diff options
Diffstat (limited to 'gnu/packages/python-science.scm')
| -rw-r--r-- | gnu/packages/python-science.scm | 176 |
1 files changed, 154 insertions, 22 deletions
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 7d3319e367..938deaec6a 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -9,7 +9,7 @@ ;;; Copyright © 2019, 2021, 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com> ;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autistici.org> ;;; Copyright © 2020 Pierre Langlois <pierre.langlois@gmx.com> -;;; Copyright © 2020, 2021, 2022 Vinicius Monego <monego@posteo.net> +;;; Copyright © 2020, 2021, 2022, 2023 Vinicius Monego <monego@posteo.net> ;;; Copyright © 2021 Greg Hogan <code@greghogan.com> ;;; Copyright © 2021 Roel Janssen <roel@gnu.org> ;;; Copyright © 2021 Paul Garlick <pgarlick@tourbillion-technology.com> @@ -324,13 +324,13 @@ implements several methods for sequential model-based optimization. (define-public python-trimesh (package (name "python-trimesh") - (version "3.10.7") + (version "3.22.1") (source (origin (method url-fetch) (uri (pypi-uri "trimesh" version)) (sha256 - (base32 "0bw55cwxlxds0j54naijh64sdb0rkscx4i1fy0ql94h96kw2p2ir")))) + (base32 "1ck4dkhz1x6sznd83c1hlvsv2m6d22fr82na0947j5jf47a4c1gl")))) (build-system python-build-system) (propagated-inputs (list python-numpy)) @@ -346,7 +346,7 @@ implements several methods for sequential model-based optimization. (modify-phases %standard-phases (add-after 'unpack 'fix-build (lambda _ - (substitute* "trimesh/resources/templates/blender_boolean.py" + (substitute* "trimesh/resources/templates/blender_boolean.py.tmpl" (("\\$MESH_PRE") "'$MESH_PRE'"))))))) (home-page "https://github.com/mikedh/trimesh") @@ -669,27 +669,55 @@ provides an example implementation of the algorithm as well as scripts necessary for reproducing the experiments in the paper.") (license license:expat))) +(define-public python-einops + (package + (name "python-einops") + (version "0.6.1") + (source (origin + (method git-fetch) ;PyPI misses .ipynb files required for tests + (uri (git-reference + (url "https://github.com/arogozhnikov/einops") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1h8p39kd7ylg99mh620xr20hg7v78x1jnj6vxwk31rlw2dmv2dpr")))) + (build-system pyproject-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (add-after 'unpack 'set-backend + (lambda _ + ;; Einops supports different backends, but we test + ;; only NumPy for availability and simplicity. + (setenv "EINOPS_TEST_BACKENDS" "numpy")))))) + (native-inputs (list jupyter + python-hatchling + python-nbconvert + python-nbformat + python-parameterized + python-pytest)) + (propagated-inputs (list python-numpy)) + (home-page "https://einops.rocks/") + (synopsis "Tensor operations for different backends") + (description "Einops provides a set of tensor operations for NumPy and +multiple deep learning frameworks.") + (license license:expat))) + (define-public python-xarray (package (name "python-xarray") - (version "0.15.1") + (version "2023.6.0") (source (origin (method url-fetch) (uri (pypi-uri "xarray" version)) (sha256 (base32 - "1yx8j66b7rn10m2l6gmn8yr9cn38pi5cj0x0wwpy4hdnhy6i7qv4")))) - (build-system python-build-system) + "1339fz5gxkizq02h6vn19546x9p4c3nd9ipzpcg39h7gwhg26yi6")))) + (build-system pyproject-build-system) (native-inputs (list python-setuptools-scm python-pytest)) (propagated-inputs (list python-numpy python-pandas)) - (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (lambda _ - (invoke "pytest")))))) (home-page "https://github.com/pydata/xarray") (synopsis "N-D labeled arrays and datasets") (description "Xarray (formerly xray) makes working with labelled @@ -702,6 +730,107 @@ large and growing library of domain-agnostic functions for advanced analytics and visualization with these data structures.") (license license:asl2.0))) +(define-public python-xarray-einstats + (package + (name "python-xarray-einstats") + (version "0.5.1") + (source (origin + (method git-fetch) ; no tests in PyPI + (uri (git-reference + (url "https://github.com/arviz-devs/xarray-einstats") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1gg7p2lq7zxic64nbr6a8ynizs8rjzb29fnqib7hw3lmp13wsfm0")))) + (build-system pyproject-build-system) + (native-inputs (list python-einops python-flit-core python-numba + python-pytest)) + (propagated-inputs (list python-numpy python-scipy python-xarray)) + (home-page "https://einstats.python.arviz.org/en/latest/") + (synopsis "Stats, linear algebra and einops for xarray") + (description + "@code{xarray_einstats} provides wrappers around some NumPy and SciPy +functions and around einops with an API and features adapted to xarray.") + (license license:asl2.0))) + +(define-public python-pytensor + (package + (name "python-pytensor") + (version "2.12.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pymc-devs/pytensor") + (commit (string-append "rel-" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1445fwbmzkdbndkq9hxiagdkfclgrnmpfzad40zqn6m5ry8192x8")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + ;; Replace version manually because pytensor uses + ;; versioneer, which requires git metadata. + (add-after 'unpack 'versioneer + (lambda _ + (with-output-to-file "setup.cfg" + (lambda () + (display "\ +[versioneer] +VCS = git +style = pep440 +versionfile_source = pytensor/_version.py +versionfile_build = pytensor/_version.py +tag_prefix = +parentdir_prefix = pytensor- +"))) + (invoke "versioneer" "install") + (substitute* "setup.py" + (("versioneer.get_version\\(\\)") + (string-append "\"" #$version "\""))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" "/tmp") ; required for most tests + ;; Test discovery fails, have to call pytest by hand. + ;; test_tensor_basic.py file requires JAX. + (invoke "python" "-m" "pytest" "-vv" + "--ignore" "tests/link/jax/test_tensor_basic.py" + ;; Skip benchmark tests. + "-k" (string-append + "not test_elemwise_speed" + " and not test_logsumexp_benchmark" + " and not test_fused_elemwise_benchmark" + " and not test_scan_multiple_output" + " and not test_vector_taps_benchmark" + " and not test_cython_performance") + ;; Skip computationally intensive tests. + "--ignore" "tests/scan/" + "--ignore" "tests/tensor/" + "--ignore" "tests/sandbox/" + "--ignore" "tests/sparse/sandbox/"))))))) + (native-inputs (list python-cython python-pytest python-versioneer)) + (propagated-inputs (list python-cons + python-etuples + python-filelock + python-logical-unification + python-minikanren + python-numba + python-numpy + python-scipy + python-typing-extensions)) + (home-page "https://pytensor.readthedocs.io/en/latest/") + (synopsis + "Library for mathematical expressions in multi-dimensional arrays") + (description + "PyTensor is a Python library that allows one to define, optimize, and +efficiently evaluate mathematical expressions involving multi-dimensional +arrays. It is a fork of the Aesara library.") + (license license:bsd-3))) + (define-public python-msgpack-numpy (package (name "python-msgpack-numpy") @@ -891,18 +1020,18 @@ two-dimensional renderings such as scatter plots and histograms. (define-public python-pandas-flavor (package (name "python-pandas-flavor") - (version "0.2.0") + (version "0.5.0") (source (origin (method url-fetch) (uri (pypi-uri "pandas_flavor" version)) (sha256 (base32 - "12g4av8gpl6l83yza3h97j3f2jblqv69frlidrvdq8ny2rc6awbq")))) + "0473lkbdnsag3w5x65sxwjlyq0i7z938ssxqwn2cpcml282vksx1")))) (build-system python-build-system) (propagated-inputs - (list python-pandas python-xarray)) - (home-page "https://github.com/Zsailer/pandas_flavor") + (list python-lazy-loader python-packaging python-pandas python-xarray)) + (home-page "https://github.com/pyjanitor-devs/pandas_flavor") (synopsis "Write your own flavor of Pandas") (description "Pandas 0.23 added a simple API for registering accessors with Pandas objects. Pandas-flavor extends Pandas' extension API by @@ -1154,6 +1283,9 @@ Mathematics (GLM) library to Python.") " and not test_exception_text" " and not test_worker_bad_args" + ;; These time out + " and not test_nanny_timeout" + ;; These tests are rather flaky " and not test_quiet_quit_when_cluster_leaves" " and not multiple_clients_restart")) @@ -1341,7 +1473,7 @@ aggregated sum and more.") (define-public python-pyvista (package (name "python-pyvista") - (version "0.36.1") + (version "0.39.1") (source ;; The PyPI tarball does not contain the tests. ;; (However, we don't yet actually run the tests.) @@ -1352,15 +1484,15 @@ aggregated sum and more.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1kjilcrz2cyh67n79r8dpxrans99mlviz2whc6g7j8hgn7v14z2n")))) + (base32 "00nij00z5r35f6dx7mwndsrpmiw43adjk8x35mk308c369ylbv9p")))) (build-system python-build-system) (propagated-inputs - (list python-appdirs - python-imageio + (list python-imageio python-matplotlib python-meshio python-numpy python-pillow + python-pooch python-scooby vtk)) (arguments @@ -1371,7 +1503,7 @@ aggregated sum and more.") (delete 'check) ;; Disable the sanity check, which fails with the following error: ;; - ;; ...checking requirements: ERROR: pyvista==0.34.0 DistributionNotFound(Requirement.parse('vtk'), {'pyvista'}) + ;; ...checking requirements: ERROR: pyvista==0.39.1 DistributionNotFound(Requirement.parse('vtk'), {'pyvista'}) (delete 'sanity-check)))) (home-page "https://docs.pyvista.org/") (synopsis "3D plotting and mesh analysis through VTK") |