | (source
|
| 3160 | (origin
|
| 3161 | (method git-fetch)
|
| 3162 | (uri (git-reference
|
| 3163 | (url "https://github.com/SALib/SALib")
|
| 3164 | (commit (string-append "v" version))))
|
| 3165 | (file-name (git-file-name name version))
|
| 3166 | (sha256
|
| 3167 | (base32 "0v7l6qbxgclz644fq1vmakfasxcdhg1g019b5w47hlxqw8fx0ipl"))))
|
| 3168 | (build-system pyproject-build-system)
|
| 3169 | |
| 3170 | (native-inputs
|
| 3171 | (list python-hatch-vcs
|
| 3172 | python-hatchling
|
| 3173 | python-pytest))
|
| 3174 | (propagated-inputs
|
| 3175 | (list python-matplotlib
|
| 3176 | python-multiprocess
|
| 3177 | python-numpy
|
| 3178 | python-pandas
|
| 3179 | python-scipy))
|
| 3180 | (home-page "https://salib.readthedocs.io/en/latest/")
|
| 3181 | (synopsis "Tools for global sensitivity analysis")
|
| 3182 | (description "SALib provides tools for global sensitivity analysis. It
|
| 3183 | contains Sobol', Morris, FAST, DGSM, PAWN, HDMR, Moment Independent and
|
| 3184 | fractional factorial methods.")
|
| 3185 | (license license:expat)))
|
| 3186 |
|
| 3187 | (define-public python-scikit-allel
|
| 3188 | (package
|
| 3189 | (name "python-scikit-allel")
|
| 3190 | (version "1.3.13")
|
| 3191 | (source
|
| 3192 | (origin
|
| 3193 | (method url-fetch)
|
| 3194 | (uri (pypi-uri "scikit_allel" version))
|
| 3195 | (sha256
|
| 3196 | (base32 "0d9yadzhsjjqkh6rz273f53iwczk0c7pv9dajzcrmfnk036b8f4s"))))
|
| 3197 | (build-system pyproject-build-system)
|
| 3198 | (arguments
|
| 3199 | (list
|
| 3200 | #:test-flags
|
| 3201 | '(list "-k"
|
| 3202 | (string-append
|
| 3203 | |
| 3204 | "not test_vcf_to_hdf5"
|
| 3205 | " and not test_vcf_to_hdf5_exclude"
|
| 3206 | " and not test_vcf_to_hdf5_rename"
|
| 3207 | " and not test_vcf_to_hdf5_group"
|
| 3208 | " and not test_vcf_to_hdf5_ann"
|
| 3209 | |
| 3210 | " and not test_roh_mhmm_0pct"
|
| 3211 | " and not test_roh_mhmm_100pct"))
|
| 3212 | #:phases
|
| 3213 | '(modify-phases %standard-phases
|
| 3214 | (add-before 'check 'build-ext
|
| 3215 | (lambda _
|
| 3216 | (invoke "python" "setup.py" "build_ext" "--inplace"))))))
|
| 3217 | (propagated-inputs
|
| 3218 | (list python-dask python-numpy))
|
| 3219 | (native-inputs
|
| 3220 | (list htslib
|
| 3221 | python-cython
|
| 3222 | python-h5py
|
| 3223 | python-hmmlearn
|
| 3224 | python-numexpr
|
| 3225 | python-numpy
|
| 3226 | python-pytest
|
| 3227 | python-setuptools
|
| 3228 | python-setuptools-scm
|
| 3229 | python-wheel
|
| 3230 | python-zarr))
|
| 3231 | (home-page "https://github.com/cggh/scikit-allel")
|
| 3232 | (synopsis "Explore and analyze genetic variation data")
|
| 3233 | (description
|
| 3234 | "This package provides utilities for exploratory analysis of large scale
|
| 3235 | genetic variation data.")
|
| 3236 | (license license:expat)))
|
| 3237 |
|
| 3238 | (define-public python-scikit-base
|
| 3239 | (package
|
| 3240 | (name "python-scikit-base")
|
| 3241 | (version "1.0.2")
|
| 3242 | (source
|
| 3243 | (origin
|
| 3244 | (method git-fetch)
|
| 3245 | (uri (git-reference
|
| 3246 | (url "https://github.com/sktime/skbase")
|
| 3247 | (commit (string-append "v" version))))
|
| 3248 | (file-name (git-file-name name version))
|
| 3249 | (sha256
|
| 3250 | (base32 "1436l0jr6avyhz2dg3driykn6rwskwyf57aig7x3pwak6w3il6rv"))))
|
| 3251 | (build-system pyproject-build-system)
|
| 3252 | (native-inputs
|
| 3253 | (list python-numpy
|
| 3254 | python-pandas-minimal
|
| 3255 | python-pytest
|
| 3256 | python-scikit-learn
|
| 3257 | python-scipy-minimal
|
| 3258 | python-setuptools
|
| 3259 | python-toml))
|
| 3260 | (home-page "https://github.com/sktime/skbase")
|
| 3261 | (synopsis "Base classes for sklearn-like parametric objects")
|
| 3262 | (description
|
| 3263 | "@code{skbase} provides base classes for creating scikit-learn-like
|
| 3264 | parametric objects, along with tools to make it easier to build your own
|
| 3265 | packages that follow these design patterns.")
|
| 3266 | (license license:bsd-3)))
|
| 3267 |
|
| 3268 | (define-public python-scikit-build-core
|
| 3269 | (package
|
| 3270 | (name "python-scikit-build-core")
|
| 3271 | (version "0.12.2")
|
| 3272 | (source
|
| 3273 | (origin
|
| 3274 | (method git-fetch)
|
| 3275 | (uri (git-reference
|
| 3276 | (url "https://github.com/scikit-build/scikit-build-core")
|
| 3277 | (commit (string-append "v" version))))
|
| 3278 | (file-name (git-file-name name version))
|
| 3279 | (sha256
|
| 3280 | (base32 "18xh572ndd0dww7czic775p6n8y5kxd072fj7xdhxwykdxr0bl2g"))))
|
| 3281 | (build-system pyproject-build-system)
|
| 3282 | (arguments
|
| 3283 | (list
|
| 3284 | |
| 3285 | #:test-flags
|
| 3286 | |
| 3287 | #~(list "--ignore=tests/test_cmake_config.py"
|
| 3288 | "--ignore=tests/test_custom_modules.py"
|
| 3289 | "--ignore=tests/test_editable.py"
|
| 3290 | "--ignore=tests/test_editable_generated.py"
|
| 3291 | "--ignore=tests/test_get_requires.py"
|
| 3292 | "--ignore=tests/test_hatchling.py"
|
| 3293 | "--ignore=tests/test_prepare_metadata.py"
|
| 3294 | "--ignore=tests/test_program_search.py"
|
| 3295 | "--ignore=tests/test_pyproject_pep518.py"
|
| 3296 | "--ignore=tests/test_pyproject_pep660.py"
|
| 3297 | "--ignore=tests/test_settings_overrides.py"
|
| 3298 | "--ignore=tests/test_setuptools_pep518.py")))
|
| 3299 | (native-inputs
|
| 3300 | (list python-cattrs
|
| 3301 | python-hatch-vcs
|
| 3302 | python-hatchling
|
| 3303 | python-pypa-build
|
| 3304 | python-pytest
|
| 3305 | python-virtualenv))
|
| 3306 | (propagated-inputs
|
| 3307 | (list cmake-minimal
|
| 3308 | |
| 3309 | python-packaging
|
| 3310 | python-pathspec))
|
| 3311 | (home-page "https://github.com/scikit-build/scikit-build-core")
|
| 3312 | (synopsis "Build backend for CMake based projects")
|
| 3313 | (description "Scikit-build-core is a build backend for Python that uses
|
| 3314 | CMake to build extension modules. It has a simple yet powerful static
|
| 3315 | configuration system in pyproject.toml, and supports almost unlimited
|
| 3316 | flexibility via CMake. It was initially developed to support the demanding
|
| 3317 | needs of scientific users, but can build any sort of package that uses
|
| 3318 | CMake.")
|
| 3319 | (license license:asl2.0)))
|
| 3320 |
|
| 3321 | (define-public python-scikit-fem
|
| 3322 | (package
|
| 3323 | (name "python-scikit-fem")
|
| 3324 | (version "11.0.0")
|
| 3325 | (source
|
| 3326 | (origin
|
| 3327 | (method git-fetch) |
| 3328 | (uri (git-reference
|
| 3329 | (url "https://github.com/kinnala/scikit-fem")
|
| 3330 | (commit version)))
|
| 3331 | (file-name (git-file-name name version))
|
| 3332 | (sha256
|
| 3333 | (base32 "13zh57raz2qcdfhsvpdlyiba5q0s0lh5b3gmsmh4cfrncrkdh6mh"))))
|
| 3334 | (build-system pyproject-build-system)
|
| 3335 | (arguments
|
| 3336 | (list
|
| 3337 | #:test-flags #~(list
|
| 3338 | |
| 3339 | "--ignore=tests/test_autodiff.py"
|
| 3340 | "--ignore=tests/test_examples.py")))
|
| 3341 | (native-inputs
|
| 3342 | (list python-autograd
|
| 3343 | python-pyamg
|
| 3344 | |
| 3345 | python-pytest
|
| 3346 | python-shapely
|
| 3347 | python-setuptools))
|
| 3348 | (propagated-inputs
|
| 3349 | (list python-meshio
|
| 3350 | python-numpy
|
| 3351 | python-matplotlib
|
| 3352 | python-scipy))
|
| 3353 | (home-page "https://scikit-fem.readthedocs.io/en/latest/")
|
| 3354 | (synopsis "Library for performing finite element assembly")
|
| 3355 | (description
|
| 3356 | "@code{scikit-fem} is a library for performing finite element assembly.
|
| 3357 | Its main purpose is the transformation of bilinear forms into sparse matrices
|
| 3358 | and linear forms into vectors.")
|
| 3359 | (license license:bsd-3)))
|
| 3360 |
|
| 3361 | (define-public python-scikit-fuzzy
|
| 3362 | (package
|
| 3363 | (name "python-scikit-fuzzy")
|
| 3364 | (version "0.5.0")
|
| 3365 | (source
|
| 3366 | (origin
|
| 3367 | (method url-fetch)
|
| 3368 | (uri (pypi-uri "scikit_fuzzy" version))
|
| 3369 | (sha256
|
| 3370 | (base32 "0zsfyd8cpd2l82fwh3smxbwhb3bkqwlq17cbav53axma4c2k9r9f"))))
|
| 3371 | (build-system pyproject-build-system)
|
| 3372 | (arguments
|
| 3373 | (list
|
| 3374 | #:test-flags #~(list "--pyargs" "skfuzzy")))
|
| 3375 | (native-inputs
|
| 3376 | (list python-pytest python-setuptools python-wheel))
|
| 3377 | (propagated-inputs
|
| 3378 | (list python-networkx python-numpy python-scipy))
|
| 3379 | (home-page "https://github.com/scikit-fuzzy/scikit-fuzzy")
|
| 3380 | (synopsis "Fuzzy logic toolkit for SciPy")
|
| 3381 | (description
|
| 3382 | "This package implements many useful tools for projects involving fuzzy
|
| 3383 | logic, also known as grey logic.")
|
| 3384 | (license license:bsd-3)))
|
| 3385 |
|
| 3386 | (define-public python-scikit-image
|
| 3387 | (package
|
| 3388 | (name "python-scikit-image")
|
| 3389 | (version "0.26.0")
|
| 3390 | (source
|
| 3391 | (origin
|
| 3392 | (method git-fetch)
|
| 3393 | (uri (git-reference
|
| 3394 | (url "https://github.com/scikit-image/scikit-image")
|
| 3395 | (commit (string-append "v" version))))
|
| 3396 | (file-name (git-file-name name version))
|
| 3397 | |
| 3398 | |
| 3399 | (patches
|
| 3400 | (search-patches "python-scikit-image-fix-python-pillow.patch"))
|
| 3401 | (sha256
|
| 3402 | (base32 "1x90jad3jqin8ws1j1i89zrajpcbn1h87nl5yxxf5cs3b7ha13rf"))))
|
| 3403 | (build-system pyproject-build-system)
|
| 3404 | (arguments
|
| 3405 | (list
|
| 3406 | #:test-flags
|
| 3407 | #~(list "--ignore=benchmarks/"
|
| 3408 | |
| 3409 | |
| 3410 | |
| 3411 | "-k" "not test_ellipse_parameter_stability")))
|
| 3412 | (propagated-inputs
|
| 3413 | (list python-imageio
|
| 3414 | python-lazy-loader
|
| 3415 | python-networkx
|
| 3416 | python-numpy
|
| 3417 | python-packaging
|
| 3418 | python-pillow
|
| 3419 | python-scipy
|
| 3420 | python-tifffile
|
| 3421 | |
| 3422 | |
| 3423 | |
| 3424 | |
| 3425 | |
| 3426 | |
| 3427 | |
| 3428 | |
| 3429 | |
| 3430 | #;python-simpleitk))
|
| 3431 | (native-inputs
|
| 3432 | (list python-meson
|
| 3433 | python-pytest
|
| 3434 | python-pytest-localserver
|
| 3435 | python-pytest-pretty
|
| 3436 | python-pythran))
|
| 3437 | (home-page "https://scikit-image.org/")
|
| 3438 | (synopsis "Image processing in Python")
|
| 3439 | (description
|
| 3440 | "Scikit-image is a collection of algorithms for image processing.")
|
| 3441 | (license license:bsd-3)))
|
| 3442 |
|
| 3443 | (define-public python-scikit-misc
|
| 3444 | (package
|
| 3445 | (name "python-scikit-misc")
|
| 3446 | (version "0.5.1")
|
| 3447 | (source
|
| 3448 | (origin
|
| 3449 | (method url-fetch)
|
| 3450 | (uri (pypi-uri "scikit_misc" version))
|
| 3451 | (sha256
|
| 3452 | (base32 "18sj7qa3kk4pqh3rzg2c64lf03nciv9cf985yh1h2kpqqndgdhf5"))))
|
| 3453 | (build-system pyproject-build-system)
|
| 3454 | (arguments
|
| 3455 | (list
|
| 3456 | #:test-flags
|
| 3457 | '(list "--pyargs" "skmisc")
|
| 3458 | #:phases
|
| 3459 | #~(modify-phases %standard-phases
|
| 3460 | (add-after 'unpack 'fix-version
|
| 3461 | (lambda _
|
| 3462 | (call-with-output-file "skmisc/_version.py"
|
| 3463 | (lambda (port)
|
| 3464 | (display (string-append "__version__ = \"" #$version "\"")
|
| 3465 | port)))
|
| 3466 | (substitute* "meson.build"
|
| 3467 | (("^ version: run_command.*")
|
| 3468 | (string-append " version: '" #$version "',\n")))
|
| 3469 | (substitute* "pyproject.toml"
|
| 3470 | (("dynamic = \\['version'\\]")
|
| 3471 | (string-append "version = \"" #$version "\""))))))))
|
| 3472 | (native-inputs
|
| 3473 | (list gfortran
|
| 3474 | python-meson
|
| 3475 | python-spin
|
| 3476 | python-pytest
|
| 3477 | python-setuptools))
|
| 3478 | (propagated-inputs
|
| 3479 | (list python-numpy))
|
| 3480 | (home-page "https://has2k1.github.io/scikit-misc/stable")
|
| 3481 | (synopsis "Miscellaneous tools for scientific computing.")
|
| 3482 | (description "This package provides miscellaneous tools for data analysis
|
| 3483 | and scientific computing.")
|
| 3484 | (license license:bsd-3)))
|
| 3485 |
|
| 3486 | (define-public python-scikit-opt
|
| 3487 | (package
|
| 3488 | (name "python-scikit-opt")
|
| 3489 | (version "0.6.6")
|
| 3490 | (source
|
| 3491 | (origin
|
| 3492 | (method url-fetch)
|
| 3493 | (uri (pypi-uri "scikit-opt" version))
|
| 3494 | (sha256
|
| 3495 | (base32 "0ycqizgsj7q57asc1bphzhf1fx9zqn0vx5rli7q541bas64hfqiy"))))
|
| 3496 | (build-system pyproject-build-system)
|
| 3497 | (native-inputs
|
| 3498 | (list python-pytest
|
| 3499 | python-setuptools))
|
| 3500 | (propagated-inputs
|
| 3501 | (list python-numpy
|
| 3502 | python-pytorch
|
| 3503 | python-scipy))
|
| 3504 | (home-page "https://github.com/guofei9987/scikit-opt")
|
| 3505 | (synopsis "Swarm intelligence algorithms in Python")
|
| 3506 | (description
|
| 3507 | "Scikit-opt (or sko) is a Python module implementing @dfn{swarm
|
| 3508 | intelligence} algorithms: genetic algorithm, particle swarm optimization,
|
| 3509 | simulated annealing, ant colony algorithm, immune algorithm, artificial fish
|
| 3510 | swarm algorithm.")
|
| 3511 | (license license:expat)))
|
| 3512 |
|
| 3513 | (define-public python-scikit-optimize
|
| 3514 | |
| 3515 | |
| 3516 | (package
|
| 3517 | (name "python-scikit-optimize")
|
| 3518 | (version "0.10.2")
|
| 3519 | (source
|
| 3520 | (origin
|
| 3521 | (method git-fetch)
|
| 3522 | (uri (git-reference
|
| 3523 | (url "https://github.com/holgern/scikit-optimize")
|
| 3524 | (commit (string-append "v" version))))
|
| 3525 | (file-name (git-file-name name version))
|
| 3526 | (sha256
|
| 3527 | (base32 "0pc6avzxz8l32km5jvv3maih0a5x2akxybvxl2hdg04qz2l0kz8b"))))
|
| 3528 | (build-system pyproject-build-system)
|
| 3529 | (arguments
|
| 3530 | (list
|
| 3531 | |
| 3532 | #:test-flags
|
| 3533 | #~(list "--numprocesses" (number->string (parallel-job-count))
|
| 3534 | "-k" (string-join
|
| 3535 | |
| 3536 | |
| 3537 | (list "not test_acq_optimizer"
|
| 3538 | "test_acq_optimizer_with_time_api"
|
| 3539 | "test_categorical_init_vals"
|
| 3540 | "test_consistent_x_iter_dimensions"
|
| 3541 | "test_early_stopping_delta_x"
|
| 3542 | "test_early_stopping_delta_x_empty_result_object"
|
| 3543 | "test_early_stopping_delta_y"
|
| 3544 | "test_early_stopping_delta_y_with_x0"
|
| 3545 | "test_exhaust_initial_calls"
|
| 3546 | "test_fixed_random_states"
|
| 3547 | "test_init_points_and_models"
|
| 3548 | "test_init_vals"
|
| 3549 | "test_init_vals_and_models"
|
| 3550 | "test_minimizer_api"
|
| 3551 | "test_minimizer_api_random_only"
|
| 3552 | "test_minimizer_space_constraint"
|
| 3553 | "test_minimizer_with_space"
|
| 3554 | "test_mixed_spaces"
|
| 3555 | "test_optimizer_base_estimator_string_smoke"
|
| 3556 | "test_optimizer_base_estimator_string_smoke_njobs"
|
| 3557 | "test_per_second_api"
|
| 3558 | "test_repeated_x"
|
| 3559 | "test_tree_based_minimize")
|
| 3560 | " and not "))))
|
| 3561 | (native-inputs
|
| 3562 | (list python-pytest
|
| 3563 | python-pytest-xdist
|
| 3564 | python-setuptools))
|
| 3565 | (propagated-inputs
|
| 3566 | (list python-joblib
|
| 3567 | python-matplotlib
|
| 3568 | python-numpy
|
| 3569 | python-pyaml
|
| 3570 | python-scikit-learn
|
| 3571 | python-scipy))
|
| 3572 | (home-page "https://scikit-optimize.github.io/")
|
| 3573 | (synopsis "Sequential model-based optimization toolbox")
|
| 3574 | (description
|
| 3575 | "Scikit-Optimize, or @code{skopt}, is a simple and efficient library to
|
| 3576 | minimize (very) expensive and noisy black-box functions. It implements
|
| 3577 | several methods for sequential model-based optimization. @code{skopt} aims to
|
| 3578 | be accessible and easy to use in many contexts.")
|
| 3579 | (license license:bsd-3)))
|
| 3580 |
|
| 3581 | (define-public python-scikit-surprise
|
| 3582 | (package
|
| 3583 | (name "python-scikit-surprise")
|
| 3584 | (version "1.1.5")
|
| 3585 | (source
|
| 3586 | (origin
|
| 3587 | (method git-fetch)
|
| 3588 | (uri (git-reference
|
| 3589 | (url "https://github.com/NicolasHug/Surprise")
|
| 3590 | (commit (string-append "v" version))))
|
| 3591 | (file-name (git-file-name name version))
|
| 3592 | (sha256
|
| 3593 | (base32 "1jw05xb8w7d5vx0v8gjd51a5bp1zwqy5adcpaf8fy5mfrdjn6hpp"))))
|
| 3594 | (build-system pyproject-build-system)
|
| 3595 | (arguments
|
| 3596 | (list
|
| 3597 | |
| 3598 | #:phases
|
| 3599 | #~(modify-phases %standard-phases
|
| 3600 | (add-before 'sanity-check 'set-home
|
| 3601 | (lambda _
|
| 3602 | |
| 3603 | |
| 3604 | (setenv "HOME" "/tmp"))))))
|
| 3605 | (native-inputs
|
| 3606 | (list python-cython
|
| 3607 | python-pandas-minimal
|
| 3608 | python-pytest
|
| 3609 | python-setuptools))
|
| 3610 | (propagated-inputs
|
| 3611 | (list python-joblib
|
| 3612 | python-numpy
|
| 3613 | python-scikit-learn))
|
| 3614 | (home-page "https://surpriselib.com/")
|
| 3615 | (synopsis "Recommender system library for Scikit-learn")
|
| 3616 | (description
|
| 3617 | "This package provides a Python library for building and analyzing
|
| 3618 | recommender systems that deal with explicit rating data. It was designed with
|
| 3619 | the following purposes in mind:
|
| 3620 | @itemize
|
| 3621 | @item Provide tools to handle downloaded or user-provided datasets.
|
| 3622 | @item Provide ready-to-use prediction algorithms and similarity measures.
|
| 3623 | @item Provide a base for creating custom algorithms.
|
| 3624 | @item Provide tools to evaluate, analyse and compare algorithm performance.
|
| 3625 | @item Provide documentation with precise details regarding library algorithms.
|
| 3626 | @end itemize")
|
| 3627 | (license license:bsd-3)))
|
| 3628 |
|
| 3629 | (define-public python-scikit-survival
|
| 3630 | (package
|
| 3631 | (name "python-scikit-survival")
|
| 3632 | (version "0.26.0")
|
| 3633 | (source
|
| 3634 | (origin
|
| 3635 | (method git-fetch)
|
| 3636 | (uri (git-reference
|
| 3637 | (url "https://github.com/sebp/scikit-survival")
|
| 3638 | (commit (string-append "v" version))
|
| 3639 | |
| 3640 | |
| 3641 | |
| 3642 | (recursive? #true)))
|
| 3643 | (file-name (git-file-name name version))
|
| 3644 | (sha256
|
| 3645 | (base32 "0r0xi9saz247ph6bgrc3iknq0m60d8rs4sl4mdv4s1zja80w1cp8"))))
|
| 3646 | (build-system pyproject-build-system)
|
| 3647 | (arguments
|
| 3648 | (list
|
| 3649 | |
| 3650 | #:test-flags
|
| 3651 | #~(list "--durations=10" |
| 3652 | "--numprocesses" (number->string (min 4 (parallel-job-count))))))
|
| 3653 | (propagated-inputs
|
| 3654 | (list python-ecos
|
| 3655 | python-joblib
|
| 3656 | python-numexpr
|
| 3657 | python-numpy
|
| 3658 | python-osqp
|
| 3659 | python-pandas
|
| 3660 | python-scikit-learn
|
| 3661 | python-scipy))
|
| 3662 | (native-inputs
|
| 3663 | (list python-cython
|
| 3664 | python-packaging
|
| 3665 | python-pytest
|
| 3666 | python-pytest-xdist
|
| 3667 | python-setuptools
|
| 3668 | python-setuptools-scm))
|
| 3669 | (home-page "https://github.com/sebp/scikit-survival")
|
| 3670 | (synopsis "Survival analysis built on top of scikit-learn")
|
| 3671 | (description "Scikit-survival is a Python module for survival analysis
|
| 3672 | built on top of scikit-learn. It allows doing survival analysis while
|
| 3673 | utilizing the power of scikit-learn, e.g., for pre-processing or doing
|
| 3674 | cross-validation.")
|
| 3675 | (license license:gpl3+)))
|
| 3676 |
|
| 3677 | (define-public python-scipy
|
| 3678 | (package
|
| 3679 | (name "python-scipy")
|
| 3680 | (version "1.16.3")
|
| 3681 | |
| 3682 | |
| 3683 | |
| 3684 | |
| 3685 | |
| 3686 | (source
|
| 3687 | (origin
|
| 3688 | (method url-fetch)
|
| 3689 | (uri (pypi-uri "scipy" version))
|
| 3690 | (sha256
|
| 3691 | (base32 "1jxf6mjr3whbh23p8bnlcyiss5rsamq37qgys8xz8qi781cpds01"))))
|
| 3692 | (build-system pyproject-build-system)
|
| 3693 | (arguments
|
| 3694 | (list
|
| 3695 | |
| 3696 | #:configure-flags
|
| 3697 | ''(("setup-args" . #("-Duse-system-libraries=all")))
|
| 3698 | #:test-flags
|
| 3699 | #~(list "--durations=10"
|
| 3700 | "--numprocesses" (number->string (min 4 (parallel-job-count)))
|
| 3701 | "--pyargs" "scipy"
|
| 3702 | "-k" (string-join
|
| 3703 | |
| 3704 | (list "not test_ascent"
|
| 3705 | "test_electrocardiogram"
|
| 3706 | "test_existence_all"
|
| 3707 | "test_face"
|
| 3708 | |
| 3709 | "test_callbacks"
|
| 3710 | "test_bad_callbacks"
|
| 3711 | |
| 3712 | |
| 3713 | "test_expm1_complex"
|
| 3714 | |
| 3715 | "test_log1p_complex"
|
| 3716 | |
| 3717 | "test_nctdtr_accuracy[3.0-5.0--2.0-1.5645373999149622e-09-5e-09]"
|
| 3718 | |
| 3719 | |
| 3720 | "test_spherical_in_complex"
|
| 3721 | "test_spherical_jn_complex"
|
| 3722 | "test_spherical_kn"
|
| 3723 | "test_spherical_yn_complex"
|
| 3724 | |
| 3725 | "test_negative_real_gh14582[spherical_in-False]"
|
| 3726 | "test_negative_real_gh14582[spherical_in-True]"
|
| 3727 | "test_negative_real_gh14582[spherical_jn-False]"
|
| 3728 | "test_negative_real_gh14582[spherical_jn-True]"
|
| 3729 | "test_negative_real_gh14582[spherical_yn-False]"
|
| 3730 | "test_negative_real_gh14582[spherical_yn-True]"
|
| 3731 | |
| 3732 | |
| 3733 | "test_boost_eval_issue_14606")
|
| 3734 | " and not "))
|
| 3735 | #:phases
|
| 3736 | #~(modify-phases %standard-phases
|
| 3737 | (add-after 'set-paths 'hide-gfortran
|
| 3738 | |
| 3739 | (lambda* (#:key inputs #:allow-other-keys)
|
| 3740 | (let ((gfortran #$(this-package-native-input "gfortran")))
|
| 3741 | (setenv "CPLUS_INCLUDE_PATH"
|
| 3742 | (string-join
|
| 3743 | (delete (string-append gfortran "/include/c++")
|
| 3744 | (string-split (getenv "CPLUS_INCLUDE_PATH") #\:))
|
| 3745 | ":")))))
|
| 3746 | (replace 'check
|
| 3747 | (lambda* (#:key test-flags tests? #:allow-other-keys)
|
| 3748 | (when tests?
|
| 3749 | |
| 3750 | |
| 3751 | |
| 3752 | (with-directory-excursion "/tmp"
|
| 3753 | (setenv "HOME" "/tmp")
|
| 3754 | (setenv "PYTHONOPTIMIZE" "2")
|
| 3755 | (apply invoke "pytest" "-vv" test-flags))))))))
|
| 3756 | (native-inputs
|
| 3757 | (list gfortran
|
| 3758 | pkg-config
|
| 3759 | python-click
|
| 3760 | python-doit
|
| 3761 | python-hypothesis
|
| 3762 | python-meson
|
| 3763 | python-mpmath
|
| 3764 | python-numpydoc
|
| 3765 | python-pooch
|
| 3766 | python-pycodestyle
|
| 3767 | python-pydevtool
|
| 3768 | python-pytest
|
| 3769 | python-pytest-timeout
|
| 3770 | python-pytest-xdist
|
| 3771 | python-pythran
|
| 3772 | python-rich-click
|
| 3773 | python-threadpoolctl
|
| 3774 | python-typing-extensions))
|
| 3775 | (inputs
|
| 3776 | (list boost-1.88
|
| 3777 | openblas
|
| 3778 | pybind11-2
|
| 3779 | qhull
|
| 3780 | xsimd))
|
| 3781 | (propagated-inputs
|
| 3782 | (list python-numpy))
|
| 3783 | (home-page "https://scipy.org/")
|
| 3784 | (synopsis "The Scipy library provides efficient numerical routines")
|
| 3785 | (description "The SciPy library is one of the core packages that make up
|
| 3786 | the SciPy stack. It provides many user-friendly and efficient numerical
|
| 3787 | routines such as routines for numerical integration and optimization.")
|
| 3788 | (license license:bsd-3)))
|
| 3789 |
|
| 3790 | |
| 3791 | |
| 3792 | (define-public python-scipy-minimal
|
| 3793 | (package/inherit python-scipy
|
| 3794 | (name "python-scipy-minimal")
|
| 3795 | (arguments
|
| 3796 | (substitute-keyword-arguments arguments
|
| 3797 | ((#:tests? _ #t) #f)))
|
| 3798 | (native-inputs
|
| 3799 | (list gfortran
|
| 3800 | pkg-config
|
| 3801 | python-meson
|
| 3802 | python-pythran))))
|
| 3803 |
|
| 3804 | (define-public python-simple-pid
|
| 3805 | (package
|
| 3806 | (name "python-simple-pid")
|
| 3807 | (version "2.0.1")
|
| 3808 | (source (origin
|
| 3809 | (method url-fetch)
|
| 3810 | (uri (pypi-uri "simple_pid" version))
|
| 3811 | (sha256
|
| 3812 | (base32
|
| 3813 | "17p9bgka5yv5lbnbk374yjccrlizm572wv3xb479072lahf7cwap"))))
|
| 3814 | (build-system pyproject-build-system)
|
| 3815 | (native-inputs
|
| 3816 | (list python-pytest python-setuptools python-wheel))
|
| 3817 | (home-page "https://github.com/m-lundberg/simple-pid")
|
| 3818 | (synopsis "Easy to use PID controller")
|
| 3819 | (description "This package provides a simple and easy-to-use @acronym{PID,
|
| 3820 | proportional-integral-derivative} controller.")
|
| 3821 | (license license:expat)))
|
| 3822 |
|
| 3823 | (define-public python-snakemake-interface-common
|
| 3824 | (package
|
| 3825 | (name "python-snakemake-interface-common")
|
| 3826 | (version "1.17.4")
|
| 3827 | (source
|
| 3828 | (origin
|
| 3829 | (method git-fetch)
|
| 3830 | (uri (git-reference
|
| 3831 | (url "https://github.com/snakemake/snakemake-interface-common")
|
| 3832 | (commit (string-append "v" version))))
|
| 3833 | (file-name (git-file-name name version))
|
| 3834 | (sha256
|
| 3835 | (base32 "19fyqs048zdvrmq5sdayzch850kwsyv2x6xn57cjjzcm4zpjrh9w"))))
|
| 3836 | (build-system pyproject-build-system)
|
| 3837 | (arguments
|
| 3838 | (list #:phases
|
| 3839 | #~(modify-phases %standard-phases
|
| 3840 | (replace 'check
|
| 3841 | (lambda* (#:key tests? #:allow-other-keys)
|
| 3842 | (when tests?
|
| 3843 | (invoke "python3" "tests/tests.py")))))))
|
| 3844 | (native-inputs (list python-poetry-core python-pytest))
|
| 3845 | (propagated-inputs (list python-argparse-dataclass python-configargparse))
|
| 3846 | (home-page "https://github.com/snakemake/snakemake-interface-common")
|
| 3847 | (synopsis "Common functions and classes for Snakemake and its plugins")
|
| 3848 | (description "This package provides common functions and classes
|
| 3849 | for Snakemake and its plugins.")
|
| 3850 | (license license:expat)))
|
| 3851 |
|
| 3852 | (define-public python-snakemake-interface-executor-plugins
|
| 3853 | (package
|
| 3854 | (name "python-snakemake-interface-executor-plugins")
|
| 3855 | (version "9.3.3")
|
| 3856 | (source
|
| 3857 | (origin
|
| 3858 | (method git-fetch)
|
| 3859 | (uri (git-reference
|
| 3860 | (url (string-append "https://github.com/snakemake/"
|
| 3861 | "snakemake-interface-executor-plugins"))
|
| 3862 | (commit (string-append "v" version))))
|
| 3863 | (file-name (git-file-name name version))
|
| 3864 | (sha256
|
| 3865 | (base32 "1kjjcgkk1rbavb687x5ayw35ayhsnhpg9262k317x911wqpsj2fm"))))
|
| 3866 | (build-system pyproject-build-system)
|
| 3867 | (arguments
|
| 3868 | (list
|
| 3869 | #:phases
|
| 3870 | #~(modify-phases %standard-phases
|
| 3871 | (replace 'check
|
| 3872 | (lambda* (#:key tests? #:allow-other-keys)
|
| 3873 | (when tests?
|
| 3874 | (invoke "python3" "tests/tests.py")))))))
|
| 3875 | (propagated-inputs (list python-argparse-dataclass
|
| 3876 | python-snakemake-interface-common
|
| 3877 | python-throttler))
|
| 3878 | (native-inputs (list python-poetry-core python-pytest))
|
| 3879 | (home-page (string-append "https://github.com/snakemake/"
|
| 3880 | "python-snakemake-interface-executor-plugins"))
|
| 3881 | (synopsis "Interface for Snakemake executor plugins")
|
| 3882 | (description
|
| 3883 | "This package provides a stable interface for interactions between Snakemake and
|
| 3884 | its executor plugins.")
|
| 3885 | (license license:expat)))
|
| 3886 |
|
| 3887 | (define-public python-snakemake-interface-report-plugins
|
| 3888 | (package
|
| 3889 | (name "python-snakemake-interface-report-plugins")
|
| 3890 | (version "1.1.0")
|
| 3891 | (source
|
| 3892 | (origin
|
| 3893 | (method git-fetch)
|
| 3894 | (uri (git-reference
|
| 3895 | (url (string-append "https://github.com/snakemake/"
|
| 3896 | "snakemake-interface-report-plugins"))
|
| 3897 | (commit (string-append "v" version))))
|
| 3898 | (file-name (git-file-name name version))
|
| 3899 | (sha256
|
| 3900 | (base32 "0i6z9vk6nv2m3jsym0glrb7h9isdlfza2yq14vbqcslybdi9ykfa"))))
|
| 3901 | (build-system pyproject-build-system)
|
| 3902 | (arguments
|
| 3903 | (list
|
| 3904 | #:tests? #f |
| 3905 | #:phases
|
| 3906 | #~(modify-phases %standard-phases
|
| 3907 | (replace 'check
|
| 3908 | (lambda* (#:key tests? #:allow-other-keys)
|
| 3909 | (when tests?
|
| 3910 | (invoke "python3" "tests/tests.py")))))))
|
| 3911 | (propagated-inputs (list python-snakemake-interface-common python-pytest))
|
| 3912 | (native-inputs (list python-poetry-core))
|
| 3913 | (home-page (string-append "https://github.com/snakemake/"
|
| 3914 | "python-snakemake-interface-report-plugins"))
|
| 3915 | (synopsis "Interface for Snakemake report plugins")
|
| 3916 | (description "This package provides a stable interface for interactions
|
| 3917 | between Snakemake and its report plugins.")
|
| 3918 | (license license:expat)))
|
| 3919 |
|
| 3920 | (define-public python-snakemake-interface-software-deployment-plugins
|
| 3921 | (package
|
| 3922 | (name "python-snakemake-interface-software-deployment-plugins")
|
| 3923 | (version "0.6.1")
|
| 3924 | (source
|
| 3925 | (origin
|
| 3926 | (method git-fetch)
|
| 3927 | (uri (git-reference
|
| 3928 | (url (string-append "https://github.com/snakemake/"
|
| 3929 | "snakemake-interface-software-deployment-plugins"))
|
| 3930 | (commit (string-append "v" version))))
|
| 3931 | (file-name (git-file-name name version))
|
| 3932 | (sha256
|
| 3933 | (base32 "0b4kkznfyfck9f92pkimhyl13ljisfn67rsilm1a5inq2ywpmxba"))))
|
| 3934 | (build-system pyproject-build-system)
|
| 3935 | (arguments
|
| 3936 | (list
|
| 3937 | #:phases
|
| 3938 | #~(modify-phases %standard-phases
|
| 3939 | (replace 'check
|
| 3940 | (lambda* (#:key tests? #:allow-other-keys)
|
| 3941 | (when tests?
|
| 3942 | (invoke "python3" "tests/tests.py")))))))
|
| 3943 | (propagated-inputs (list python-argparse-dataclass
|
| 3944 | python-snakemake-interface-common))
|
| 3945 | (native-inputs (list python-poetry-core))
|
| 3946 | (home-page (string-append "https://github.com/snakemake/"
|
| 3947 | "snakemake-interface-software-deployment-plugins"))
|
| 3948 | (synopsis "Interface for Snakemake software deployment plugins")
|
| 3949 | (description
|
| 3950 | "This package provides a stable interface for interactions between Snakemake and
|
| 3951 | its software deployment plugins.")
|
| 3952 | (license license:expat)))
|
| 3953 |
|
| 3954 | (define-public python-snakemake-interface-storage-plugins
|
| 3955 | (package
|
| 3956 | (name "python-snakemake-interface-storage-plugins")
|
| 3957 | (version "3.6.0")
|
| 3958 | (source
|
| 3959 | (origin
|
| 3960 | (method git-fetch)
|
| 3961 | (uri (git-reference
|
| 3962 | (url (string-append "https://github.com/snakemake/"
|
| 3963 | "snakemake-interface-storage-plugins"))
|
| 3964 | (commit (string-append "v" version))))
|
| 3965 | (file-name (git-file-name name version))
|
| 3966 | (sha256
|
| 3967 | (base32 "1dh52nkvq9zhh28xmbbq74kzhzagcy48d3vgb39bd3ckjz8libgy"))))
|
| 3968 | (build-system pyproject-build-system)
|
| 3969 | (arguments
|
| 3970 | (list
|
| 3971 | #:tests? #f |
| 3972 | #:phases
|
| 3973 | #~(modify-phases %standard-phases
|
| 3974 | (add-after 'unpack 'relax-requirements
|
| 3975 | (lambda _
|
| 3976 | (substitute* "pyproject.toml"
|
| 3977 | (("wrapt = \".*\"")
|
| 3978 | "wrapt = \"*\""))))
|
| 3979 | (replace 'check
|
| 3980 | (lambda* (#:key tests? #:allow-other-keys)
|
| 3981 | (when tests?
|
| 3982 | (invoke "python3" "tests/tests.py")))))))
|
| 3983 | (propagated-inputs (list python-reretry python-snakemake-interface-common
|
| 3984 | python-throttler python-wrapt))
|
| 3985 | (native-inputs (list python-poetry-core python-pytest))
|
| 3986 | (home-page (string-append "https://github.com/snakemake/"
|
| 3987 | "snakemake-interface-storage-plugins"))
|
| 3988 | (synopsis "Interface for Snakemake storage plugins")
|
| 3989 | (description
|
| 3990 | "This package provides a stable interface for interactions between
|
| 3991 | Snakemake and its storage plugins.")
|
| 3992 | (license license:expat)))
|
| 3993 |
|
| 3994 | (define-public python-snakemake-executor-plugin-slurm-jobstep
|
| 3995 | (package
|
| 3996 | (name "python-snakemake-executor-plugin-slurm-jobstep")
|
| 3997 | (version "0.3.0")
|
| 3998 | (home-page "https://github.com/snakemake/snakemake-executor-plugin-slurm-jobstep")
|
| 3999 | (source
|
| 4000 | (origin
|
| 4001 | (method git-fetch)
|
| 4002 | (uri (git-reference
|
| 4003 | (url home-page)
|
| 4004 | (commit (string-append "v" version))))
|
| 4005 | (file-name (git-file-name name version))
|
| 4006 | (sha256
|
| 4007 | (base32 "0ly15ywmbfcm5z7jy7dxiidpw3immsdd2k80vrm4pza721irxcar"))))
|
| 4008 | (build-system pyproject-build-system)
|
| 4009 | (arguments
|
| 4010 | (list #:phases
|
| 4011 | #~(modify-phases %standard-phases
|
| 4012 | (replace 'check
|
| 4013 | (lambda* (#:key tests? #:allow-other-keys)
|
| 4014 | (when tests?
|
| 4015 | (invoke "python3" "tests/tests.py")))))))
|
| 4016 | (native-inputs (list python-poetry-core
|
| 4017 | snakemake))
|
| 4018 | (synopsis "Snakemake executor plugin: slurm-jobstep")
|
| 4019 | (description "A Snakemake executor plugin for running srun jobs inside of
|
| 4020 | SLURM jobs (meant for internal use by python-snakemake-executor-plugin-slurm).")
|
| 4021 | (license license:expat)))
|
| 4022 |
|
| 4023 | (define-public python-snakemake-executor-plugin-slurm
|
| 4024 | (package
|
| 4025 | (name "python-snakemake-executor-plugin-slurm")
|
| 4026 | (version "1.7.0")
|
| 4027 | (home-page "https://github.com/snakemake/snakemake-executor-plugin-slurm/")
|
| 4028 | (source
|
| 4029 | (origin
|
| 4030 | (method git-fetch)
|
| 4031 | (uri (git-reference
|
| 4032 | (url home-page)
|
| 4033 | (commit (string-append "v" version))))
|
| 4034 | (file-name (git-file-name name version))
|
| 4035 | (sha256
|
| 4036 | (base32 "0x7ghrkvmxqbcjl69hxp5axa1av3s0mdc0i9xjg8qjnd3hgd82r3"))))
|
| 4037 | (build-system pyproject-build-system)
|
| 4038 | (arguments
|
| 4039 | (list #:phases
|
| 4040 | #~(modify-phases %standard-phases
|
| 4041 | (replace 'check
|
| 4042 | (lambda* (#:key tests? #:allow-other-keys)
|
| 4043 | (when tests?
|
| 4044 | (invoke "python3" "tests/tests.py")))))))
|
| 4045 | (native-inputs (list python-pandas
|
| 4046 | python-poetry-core
|
| 4047 | python-pytest
|
| 4048 | python-snakemake-executor-plugin-slurm-jobstep
|
| 4049 | snakemake))
|
| 4050 | (synopsis "Snakemake executor plugin: slurm")
|
| 4051 | (description "A Snakemake executor plugin for running SLURM jobs.")
|
| 4052 | (license license:expat)))
|
| 4053 |
|
| 4054 | (define-public python-sparse
|
| 4055 | (package
|
| 4056 | (name "python-sparse")
|
| 4057 | (version "0.18.0")
|
| 4058 | (source
|
| 4059 | (origin
|
| 4060 | (method url-fetch)
|
| 4061 | (uri (pypi-uri "sparse" version))
|
| 4062 | (sha256
|
| 4063 | (base32
|
| 4064 | "1x5zkgbsgmpr6nis0k2y5vrsg7l61ly2zishnijcgh0fxdhjdyap"))))
|
| 4065 | (build-system pyproject-build-system)
|
| 4066 | (propagated-inputs
|
| 4067 | (list python-numba python-numpy python-scipy))
|
| 4068 | (native-inputs
|
| 4069 | (list python-dask
|
| 4070 | python-pytest
|
| 4071 | python-setuptools
|
| 4072 | python-setuptools-scm))
|
| 4073 | (home-page "https://github.com/pydata/sparse/")
|
| 4074 | (synopsis "Library for multi-dimensional sparse arrays")
|
| 4075 | (description
|
| 4076 | "This package implements sparse arrays of arbitrary dimension on top of
|
| 4077 | @code{numpy} and @code{scipy.sparse}. Sparse array is a matrix in which most
|
| 4078 | of the elements are zero. @code{python-sparse} generalizes the
|
| 4079 | @code{scipy.sparse.coo_matrix} and @code{scipy.sparse.dok_matrix} layouts, but
|
| 4080 | extends beyond just rows and columns to an arbitrary number of dimensions.
|
| 4081 | Additionally, this project maintains compatibility with the
|
| 4082 | @code{numpy.ndarray} interface rather than the @code{numpy.matrix} interface
|
| 4083 | used in @code{scipy.sparse}. These differences make this project useful in
|
| 4084 | certain situations where @code{scipy.sparse} matrices are not well suited, but
|
| 4085 | it should not be considered a full replacement. It lacks layouts that are not
|
| 4086 | easily generalized like @dfn{compressed sparse row/column}(CSR/CSC) and
|
| 4087 | depends on @code{scipy.sparse} for some computations.")
|
| 4088 | (license license:bsd-3)))
|
| 4089 |
|
| 4090 | (define-public python-tdda
|
| 4091 | (package
|
| 4092 | (name "python-tdda")
|
| 4093 | (version "3.0.02")
|
| 4094 | (source
|
| 4095 | (origin
|
| 4096 | (method git-fetch)
|
| 4097 | (uri (git-reference
|
| 4098 | (url "https://github.com/tdda/tdda")
|
| 4099 | (commit (string-append "v" version))))
|
| 4100 | (file-name (git-file-name name version))
|
| 4101 | (sha256
|
| 4102 | (base32 "0agqy4v895qbrg149w2fkyh8kdfbk650iqp77aw8542ry1333lgs"))))
|
| 4103 | (build-system pyproject-build-system)
|
| 4104 | (arguments
|
| 4105 | (list
|
| 4106 | #:test-flags
|
| 4107 | #~(list
|
| 4108 | (string-append "--deselect=tdda/test_tdda.py::"
|
| 4109 | "TestTDDAUtils::test_handle_tilde_strings")
|
| 4110 | (string-append "--deselect=tdda/test_tdda.py::"
|
| 4111 | "TestPandasCommandLine::testDetectE118Cmd")
|
| 4112 | (string-append "--deselect=tdda/test_tdda.py::"
|
| 4113 | "TestPandasCommandLine::testDetectE118CmdInterleaved")
|
| 4114 | (string-append "--deselect=tdda/test_tdda.py::"
|
| 4115 | "TestPandasCommandLine::testDetectE118ParquetCmd")
|
| 4116 | (string-append "--deselect=tdda/test_tdda.py::"
|
| 4117 | "TestPandasCommandLine::testDiscoverCmd")
|
| 4118 | (string-append "--deselect=tdda/test_tdda.py::"
|
| 4119 | "TestPandasCommandLine::testVerifyE118Cmd")
|
| 4120 | (string-append "--deselect=tdda/test_tdda.py::"
|
| 4121 | "TestPandasCommandLine::testVerifyE92Cmd")
|
| 4122 | (string-append "--deselect=tdda/test_tdda.py::"
|
| 4123 | "TestPandasCommandLine::testVerifyEpsilon")
|
| 4124 | (string-append "--deselect=tdda/test_tdda.py::"
|
| 4125 | "TestPandasCommandLine::testVerifyOptionFlags"))))
|
| 4126 | (native-inputs
|
| 4127 | (list python-pytest python-setuptools))
|
| 4128 | (propagated-inputs
|
| 4129 | (list python-chardet
|
| 4130 | python-numpy
|
| 4131 | python-pandas
|
| 4132 | python-polars
|
| 4133 | python-pyarrow
|
| 4134 | python-pyyaml
|
| 4135 | python-regex
|
| 4136 | python-requests
|
| 4137 | python-rich
|
| 4138 | python-tomli
|
| 4139 | python-tomli-w))
|
| 4140 | (home-page "https://tdda.readthedocs.io/en/stable")
|
| 4141 | (synopsis "Test-driven data analysis library for Python")
|
| 4142 | (description
|
| 4143 | "The TDDA Python module provides command-line and Python API support
|
| 4144 | for the overall process of data analysis, through tools that perform
|
| 4145 | reference testing, constraint discovery for data, automatic inference
|
| 4146 | of regular expressions from text data and automatic test generation.")
|
| 4147 | (license license:expat))) |
| 4148 |
|
| 4149 | (define-public python-traittypes
|
| 4150 | (package
|
| 4151 | (name "python-traittypes")
|
| 4152 | (version "0.2.1")
|
| 4153 | (source
|
| 4154 | (origin
|
| 4155 | (method url-fetch)
|
| 4156 | (uri (pypi-uri "traittypes" version))
|
| 4157 | (sha256
|
| 4158 | (base32 "1mlv93irdrgxrhnhq3ksi9585d55bpi4mv9dha4p8gkkjiia4vxy"))))
|
| 4159 | (build-system pyproject-build-system)
|
| 4160 | (arguments
|
| 4161 | (list
|
| 4162 | |
| 4163 | #:test-flags '(list "-k" "not test_bad_values")
|
| 4164 | #:phases
|
| 4165 | '(modify-phases %standard-phases
|
| 4166 | (add-after 'unpack 'numpy-compatibility
|
| 4167 | (lambda _
|
| 4168 | (substitute* "traittypes/tests/test_traittypes.py"
|
| 4169 | (("np\\.int") "int")))))))
|
| 4170 | (propagated-inputs (list python-traitlets))
|
| 4171 | (native-inputs
|
| 4172 | (list python-numpy
|
| 4173 | python-pandas
|
| 4174 | python-pynose
|
| 4175 | python-pytest
|
| 4176 | python-setuptools
|
| 4177 | python-xarray))
|
| 4178 | (home-page "https://github.com/jupyter-widgets/traittypes")
|
| 4179 | (synopsis "Trait types for NumPy, SciPy and friends")
|
| 4180 | (description "The goal of this package is to provide a reference
|
| 4181 | implementation of trait types for common data structures used in the scipy
|
| 4182 | stack such as numpy arrays or pandas and xarray data structures. These are
|
| 4183 | out of the scope of the main traitlets project but are a common requirement to
|
| 4184 | build applications with traitlets in combination with the scipy stack.")
|
| 4185 | (license license:bsd-3)))
|
| 4186 |
|
| 4187 | (define-public python-trimesh
|
| 4188 | (package
|
| 4189 | (name "python-trimesh")
|
| 4190 | (version "4.5.3")
|
| 4191 | (source
|
| 4192 | (origin
|
| 4193 | (method git-fetch) |
| 4194 | (uri (git-reference
|
| 4195 | (url "https://github.com/mikedh/trimesh")
|
| 4196 | (commit version)))
|
| 4197 | (file-name (git-file-name name version))
|
| 4198 | (sha256
|
| 4199 | (base32 "17fyapp8nffnnf95bmcvllvg41fjlpvlv6qndbm048hnyayixxld"))))
|
| 4200 | (build-system pyproject-build-system)
|
| 4201 | (arguments
|
| 4202 | (list
|
| 4203 | #:test-flags
|
| 4204 | |
| 4205 | |
| 4206 | |
| 4207 | |
| 4208 | #~(list "-k" (string-join
|
| 4209 | (list "not test_bezier_example"
|
| 4210 | "test_discrete"
|
| 4211 | "test_dxf"
|
| 4212 | "test_ply_path_bezier"
|
| 4213 | "test_ply_path_line"
|
| 4214 | "test_ply_path_multi"
|
| 4215 | "test_revolve"
|
| 4216 | "test_screw"
|
| 4217 | "test_simple_closed"
|
| 4218 | "test_simple_extrude"
|
| 4219 | "test_simple_open"
|
| 4220 | "test_slice_onplane"
|
| 4221 | "test_spline_3D"
|
| 4222 | "test_svg"
|
| 4223 | |
| 4224 | "test_fuze"
|
| 4225 | "test_remote")
|
| 4226 | " and not "))
|
| 4227 | #:phases
|
| 4228 | #~(modify-phases %standard-phases
|
| 4229 | |
| 4230 | |
| 4231 | (delete 'sanity-check))))
|
| 4232 | (native-inputs
|
| 4233 | (list python-pyinstrument
|
| 4234 | python-pytest))
|
| 4235 | (propagated-inputs
|
| 4236 | (list |
| 4237 | python-chardet
|
| 4238 | python-colorlog
|
| 4239 | python-httpx
|
| 4240 | python-jsonschema
|
| 4241 | python-lxml
|
| 4242 | |
| 4243 | |
| 4244 | python-meshio
|
| 4245 | python-networkx
|
| 4246 | python-numpy
|
| 4247 | |
| 4248 | python-pillow
|
| 4249 | python-psutil
|
| 4250 | python-pycollada
|
| 4251 | python-pyglet
|
| 4252 | python-requests
|
| 4253 | python-rtree
|
| 4254 | python-scikit-image
|
| 4255 | python-scipy
|
| 4256 | python-setuptools
|
| 4257 | python-shapely
|
| 4258 | |
| 4259 | python-sympy
|
| 4260 | |
| 4261 | |
| 4262 | python-xxhash))
|
| 4263 | (home-page "https://github.com/mikedh/trimesh")
|
| 4264 | (synopsis "Python library for loading and using triangular meshes")
|
| 4265 | (description
|
| 4266 | "Trimesh is a pure Python library for loading and using triangular meshes
|
| 4267 | with an emphasis on watertight surfaces. The goal of the library is to
|
| 4268 | provide a full featured and well tested Trimesh object which allows for easy
|
| 4269 | manipulation and analysis, in the style of the Polygon object in the Shapely
|
| 4270 | library.")
|
| 4271 | (license license:expat)))
|
| 4272 |
|
| 4273 | (define-public python-tspex
|
| 4274 | (package
|
| 4275 | (name "python-tspex")
|
| 4276 | |
| 4277 | |
| 4278 | (properties '((commit . "d393ff497b7c14d673e792bd6c84ddd734be1239")
|
| 4279 | (revision . "0")))
|
| 4280 | (version (git-version "0.6.3"
|
| 4281 | (assoc-ref properties 'revision)
|
| 4282 | (assoc-ref properties 'commit)))
|
| 4283 | (source
|
| 4284 | (origin
|
| 4285 | (method git-fetch)
|
| 4286 | (uri (git-reference
|
| 4287 | (url "https://github.com/apcamargo/tspex")
|
| 4288 | (commit (assoc-ref properties 'commit))))
|
| 4289 | (file-name (git-file-name name version))
|
| 4290 | (sha256
|
| 4291 | (base32 "0khhnahhn0jp9y14q6wgq0xqadqszwn1iq3y562bhfmv09f4j1ik"))))
|
| 4292 | (build-system pyproject-build-system)
|
| 4293 | (arguments
|
| 4294 | (list
|
| 4295 | #:phases
|
| 4296 | #~(modify-phases %standard-phases
|
| 4297 | |
| 4298 | (add-after 'unpack 'fix-seaborn
|
| 4299 | (lambda _
|
| 4300 | (substitute* (find-files "." ".py$")
|
| 4301 | (("seaborn-") "seaborn-v0_8-")))))))
|
| 4302 | (native-inputs
|
| 4303 | (list python-pytest
|
| 4304 | python-setuptools))
|
| 4305 | (propagated-inputs
|
| 4306 | (list python-matplotlib
|
| 4307 | python-numpy
|
| 4308 | python-pandas
|
| 4309 | python-seaborn
|
| 4310 | python-xlrd))
|
| 4311 | (home-page "https://apcamargo.github.io/tspex/")
|
| 4312 | (synopsis "Calculate tissue-specificity metrics for gene expression")
|
| 4313 | (description
|
| 4314 | "This package provides a Python package for calculating
|
| 4315 | tissue-specificity metrics for gene expression.")
|
| 4316 | (license license:gpl3+)))
|
| 4317 |
|
| 4318 | (define-public python-pandas
|
| 4319 | (package
|
| 4320 | (name "python-pandas")
|
| 4321 | (version "2.3.3")
|
| 4322 | (source
|
| 4323 | (origin
|
| 4324 | (method git-fetch)
|
| 4325 | (uri (git-reference
|
| 4326 | (url "https://github.com/pandas-dev/pandas")
|
| 4327 | (commit (string-append "v" version))))
|
| 4328 | (file-name (git-file-name name version))
|
| 4329 | (sha256
|
| 4330 | (base32 "0qf4frgj31kd9i544n8v03a0bv9mgml3f7n9n1rik187q3r8ygfg"))
|
| 4331 | (patches (search-patches "python-pandas-2-no-pytz_datetime.patch"))))
|
| 4332 | (build-system pyproject-build-system)
|
| 4333 | (arguments
|
| 4334 | (list
|
| 4335 | |
| 4336 | #:test-flags
|
| 4337 | #~(list "-m" (string-join
|
| 4338 | (list "not db" "network" "single_cpu" "slow" "slow_arm")
|
| 4339 | " and not ")
|
| 4340 | "--numprocesses" (number->string (min 4 (parallel-job-count)))
|
| 4341 | "-k" (string-join
|
| 4342 | (list "not test_git_version"
|
| 4343 | "test_parsing_tzlocal_deprecated"
|
| 4344 | "test_show_versions_console"
|
| 4345 | |
| 4346 | #$@(if (target-64bit?)
|
| 4347 | '()
|
| 4348 | '("test_rolling_var_numerical_issues")))
|
| 4349 | " and not "))
|
| 4350 | #:phases
|
| 4351 | #~(modify-phases %standard-phases
|
| 4352 | (add-after 'unpack 'patch-generate-version
|
| 4353 | (lambda _
|
| 4354 | |
| 4355 | (substitute* "generate_version.py"
|
| 4356 | (("version =.*")
|
| 4357 | (format #f "version = ~s~%" #$version))
|
| 4358 | (("git_version =.*")
|
| 4359 | (format #f "git_version = ~s~%" #$version)))))
|
| 4360 | (replace 'check
|
| 4361 | (lambda* (#:key inputs outputs test-flags tests? #:allow-other-keys)
|
| 4362 | (when tests?
|
| 4363 | (setenv "HOME" "/tmp")
|
| 4364 | (with-directory-excursion
|
| 4365 | (string-append (string-append (site-packages inputs outputs)
|
| 4366 | "/pandas"))
|
| 4367 | (apply invoke "pytest" "-vv" test-flags))))))))
|
| 4368 | (propagated-inputs
|
| 4369 | (list python-numpy
|
| 4370 | python-dateutil
|
| 4371 | python-pytz
|
| 4372 | python-tzdata
|
| 4373 | |
| 4374 | |
| 4375 | |
| 4376 | |
| 4377 | |
| 4378 | |
| 4379 | |
| 4380 | |
| 4381 | |
| 4382 | |
| 4383 | |
| 4384 | |
| 4385 | |
| 4386 | |
| 4387 | |
| 4388 | |
| 4389 | |
| 4390 | |
| 4391 | |
| 4392 | |
| 4393 | |
| 4394 | |
| 4395 | |
| 4396 | |
| 4397 | |
| 4398 | |
| 4399 | |
| 4400 | |
| 4401 | |
| 4402 | |
| 4403 | |
| 4404 | |
| 4405 | |
| 4406 | |
| 4407 | |
| 4408 | |
| 4409 | |
| 4410 | |
| 4411 | |
| 4412 | |
| 4413 | #;python-zstandard))
|
| 4414 | (inputs
|
| 4415 | (list xclip xsel))
|
| 4416 | (native-inputs
|
| 4417 | (list python-meson
|
| 4418 | python-lxml
|
| 4419 | python-pytest
|
| 4420 | python-pytest-asyncio
|
| 4421 | python-pytest-xdist
|
| 4422 | python-versioneer
|
| 4423 | tzdata-for-tests))
|
| 4424 | (home-page "https://pandas.pydata.org")
|
| 4425 | (synopsis "Data structures for data analysis, time series, and statistics")
|
| 4426 | (description
|
| 4427 | "Pandas is a Python package providing fast, flexible, and expressive data
|
| 4428 | structures designed to make working with structured (tabular,
|
| 4429 | multidimensional, potentially heterogeneous) and time series data both easy
|
| 4430 | and intuitive. It aims to be the fundamental high-level building block for
|
| 4431 | doing practical, real world data analysis in Python.")
|
| 4432 | (license license:bsd-3)))
|
| 4433 |
|
| 4434 | |
| 4435 | |
| 4436 | |
| 4437 | (define-public python-pandas-minimal
|
| 4438 | (package/inherit python-pandas
|
| 4439 | (name "python-pandas-minimal")
|
| 4440 | (arguments
|
| 4441 | (substitute-keyword-arguments arguments
|
| 4442 | ((#:tests? _ #t) #f)))
|
| 4443 | (native-inputs
|
| 4444 | (list python-meson
|
| 4445 | python-versioneer))
|
| 4446 | (propagated-inputs
|
| 4447 | (list python-numpy
|
| 4448 | python-dateutil
|
| 4449 | python-pytz))))
|
| 4450 |
|
| 4451 | (define-public python-pandas-stubs
|
| 4452 | (package
|
| 4453 | (name "python-pandas-stubs")
|
| 4454 | |
| 4455 | |
| 4456 | (version "2.3.3.251219")
|
| 4457 | (source
|
| 4458 | (origin
|
| 4459 | (method git-fetch)
|
| 4460 | (uri (git-reference
|
| 4461 | (url "https://github.com/pandas-dev/pandas-stubs")
|
| 4462 | (commit (string-append "v" version))))
|
| 4463 | (file-name (git-file-name name version))
|
| 4464 | (sha256
|
| 4465 | (base32 "1xh753wv5dbc59qp7fas323181mlblvhqmd9a4g7zzhaa2mxmzqs"))))
|
| 4466 | (build-system pyproject-build-system)
|
| 4467 | (arguments
|
| 4468 | (list
|
| 4469 | |
| 4470 | #:test-flags
|
| 4471 | #~(list
|
| 4472 | |
| 4473 | "--deselect=tests/test_io.py::test_read_excel"
|
| 4474 | "--deselect=tests/test_io.py::test_excel_reader")))
|
| 4475 | (native-inputs
|
| 4476 | (list python-beautifulsoup4
|
| 4477 | python-fsspec
|
| 4478 | python-html5lib
|
| 4479 | python-jinja2
|
| 4480 | python-loguru
|
| 4481 | python-lxml
|
| 4482 | python-matplotlib
|
| 4483 | python-mypy
|
| 4484 | python-numexpr
|
| 4485 | python-odfpy
|
| 4486 | python-openpyxl
|
| 4487 | python-pandas
|
| 4488 | python-poetry-core
|
| 4489 | python-pyarrow
|
| 4490 | python-pyreadstat
|
| 4491 | python-pytest
|
| 4492 | python-scipy
|
| 4493 | python-sqlalchemy-2
|
| 4494 | python-tabulate
|
| 4495 | python-typing-extensions
|
| 4496 | python-xarray
|
| 4497 | python-xlrd
|
| 4498 | python-xlsxwriter
|
| 4499 | |
| 4500 | |
| 4501 | |
| 4502 | |
| 4503 | |
| 4504 | |
| 4505 | |
| 4506 | |
| 4507 | |
| 4508 | |
| 4509 | |
| 4510 | tzdata-for-tests))
|
| 4511 | (propagated-inputs
|
| 4512 | (list python-numpy
|
| 4513 | python-types-pytz))
|
| 4514 | (home-page "https://pandas.pydata.org")
|
| 4515 | (synopsis "Type annotations for pandas")
|
| 4516 | (description
|
| 4517 | "This package contains public type stubs for @code{python-pandas}, following
|
| 4518 | the convention of providing stubs in a separate package, as specified in
|
| 4519 | @acronym{PEP, Python Enhancement Proposal} 561. The stubs cover the most
|
| 4520 | typical use cases of @code{python-pandas}. In general, these stubs are
|
| 4521 | narrower than what is possibly allowed by @code{python-pandas}, but follow a
|
| 4522 | convention of suggesting best recommended practices for using
|
| 4523 | @code{python-pandas}.")
|
| 4524 | (license license:bsd-3)))
|
| 4525 |
|
| 4526 | (define-public python-pandarallel
|
| 4527 | (package
|
| 4528 | (name "python-pandarallel")
|
| 4529 | (version "1.6.5")
|
| 4530 | (source
|
| 4531 | (origin
|
| 4532 | (method git-fetch) |
| 4533 | (uri (git-reference
|
| 4534 | (url "https://github.com/nalepae/pandarallel/")
|
| 4535 | (commit (string-append "v" version))))
|
| 4536 | (file-name (git-file-name name version))
|
| 4537 | (sha256
|
| 4538 | (base32 "0r2wlxlwp4wia0vm15k4cp421mwa20k4k5g2ml01inprj8bl1p0p"))))
|
| 4539 | (build-system pyproject-build-system)
|
| 4540 | (arguments
|
| 4541 | (list
|
| 4542 | #:test-flags #~(list "-n" (number->string (parallel-job-count)))))
|
| 4543 | (propagated-inputs
|
| 4544 | (list python-dill
|
| 4545 | python-pandas
|
| 4546 | python-psutil))
|
| 4547 | (native-inputs
|
| 4548 | (list python-mkdocs-material
|
| 4549 | python-numpy
|
| 4550 | python-pytest
|
| 4551 | python-pytest-xdist
|
| 4552 | python-setuptools
|
| 4553 | python-wheel))
|
| 4554 | (home-page "https://nalepae.github.io/pandarallel/")
|
| 4555 | (synopsis "Tool to parallelize Pandas operations across CPUs")
|
| 4556 | (description
|
| 4557 | "@code{pandarallel} allows any Pandas user to take advantage of their
|
| 4558 | multi-core computer, while Pandas uses only one core. @code{pandarallel} also
|
| 4559 | offers nice progress bars (available on Notebook and terminal) to get an rough
|
| 4560 | idea of the remaining amount of computation to be done.")
|
| 4561 | (license license:bsd-3)))
|
| 4562 |
|
| 4563 | (define-public python-pandera
|
| 4564 | (package
|
| 4565 | (name "python-pandera")
|
| 4566 | (version "0.27.1")
|
| 4567 | (source
|
| 4568 | (origin
|
| 4569 | (method url-fetch)
|
| 4570 | (uri (pypi-uri "pandera" version))
|
| 4571 | (sha256
|
| 4572 | (base32 "1x5vjp1ra252ncyfsfrc7vck5snx807mpwzd0hvv0vpi9v096934"))))
|
| 4573 | (build-system pyproject-build-system)
|
| 4574 | (arguments
|
| 4575 | (list
|
| 4576 | |
| 4577 | #:test-flags
|
| 4578 | |
| 4579 | #~(list "--numprocesses" (number->string (min 4 (parallel-job-count)))
|
| 4580 | |
| 4581 | |
| 4582 | "--ignore=tests/ibis"
|
| 4583 | "--ignore=tests/polars"
|
| 4584 | "--ignore=tests/pyspark"
|
| 4585 | |
| 4586 | "--ignore=tests/pandas/test_docs_setting_column_widths.py"
|
| 4587 | |
| 4588 | "--ignore=tests/fastapi/test_app.py"
|
| 4589 | |
| 4590 | |
| 4591 | "-k" (string-join
|
| 4592 | (list "not test_schema_model[data0-True]"
|
| 4593 | "test_schema_from_dataframe[data1-True]"
|
| 4594 | "test_schema_no_geometry"
|
| 4595 | |
| 4596 | "test_pandas_stubs_false_positives")
|
| 4597 | " and not "))))
|
| 4598 | (native-inputs
|
| 4599 | (list python-joblib
|
| 4600 | python-pytest
|
| 4601 | python-pytest-asyncio
|
| 4602 | python-pytest-xdist
|
| 4603 | python-setuptools
|
| 4604 | python-setuptools-scm
|
| 4605 | python-uvicorn))
|
| 4606 | (inputs
|
| 4607 | |
| 4608 | |
| 4609 | |
| 4610 | |
| 4611 | |
| 4612 | (list python-dask
|
| 4613 | python-distributed
|
| 4614 | python-geopandas
|
| 4615 | python-hypothesis
|
| 4616 | |
| 4617 | python-modin
|
| 4618 | python-numpy
|
| 4619 | python-pandas
|
| 4620 | |
| 4621 | |
| 4622 | |
| 4623 | python-scipy
|
| 4624 | python-shapely))
|
| 4625 | (propagated-inputs
|
| 4626 | (list python-packaging
|
| 4627 | python-pydantic
|
| 4628 | python-typeguard
|
| 4629 | python-typing-extensions
|
| 4630 | python-typing-inspect))
|
| 4631 | (home-page "https://github.com/unionai-oss/pandera")
|
| 4632 | (synopsis "Perform data validation on dataframe-like objects")
|
| 4633 | (description
|
| 4634 | "@code{python-pandera} provides a flexible and expressive API for
|
| 4635 | performing data validation on dataframe-like objects to make data processing
|
| 4636 | pipelines more readable and robust. Dataframes contain information that
|
| 4637 | @code{python-pandera} explicitly validates at runtime. This is useful in
|
| 4638 | production-critical data pipelines or reproducible research settings. With
|
| 4639 | @code{python-pandera}, you can:
|
| 4640 |
|
| 4641 | @itemize
|
| 4642 | @item Define a schema once and use it to validate different dataframe types.
|
| 4643 | @item Check the types and properties of columns.
|
| 4644 | @item Perform more complex statistical validation like hypothesis testing.
|
| 4645 | @item Seamlessly integrate with existing data pipelines via function decorators.
|
| 4646 | @item Define dataframe models with the class-based API with pydantic-style syntax.
|
| 4647 | @item Synthesize data from schema objects for property-based testing.
|
| 4648 | @item Lazily validate dataframes so that all validation rules are executed.
|
| 4649 | @item Integrate with a rich ecosystem of tools like @code{python-pydantic},
|
| 4650 | @code{python-fastapi} and @code{python-mypy}.
|
| 4651 | @end itemize")
|
| 4652 | (license license:expat)))
|
| 4653 |
|
| 4654 | (define-public python-pyjanitor
|
| 4655 | (package
|
| 4656 | (name "python-pyjanitor")
|
| 4657 | (version "0.32.5")
|
| 4658 | (source
|
| 4659 | (origin
|
| 4660 | (method git-fetch)
|
| 4661 | (uri (git-reference
|
| 4662 | (url "https://github.com/pyjanitor-devs/pyjanitor")
|
| 4663 | (commit (string-append "v" version))))
|
| 4664 | (file-name (git-file-name name version))
|
| 4665 | (sha256
|
| 4666 | (base32 "058w2mq42v55xkqv3cvxry53sj2qh1v64ad4gc5qb8a3is453a07"))))
|
| 4667 | (build-system pyproject-build-system)
|
| 4668 | |
| 4669 | |
| 4670 | (arguments
|
| 4671 | (list
|
| 4672 | |
| 4673 | #:test-flags
|
| 4674 | |
| 4675 | |
| 4676 | |
| 4677 | |
| 4678 | |
| 4679 | #~(list |
| 4680 | |
| 4681 | "--ignore=tests/io/test_read_csvs.py"
|
| 4682 | |
| 4683 | "--ignore=tests/polars/"
|
| 4684 | |
| 4685 | "--ignore=tests/spark/"
|
| 4686 | |
| 4687 | "-k" (string-append "not test_is_connected"
|
| 4688 | |
| 4689 | " and not test_read_commandline_bad_cmd"
|
| 4690 | |
| 4691 | " and not test_maccs_keys_fingerprint"
|
| 4692 | " and not test_morgan_fingerprint_counts"
|
| 4693 | " and not test_morgan_fingerprint_bits"
|
| 4694 | |
| 4695 | |
| 4696 | " and not test_various_sorted"))
|
| 4697 | #:phases
|
| 4698 | #~(modify-phases %standard-phases
|
| 4699 | (add-before 'check 'set-env-ci
|
| 4700 | (lambda _
|
| 4701 | |
| 4702 | |
| 4703 | (setenv "JANITOR_CI_MACHINE" "1"))))))
|
| 4704 | (propagated-inputs (list python-multipledispatch
|
| 4705 | python-natsort
|
| 4706 | python-pandas-flavor
|
| 4707 | python-scipy
|
| 4708 | |
| 4709 | python-biopython
|
| 4710 | python-unyt))
|
| 4711 | (native-inputs (list python-numba
|
| 4712 | python-openpyxl
|
| 4713 | python-pytest
|
| 4714 | |
| 4715 | |
| 4716 | |
| 4717 | python-requests
|
| 4718 | python-setuptools
|
| 4719 | rdkit))
|
| 4720 | (home-page "https://github.com/pyjanitor-devs/pyjanitor")
|
| 4721 | (synopsis "Tools for cleaning and transforming Pandas DataFrames")
|
| 4722 | (description
|
| 4723 | "@code{pyjanitor} provides a set of data cleaning routines for
|
| 4724 | @code{pandas} DataFrames. These routines extend the method chaining API
|
| 4725 | defined by @code{pandas} for a subset of its methods. Originally, this
|
| 4726 | package was a port of the R package by the same name and it is inspired by the
|
| 4727 | ease-of-use and expressiveness of the @code{dplyr} package.")
|
| 4728 | (license license:expat)))
|
| 4729 |
|
| 4730 | (define-public python-pymcubes
|
| 4731 | (package
|
| 4732 | (name "python-pymcubes")
|
| 4733 | (version "0.1.6")
|
| 4734 | (source
|
| 4735 | (origin
|
| 4736 | (method git-fetch) |
| 4737 | (uri (git-reference
|
| 4738 | (url "https://github.com/pmneila/PyMCubes")
|
| 4739 | (commit (string-append "v" version))))
|
| 4740 | (file-name (git-file-name name version))
|
| 4741 | (sha256
|
| 4742 | (base32 "1v2qhc4pwanx6a8k843mbh45yk77n3w63sy5lzk5c3q4pkvfj1b9"))))
|
| 4743 | (build-system pyproject-build-system)
|
| 4744 | (arguments
|
| 4745 | (list
|
| 4746 | #:phases
|
| 4747 | #~(modify-phases %standard-phases
|
| 4748 | (add-before 'check 'prepare-test-environment
|
| 4749 | (lambda _
|
| 4750 | |
| 4751 | |
| 4752 | (mkdir "output")
|
| 4753 | (invoke "python" "setup.py" "build_ext" "--inplace"))))))
|
| 4754 | (native-inputs
|
| 4755 | (list python-cython
|
| 4756 | python-pytest
|
| 4757 | python-setuptools
|
| 4758 | python-wheel))
|
| 4759 | (propagated-inputs
|
| 4760 | (list python-pycollada
|
| 4761 | python-numpy
|
| 4762 | python-scipy))
|
| 4763 | (home-page "https://github.com/pmneila/PyMCubes")
|
| 4764 | (synopsis "Marching cubes for Python")
|
| 4765 | (description
|
| 4766 | "@code{PyMCubes} is an implementation of the marching cubes algorithm to
|
| 4767 | extract iso-surfaces from volumetric data. The volumetric data can be given
|
| 4768 | as a three-dimensional @code{NumPy} array or as a Python function @code{f(x,
|
| 4769 | y, z)}.")
|
| 4770 | (license license:bsd-3)))
|
| 4771 |
|
| 4772 | (define-public python-pythran
|
| 4773 | (package
|
| 4774 | (name "python-pythran")
|
| 4775 | (version "0.17.0")
|
| 4776 | (source
|
| 4777 | (origin
|
| 4778 | (method git-fetch)
|
| 4779 | (uri (git-reference
|
| 4780 | (url "https://github.com/serge-sans-paille/pythran")
|
| 4781 | (commit (string-append "v" version))))
|
| 4782 | (file-name (git-file-name name version))
|
| 4783 | (sha256
|
| 4784 | (base32 "1rm9lfbz5qvah1m0rr5gaaahkf1gzwlw1ysvym2l2yh0clglav94"))))
|
| 4785 | (build-system pyproject-build-system)
|
| 4786 | (arguments
|
| 4787 | (list
|
| 4788 | |
| 4789 | |
| 4790 | |
| 4791 | #:tests? #f))
|
| 4792 | (native-inputs
|
| 4793 | (list python-setuptools))
|
| 4794 | (propagated-inputs
|
| 4795 | (list boost |
| 4796 | xsimd
|
| 4797 | python-beniget
|
| 4798 | python-gast
|
| 4799 | python-numpy
|
| 4800 | python-ply))
|
| 4801 | (home-page "https://github.com/serge-sans-paille/pythran")
|
| 4802 | (synopsis "Ahead of Time compiler for numeric kernels")
|
| 4803 | (description
|
| 4804 | "Pythran is an ahead of time compiler for a subset of the Python
|
| 4805 | language, with a focus on scientific computing. It takes a Python module
|
| 4806 | annotated with a few interface descriptions and turns it into a native
|
| 4807 | Python module with the same interface, but (hopefully) faster.")
|
| 4808 | (license license:bsd-3)))
|
| 4809 |
|
| 4810 | (define-public python-pyts
|
| 4811 | (let ((commit "4f3d97bcb1016d33dbfaef68c0931756a4552410")
|
| 4812 | (revision "0"))
|
| 4813 | (package
|
| 4814 | (name "python-pyts")
|
| 4815 | (version (git-version "0.13.0" revision commit))
|
| 4816 | (source
|
| 4817 | (origin
|
| 4818 | (method git-fetch)
|
| 4819 | (uri (git-reference
|
| 4820 | (url "https://github.com/johannfaouzi/pyts")
|
| 4821 | (commit commit)))
|
| 4822 | (file-name (git-file-name name version))
|
| 4823 | (sha256
|
| 4824 | (base32 "16hlxwajdz44qs8vi7bhiania2b3201fv3pqiwsx79rb554bvl66"))))
|
| 4825 | (build-system pyproject-build-system)
|
| 4826 | (arguments
|
| 4827 | (list
|
| 4828 | #:test-flags
|
| 4829 | #~(list "--pyargs" "pyts"
|
| 4830 | |
| 4831 | "--deselect=preprocessing/transformer.py::\
|
| 4832 | pyts.preprocessing.transformer.QuantileTransformer")))
|
| 4833 | (propagated-inputs
|
| 4834 | (list python-joblib
|
| 4835 | python-numba
|
| 4836 | python-numpy
|
| 4837 | python-scikit-learn
|
| 4838 | python-scipy))
|
| 4839 | (native-inputs
|
| 4840 | (list python-pytest python-setuptools))
|
| 4841 | (home-page "https://github.com/johannfaouzi/pyts")
|
| 4842 | (synopsis "Python package for time series classification")
|
| 4843 | (description
|
| 4844 | "pyts is a Python package for time series classification. It aims to
|
| 4845 | make time series classification easily accessible by providing preprocessing
|
| 4846 | and utility tools, and implementations of state-of-the-art algorithms. Most
|
| 4847 | of these algorithms transform time series, thus pyts provides several tools to
|
| 4848 | perform these transformations.")
|
| 4849 | (license license:bsd-3))))
|
| 4850 |
|
| 4851 | (define-public python-spin
|
| 4852 | (package
|
| 4853 | (name "python-spin")
|
| 4854 | (version "0.8")
|
| 4855 | (source
|
| 4856 | (origin
|
| 4857 | (method url-fetch)
|
| 4858 | (uri (pypi-uri "spin" version))
|
| 4859 | (sha256
|
| 4860 | (base32 "0ff48nagfaai3j26g1db4zq2bwdv6kj5l7xhcs2l9kzg7qzrmhr7"))))
|
| 4861 | (build-system pyproject-build-system)
|
| 4862 | (propagated-inputs (list python-click python-colorama python-tomli))
|
| 4863 | (native-inputs (list python-pytest python-setuptools python-wheel))
|
| 4864 | (home-page "https://github.com/scientific-python/spin")
|
| 4865 | (synopsis "Developer tool for scientific Python libraries")
|
| 4866 | (description "@code{spin} is a simple interface for common development
|
| 4867 | tasks. It comes with a few common build commands out the box, but can
|
| 4868 | easily be customized per project.
|
| 4869 |
|
| 4870 | The impetus behind developing the tool was the mass migration of scientific
|
| 4871 | Python libraries (SciPy, scikit-image, and NumPy, etc.) to Meson, after
|
| 4872 | distutils was deprecated. When many of the build and installation commands
|
| 4873 | changed, it made sense to abstract away the nuisance of having to re-learn
|
| 4874 | them.")
|
| 4875 | (license license:bsd-3)))
|
| 4876 |
|
| 4877 | (define-public python-uhi
|
| 4878 | (package
|
| 4879 | (name "python-uhi")
|
| 4880 | (version "0.5.0")
|
| 4881 | (source
|
| 4882 | (origin
|
| 4883 | (method url-fetch)
|
| 4884 | (uri (pypi-uri "uhi" version))
|
| 4885 | (sha256
|
| 4886 | (base32 "0753b7yw0zi06g4azafnk3w8i3q6js9i6wwg3pya464gygrbnncm"))))
|
| 4887 | (build-system pyproject-build-system)
|
| 4888 | (propagated-inputs (list python-numpy))
|
| 4889 | (native-inputs (list python-boost-histogram
|
| 4890 | python-fastjsonschema
|
| 4891 | python-hatch-vcs
|
| 4892 | python-hatchling
|
| 4893 | python-pytest))
|
| 4894 | (home-page "https://github.com/scikit-hep/uhi")
|
| 4895 | (synopsis "Universal Histogram Interface")
|
| 4896 | (description "This is a package meant primarily for documenting histogram
|
| 4897 | indexing and the PlottableHistogram Protocol and any future cross-library
|
| 4898 | standards. It also contains the code for the PlottableHistogram Protocol, to
|
| 4899 | be used in type checking libraries wanting to conform to the protocol. It is
|
| 4900 | not usually a runtime dependency, but only a type checking, testing, and/or
|
| 4901 | docs dependency in support of other libraries.")
|
| 4902 | (license license:bsd-3)))
|
| 4903 |
|
| 4904 | (define-public python-unyt
|
| 4905 | (package
|
| 4906 | (name "python-unyt")
|
| 4907 | (version "3.1.0")
|
| 4908 | (source
|
| 4909 | (origin
|
| 4910 | (method url-fetch)
|
| 4911 | (uri (pypi-uri "unyt" version))
|
| 4912 | (sha256
|
| 4913 | (base32 "07g5rasgikp8a4x0cylz8xxzgh3536djdjppcadiqlhygyl845bp"))))
|
| 4914 | (build-system pyproject-build-system)
|
| 4915 | |
| 4916 | (native-inputs
|
| 4917 | (list python-flit-core
|
| 4918 | python-pytest))
|
| 4919 | (propagated-inputs
|
| 4920 | (list python-numpy
|
| 4921 | python-packaging
|
| 4922 | python-sympy))
|
| 4923 | (home-page "https://unyt.readthedocs.io")
|
| 4924 | (synopsis "Library for working with data that has physical units")
|
| 4925 | (description
|
| 4926 | "@code{unyt} is a Python library working with data that has physical
|
| 4927 | units. It defines the @code{unyt.array.unyt_array} and
|
| 4928 | @code{unyt.array.unyt_quantity} classes (subclasses of NumPy’s ndarray class)
|
| 4929 | for handling arrays and scalars with units,respectively")
|
| 4930 | (license license:bsd-3)))
|
| 4931 |
|
| 4932 | (define-public python-uproot
|
| 4933 | (package
|
| 4934 | (name "python-uproot")
|
| 4935 | (version "5.6.4")
|
| 4936 | (source
|
| 4937 | (origin
|
| 4938 | (method url-fetch)
|
| 4939 | (uri (pypi-uri "uproot" version))
|
| 4940 | (sha256
|
| 4941 | (base32 "024k5kjwcd2nw5hfxhpl0x9p5aq0qrg0nlh9v24vr39rcqadh52a"))))
|
| 4942 | (build-system pyproject-build-system)
|
| 4943 | (arguments
|
| 4944 | (list
|
| 4945 | #:test-flags
|
| 4946 | #~(list
|
| 4947 | |
| 4948 | "--noconftest"
|
| 4949 | |
| 4950 | |
| 4951 | "tests/test_0351_write_TList.py"
|
| 4952 | "tests/test_0352_write_THashList.py"
|
| 4953 | "tests/test_0439_check_awkward_before_numpy.py"
|
| 4954 | "tests/test_0976_path_object_split.py"
|
| 4955 | "tests/test_1198_coalesce.py"
|
| 4956 | "tests/test_1264_write_NumPy_array_of_strings.py"
|
| 4957 | "tests/test_1318_dont_compare_big_endian_in_awkward.py")
|
| 4958 | #:phases
|
| 4959 | #~(modify-phases %standard-phases
|
| 4960 | (add-after 'unpack 'set-version
|
| 4961 | (lambda _
|
| 4962 | |
| 4963 | (substitute* "pyproject.toml"
|
| 4964 | (("\\[project\\]")
|
| 4965 | (string-append "[project]" "\n" "version = \""
|
| 4966 | #$version "\""))
|
| 4967 | (("\"version\"") "")))))))
|
| 4968 | (native-inputs
|
| 4969 | (list python-hatch-vcs
|
| 4970 | python-pytest
|
| 4971 | python-pytest-timeout
|
| 4972 | python-setuptools))
|
| 4973 | (propagated-inputs
|
| 4974 | (list python-awkward
|
| 4975 | python-cramjam
|
| 4976 | python-fsspec
|
| 4977 | python-numpy
|
| 4978 | python-packaging
|
| 4979 | python-xxhash))
|
| 4980 | (home-page "https://uproot.readthedocs.io")
|
| 4981 | (synopsis "ROOT I/O in Python using NumPy")
|
| 4982 | (description
|
| 4983 | "Uproot is a Python library for reading and writing ROOT files. It uses
|
| 4984 | NumPy and does not depend on C++ ROOT.")
|
| 4985 | (license license:bsd-3)))
|
| 4986 |
|
| 4987 | (define-public python-upsetplot
|
| 4988 | (package
|
| 4989 | (name "python-upsetplot")
|
| 4990 | (version "0.9.0")
|
| 4991 | (source
|
| 4992 | (origin
|
| 4993 | (method url-fetch)
|
| 4994 | (uri (pypi-uri "UpSetPlot" version))
|
| 4995 | (sha256
|
| 4996 | (base32
|
| 4997 | "14l5gcj88cclkj1mf74bcy1pxq1hgsiy27fa3vxrsk32ik1nmdwm"))))
|
| 4998 | (build-system pyproject-build-system)
|
| 4999 | (propagated-inputs
|
| 5000 | (list python-matplotlib python-pandas))
|
| 5001 | (native-inputs
|
| 5002 | (list python-pytest python-setuptools))
|
| 5003 | (home-page "https://upsetplot.readthedocs.io")
|
| 5004 | (synopsis "Draw UpSet plots with Pandas and Matplotlib")
|
| 5005 | (description
|
| 5006 | "This is a Python implementation of UpSet plots by Lex et al.
|
| 5007 | UpSet plots are used to visualize set overlaps; like Venn diagrams but more
|
| 5008 | readable.")
|
| 5009 | (license license:bsd-3)))
|
| 5010 |
|
| 5011 | (define-public python-vaex-core
|
| 5012 | (package
|
| 5013 | (name "python-vaex-core")
|
| 5014 | (version "4.19.0")
|
| 5015 | (source
|
| 5016 | (origin
|
| 5017 | (method git-fetch)
|
| 5018 | (uri (git-reference
|
| 5019 | (url "https://www.github.com/maartenbreddels/vaex")
|
| 5020 | (commit (string-append "core-v" version))))
|
| 5021 | (file-name (git-file-name name version))
|
| 5022 | (sha256
|
| 5023 | (base32 "1m6h6m0vm8vdx2nk26nvlbyfvlj0g9ph8cdh38258gn18fd2db0l"))
|
| 5024 | (patches
|
| 5025 | (search-patches "python-vaex-core-fix-tsl-use.patch"))
|
| 5026 | (modules '((guix build utils)
|
| 5027 | (ice-9 ftw)))
|
| 5028 | (snippet
|
| 5029 | #~(begin
|
| 5030 | |
| 5031 | (define (delete-except exception)
|
| 5032 | (lambda (file)
|
| 5033 | (unless (member file `("." ".." ,exception))
|
| 5034 | (delete-file-recursively file))))
|
| 5035 | (for-each (delete-except "packages") (scandir "."))
|
| 5036 | (with-directory-excursion "packages"
|
| 5037 | (for-each (delete-except "vaex-core") (scandir ".")))
|
| 5038 | (for-each (lambda (file)
|
| 5039 | (unless (member file '("." ".."))
|
| 5040 | (rename-file
|
| 5041 | (string-append "packages/vaex-core/" file)
|
| 5042 | file)))
|
| 5043 | (scandir "packages/vaex-core"))
|
| 5044 | (delete-file-recursively "packages")
|
| 5045 | (delete-file-recursively "vendor")))))
|
| 5046 | (build-system pyproject-build-system)
|
| 5047 | (arguments
|
| 5048 | (list
|
| 5049 | |
| 5050 | |
| 5051 | #:tests? #f
|
| 5052 | #:phases
|
| 5053 | #~(modify-phases %standard-phases
|
| 5054 | (add-after 'unpack 'relax-requirements
|
| 5055 | (lambda _
|
| 5056 | (substitute* "setup.py"
|
| 5057 | |
| 5058 | |
| 5059 | |
| 5060 | ((",<2024.9") ""))))
|
| 5061 | (add-before 'build 'patch-missing-include
|
| 5062 | (lambda _
|
| 5063 | |
| 5064 | |
| 5065 | (substitute* "src/string_utils.hpp"
|
| 5066 | (("#include <nonstd/string_view.hpp>")
|
| 5067 | "#include <cstdint>\n#include <nonstd/string_view.hpp>")))))))
|
| 5068 | (native-inputs
|
| 5069 | (list pybind11-2
|
| 5070 | python-cython
|
| 5071 | python-setuptools))
|
| 5072 | (inputs
|
| 5073 | (list boost
|
| 5074 | pcre
|
| 5075 | string-view-lite
|
| 5076 | tsl-hopscotch-map))
|
| 5077 | (propagated-inputs
|
| 5078 | (list python-aplus
|
| 5079 | python-blake3
|
| 5080 | python-cloudpickle
|
| 5081 | python-dask
|
| 5082 | python-filelock
|
| 5083 | python-frozendict
|
| 5084 | python-future
|
| 5085 | python-nest-asyncio
|
| 5086 | python-numpy
|
| 5087 | python-pandas
|
| 5088 | python-pyarrow
|
| 5089 | python-pydantic
|
| 5090 | python-pyyaml
|
| 5091 | python-rich
|
| 5092 | python-six |
| 5093 | python-tabulate
|
| 5094 | |
| 5095 | python-diskcache
|
| 5096 | python-fsspec
|
| 5097 | |
| 5098 | python-graphviz
|
| 5099 | python-h5py
|
| 5100 | python-httpx
|
| 5101 | |
| 5102 | python-psutil
|
| 5103 | python-s3fs))
|
| 5104 | (home-page "https://www.github.com/maartenbreddels/vaex")
|
| 5105 | (synopsis "Core of Vaex library for exploring tabular datasets")
|
| 5106 | (description "Vaex is a high performance Python library for lazy
|
| 5107 | Out-of-Core DataFrames (similar to Pandas), to visualize and explore big
|
| 5108 | tabular datasets. This package provides the core modules of Vaex.")
|
| 5109 | (license license:expat)))
|
| 5110 |
|
| 5111 | (define-public python-vector
|
| 5112 | (package
|
| 5113 | (name "python-vector")
|
| 5114 | (version "1.8.0")
|
| 5115 | (source
|
| 5116 | (origin
|
| 5117 | (method url-fetch)
|
| 5118 | (uri (pypi-uri "vector" version))
|
| 5119 | (sha256
|
| 5120 | (base32 "19jc889z6jxfyyqya5c6sx0hps6j5zgj0shp6k552f264jg5xyaq"))))
|
| 5121 | (build-system pyproject-build-system)
|
| 5122 | (arguments
|
| 5123 | (list
|
| 5124 | |
| 5125 | #:test-flags
|
| 5126 | |
| 5127 | #~(list "--deselect=tests/test_issues.py::test_issue_443" )))
|
| 5128 | (native-inputs
|
| 5129 | (list |
| 5130 | python-hatch-vcs
|
| 5131 | python-hatchling
|
| 5132 | |
| 5133 | python-notebook
|
| 5134 | python-optree
|
| 5135 | python-papermill
|
| 5136 | python-pytest
|
| 5137 | #;python-spark-parse)) |
| 5138 | (propagated-inputs
|
| 5139 | (list python-numpy
|
| 5140 | python-packaging
|
| 5141 | |
| 5142 | python-awkward
|
| 5143 | python-numba
|
| 5144 | python-sympy))
|
| 5145 | (home-page "https://github.com/scikit-hep/vector")
|
| 5146 | (synopsis "Arrays of 2D, 3D, and Lorentz vectors")
|
| 5147 | (description "Vector is a Python library for 2D and 3D spatial vectors, as
|
| 5148 | well as 4D space-time vectors. It is especially intended for performing
|
| 5149 | geometric calculations on arrays of vectors, rather than one vector at a time
|
| 5150 | in a Python @code{for} loop.")
|
| 5151 | (license license:bsd-3)))
|
| 5152 |
|
| 5153 | (define-public python-vedo
|
| 5154 | (package
|
| 5155 | (name "python-vedo")
|
| 5156 | (version "2025.5.4")
|
| 5157 | (source
|
| 5158 | (origin
|
| 5159 | (method git-fetch)
|
| 5160 | (uri (git-reference
|
| 5161 | (url "https://github.com/marcomusy/vedo")
|
| 5162 | (commit (string-append "v" version))))
|
| 5163 | (file-name (git-file-name name version))
|
| 5164 | (sha256
|
| 5165 | (base32 "17lrx30pdag0d3d5a2cycfylsbhad4ywikza784h2fg95w77y1va"))))
|
| 5166 | (build-system pyproject-build-system)
|
| 5167 | (arguments
|
| 5168 | (list
|
| 5169 | |
| 5170 | |
| 5171 | |
| 5172 | #:tests? #f
|
| 5173 | #:phases
|
| 5174 | #~(modify-phases %standard-phases
|
| 5175 | (add-after 'unpack 'relax-requirements
|
| 5176 | |
| 5177 | |
| 5178 | |
| 5179 | |
| 5180 | (lambda _
|
| 5181 | (substitute* "pyproject.toml"
|
| 5182 | (("\"vtk\",") "")))))))
|
| 5183 | (native-inputs
|
| 5184 | (list pkg-config
|
| 5185 | python-pkgconfig
|
| 5186 | python-setuptools
|
| 5187 | python-wheel))
|
| 5188 | (propagated-inputs
|
| 5189 | (list python-deprecated
|
| 5190 | python-matplotlib
|
| 5191 | python-numpy
|
| 5192 | python-pygments
|
| 5193 | vtk))
|
| 5194 | (home-page "https://github.com/marcomusy/vedo")
|
| 5195 | (synopsis
|
| 5196 | "Analysis and visualization of 3D objects and point clouds")
|
| 5197 | (description
|
| 5198 | "@code{vedo} is a fast and lightweight python module for
|
| 5199 | scientific analysis and visualization. The package provides a wide
|
| 5200 | range of functionalities for working with three-dimensional meshes and
|
| 5201 | point clouds. It can also be used to generate high quality
|
| 5202 | two-dimensional renderings such as scatter plots and histograms.
|
| 5203 | @code{vedo} is based on @code{vtk} and @code{numpy}.")
|
| 5204 | |
| 5205 | |
| 5206 | |
| 5207 | (license (list license:expat
|
| 5208 | license:silofl1.1
|
| 5209 | license:cc0
|
| 5210 | license:public-domain))))
|
| 5211 |
|
| 5212 | (define-public python-xarray
|
| 5213 | (package
|
| 5214 | (name "python-xarray")
|
| 5215 | (version "2025.12.0")
|
| 5216 | (source (origin
|
| 5217 | (method url-fetch)
|
| 5218 | (uri (pypi-uri "xarray" version))
|
| 5219 | (sha256
|
| 5220 | (base32
|
| 5221 | "1vczqm5daz79n7w3ycd0m1wf0bf78wd84w6xbgac8sfcvkxadxkk"))))
|
| 5222 | (build-system pyproject-build-system)
|
| 5223 | (arguments
|
| 5224 | (list
|
| 5225 | |
| 5226 | #:phases
|
| 5227 | #~(modify-phases %standard-phases
|
| 5228 | (add-after 'unpack 'fix-pytest-config
|
| 5229 | (lambda _
|
| 5230 | (substitute* "pyproject.toml"
|
| 5231 | ((".*--mypy-.*") "")))))))
|
| 5232 | (native-inputs
|
| 5233 | (list python-pytest
|
| 5234 | python-pytest-asyncio
|
| 5235 | python-setuptools
|
| 5236 | python-setuptools-scm))
|
| 5237 | (propagated-inputs
|
| 5238 | (list python-numpy
|
| 5239 | python-packaging
|
| 5240 | python-pandas))
|
| 5241 | (home-page "https://github.com/pydata/xarray")
|
| 5242 | (synopsis "N-D labeled arrays and datasets")
|
| 5243 | (description "Xarray (formerly xray) makes working with labelled
|
| 5244 | multi-dimensional arrays simple, efficient, and fun!
|
| 5245 |
|
| 5246 | Xarray introduces labels in the form of dimensions, coordinates and attributes
|
| 5247 | on top of raw NumPy-like arrays, which allows for a more intuitive, more
|
| 5248 | concise, and less error-prone developer experience. The package includes a
|
| 5249 | large and growing library of domain-agnostic functions for advanced analytics
|
| 5250 | and visualization with these data structures.")
|
| 5251 | (license license:asl2.0)))
|
| 5252 |
|
| 5253 | (define-public python-xarray-dataclass
|
| 5254 | (package
|
| 5255 | (name "python-xarray-dataclass")
|
| 5256 | (version "3.0.0")
|
| 5257 | (source
|
| 5258 | (origin
|
| 5259 | (method git-fetch)
|
| 5260 | (uri (git-reference
|
| 5261 | (url "https://github.com/xarray-contrib/xarray-dataclass/")
|
| 5262 | (commit (string-append "v" version))))
|
| 5263 | (file-name (git-file-name name version))
|
| 5264 | (sha256
|
| 5265 | (base32 "1q3y9gbzrp1mh48y7gggqgggwnarxdn32h907mfax1hi9ap6ywil"))))
|
| 5266 | (build-system pyproject-build-system)
|
| 5267 | (native-inputs
|
| 5268 | (list python-pytest
|
| 5269 | python-hatchling))
|
| 5270 | (propagated-inputs
|
| 5271 | (list python-numpy
|
| 5272 | python-typing-extensions
|
| 5273 | python-xarray))
|
| 5274 | (home-page "https://github.com/xarray-contrib/xarray-dataclass/")
|
| 5275 | (synopsis "Xarray data creation by data classes")
|
| 5276 | (description
|
| 5277 | "xarray-dataclass is a Python package that makes it easy to create
|
| 5278 | @url{https://xarray.pydata.org/en/stable/index.html, xarray}'s DataArray and
|
| 5279 | Dataset objects that are \"typed\" (i.e. fixed dimensions, data type,
|
| 5280 | coordinates, attributes, and name) using
|
| 5281 | @url{https://docs.python.org/3/library/dataclasses.html, the Python's
|
| 5282 | dataclass}. It's a successor of not maintained
|
| 5283 | https://github.com/astropenguin/xarray-dataclasses.")
|
| 5284 | (license license:expat)))
|
| 5285 |
|
| 5286 | (define-public python-xarray-dataclasses
|
| 5287 | (package
|
| 5288 | (name "python-xarray-dataclasses")
|
| 5289 | (version "1.7.0")
|
| 5290 | (source
|
| 5291 | (origin
|
| 5292 | (method git-fetch)
|
| 5293 | (uri (git-reference
|
| 5294 | (url "https://github.com/astropenguin/xarray-dataclasses/")
|
| 5295 | (commit (string-append "v" version))))
|
| 5296 | (file-name (git-file-name name version))
|
| 5297 | (sha256
|
| 5298 | (base32 "043lc1hadr5y0y16g682viiafy0hfsa7q18lqmndpyvnmcgm893z"))))
|
| 5299 | (build-system pyproject-build-system)
|
| 5300 | (propagated-inputs (list python-numpy python-typing-extensions
|
| 5301 | python-xarray))
|
| 5302 | (native-inputs (list python-pytest python-poetry-core))
|
| 5303 | (home-page "https://github.com/astropenguin/xarray-dataclasses/")
|
| 5304 | (synopsis "Data creation made easy by dataclass")
|
| 5305 | (description "@code{xarray-dataclasses} is a Python package that makes it
|
| 5306 | easy to create @code{xarray}'s @code{DataArray} and @code{Datase} objects that
|
| 5307 | are \"typed\" (i.e. fixed dimensions, data type, coordinates, attributes, and
|
| 5308 | name) using the Python's @code{dataclass}.")
|
| 5309 | (license license:expat)))
|
| 5310 |
|
| 5311 | (define-public python-xarray-einstats
|
| 5312 | (package
|
| 5313 | (name "python-xarray-einstats")
|
| 5314 | (version "0.9.1")
|
| 5315 | (source
|
| 5316 | (origin
|
| 5317 | (method git-fetch)
|
| 5318 | (uri (git-reference
|
| 5319 | (url "https://github.com/arviz-devs/xarray-einstats")
|
| 5320 | (commit (string-append "v" version))))
|
| 5321 | (file-name (git-file-name name version))
|
| 5322 | (sha256
|
| 5323 | (base32 "11crz1l6swabwzmwbrxypfw8gbbp81higzgi5nsxzfigcrrqq30a"))))
|
| 5324 | (build-system pyproject-build-system)
|
| 5325 | |
| 5326 | (native-inputs
|
| 5327 | (list python-flit-core
|
| 5328 | python-pytest))
|
| 5329 | (propagated-inputs
|
| 5330 | (list python-numpy
|
| 5331 | python-scipy
|
| 5332 | python-xarray
|
| 5333 | |
| 5334 | python-einops
|
| 5335 | python-numba))
|
| 5336 | (home-page "https://einstats.python.arviz.org/en/latest/")
|
| 5337 | (synopsis "Stats, linear algebra and einops for xarray")
|
| 5338 | (description
|
| 5339 | "@code{xarray_einstats} provides wrappers around some NumPy and SciPy
|
| 5340 | functions and around einops with an API and features adapted to xarray.")
|
| 5341 | (license license:asl2.0)))
|
| 5342 |
|
| 5343 | (define-public python-xarray-schema
|
| 5344 | (package
|
| 5345 | (name "python-xarray-schema")
|
| 5346 | (version "0.0.3")
|
| 5347 | (source
|
| 5348 | (origin
|
| 5349 | (method url-fetch)
|
| 5350 | (uri (pypi-uri "xarray-schema" version))
|
| 5351 | (sha256
|
| 5352 | (base32 "08194629696z98dkc74i6c9zmy1jicvd2ajb75q0lsf0i427cv4w"))))
|
| 5353 | (build-system pyproject-build-system)
|
| 5354 | (propagated-inputs (list python-numpy python-xarray))
|
| 5355 | (native-inputs
|
| 5356 | (list python-pytest
|
| 5357 | python-setuptools
|
| 5358 | python-setuptools-scm
|
| 5359 | python-wheel))
|
| 5360 | (home-page "https://github.com/carbonplan/xarray-schema")
|
| 5361 | (synopsis "Schema validation for Xarray objects")
|
| 5362 | (description "This package implements schema validation for Xarray
|
| 5363 | objects.")
|
| 5364 | (license license:expat)))
|
| 5365 |
|
| 5366 | (define-public python-pytensor
|
| 5367 | (package
|
| 5368 | (name "python-pytensor")
|
| 5369 | (version "2.36.3")
|
| 5370 | (source (origin
|
| 5371 | (method git-fetch)
|
| 5372 | (uri (git-reference
|
| 5373 | (url "https://github.com/pymc-devs/pytensor")
|
| 5374 | (commit (string-append "rel-" version))))
|
| 5375 | (file-name (git-file-name name version))
|
| 5376 | (sha256
|
| 5377 | (base32
|
| 5378 | "0m9nmwnn0ixrk9ml0yc6qjdcw0vmw7swfcw8vahyfmp70pirhimn"))))
|
| 5379 | (build-system pyproject-build-system)
|
| 5380 | (arguments
|
| 5381 | (list
|
| 5382 | |
| 5383 | #:test-flags
|
| 5384 | |
| 5385 | |
| 5386 | |
| 5387 | |
| 5388 | |
| 5389 | |
| 5390 | |
| 5391 | |
| 5392 | |
| 5393 | #~(list "--benchmark-disable"
|
| 5394 | "--benchmark-skip"
|
| 5395 | "--durations=50"
|
| 5396 | |
| 5397 | "--ignore=tests/scan/"
|
| 5398 | "--ignore=tests/tensor/"
|
| 5399 | "--ignore=tests/sandbox/"
|
| 5400 | "--ignore=tests/sparse/sandbox/"
|
| 5401 | |
| 5402 | "--deselect=tests/link/numba/test_nlinalg.py::test_Eigh[x0-L-None]"
|
| 5403 | #$@(map (lambda (test)
|
| 5404 | (string-append "--deselect=tests/graph/rewriting/"
|
| 5405 | "test_basic.py::"
|
| 5406 | test))
|
| 5407 | |
| 5408 | |
| 5409 | |
| 5410 | (list "TestPatternNodeRewriter::test_replace_output"
|
| 5411 | "TestPatternNodeRewriter::test_nested_out_pattern"
|
| 5412 | "TestPatternNodeRewriter::test_unification_1"
|
| 5413 | "TestPatternNodeRewriter::test_replace_subgraph"
|
| 5414 | "TestPatternNodeRewriter::test_no_recurse"
|
| 5415 | "TestPatternNodeRewriter::test_multiple"
|
| 5416 | "TestPatternNodeRewriter::test_nested_even"
|
| 5417 | "TestPatternNodeRewriter::test_nested_odd"
|
| 5418 | "TestPatternNodeRewriter::test_expand"
|
| 5419 | "TestPatternNodeRewriter::test_ambiguous"
|
| 5420 | "TestPatternNodeRewriter::test_constant"
|
| 5421 | "TestPatternNodeRewriter::test_constraints"
|
| 5422 | "TestPatternNodeRewriter::test_match_same"
|
| 5423 | "TestPatternNodeRewriter::test_eq"
|
| 5424 | "TestEquilibrium::test_1"
|
| 5425 | "TestEquilibrium::test_2"
|
| 5426 | "TestEquilibrium::test_low_use_ratio"
|
| 5427 | |
| 5428 | "TestPatternNodeRewriter::test_allow_multiple_clients"
|
| 5429 | "TestPatternNodeRewriter::test_op_pattern"
|
| 5430 | "test_patternsub_values_eq_approx[out_pattern0-True]"
|
| 5431 | "test_patternsub_values_eq_approx[out_pattern0-False]"
|
| 5432 | "test_patternsub_values_eq_approx[x-True]"
|
| 5433 | "test_patternsub_values_eq_approx[x-False]"
|
| 5434 | "test_patternsub_multi_output_nodes"))
|
| 5435 | #$@(map (lambda (test)
|
| 5436 | (string-append "--deselect=tests/graph/" test))
|
| 5437 | (list "rewriting/test_kanren.py::test_kanren_basic"
|
| 5438 | "rewriting/test_kanren.py::test_KanrenRelationSub_filters"
|
| 5439 | "rewriting/test_kanren.py::test_KanrenRelationSub_dot"
|
| 5440 | "rewriting/test_unify.py::test_unify_Variable"
|
| 5441 | "rewriting/test_unify.py::test_ConstrainedVar"
|
| 5442 | "rewriting/test_unify.py::test_unify_OpPattern"
|
| 5443 | "test_destroyhandler.py::test_misc")))
|
| 5444 | #:phases
|
| 5445 | #~(modify-phases %standard-phases
|
| 5446 | (add-before 'check 'pre-check
|
| 5447 | (lambda _
|
| 5448 | |
| 5449 | (setenv "HOME" "/tmp")
|
| 5450 | |
| 5451 | |
| 5452 | (delete-file-recursively "pytensor"))))))
|
| 5453 | (native-inputs (list python-cython
|
| 5454 | python-pytest
|
| 5455 | python-pytest-benchmark
|
| 5456 | python-pytest-mock
|
| 5457 | python-pytest-xdist
|
| 5458 | python-versioneer
|
| 5459 | python-setuptools))
|
| 5460 | (propagated-inputs (list python-cons
|
| 5461 | python-etuples
|
| 5462 | python-filelock
|
| 5463 | python-logical-unification
|
| 5464 | python-minikanren
|
| 5465 | python-numba
|
| 5466 | python-numpy
|
| 5467 | python-scipy
|
| 5468 | |
| 5469 | |
| 5470 | |
| 5471 | #;python-llvmlite))
|
| 5472 | (home-page "https://pytensor.readthedocs.io/en/latest/")
|
| 5473 | (synopsis
|
| 5474 | "Library for mathematical expressions in multi-dimensional arrays")
|
| 5475 | (description
|
| 5476 | "PyTensor is a Python library that allows one to define, optimize, and
|
| 5477 | efficiently evaluate mathematical expressions involving multi-dimensional
|
| 5478 | arrays. It is a fork of the Aesara library.")
|
| 5479 | (license license:bsd-3)))
|
| 5480 |
|
| 5481 | (define-public python-scs
|
| 5482 | (package
|
| 5483 | (name "python-scs")
|
| 5484 | (version "3.2.10")
|
| 5485 | (source
|
| 5486 | (origin
|
| 5487 | (method git-fetch)
|
| 5488 | (uri (git-reference
|
| 5489 | (url "https://github.com/bodono/scs-python")
|
| 5490 | (commit version)))
|
| 5491 | (file-name (git-file-name name version))
|
| 5492 | (sha256
|
| 5493 | (base32 "1wg1g6das5hs53z3sjn2m8646023d14q9shmwfb38n23baqi468g"))))
|
| 5494 | (build-system pyproject-build-system)
|
| 5495 | (arguments
|
| 5496 | (list
|
| 5497 | |
| 5498 | #:phases
|
| 5499 | #~(modify-phases %standard-phases
|
| 5500 | (add-after 'ensure-no-mtimes-pre-1980 'substitute-git-submodules
|
| 5501 | (lambda _
|
| 5502 | (rmdir "scs_source")
|
| 5503 | (symlink #$(package-source
|
| 5504 | (this-package-native-input "scs"))
|
| 5505 | "scs_source")
|
| 5506 | (rmdir "scs/pythoncapi-compat")
|
| 5507 | (symlink #$(package-source
|
| 5508 | (this-package-native-input "pythoncapi-compat"))
|
| 5509 | "scs/pythoncapi-compat"))))))
|
| 5510 | (native-inputs
|
| 5511 | (list pkg-config
|
| 5512 | python-meson
|
| 5513 | python-pytest
|
| 5514 | pythoncapi-compat
|
| 5515 | scs))
|
| 5516 | (inputs
|
| 5517 | (list lapack
|
| 5518 | openblas))
|
| 5519 | (propagated-inputs
|
| 5520 | (list python-numpy
|
| 5521 | python-scipy))
|
| 5522 | (home-page "https://github.com/bodono/scs-python")
|
| 5523 | (synopsis "Splitting conic solver")
|
| 5524 | (description "This package provides a Python interface for the
|
| 5525 | SCS (Splitting conic solver) library.")
|
| 5526 | (license license:expat)))
|
| 5527 |
|
| 5528 | (define-public python-pandas-flavor
|
| 5529 | (package
|
| 5530 | (name "python-pandas-flavor")
|
| 5531 | (version "0.8.1")
|
| 5532 | (source
|
| 5533 | (origin
|
| 5534 | (method url-fetch)
|
| 5535 | (uri (pypi-uri "pandas_flavor" version))
|
| 5536 | (sha256
|
| 5537 | (base32
|
| 5538 | "0rn3pnracv8013j3f737qal3isf1brbc3mpxqhr03vik322sapr5"))))
|
| 5539 | (build-system pyproject-build-system)
|
| 5540 | (native-inputs
|
| 5541 | (list python-pytest
|
| 5542 | python-setuptools
|
| 5543 | python-setuptools-scm))
|
| 5544 | (propagated-inputs
|
| 5545 | (list python-pandas
|
| 5546 | python-xarray))
|
| 5547 | (home-page "https://github.com/pyjanitor-devs/pandas_flavor")
|
| 5548 | (synopsis "Write your own flavor of Pandas")
|
| 5549 | (description "Pandas 0.23 added a simple API for registering accessors
|
| 5550 | with Pandas objects. Pandas-flavor extends Pandas' extension API by
|
| 5551 |
|
| 5552 | @itemize
|
| 5553 | @item adding support for registering methods as well
|
| 5554 | @item making each of these functions backwards compatible with older versions
|
| 5555 | of Pandas
|
| 5556 | @end itemize")
|
| 5557 | (license license:expat)))
|
| 5558 |
|
| 5559 | (define-public python-pingouin
|
| 5560 | (package
|
| 5561 | (name "python-pingouin")
|
| 5562 | (version "0.5.5")
|
| 5563 | (source
|
| 5564 | (origin
|
| 5565 | (method git-fetch)
|
| 5566 | (uri (git-reference
|
| 5567 | (url "https://github.com/raphaelvallat/pingouin")
|
| 5568 | (commit (string-append "v" version))))
|
| 5569 | (file-name (git-file-name name version))
|
| 5570 | (sha256
|
| 5571 | (base32
|
| 5572 | "0i3yzdlj08di3mzi69ci57jm5myl123hp8c5vn1g35k77m4zpgvd"))))
|
| 5573 | (build-system pyproject-build-system)
|
| 5574 | (arguments
|
| 5575 | (list
|
| 5576 | |
| 5577 | #:test-flags
|
| 5578 | |
| 5579 | #~(list "--deselect=tests/test_pairwise.py::TestPairwise::test_pairwise_tests"
|
| 5580 | |
| 5581 | "--deselect=tests/test_power.py::TestPower::test_power_ttest")))
|
| 5582 | (native-inputs
|
| 5583 | (list python-pytest
|
| 5584 | python-setuptools))
|
| 5585 | (propagated-inputs
|
| 5586 | (list python-matplotlib
|
| 5587 | python-mpmath
|
| 5588 | python-numpy
|
| 5589 | python-pandas
|
| 5590 | python-pandas-flavor
|
| 5591 | python-scikit-learn
|
| 5592 | python-scipy
|
| 5593 | python-seaborn
|
| 5594 | python-statsmodels
|
| 5595 | python-tabulate))
|
| 5596 | (home-page "https://pingouin-stats.org/")
|
| 5597 | (synopsis "Statistical package for Python")
|
| 5598 | (description "Pingouin is a statistical package written in Python 3 and
|
| 5599 | based mostly on Pandas and NumPy. Its features include
|
| 5600 |
|
| 5601 | @itemize
|
| 5602 | @item ANOVAs: N-ways, repeated measures, mixed, ancova
|
| 5603 | @item Pairwise post-hocs tests (parametric and non-parametric) and pairwise
|
| 5604 | correlations
|
| 5605 | @item Robust, partial, distance and repeated measures correlations
|
| 5606 | @item Linear/logistic regression and mediation analysis
|
| 5607 | @item Bayes Factors
|
| 5608 | @item Multivariate tests
|
| 5609 | @item Reliability and consistency
|
| 5610 | @item Effect sizes and power analysis
|
| 5611 | @item Parametric/bootstrapped confidence intervals around an effect size or a
|
| 5612 | correlation coefficient
|
| 5613 | @item Circular statistics
|
| 5614 | @item Chi-squared tests
|
| 5615 | @item Plotting: Bland-Altman plot, Q-Q plot, paired plot, robust correlation,
|
| 5616 | and more
|
| 5617 | @end itemize")
|
| 5618 | (license license:gpl3)))
|
| 5619 |
|
| 5620 | (define-public python-plotly
|
| 5621 | (package
|
| 5622 | (name "python-plotly")
|
| 5623 | (version "6.8.0")
|
| 5624 | (source
|
| 5625 | (origin
|
| 5626 | (method git-fetch)
|
| 5627 | (uri (git-reference
|
| 5628 | (url "https://github.com/plotly/plotly.py")
|
| 5629 | (commit (string-append "v" version))))
|
| 5630 | (file-name (git-file-name name version))
|
| 5631 | (sha256
|
| 5632 | (base32 "147vgm22zrg4wcjc427mxszbb8v6vhs7hgchcm8678cy304hawvd"))))
|
| 5633 | (build-system pyproject-build-system)
|
| 5634 | (arguments
|
| 5635 | (list
|
| 5636 | |
| 5637 | #:test-flags
|
| 5638 | |
| 5639 | #~(list "--ignore=plotly/matplotlylib/mplexporter/tests/test_basic.py"
|
| 5640 | "--ignore=plotly/matplotlylib/mplexporter/tests/test_utils.py"
|
| 5641 | "--ignore=plotly/matplotlylib/tests/test_renderer.py"
|
| 5642 | "--ignore=tests/test_io/test_renderers.py"
|
| 5643 | "--ignore=tests/test_optional/test_kaleido/test_kaleido.py"
|
| 5644 | |
| 5645 | "-k" (string-join
|
| 5646 | (list "not test_acceptance_named"
|
| 5647 | "test_colorscale_and_levels_same_length"
|
| 5648 | "test_correct_order_param"
|
| 5649 | "test_date_in_hover"
|
| 5650 | "test_dependencies_not_imported"
|
| 5651 | "test_fips_values_same_length"
|
| 5652 | "test_from_json_output_type"
|
| 5653 | "test_get_module_exists_submodule"
|
| 5654 | "test_iplot_mpl_works"
|
| 5655 | "test_iplot_works_after_you_call_init_notebook_mode"
|
| 5656 | "test_iplot_works_without_init_notebook_mode"
|
| 5657 | "test_lazy_imports"
|
| 5658 | "test_ols_trendline_slopes"
|
| 5659 | "test_overall_trendline"
|
| 5660 | "test_read_json_from_file_string"
|
| 5661 | "test_read_json_from_filelike"
|
| 5662 | "test_read_json_from_pathlib"
|
| 5663 | "test_render_mode"
|
| 5664 | "test_scope_is_not_list"
|
| 5665 | "test_trendline_enough_values"
|
| 5666 | "test_trendline_nan_values"
|
| 5667 | "test_trendline_on_timeseries"
|
| 5668 | "test_trendline_results_passthrough")
|
| 5669 | " and not "))
|
| 5670 | #:phases
|
| 5671 | #~(modify-phases %standard-phases
|
| 5672 | (add-before 'build 'skip-npm
|
| 5673 | |
| 5674 | (lambda _
|
| 5675 | (setenv "SKIP_NPM" "T"))))))
|
| 5676 | |
| 5677 | |
| 5678 | |
| 5679 | (native-inputs
|
| 5680 | (list |
| 5681 | python-colorcet
|
| 5682 | python-geopandas
|
| 5683 | python-hatchling
|
| 5684 | python-inflect
|
| 5685 | |
| 5686 | python-numpy
|
| 5687 | python-orjson
|
| 5688 | python-pandas-minimal
|
| 5689 | |
| 5690 | python-pillow
|
| 5691 | |
| 5692 | python-polars
|
| 5693 | python-pyarrow
|
| 5694 | python-pyshp
|
| 5695 | python-pytest
|
| 5696 | python-pytz
|
| 5697 | python-scikit-image
|
| 5698 | python-scipy-minimal
|
| 5699 | python-shapely
|
| 5700 | python-statsmodels
|
| 5701 | python-xarray
|
| 5702 | tzdata-for-tests))
|
| 5703 | (propagated-inputs
|
| 5704 | (list python-narwhals
|
| 5705 | python-packaging))
|
| 5706 | (home-page "https://plotly.com/python/")
|
| 5707 | (synopsis "Interactive plotting library for Python")
|
| 5708 | (description
|
| 5709 | "Plotly's Python graphing library makes interactive,publication-quality
|
| 5710 | graphs online. Examples of how to make line plots, scatter plots, area
|
| 5711 | charts, bar charts, error bars, box plots, histograms, heatmaps, subplots,
|
| 5712 | multiple-axes, polar charts, and bubble charts.")
|
| 5713 | (license license:expat)))
|
| 5714 |
|
| 5715 | (define-public python-plotnine
|
| 5716 | (package
|
| 5717 | (name "python-plotnine")
|
| 5718 | (version "0.14.5")
|
| 5719 | (source
|
| 5720 | (origin
|
| 5721 | (method git-fetch)
|
| 5722 | (uri (git-reference
|
| 5723 | (url "https://github.com/has2k1/plotnine")
|
| 5724 | (commit (string-append "v" version))))
|
| 5725 | (file-name (git-file-name name version))
|
| 5726 | (sha256
|
| 5727 | (base32 "02ph0h312qn5a9ivh2qhv0x9sybccgbidzvb8im1hikwcqp8v2fw"))))
|
| 5728 | (build-system pyproject-build-system)
|
| 5729 | (arguments
|
| 5730 | (list
|
| 5731 | #:test-flags
|
| 5732 | |
| 5733 | |
| 5734 | |
| 5735 | |
| 5736 | `(list ,@(map (lambda (file) (string-append "--ignore=" file))
|
| 5737 | (list "tests/test_aes.py"
|
| 5738 | "tests/test_annotation_logticks.py"
|
| 5739 | "tests/test_coords.py"
|
| 5740 | "tests/test_facet_labelling.py"
|
| 5741 | "tests/test_facets.py"
|
| 5742 | "tests/test_geom_bar_col_histogram.py"
|
| 5743 | "tests/test_geom_bin_2d.py"
|
| 5744 | "tests/test_geom_boxplot.py"
|
| 5745 | "tests/test_geom_count.py"
|
| 5746 | "tests/test_geom_density_2d.py"
|
| 5747 | "tests/test_geom_density.py"
|
| 5748 | "tests/test_geom_dotplot.py"
|
| 5749 | "tests/test_geom_freqpoly.py"
|
| 5750 | "tests/test_geom_map.py"
|
| 5751 | "tests/test_geom_path_line_step.py"
|
| 5752 | "tests/test_geom_point.py"
|
| 5753 | "tests/test_geom_raster.py"
|
| 5754 | "tests/test_geom_rect_tile.py"
|
| 5755 | "tests/test_geom_ribbon_area.py"
|
| 5756 | "tests/test_geom_sina.py"
|
| 5757 | "tests/test_geom_smooth.py"
|
| 5758 | "tests/test_geom_text_label.py"
|
| 5759 | "tests/test_geom_violin.py"
|
| 5760 | "tests/test_layout.py"
|
| 5761 | "tests/test_position.py"
|
| 5762 | "tests/test_qplot.py"
|
| 5763 | "tests/test_scale_internals.py"
|
| 5764 | "tests/test_scale_labelling.py"
|
| 5765 | "tests/test_stat_ecdf.py"
|
| 5766 | "tests/test_stat_function.py"
|
| 5767 | "tests/test_stat_summary.py"
|
| 5768 | "tests/test_theme.py"))
|
| 5769 | "-k"
|
| 5770 | (string-append "not "
|
| 5771 | (string-join
|
| 5772 | (list
|
| 5773 | |
| 5774 | |
| 5775 | "test_save_method"
|
| 5776 | |
| 5777 | "test_no_after_scale_warning"
|
| 5778 | |
| 5779 | "test_non_linear_smooth"
|
| 5780 | "test_non_linear_smooth_no_ci")
|
| 5781 | " and not "
|
| 5782 | 'infix)))
|
| 5783 | #:phases
|
| 5784 | #~(modify-phases %standard-phases
|
| 5785 | (add-before 'check 'pre-check
|
| 5786 | (lambda* (#:key inputs outputs #:allow-other-keys)
|
| 5787 | |
| 5788 | |
| 5789 | (copy-recursively "plotnine/data"
|
| 5790 | (string-append (site-packages inputs
|
| 5791 | outputs)
|
| 5792 | "/plotnine/data"))
|
| 5793 | (setenv "CI" "1") |
| 5794 | |
| 5795 | |
| 5796 | (setenv "MPLCONFIGDIR" "/tmp")
|
| 5797 | (setenv "TZ" "UTC")
|
| 5798 | (setenv "TZDIR"
|
| 5799 | (search-input-directory inputs "share/zoneinfo")))))))
|
| 5800 | (propagated-inputs (list python-adjusttext
|
| 5801 | python-matplotlib
|
| 5802 | python-mizani
|
| 5803 | python-numpy
|
| 5804 | python-patsy
|
| 5805 | python-scipy
|
| 5806 | python-statsmodels))
|
| 5807 | (native-inputs (list python-geopandas
|
| 5808 | python-mock
|
| 5809 | python-pandas
|
| 5810 | python-pytest
|
| 5811 | python-setuptools
|
| 5812 | python-setuptools-scm
|
| 5813 | python-wheel
|
| 5814 | tzdata-for-tests))
|
| 5815 | (home-page "https://github.com/has2k1/plotnine")
|
| 5816 | (synopsis "Grammar of Graphics for Python")
|
| 5817 | (description
|
| 5818 | "Plotnine is a Python implementation of the Grammar of Graphics.
|
| 5819 | It is a powerful graphics concept for creating plots and visualizations in a
|
| 5820 | structured and declarative manner. It is inspired by the R package ggplot2
|
| 5821 | and aims to provide a similar API and functionality in Python.")
|
| 5822 | (license license:expat)))
|
| 5823 |
|
| 5824 | (define-public python-pytest-pyvista
|
| 5825 | (package
|
| 5826 | (name "python-pytest-pyvista")
|
| 5827 | (version "0.3.2")
|
| 5828 | (source
|
| 5829 | (origin
|
| 5830 | (method url-fetch)
|
| 5831 | (uri (pypi-uri "pytest_pyvista" version))
|
| 5832 | (sha256
|
| 5833 | (base32 "0hgk3a5wwymk3k7ih4lsmkd44dfnsd842zv5859izqxkw74j2xpn"))))
|
| 5834 | (build-system pyproject-build-system)
|
| 5835 | (arguments
|
| 5836 | (list
|
| 5837 | |
| 5838 | #:tests? #f))
|
| 5839 | (propagated-inputs (list python-numpy python-pillow python-pytest-8))
|
| 5840 | (native-inputs (list python-flit-core))
|
| 5841 | (home-page "https://github.com/pyvista/pytest-pyvista")
|
| 5842 | (synopsis "Pytest plugin for comparing PyVista plot images")
|
| 5843 | (description "This package provides a Pytest plugin that facilitates
|
| 5844 | the comparison of images produced by PyVista, generating cached images from
|
| 5845 | tests and comparing subsequent results against that cache.")
|
| 5846 | (license license:expat)))
|
| 5847 |
|
| 5848 | (define-public python-pyvista
|
| 5849 | (package
|
| 5850 | (name "python-pyvista")
|
| 5851 | (version "0.46.5")
|
| 5852 | (source
|
| 5853 | (origin
|
| 5854 | (method git-fetch)
|
| 5855 | (uri (git-reference
|
| 5856 | (url "https://github.com/pyvista/pyvista")
|
| 5857 | (commit (string-append "v" version))))
|
| 5858 | (file-name (git-file-name name version))
|
| 5859 | (sha256
|
| 5860 | (base32 "0553bp4fhbar9z0ybjv1mw1jhb5rhrr4v6q2bzmia0ww0dn8fc69"))))
|
| 5861 | (build-system pyproject-build-system)
|
| 5862 | (arguments
|
| 5863 | (list
|
| 5864 | |
| 5865 | #:test-flags
|
| 5866 | |
| 5867 | #~(list "--ignore=tests/plotting/test_charts.py"
|
| 5868 | "--ignore=tests/examples/test_download_files.py"
|
| 5869 | "--ignore=tests/examples/test_downloads.py"
|
| 5870 | "--ignore=tests/plotting/test_texture.py"
|
| 5871 | |
| 5872 | "--ignore=tests/core/test_dataobject_filters.py"
|
| 5873 | |
| 5874 | "--ignore=tests/core/test_dataset_filters.py"
|
| 5875 | |
| 5876 | "--ignore=tests/plotting/test_plotter.py"
|
| 5877 | "-k" (string-join
|
| 5878 | (list "not test_actor_texture"
|
| 5879 | "test_add_multiple"
|
| 5880 | "test_add_timer_event"
|
| 5881 | "test_avsucd_reader"
|
| 5882 | "test_binarymarchingcubesreader"
|
| 5883 | "test_bmpreader"
|
| 5884 | "test_box_axes"
|
| 5885 | "test_byureader"
|
| 5886 | "test_cast_to_numpy_raises"
|
| 5887 | "test_compute_boundary_mesh_quality"
|
| 5888 | "test_connectivity_"
|
| 5889 | "test_dataset_loader_cubemap"
|
| 5890 | "test_dataset_loader_dicom"
|
| 5891 | "test_dataset_loader_from_nested_files_and_directory"
|
| 5892 | "test_dataset_loader_from_nested_multiblock"
|
| 5893 | "test_dataset_loader_one_file"
|
| 5894 | "test_dataset_loader_two_files_both_loadable"
|
| 5895 | "test_dataset_loader_two_files_one_loadable"
|
| 5896 | "test_dcmreader"
|
| 5897 | "test_demreader"
|
| 5898 | "test_ensight_multi_block_io"
|
| 5899 | "test_ensightreader_arrays"
|
| 5900 | "test_ensightreader_time_sets"
|
| 5901 | "test_ensightreader_timepoints"
|
| 5902 | "test_facetreader"
|
| 5903 | "test_fluentcffreader"
|
| 5904 | "test_gambitreader"
|
| 5905 | "test_gaussian_cubes_reader"
|
| 5906 | "test_gesignareader"
|
| 5907 | "test_gif_reader"
|
| 5908 | "test_hdf_reader"
|
| 5909 | "test_hdr_reader"
|
| 5910 | "test_init_cmap"
|
| 5911 | "test_interpolate"
|
| 5912 | "test_jpegreader"
|
| 5913 | "test_legend_"
|
| 5914 | "test_load_dataset_no_reader"
|
| 5915 | "test_load_theme"
|
| 5916 | "test_meta_image_reader"
|
| 5917 | "test_multiblockplot3dreader"
|
| 5918 | "test_nifti_reader"
|
| 5919 | "test_nrrd_reader"
|
| 5920 | "test_objreader"
|
| 5921 | "test_only_screenshots_flag"
|
| 5922 | "test_openfoam_case_type"
|
| 5923 | "test_openfoam_cell_to_point_default"
|
| 5924 | "test_openfoam_patch_arrays"
|
| 5925 | "test_openfoam_skip_zero_time"
|
| 5926 | "test_openfoamreader_active_time"
|
| 5927 | "test_openfoamreader_arrays_time"
|
| 5928 | "test_openfoamreader_read_data_time_point"
|
| 5929 | "test_openfoamreader_read_data_time_value"
|
| 5930 | "test_particle_reader"
|
| 5931 | "test_partition"
|
| 5932 | "test_pdbreader"
|
| 5933 | "test_plot3dmetareader"
|
| 5934 | "test_plot_return_img_with_cpos"
|
| 5935 | "test_plot_return_img_without_cpos"
|
| 5936 | "test_png_reader"
|
| 5937 | "test_pnm_reader"
|
| 5938 | "test_prostar_reader"
|
| 5939 | "test_protein_ribbon"
|
| 5940 | "test_pvdreader"
|
| 5941 | "test_pvdreader_no_part_group"
|
| 5942 | "test_pvdreader_no_time_group"
|
| 5943 | "test_read_cgns"
|
| 5944 | "test_repr"
|
| 5945 | "test_save_before_close_callback"
|
| 5946 | "test_slc_reader"
|
| 5947 | "test_stlreader"
|
| 5948 | "test_tecplotreader"
|
| 5949 | "test_tiff_reader"
|
| 5950 | "test_timer"
|
| 5951 | "test_translate_direction_collinear"
|
| 5952 | "test_user_logo"
|
| 5953 | "test_xdmf_reader"
|
| 5954 | |
| 5955 | |
| 5956 | "test_check_subdtype_changes_type"
|
| 5957 | |
| 5958 | "test_read_exodus"
|
| 5959 | "test_nek5000_reader"
|
| 5960 | "test_exodus_reader_ext"
|
| 5961 | "test_exodus_reader_core"
|
| 5962 | "test_exodus_blocks"
|
| 5963 | "test_download_dataset_texture"
|
| 5964 | "test_structured_grid_cast_to_explicit_structured_grid"
|
| 5965 | "test_pad_image_multi_component_with_scalar"
|
| 5966 | "test_pad_image_raises"
|
| 5967 | "test_points_to_cells_and_cells_to_points_dimensions"
|
| 5968 | |
| 5969 | "test_meshio[cow_ugrid]"
|
| 5970 | "test_meshio[points_only]"
|
| 5971 | |
| 5972 | "test_max_positional_args_matches_pyproject")
|
| 5973 | " and not "))
|
| 5974 | #:phases
|
| 5975 | #~(modify-phases %standard-phases
|
| 5976 | |
| 5977 | (add-after 'unpack 'patch-pyproject
|
| 5978 | (lambda _
|
| 5979 | (substitute* "pyproject.toml"
|
| 5980 | (("'vtk[^']*'," all) (string-append "#" all)))))
|
| 5981 | (add-after 'unpack 'fix-failing-tests
|
| 5982 | (lambda _
|
| 5983 | (substitute* "tests/plotting/test_plotting.py"
|
| 5984 | (("\"\"\"Determine if using mesa.\"\"\"" all)
|
| 5985 | (string-append all "\n return False")))
|
| 5986 | (substitute* "tests/test_meshio.py"
|
| 5987 | (("cow = .*$" all) (string-append "#" all "\n"))
|
| 5988 | ((", cow") ""))))
|
| 5989 | |
| 5990 | (add-before 'check 'redirect-HOME
|
| 5991 | (lambda _
|
| 5992 | (setenv "HOME" "/tmp"))))))
|
| 5993 | (native-inputs
|
| 5994 | (list nss-certs-for-test
|
| 5995 | python-aiohttp
|
| 5996 | python-ipython
|
| 5997 | python-mypy
|
| 5998 | python-pandas
|
| 5999 | python-pytest-8
|
| 6000 | python-pytest-cases
|
| 6001 | python-pytest-mock
|
| 6002 | python-pytest-pyvista
|
| 6003 | python-scipy
|
| 6004 | python-tqdm
|
| 6005 | python-trimesh
|
| 6006 | which
|
| 6007 | xorg-server-for-tests))
|
| 6008 | (propagated-inputs
|
| 6009 | (list python-cmcrameri
|
| 6010 | python-cmocean
|
| 6011 | python-colorcet
|
| 6012 | python-imageio
|
| 6013 | python-matplotlib
|
| 6014 | python-meshio
|
| 6015 | python-numpy
|
| 6016 | python-pillow
|
| 6017 | python-pooch
|
| 6018 | python-scooby
|
| 6019 | vtk-9.5))
|
| 6020 | (home-page "https://docs.pyvista.org/")
|
| 6021 | (synopsis "3D plotting and mesh analysis through VTK")
|
| 6022 | (description
|
| 6023 | "PyVista is...
|
| 6024 |
|
| 6025 | @itemize
|
| 6026 | @item @emph{Pythonic VTK}: a high-level API to the Visualization
|
| 6027 | Toolkit (VTK);
|
| 6028 | @item mesh data structures and filtering methods for spatial datasets;
|
| 6029 | @item 3D plotting made simple and built for large/complex data geometries.
|
| 6030 | @end itemize
|
| 6031 |
|
| 6032 | This package provides a Pythonic, well-documented interface exposing VTK's
|
| 6033 | powerful visualization backend to facilitate rapid prototyping, analysis, and
|
| 6034 | visual integration of spatially referenced datasets.")
|
| 6035 | (license license:expat)))
|
| 6036 |
|
| 6037 | (define-public python-pyvistaqt
|
| 6038 | (package
|
| 6039 | (name "python-pyvistaqt")
|
| 6040 | (version "0.11.3")
|
| 6041 | (source
|
| 6042 | (origin
|
| 6043 | (method git-fetch)
|
| 6044 | (uri (git-reference
|
| 6045 | (url "https://github.com/pyvista/pyvistaqt")
|
| 6046 | (commit version)))
|
| 6047 | (file-name (git-file-name name version))
|
| 6048 | (sha256
|
| 6049 | (base32 "04f9cd98k463pdrpi8jby411x9mc0ih62gl0nv0h9w3r7pwl61yl"))))
|
| 6050 | (build-system pyproject-build-system)
|
| 6051 | (arguments
|
| 6052 | (list
|
| 6053 | #:phases
|
| 6054 | #~(modify-phases %standard-phases
|
| 6055 | (add-after 'unpack 'fix-pytest
|
| 6056 | (lambda _
|
| 6057 | (substitute* "tests/conftest.py"
|
| 6058 | (("pytest.skip")
|
| 6059 | "pytest.mark.skipif"))))
|
| 6060 | (add-before 'check 'before-check
|
| 6061 | (lambda _
|
| 6062 | |
| 6063 | (setenv "HOME" "/tmp")
|
| 6064 | |
| 6065 | (system "Xvfb :99 -screen 0 1024x768x24 &")
|
| 6066 | (setenv "DISPLAY" ":99.0"))))))
|
| 6067 | (propagated-inputs (list python-pyvista python-qtpy))
|
| 6068 | (native-inputs (list python-ipython
|
| 6069 | python-matplotlib
|
| 6070 | python-numpy
|
| 6071 | python-pyqt-6
|
| 6072 | python-pytest
|
| 6073 | python-pytest-qt
|
| 6074 | python-setuptools
|
| 6075 | python-sphinx-gallery
|
| 6076 | xorg-server))
|
| 6077 | (home-page "https://github.com/pyvista/pyvistaqt")
|
| 6078 | (synopsis "Qt support for PyVista")
|
| 6079 | (description
|
| 6080 | "@code{pyvistaqt} is a helper module for @code{pyvista} to enable you to
|
| 6081 | plot using Qt by placing a vtk-widget into a background renderer. This can be
|
| 6082 | quite useful when you desire to update your plot in real-time.")
|
| 6083 | (license license:expat)))
|
| 6084 |
|
| 6085 | (define-public python-simplespectral
|
| 6086 | (package
|
| 6087 | (name "python-simplespectral")
|
| 6088 | (version "1.0.0")
|
| 6089 | (source
|
| 6090 | (origin
|
| 6091 | (method url-fetch)
|
| 6092 | (uri (pypi-uri "SimpleSpectral" version))
|
| 6093 | (sha256
|
| 6094 | (base32 "0qh3xwdv9cwcqdamvglrhm586p4yaq1hd291py1fvykhk2a2d4w6"))))
|
| 6095 | (build-system pyproject-build-system)
|
| 6096 | (arguments
|
| 6097 | (list #:tests? #f)) |
| 6098 | (native-inputs
|
| 6099 | (list python-setuptools))
|
| 6100 | (propagated-inputs
|
| 6101 | (list python-numpy python-scipy))
|
| 6102 | (home-page "https://github.com/xmikos/simplespectral")
|
| 6103 | (synopsis "FFT module for Python")
|
| 6104 | (description
|
| 6105 | "This package provides a simplified @code{scipy.signal.spectral} module
|
| 6106 | to do spectral analysis in Python.")
|
| 6107 | (license license:expat)))
|
| 6108 |
|
| 6109 | (define-public python-pods
|
| 6110 | (package
|
| 6111 | (name "python-pods")
|
| 6112 | (version "0.1.17")
|
| 6113 | (source
|
| 6114 | (origin
|
| 6115 | (method url-fetch)
|
| 6116 | (uri (pypi-uri "pods" version))
|
| 6117 | (sha256
|
| 6118 | (base32 "1z57jdwml2jzr2dq20p7pzx3ayhajgfd2d0xqjvgzx576hp2z1ac"))))
|
| 6119 | (build-system pyproject-build-system)
|
| 6120 | |
| 6121 | |
| 6122 | (arguments (list #:tests? #f))
|
| 6123 | (native-inputs
|
| 6124 | (list python-poetry-core))
|
| 6125 | (propagated-inputs
|
| 6126 | (list python-pandas
|
| 6127 | python-pyyaml
|
| 6128 | python-scipy
|
| 6129 | python-tables))
|
| 6130 | (home-page "https://github.com/lawrennd/ods")
|
| 6131 | (synopsis "Python software for Open Data Science")
|
| 6132 | (description "This package provides utilities and tools for open data
|
| 6133 | science including tools for accessing data sets in Python.")
|
| 6134 | (license license:bsd-3)))
|
| 6135 |
|
| 6136 | (define-public python-polars-runtime-32
|
| 6137 | (package
|
| 6138 | (name "python-polars-runtime-32")
|
| 6139 | (version "1.38.1")
|
| 6140 | (source
|
| 6141 | (origin
|
| 6142 | (method url-fetch)
|
| 6143 | (uri (pypi-uri "polars_runtime_32" version))
|
| 6144 | (sha256
|
| 6145 | (base32 "1v72zkyhcziiizpymjlh2d5rwnkmvhlp18ln8brp31y5yp8hxwh4"))))
|
| 6146 | (build-system pyproject-build-system)
|
| 6147 | (arguments
|
| 6148 | (list
|
| 6149 | #:imported-modules `(,@%cargo-build-system-modules
|
| 6150 | ,@%pyproject-build-system-modules)
|
| 6151 | #:modules '(((guix build cargo-build-system) #:prefix cargo:)
|
| 6152 | (guix build pyproject-build-system)
|
| 6153 | (guix build utils))
|
| 6154 | |
| 6155 | #:tests? #f
|
| 6156 | #:phases
|
| 6157 | #~(modify-phases %standard-phases
|
| 6158 | (add-after 'unpack 'build-without-rust-nightly
|
| 6159 | (lambda _
|
| 6160 | |
| 6161 | (substitute* "pyproject.toml"
|
| 6162 | ((".*tool.maturin.*" all)
|
| 6163 | (string-append all "no-default-features = true\n"
|
| 6164 | "features = [\"full\"]\n")))))
|
| 6165 | (add-after 'unpack 'fix-tikv-jemallocator
|
| 6166 | (lambda _
|
| 6167 | |
| 6168 | |
| 6169 | (substitute* "Cargo.toml"
|
| 6170 | (("^tikv-jemallocator.*") ""))))
|
| 6171 | |
| 6172 | (add-before 'build 'override-jemalloc
|
| 6173 | (lambda* (#:key inputs #:allow-other-keys)
|
| 6174 | (let ((jemalloc (assoc-ref inputs "jemalloc")))
|
| 6175 | |
| 6176 | |
| 6177 | (setenv "CARGO_FEATURE_UNPREFIXED_MALLOC_ON_SUPPORTED_PLATFORMS" "1")
|
| 6178 | (setenv "JEMALLOC_OVERRIDE"
|
| 6179 | (string-append jemalloc "/lib/libjemalloc_pic.a")))))
|
| 6180 | (add-after 'unpack 'prepare-cargo-build-system
|
| 6181 | (lambda args
|
| 6182 | (for-each
|
| 6183 | (lambda (phase)
|
| 6184 | (format #t "Running cargo phase: ~a~%" phase)
|
| 6185 | (apply (assoc-ref cargo:%standard-phases phase)
|
| 6186 | #:cargo-target #$(cargo-triplet)
|
| 6187 | args))
|
| 6188 | '(prepare-rust-crates
|
| 6189 | unpack-rust-crates
|
| 6190 | configure
|
| 6191 | check-for-pregenerated-files
|
| 6192 | patch-cargo-checksums)))))))
|
| 6193 | (inputs
|
| 6194 | (cons* jemalloc
|
| 6195 | lz4
|
| 6196 | (list zstd "lib")
|
| 6197 | (cargo-inputs 'python-polars-runtime-32)))
|
| 6198 | (native-inputs
|
| 6199 | (append
|
| 6200 | (list maturin
|
| 6201 | pkg-config
|
| 6202 | rust
|
| 6203 | `(,rust "cargo"))
|
| 6204 | (or (and=> (%current-target-system)
|
| 6205 | (compose list make-rust-sysroot))
|
| 6206 | '())))
|
| 6207 | (home-page "https://pola.rs/")
|
| 6208 | (synopsis "Blazingly fast DataFrame library")
|
| 6209 | (description "Polars is an analytical query engine written for DataFrames.
|
| 6210 | It is designed to be fast, easy to use and expressive.")
|
| 6211 | (properties '(("upstream-name" . "polars-runtime-32")
|
| 6212 | (tunable? . #true)))
|
| 6213 | (license license:expat)))
|
| 6214 |
|
| 6215 | (define-public python-polars
|
| 6216 | (package
|
| 6217 | (name "python-polars")
|
| 6218 | (version "1.38.1")
|
| 6219 | (source
|
| 6220 | (origin
|
| 6221 | (method url-fetch)
|
| 6222 | (uri (pypi-uri "polars" version))
|
| 6223 | (sha256
|
| 6224 | (base32 "0fc2fx2p72g01nhhhfs1fzbwz58rcj7zppascanq1y2f6kjjnfl0"))))
|
| 6225 | (build-system pyproject-build-system)
|
| 6226 | |
| 6227 | |
| 6228 | |
| 6229 | |
| 6230 | (arguments (list #:tests? #f))
|
| 6231 | (propagated-inputs (list python-polars-runtime-32))
|
| 6232 | (native-inputs (list python-setuptools))
|
| 6233 | (home-page "https://pola.rs/")
|
| 6234 | (synopsis "Blazingly fast DataFrame library")
|
| 6235 | (description
|
| 6236 | "Polars is a DataFrame library for manipulating structured data.")
|
| 6237 | (license license:expat)))
|
| 6238 |
|
| 6239 | (define-public python-pydicom
|
| 6240 | (package
|
| 6241 | (name "python-pydicom")
|
| 6242 | (version "2.4.4")
|
| 6243 | (source (origin
|
| 6244 | (method git-fetch)
|
| 6245 | (uri (git-reference
|
| 6246 | (url "https://github.com/pydicom/pydicom")
|
| 6247 | (commit (string-append "v" version))))
|
| 6248 | (file-name (git-file-name name version))
|
| 6249 | (sha256
|
| 6250 | (base32
|
| 6251 | "0ksyyc1hbhyqy289a2frn84ss29fb7czirx3dkxx56f4ia33b4c8"))))
|
| 6252 | (build-system pyproject-build-system)
|
| 6253 | (arguments
|
| 6254 | (list
|
| 6255 | #:test-flags
|
| 6256 | |
| 6257 | #~(list "-k" (string-append
|
| 6258 | "not test_jpeg_ls_pixel_data.py"
|
| 6259 | " and not test_gdcm_pixel_data.py"
|
| 6260 | " and not test_pillow_pixel_data.py"
|
| 6261 | " and not test_rle_pixel_data.py"
|
| 6262 | " and not Test_JPEG_LS_Lossless_transfer_syntax"
|
| 6263 | " and not test_numpy_pixel_data.py"
|
| 6264 | " and not test_data_manager.py"
|
| 6265 | " and not test_handler_util.py"
|
| 6266 | " and not test_overlay_np.py"
|
| 6267 | " and not test_encoders_pydicom.py"
|
| 6268 | " and not test_encaps.py"
|
| 6269 | " and not test_reading_ds_with_known_tags_with_UN_VR"
|
| 6270 | " and not TestDatasetOverlayArray"
|
| 6271 | " and not TestReader"
|
| 6272 | " and not test_filewriter.py"))))
|
| 6273 | (native-inputs (list python-pytest python-flit-core))
|
| 6274 | (inputs (list gdcm libjpeg-turbo))
|
| 6275 | (propagated-inputs (list python-numpy python-pillow))
|
| 6276 | (home-page "https://github.com/pydicom/pydicom")
|
| 6277 | (synopsis "Python library for reading and writing DICOM data")
|
| 6278 | (description "@code{python-pydicom} is a Python library for reading and
|
| 6279 | writing DICOM medical imaging data. It can read, modify and write DICOM
|
| 6280 | data.")
|
| 6281 | (license license:expat)))
|
| 6282 |
|
| 6283 | (define-public python-supersmoother
|
| 6284 | |
| 6285 | |
| 6286 | (let ((commit "0a81544ac6bb33bdb08deeba69e97a4ceebcebcf")
|
| 6287 | (revision "0"))
|
| 6288 | (package
|
| 6289 | (name "python-supersmoother")
|
| 6290 | (version (git-version "0.4" revision commit))
|
| 6291 | (source
|
| 6292 | (origin
|
| 6293 | (method git-fetch) |
| 6294 | (uri (git-reference
|
| 6295 | (url "https://github.com/jakevdp/supersmoother")
|
| 6296 | (commit commit)))
|
| 6297 | (file-name (git-file-name name version))
|
| 6298 | (sha256
|
| 6299 | (base32 "1r79nssw4a44zizvqg8y685nv3asdfj440s227phfww6kz33s3la"))))
|
| 6300 | (build-system pyproject-build-system)
|
| 6301 | (native-inputs
|
| 6302 | (list python-pytest
|
| 6303 | python-scipy
|
| 6304 | python-setuptools))
|
| 6305 | (propagated-inputs
|
| 6306 | (list python-numpy))
|
| 6307 | (home-page "http://github.com/jakevdp/supersmoother")
|
| 6308 | (synopsis "Python implementation of Friedman's Supersmoother")
|
| 6309 | (description
|
| 6310 | "This package provides an efficient implementation of
|
| 6311 | @url{https://www.slac.stanford.edu/pubs/slacpubs/3250/slac-pub-3477.pdf,
|
| 6312 | Friedman's SuperSmoother} based in Python. It makes use of numpy for fast
|
| 6313 | numerical computation.")
|
| 6314 | (license license:bsd-2))))
|
| 6315 |
|
| 6316 | (define-public python-pylems
|
| 6317 | (package
|
| 6318 | (name "python-pylems")
|
| 6319 | (version "0.6.9")
|
| 6320 | (source
|
| 6321 | (origin
|
| 6322 | (method git-fetch)
|
| 6323 | (uri (git-reference
|
| 6324 | (url "https://github.com/LEMS/pylems")
|
| 6325 | (commit (string-append "v" version))))
|
| 6326 | (file-name (git-file-name name version))
|
| 6327 | (sha256
|
| 6328 | (base32 "0gimdx89cdla1b6zzkdrmj979nn2zy2475qvpwxxas0iv27ql0vj"))))
|
| 6329 | (build-system pyproject-build-system)
|
| 6330 | (arguments
|
| 6331 | |
| 6332 | (list #:test-flags #~(list "./lems/test" "-k" "not test_load_write_xml")))
|
| 6333 | (native-inputs (list python-setuptools python-pytest))
|
| 6334 | (propagated-inputs (list python-lxml python-matplotlib))
|
| 6335 | (home-page "https://github.com/LEMS/pylems")
|
| 6336 | (synopsis
|
| 6337 | "Python support for the Low Entropy Model Specification language (LEMS)")
|
| 6338 | (description "A @acronym{LEMS, Low Entropy Model Specification} simulator
|
| 6339 | written in Python which can be used to run NeuroML2 models.")
|
| 6340 | (license license:lgpl3)))
|
| 6341 |
|
| 6342 | (define-public python-pynrrd
|
| 6343 | (package
|
| 6344 | (name "python-pynrrd")
|
| 6345 | (version "1.1.3")
|
| 6346 | (source (origin
|
| 6347 | (method git-fetch)
|
| 6348 | (uri (git-reference
|
| 6349 | (url "https://github.com/mhe/pynrrd")
|
| 6350 | (commit (string-append "v" version))))
|
| 6351 | (file-name (git-file-name name version))
|
| 6352 | (sha256
|
| 6353 | (base32
|
| 6354 | "1l0hjbqzf5i1bmpxpblpyyqkhci3mb5n07x6hqf2a91hggfyrvda"))))
|
| 6355 | (build-system pyproject-build-system)
|
| 6356 | (native-inputs
|
| 6357 | (list python-pytest python-setuptools))
|
| 6358 | (propagated-inputs
|
| 6359 | (list python-numpy))
|
| 6360 | (home-page "https://github.com/mhe/pynrrd")
|
| 6361 | (synopsis "Python module for reading and writing NRRD files")
|
| 6362 | (description
|
| 6363 | "@code{pynrrd} is a Python module for reading and writing @acronym{NRRD,
|
| 6364 | Nearly Raw Raster Data} files (format designed to support scientific
|
| 6365 | visualization and image processing involving N-dimensional raster data) into
|
| 6366 | and from numpy arrays.")
|
| 6367 | (license license:expat)))
|
| 6368 |
|
| 6369 | (define-public python-pynsee
|
| 6370 | (package
|
| 6371 | (name "python-pynsee")
|
| 6372 | (version "0.1.8")
|
| 6373 | (source
|
| 6374 | (origin
|
| 6375 | (method url-fetch)
|
| 6376 | (uri (pypi-uri "pynsee" version))
|
| 6377 | (sha256
|
| 6378 | (base32 "1w084ynwdd9f4wpcnakqc0nxcbj9gr8vppv4rd258i3dp1qq4sw5"))))
|
| 6379 | (build-system pyproject-build-system)
|
| 6380 | (arguments (list #:tests? #f)) |
| 6381 | (native-inputs
|
| 6382 | (list python-setuptools
|
| 6383 | python-wheel))
|
| 6384 | (propagated-inputs
|
| 6385 | (list python-appdirs
|
| 6386 | python-openpyxl
|
| 6387 | python-pandas
|
| 6388 | python-platformdirs
|
| 6389 | python-pyarrow
|
| 6390 | python-requests
|
| 6391 | python-shapely
|
| 6392 | python-tqdm
|
| 6393 | python-unidecode
|
| 6394 | python-urllib3
|
| 6395 | python-xlrd))
|
| 6396 | (home-page "https://pynsee.readthedocs.io")
|
| 6397 | (synopsis
|
| 6398 | "Tools to Easily Search and Download French Data From INSEE and IGN APIs")
|
| 6399 | (description
|
| 6400 | "This package provides tools to easily search and download French data
|
| 6401 | from INSEE and IGN APIs. This data includes more than 150 000 macroeconomic
|
| 6402 | series, a dozen datasets of local french data, numerous sources available on
|
| 6403 | @url{insee.fr}, geographical limits of administrative areas taken from IGN as
|
| 6404 | well as key metadata and SIRENE database containing data on all French
|
| 6405 | compagnies.")
|
| 6406 | (license license:expat)))
|
| 6407 |
|
| 6408 | (define-public python-pyqtgraph
|
| 6409 | (package
|
| 6410 | (name "python-pyqtgraph")
|
| 6411 | (version "0.13.7")
|
| 6412 | (source
|
| 6413 | (origin
|
| 6414 | (method url-fetch)
|
| 6415 | (uri (pypi-uri "pyqtgraph" version))
|
| 6416 | (sha256
|
| 6417 | (base32 "1qyr461hcvhgy02slfkgrbip2xwa8zz6dvmi1476v6f66lclzy34"))))
|
| 6418 | (build-system pyproject-build-system)
|
| 6419 | (arguments
|
| 6420 | |
| 6421 | (list #:test-flags
|
| 6422 | |
| 6423 | #~(list "--deselect=tests/exporters/test_svg.py::test_plotscene"
|
| 6424 | |
| 6425 | |
| 6426 | "-k" "not test_reload"
|
| 6427 | |
| 6428 | "tests")
|
| 6429 | #:phases
|
| 6430 | #~(modify-phases %standard-phases
|
| 6431 | (add-before 'check 'set-qpa
|
| 6432 | (lambda _
|
| 6433 | (setenv "QT_QPA_PLATFORM" "offscreen"))))))
|
| 6434 | (native-inputs
|
| 6435 | (list python-pytest
|
| 6436 | |
| 6437 | |
| 6438 | |
| 6439 | |
| 6440 | python-pyqt-6
|
| 6441 | python-pytest-qt
|
| 6442 | python-setuptools))
|
| 6443 | (propagated-inputs
|
| 6444 | (list python-h5py
|
| 6445 | python-numpy
|
| 6446 | python-pyopengl
|
| 6447 | python-scipy))
|
| 6448 | (home-page "https://www.pyqtgraph.org")
|
| 6449 | (synopsis "Scientific graphics and GUI library for Python")
|
| 6450 | (description
|
| 6451 | "PyQtGraph is a Pure-python graphics library for PyQt5, PyQt6, PySide2
|
| 6452 | and PySide6. It is intended for use in mathematics, scientific or engineering
|
| 6453 | applications.")
|
| 6454 | (license license:expat)))
|
| 6455 |
|
| 6456 | (define-public pyzo
|
| 6457 | (package
|
| 6458 | (name "pyzo")
|
| 6459 | (version "4.20.0")
|
| 6460 | (source
|
| 6461 | (origin
|
| 6462 | (method git-fetch)
|
| 6463 | (uri (git-reference
|
| 6464 | (url "https://github.com/pyzo/pyzo")
|
| 6465 | (commit (string-append "v" version))))
|
| 6466 | (file-name (git-file-name name version))
|
| 6467 | (sha256
|
| 6468 | (base32 "1a82k7hjmv20lrwiwsdrvczrm21wq16m4snwsirwhj0jh5k1x9iw"))))
|
| 6469 | (build-system pyproject-build-system)
|
| 6470 | (arguments
|
| 6471 | (list
|
| 6472 | #:test-flags
|
| 6473 | #~(list "--ignore-glob=pyzo/yoton/tests/*" |
| 6474 | "--ignore=pyzo/codeeditor/_test.py"))) |
| 6475 | (native-inputs
|
| 6476 | (list python-flit-core
|
| 6477 | python-pytest
|
| 6478 | python-setuptools))
|
| 6479 | (inputs (list python-pyside-6))
|
| 6480 | (home-page "https://pyzo.org")
|
| 6481 | (synopsis "Python IDE for scientific computing")
|
| 6482 | (description
|
| 6483 | "Pyzo is a Python IDE focused on interactivity and introspection,which
|
| 6484 | makes it very suitable for scientific computing. Its practical design is
|
| 6485 | aimed at simplicity and efficiency.
|
| 6486 |
|
| 6487 | It consists of two main components, the editor and the shell, and uses a set
|
| 6488 | of pluggable tools to help the programmer in various ways. Some example tools
|
| 6489 | are source structure, project manager, interactive help, workspace...")
|
| 6490 | (license license:bsd-2)))
|
| 6491 |
|
| 6492 | (define-public snakemake
|
| 6493 | (package
|
| 6494 | (name "snakemake")
|
| 6495 | (version "8.30.0")
|
| 6496 | (source
|
| 6497 | (origin
|
| 6498 | (method url-fetch)
|
| 6499 | (uri (pypi-uri "snakemake" version))
|
| 6500 | (sha256
|
| 6501 | (base32 "08k6qk886a6f79higkd0pjjrq9sn6w5gk0gdgx88rhr1aln1qk7x"))))
|
| 6502 | (build-system pyproject-build-system)
|
| 6503 | (arguments
|
| 6504 | (list
|
| 6505 | #:test-flags
|
| 6506 | #~(list
|
| 6507 | |
| 6508 | "--ignore=tests/test_report_href/test_script.py"
|
| 6509 | "--ignore=tests/test_script_py/scripts/test_explicit_import.py"
|
| 6510 | "--ignore=tests/test_output_index.py"
|
| 6511 | |
| 6512 | "--ignore=tests/test_conda_python_3_7_script/test_script_python_3_7.py"
|
| 6513 | |
| 6514 | "--ignore=tests/test_api.py"
|
| 6515 | "--ignore=tests/test_executor_test_suite.py"
|
| 6516 | |
| 6517 | "--ignore=tests/test_linting.py"
|
| 6518 | |
| 6519 | |
| 6520 | "--ignore=tests/test_tibanna"
|
| 6521 | |
| 6522 | |
| 6523 | "--ignore=tests/test_google_lifesciences")
|
| 6524 | #:phases
|
| 6525 | #~(modify-phases %standard-phases
|
| 6526 | (add-after 'unpack 'avoid-assets-download
|
| 6527 | (lambda _
|
| 6528 | (substitute* "setup.py"
|
| 6529 | (("^from assets import Assets") "")
|
| 6530 | (("^Assets\\.deploy\\(\\)") ""))))
|
| 6531 | |
| 6532 | |
| 6533 | |
| 6534 | (add-after 'unpack 'call-wrapper-not-wrapped-snakemake
|
| 6535 | (lambda _
|
| 6536 | (substitute* "snakemake/executors/__init__.py"
|
| 6537 | (("self\\.get_python_executable\\(\\),")
|
| 6538 | "")
|
| 6539 | (("\"-m snakemake\"")
|
| 6540 | (string-append "\"" #$output
|
| 6541 | "/bin/snakemake" "\""))
|
| 6542 | |
| 6543 | |
| 6544 | |
| 6545 | |
| 6546 | |
| 6547 | |
| 6548 | |
| 6549 | |
| 6550 | |
| 6551 | |
| 6552 | |
| 6553 | (("tibanna_args.command = command")
|
| 6554 | (string-append
|
| 6555 | "tibanna_args.command = command.replace('"
|
| 6556 | #$output "/bin/snakemake', 'python3 -m snakemake')")))))
|
| 6557 | (add-before 'check 'pre-check
|
| 6558 | (lambda* (#:key tests? #:allow-other-keys)
|
| 6559 | (when tests?
|
| 6560 | (setenv "HOME" "/tmp")))))))
|
| 6561 | (propagated-inputs
|
| 6562 | (list python-appdirs
|
| 6563 | python-conda-inject
|
| 6564 | python-configargparse
|
| 6565 | python-connection-pool
|
| 6566 | python-dpath
|
| 6567 | python-gitpython
|
| 6568 | python-humanfriendly
|
| 6569 | python-immutables
|
| 6570 | python-jinja2
|
| 6571 | python-jsonschema
|
| 6572 | python-nbformat
|
| 6573 | python-packaging
|
| 6574 | python-psutil
|
| 6575 | python-pulp
|
| 6576 | python-pyyaml
|
| 6577 | python-requests
|
| 6578 | python-reretry
|
| 6579 | python-smart-open
|
| 6580 | python-snakemake-interface-common
|
| 6581 | python-snakemake-interface-executor-plugins
|
| 6582 | python-snakemake-interface-report-plugins
|
| 6583 | python-snakemake-interface-storage-plugins
|
| 6584 | python-tabulate
|
| 6585 | python-throttler
|
| 6586 | python-wrapt
|
| 6587 | python-yte))
|
| 6588 | (native-inputs
|
| 6589 | (list python-docutils
|
| 6590 | python-numpy
|
| 6591 | python-pandas
|
| 6592 | python-setuptools
|
| 6593 | python-tomli))
|
| 6594 | (home-page "https://snakemake.readthedocs.io")
|
| 6595 | (synopsis "Python-based execution environment for make-like workflows")
|
| 6596 | (description
|
| 6597 | "Snakemake aims to reduce the complexity of creating workflows by
|
| 6598 | providing a clean and modern domain specific specification language (DSL) in
|
| 6599 | Python style, together with a fast and comfortable execution environment.")
|
| 6600 | (license license:expat)))
|
| 6601 |
|
| 6602 | (define-public python-orsopy
|
| 6603 | (package
|
| 6604 | (name "python-orsopy")
|
| 6605 | (version "1.2.1")
|
| 6606 | (source
|
| 6607 | (origin
|
| 6608 | (method git-fetch)
|
| 6609 | (uri (git-reference
|
| 6610 | (url "https://github.com/reflectivity/orsopy")
|
| 6611 | (commit (string-append "v" version))))
|
| 6612 | (file-name (git-file-name name version))
|
| 6613 | (sha256
|
| 6614 | (base32 "15av7b38h9x0f09dzxb111r2kxm6an461l9ajb01r8r7mv7m5bw9"))))
|
| 6615 | (build-system pyproject-build-system)
|
| 6616 | (arguments
|
| 6617 | (list
|
| 6618 | #:test-flags
|
| 6619 | |
| 6620 | #~(cons* "--ignore=orsopy/slddb/tests/test_webapi.py"
|
| 6621 | (map (lambda (test)
|
| 6622 | (string-append "--deselect=orsopy/fileio/tests/"
|
| 6623 | "test_model_language.py::" test))
|
| 6624 | (list "TestSubStack::test_resolve_layers"
|
| 6625 | "TestMaterial::test_density_lookup_elements"
|
| 6626 | "TestSampleModel::test_resolve_to_layers")))))
|
| 6627 | (propagated-inputs
|
| 6628 | (list python-numpy python-pyyaml python-jsonschema python-h5py))
|
| 6629 | (native-inputs
|
| 6630 | (list python-pint python-pytest python-setuptools))
|
| 6631 | (home-page "https://github.com/reflectivity/orsopy")
|
| 6632 | (synopsis "Open Reflectometry Standards Organization Python tools")
|
| 6633 | (description
|
| 6634 | "This package provides Python tools for the Open Reflectometry Standards
|
| 6635 | Organization (ORSO). It includes utilities for working with reflectometry
|
| 6636 | data files and the ORSO file format.")
|
| 6637 | (license license:expat)))
|
| 6638 |
|
| 6639 | |
| 6640 | |
| 6641 | |
| 6642 | |
| 6643 | |