diff options
Diffstat (limited to 'gnu/packages/python-science.scm')
| -rw-r--r-- | gnu/packages/python-science.scm | 648 |
1 files changed, 471 insertions, 177 deletions
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index efddd060a4..3422302a87 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015, 2016, 2020, 2021, 2022, 2023 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015, 2016, 2020, 2021, 2022, 2023, 2024 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch> ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com> @@ -14,7 +14,7 @@ ;;; Copyright © 2021 Roel Janssen <roel@gnu.org> ;;; Copyright © 2021 Paul Garlick <pgarlick@tourbillion-technology.com> ;;; Copyright © 2021 Arun Isaac <arunisaac@systemreboot.net> -;;; Copyright © 2021 Felix Gruber <felgru@posteo.net> +;;; Copyright © 2021, 2023 Felix Gruber <felgru@posteo.net> ;;; Copyright © 2022 Malte Frank Gerdes <malte.f.gerdes@gmail.com> ;;; Copyright © 2022 Guillaume Le Vaillant <glv@posteo.net> ;;; Copyright © 2022 Paul A. Patience <paul@apatience.com> @@ -22,6 +22,7 @@ ;;; Copyright © 2022 Eric Bavier <bavier@posteo.net> ;;; Copyright © 2022 Antero Mejr <antero@mailbox.org> ;;; Copyright © 2022 jgart <jgart@dismail.de> +;;; Copyright © 2023 Troy Figiel <troy@troyfigiel.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -83,21 +84,16 @@ (define-public python-scipy (package (name "python-scipy") - (version "1.10.1") + (version "1.11.4") (source (origin (method url-fetch) (uri (pypi-uri "scipy" version)) (sha256 - (base32 "19gk88nvrxl050nasz25qpmmqvbdk247bkj09jx8jibv1awdzy9c")))) + (base32 "1amfxpnni0cagwjpb0i1kdgnh4sh484ryn4gfkgbjcspgy7bg8lh")))) (build-system pyproject-build-system) (arguments (list - ;; FIXME: The default 'mesonpy' build system doesn't seem to work with - ;; our pyproject-build-system, errors with: AttributeError: 'list' - ;; object has no attribute 'items' (see: - ;; https://issues.guix.gnu.org/62781). - #:build-backend "setuptools.build_meta" #:phases #~(modify-phases %standard-phases (replace 'check @@ -140,7 +136,7 @@ (format #t "sphinx-build not found, skipping~%")))))))) (propagated-inputs (list python-numpy python-matplotlib python-pyparsing python-pythran)) - (inputs (list openblas pybind11)) + (inputs (list openblas pybind11-2.10)) (native-inputs (list gfortran ;; XXX: Adding gfortran shadows GCC headers, causing a compilation @@ -148,7 +144,11 @@ gcc meson-python pkg-config - python-cython + python-click + python-cython-0.29.35 + python-doit + python-pooch + python-pydevtool python-pytest python-pytest-xdist python-threadpoolctl)) @@ -263,31 +263,31 @@ logic, also known as grey logic.") (define-public python-scikit-image (package (name "python-scikit-image") - (version "0.19.3") + (version "0.22.0") (source (origin - (method url-fetch) - (uri (pypi-uri "scikit-image" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/scikit-image/scikit-image") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 - (base32 "0l645smf7w1kail70z8d9r3xmvz7qh6g7n3d2bpacbbnw5ykdd94")))) - (build-system python-build-system) + (base32 "10fzyq2w1ldvfkmj374l375yrx33xrlw39xc9kmk8fxfi77jpykd")))) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-before 'build 'change-home-dir - (lambda _ - ;; Change from /homeless-shelter to /tmp for write permission. - (setenv "HOME" "/tmp") - #t)) - (replace 'build - (lambda _ - (invoke "make"))) - (replace 'check - (lambda _ - ;; The following tests require online data. - (invoke "python" "-m" "pytest" "skimage" "--doctest-modules" "-k" - (string-append "not test_ndim" - " and not test_skin"))))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'change-home-dir + (lambda _ + ;; Change from /homeless-shelter to /tmp for write permission. + (setenv "HOME" "/tmp"))) + (replace 'check + (lambda* (#:key tests? test-flags #:allow-other-keys) + (when tests? + (with-directory-excursion "/tmp" + (apply invoke "pytest" "-v" "--doctest-modules" + (append test-flags (list #$output)))))))))) ;; See requirements/ for the list of build and run time requirements. ;; NOTE: scikit-image has an optional dependency on python-pooch, however ;; propagating it would enable many more tests that require online data. @@ -295,6 +295,7 @@ logic, also known as grey logic.") (list python-cloudpickle python-dask python-imageio + python-lazy-loader python-matplotlib python-networkx python-numpy @@ -304,9 +305,13 @@ logic, also known as grey logic.") python-scipy python-tifffile)) (native-inputs - (list python-cython + (list meson-python + python-cython + python-numpydoc + python-packaging python-pytest - python-pytest-localserver)) + python-pytest-localserver + python-wheel)) (home-page "https://scikit-image.org/") (synopsis "Image processing in Python") (description @@ -330,7 +335,15 @@ logic, also known as grey logic.") ;; These are for compatibility with more recent versions of ;; numpy and scikit-learn. (search-patches "python-scikit-optimize-1148.patch" - "python-scikit-optimize-1150.patch")))) + "python-scikit-optimize-1150.patch")) + (modules '((guix build utils))) + (snippet + ;; Since scikit-learn 1.3 max_features no longer supports + ;; 'auto', which is identical to 'sqrt' + '(substitute* '("skopt/learning/forest.py" + "skopt/learning/tests/test_forest.py") + (("max_features=['\"]auto['\"]") + "max_features='sqrt'"))))) (build-system pyproject-build-system) (propagated-inputs (list python-joblib @@ -349,6 +362,38 @@ implements several methods for sequential model-based optimization. @code{skopt} aims to be accessible and easy to use in many contexts.") (license license:bsd-3))) +(define-public python-tdda + (package + (name "python-tdda") + (version "2.0.9") + (source + (origin + (method url-fetch) + (uri (pypi-uri "tdda" version)) + (sha256 + (base32 "1xs91s8b7cshjcqw88qsrjh10xly799k5rf2ycawqfz2mw8sy3br")))) + (build-system pyproject-build-system) + (arguments + '(#:phases (modify-phases %standard-phases + (add-after 'unpack 'relax-requirements + (lambda _ + (substitute* "setup.py" + (("pandas>=1.5.2") + "pandas")))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "tdda" "test"))))))) + (native-inputs (list python-numpy python-pandas)) + (home-page "https://www.stochasticsolutions.com") + (synopsis "Test-driven data analysis library for Python") + (description + "The TDDA Python module provides command-line and Python API support +for the overall process of data analysis, through tools that peform +reference testing, constraint discovery for data, automatic inference +of regular expressions from text data and automatic test generation.") + (license license:expat))) ; MIT License + (define-public python-trimesh (package (name "python-trimesh") @@ -387,6 +432,31 @@ manipulation and analysis, in the style of the Polygon object in the Shapely library.") (license license:expat))) +(define-public python-meshzoo + (package + (name "python-meshzoo") + (version "0.9.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/diego-hayashi/meshzoo") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "107byfppbq16fqyp2hw7ydcvvahspzq0hzvlvzqg2zxi1aigbr68")))) + (build-system pyproject-build-system) + (propagated-inputs + (list python-numpy)) + (native-inputs (list python-flit-core python-matplotlib python-pytest)) + (home-page "https://github.com/diego-hayashi/meshzoo") + (synopsis "Mesh generator for simple geometries") + (description + "@code{meshzoo} is a mesh generator for finite element or finite +volume computations for simple domains like regular polygons, disks, +spheres, cubes, etc.") + (license license:gpl3+))) + (define-public python-tspex (package (name "python-tspex") @@ -410,71 +480,73 @@ tissue-specificity metrics for gene expression.") (define-public python-pandas (package (name "python-pandas") - (version "1.4.4") + (version "1.5.3") (source (origin (method url-fetch) (uri (pypi-uri "pandas" version)) (sha256 - (base32 "0ryv66s9cvd27q6a985vv556k2qlnlrdna2z7qc7bdhphrrhsv5b")))) - (build-system python-build-system) + (base32 "1cdhngylzh352wx5s3sjyznn7a6kmjqcfg97hgqm5h3yb9zgv8vl")))) + (build-system pyproject-build-system) (arguments - `(#:modules ((guix build utils) - (guix build python-build-system) - (ice-9 ftw) - (srfi srfi-1) - (srfi srfi-26)) - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'enable-parallel-build - (lambda _ - (substitute* "setup.py" - (("\"-j\", type=int, default=1") - (format #f "\"-j\", type=int, default=~a" - (parallel-job-count)))))) - (add-after 'unpack 'patch-which - (lambda* (#:key inputs #:allow-other-keys) - (let ((which (assoc-ref inputs "which"))) - (substitute* "pandas/io/clipboard/__init__.py" - (("^WHICH_CMD = .*") - (string-append "WHICH_CMD = \"" which "\"\n")))))) - (add-before 'check 'prepare-x - (lambda _ - (system "Xvfb &") - (setenv "DISPLAY" ":0") - ;; xsel needs to write a log file. - (setenv "HOME" "/tmp"))) - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (let ((build-directory - (string-append - (getcwd) "/build/" - (first (scandir "build" - (cut string-prefix? "lib." <>)))))) + (list + #:test-flags + '(list "--pyargs" "pandas" + "-n" (number->string (parallel-job-count)) + "-m" "not slow and not network and not db" + "-k" + (string-append + ;; TODO: Missing input + "not TestS3" + " and not s3" + ;; No module named 'pandas.io.sas._sas' + " and not test_read_expands_user_home_dir" + " and not test_read_non_existent" + ;; Unknown failures + " and not test_switch_options" + ;; Crashes + " and not test_bytes_exceed_2gb" + ;; get_subplotspec() returns None; possibly related to + ;; https://github.com/pandas-dev/pandas/issues/54577 + " and not test_plain_axes" + ;; This test fails when run with pytest-xdist + ;; (see https://github.com/pandas-dev/pandas/issues/39096). + " and not test_memory_usage")) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-build-system + (lambda _ (substitute* "pyproject.toml" ;; Not all data files are distributed with the tarball. - (("--strict-data-files ") "")) - (with-directory-excursion build-directory - (when tests? - (invoke "pytest" "-vv" "pandas" "--skip-slow" - "--skip-network" - "-n" (number->string (parallel-job-count)) - "-k" - (string-append - ;; These test access the internet (see: - ;; https://github.com/pandas-dev/pandas/issues/45085).: - ;; pandas/tests/io/xml/test_xml.py::test_wrong_url[lxml] - ;; pandas/tests/io/xml/test_xml.py::test_wrong_url[etree] - "not test_wrong_url" - ;; TODO: Missing input - " and not TestS3" - " and not s3" - ;; This test fails when run with pytest-xdist - ;; (see: - ;; https://github.com/pandas-dev/pandas/issues/39096). - " and not test_memory_usage")))))))))) + (("--strict-data-files ") "") + ;; Unknown property "asyncio_mode" + (("asyncio_mode = \"strict\"") "")))) + (add-after 'unpack 'patch-which + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "pandas/io/clipboard/__init__.py" + (("^WHICH_CMD = .*") + (string-append "WHICH_CMD = \"" + (search-input-file inputs "/bin/which") + "\"\n"))))) + (add-before 'check 'prepare-x + (lambda _ + (system "Xvfb &") + (setenv "DISPLAY" ":0") + ;; xsel needs to write a log file. + (setenv "HOME" "/tmp"))) + ;; The compiled libraries are only in the output at this point, + ;; but they are needed to run tests. + ;; FIXME: This should be handled by the pyargs pytest argument, + ;; but is not for some reason. + (add-before 'check 'pre-check + (lambda* (#:key inputs outputs #:allow-other-keys) + (copy-recursively + (string-append (site-packages inputs outputs) + "/pandas/_libs") + "pandas/_libs")))))) (propagated-inputs (list python-jinja2 + python-matplotlib python-numpy python-openpyxl python-pytz @@ -484,7 +556,7 @@ tissue-specificity metrics for gene expression.") (inputs (list which xclip xsel)) (native-inputs - (list python-cython + (list python-cython-0.29.35 python-beautifulsoup4 python-lxml python-html5lib @@ -503,6 +575,155 @@ and intuitive. It aims to be the fundamental high-level building block for doing practical, real world data analysis in Python.") (license license:bsd-3))) +(define-public python-pandas-stubs + (package + (name "python-pandas-stubs") + ;; The versioning follows that of Pandas and uses the date of the + ;; python-pandas-stubs release. This is the latest version of + ;; python-pandas-stubs for python-pandas 1.5.3. + (version "1.5.3.230321") + (source + (origin + ;; No tests in the PyPI tarball. + (method git-fetch) + (uri (git-reference + (url "https://github.com/pandas-dev/pandas-stubs") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1blwlq5053pxnmx721zdd6v8njiybz4azribx2ygq33jcpmknda6")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags #~(list "-k" + (string-append + ;; The python-pyarrow package in Guix is not built + ;; with ORC integration, causing these tests to + ;; fail. + "not test_orc" + " and not test_orc_path" + " and not test_orc_buffer" + " and not test_orc_columns" + " and not test_orc_bytes")) + #:phases '(modify-phases %standard-phases + (add-before 'check 'prepare-x + (lambda _ + (system "Xvfb &") + (setenv "DISPLAY" ":0") + ;; xsel needs to write a log file. + (setenv "HOME" + (getcwd))))))) + (propagated-inputs (list python-types-pytz)) + ;; Add python-fastparquet to native inputs once it has been packaged. Its + ;; tests will be skipped for now. + (native-inputs (list python-lxml + python-matplotlib + python-odfpy + python-pandas + python-poetry-core + python-pyarrow + python-pyreadstat + python-pytest + python-scipy + python-sqlalchemy + python-tables + python-tabulate + python-xarray + ;; Needed to test clipboard support. + which + xclip + xorg-server-for-tests + xsel)) + (home-page "https://pandas.pydata.org") + (synopsis "Type annotations for pandas") + (description + "This package contains public type stubs for @code{python-pandas}, +following the convention of providing stubs in a separate package, as +specified in @acronym{PEP, Python Enhancement Proposal} 561. The stubs cover +the most typical use cases of @code{python-pandas}. In general, these stubs +are narrower than what is possibly allowed by @code{python-pandas}, but follow +a convention of suggesting best recommended practices for using +@code{python-pandas}.") + (license license:bsd-3))) + +(define-public python-pandera + (package + (name "python-pandera") + (version "0.17.2") + (source + (origin + ;; No tests in the PyPI tarball. + (method git-fetch) + (uri (git-reference + (url "https://github.com/unionai-oss/pandera") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1mnqk583z90k1n0z3lfa4rd0ng40v7hqfk7phz5gjmxlzfjbxa1x")) + (modules '((guix build utils))) + ;; These tests require PySpark and Modin. We need to remove the entire + ;; directory, since the conftest.py in these directories contain + ;; imports. (See: https://github.com/pytest-dev/pytest/issues/7452) + (snippet '(begin + (delete-file-recursively "tests/pyspark") + (delete-file-recursively "tests/modin"))))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags '(list "-k" + (string-append + ;; Mypy functionality is experimental and relying + ;; on pandas-stubs can lead to false + ;; positives. These tests currently fail. + "not test_python_std_list_dict_generics" + " and not test_python_std_list_dict_empty_and_none" + " and not test_pandas_modules_importable")))) + ;; Pandera comes with a lot of extras. We test as many as possible, but do + ;; not include all of them in the propagated-inputs. Currently, we have to + ;; skip the pyspark and io tests due to missing packages python-pyspark + ;; and python-frictionless. + (propagated-inputs (list python-hypothesis ;strategies extra + python-multimethod + python-numpy + python-packaging + python-pandas + python-pandas-stubs ;mypy extra + python-pydantic + python-scipy ;hypotheses extra + python-typeguard-4 + python-typing-inspect + python-wrapt)) + (native-inputs (list python-dask ;dask extra + python-fastapi ;fastapi extra + python-geopandas ;geopandas extra + python-pyarrow ;needed to run fastapi tests + python-pytest + python-pytest-asyncio + python-sphinx + python-uvicorn)) ;needed to run fastapi tests + (home-page "https://github.com/unionai-oss/pandera") + (synopsis "Perform data validation on dataframe-like objects") + (description + "@code{python-pandera} provides a flexible and expressive API for +performing data validation on dataframe-like objects to make data processing +pipelines more readable and robust. Dataframes contain information that +@code{python-pandera} explicitly validates at runtime. This is useful in +production-critical data pipelines or reproducible research settings. With +@code{python-pandera}, you can: + +@itemize +@item Define a schema once and use it to validate different dataframe types. +@item Check the types and properties of columns. +@item Perform more complex statistical validation like hypothesis testing. +@item Seamlessly integrate with existing data pipelines via function decorators. +@item Define dataframe models with the class-based API with pydantic-style syntax. +@item Synthesize data from schema objects for property-based testing. +@item Lazily validate dataframes so that all validation rules are executed. +@item Integrate with a rich ecosystem of tools like @code{python-pydantic}, +@code{python-fastapi} and @code{python-mypy}. +@end itemize") + (license license:expat))) + (define-public python-pythran (package (name "python-pythran") @@ -759,18 +980,21 @@ multiple deep learning frameworks.") (define-public python-xarray (package (name "python-xarray") - (version "2023.6.0") + (version "2023.12.0") (source (origin (method url-fetch) (uri (pypi-uri "xarray" version)) (sha256 (base32 - "1339fz5gxkizq02h6vn19546x9p4c3nd9ipzpcg39h7gwhg26yi6")))) + "0cyldwchcrmbm1y7l1ry70kk8zdh7frxci3c6iwf4iyyj34dnra5")))) (build-system pyproject-build-system) + (arguments + ;; This needs a more recent version of python-hypothesis + (list #:test-flags '(list "--ignore=xarray/tests/test_strategies.py"))) (native-inputs (list python-setuptools-scm python-pytest)) (propagated-inputs - (list python-numpy python-pandas)) + (list python-numpy python-packaging python-pandas)) (home-page "https://github.com/pydata/xarray") (synopsis "N-D labeled arrays and datasets") (description "Xarray (formerly xray) makes working with labelled @@ -810,7 +1034,7 @@ functions and around einops with an API and features adapted to xarray.") (define-public python-pytensor (package (name "python-pytensor") - (version "2.14.2") + (version "2.18.1") (source (origin (method git-fetch) (uri (git-reference @@ -819,7 +1043,7 @@ functions and around einops with an API and features adapted to xarray.") (file-name (git-file-name name version)) (sha256 (base32 - "1428l1v7yrnls8875xjx1svn48cmz0q83sv7sg0xdqghkfnyi7xx")))) + "0qa0y13xfm6w7ry7gp0lv84c8blyg34a9ns7ynwqyhf9majq08s5")))) (build-system pyproject-build-system) (arguments (list @@ -1316,6 +1540,7 @@ Mathematics (GLM) library to Python.") "test_shutdown" "test_shutdown_localcluster" "test_teardown_failure_doesnt_crash_scheduler" + "test_tell_workers_when_peers_have_left" "test_threadpoolworkers_pick_correct_ioloop" "test_tls_listen_connect" "test_tls_temporary_credentials_functional" @@ -1531,91 +1756,90 @@ aggregated sum and more.") (define-public python-plotnine (package (name "python-plotnine") - ;; XXX Version 0.12.x exists, but we can't build it because we're still at - ;; matplotlib 3.5. We'd need at least 3.6. (version "0.10.1") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/has2k1/plotnine") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0lg53wcm00lj8zbb4q9yj4a0n0fqaqq7c7vj18bda0k56gg0fpwl")))) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/has2k1/plotnine") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0lg53wcm00lj8zbb4q9yj4a0n0fqaqq7c7vj18bda0k56gg0fpwl")))) (build-system pyproject-build-system) (arguments (list #:test-flags + ;; XXX: Check for any new failing tests during next update cycle. ;; These all fail because the images are considered to be too different, ;; though they really do look fine. - '(list "-k" (string-append - "not TestThemes" - (string-join - (list - ;; Image tests - "test_adjust_text" - "test_annotation_logticks_coord_flip_discrete" - "test_annotation_logticks_faceting" - "test_arrow" - "test_aslabeller_dict_0tag" - "test_caption_simple" - "test_continuous_x" - "test_continuous_x_fullrange" - "test_coord_trans_backtransforms" - "test_coord_trans_se_false" - "test_datetime_scale_limits" - "test_dir_v_ncol" - "test_discrete_x" - "test_discrete_x_fullrange" - "test_facet_grid_drop_false" - "test_facet_grid_expression" - "test_facet_grid_space_ratios" - "test_facet_wrap" - "test_facet_wrap_expression" - "test_facet_wrap_label_both" - "test_label_context_wrap2vars" - "test_labeller_cols_both_grid" - "test_labeller_cols_both_wrap" - "test_labeller_towords" - "test_missing_data_discrete_scale" - "test_ribbon_facetting" - "test_stack_non_linear_scale" - "test_uneven_num_of_lines" - - ;; Missing optional modules - "test_non_linear_smooth" - "test_non_linear_smooth_no_ci") - " and not " 'prefix))) - #:phases - '(modify-phases %standard-phases - (add-before 'check 'pre-check - (lambda* (#:key inputs outputs #:allow-other-keys) - ;; The data files are referenced by the tests but they are not - ;; installed. - (copy-recursively "plotnine/data" - (string-append (site-packages inputs outputs) - "/plotnine/data")) - ;; Matplotlib needs to be able to write its configuration file - ;; somewhere. - (setenv "MPLCONFIGDIR" "/tmp") - (setenv "TZ" "UTC") - (setenv "TZDIR" - (search-input-directory inputs "share/zoneinfo"))))))) - (propagated-inputs - (list python-adjusttext - python-matplotlib - python-mizani - python-numpy - python-patsy - python-scipy - python-statsmodels)) - (native-inputs - (list python-geopandas - python-mock - python-pandas - python-pytest python-pytest-cov - tzdata-for-tests)) + '(list "-k" + (string-append "not TestThemes" + (string-join (list + ;; Image tests + "test_adjust_text" + "test_annotation_logticks_coord_flip_discrete" + "test_annotation_logticks_faceting" + "test_arrow" + "test_aslabeller_dict_0tag" + "test_caption_simple" + "test_continuous_x" + "test_continuous_x_fullrange" + "test_coord_trans_backtransforms" + "test_coord_trans_se_false" + "test_custom_shape" + "test_datetime_scale_limits" + "test_dir_v_ncol" + "test_discrete_x" + "test_discrete_x_fullrange" + "test_facet_grid_drop_false" + "test_facet_grid_expression" + "test_facet_grid_space_ratios" + "test_facet_wrap" + "test_facet_wrap_expression" + "test_facet_wrap_label_both" + "test_label_context_wrap2vars" + "test_labeller_cols_both_grid" + "test_labeller_cols_both_wrap" + "test_labeller_towords" + "test_missing_data_discrete_scale" + "test_ribbon_facetting" + "test_stack_non_linear_scale" + "test_uneven_num_of_lines" + + ;; Missing optional modules + "test_non_linear_smooth" + "test_non_linear_smooth_no_ci") + " and not " + 'prefix))) + #:phases '(modify-phases %standard-phases + (add-before 'check 'pre-check + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; The data files are referenced by the tests but they are not + ;; installed. + (copy-recursively "plotnine/data" + (string-append (site-packages inputs + outputs) + "/plotnine/data")) + ;; Matplotlib needs to be able to write its configuration file + ;; somewhere. + (setenv "MPLCONFIGDIR" "/tmp") + (setenv "TZ" "UTC") + (setenv "TZDIR" + (search-input-directory inputs "share/zoneinfo"))))))) + (propagated-inputs (list python-adjusttext + python-matplotlib + python-mizani + python-numpy + python-patsy + python-scipy + python-statsmodels)) + (native-inputs (list python-geopandas + python-mock + python-pandas + python-pytest + python-pytest-cov + tzdata-for-tests)) (home-page "https://github.com/has2k1/plotnine") (synopsis "Grammar of Graphics for Python") (description @@ -1814,7 +2038,11 @@ for parameterized model creation and handling. Its features include: (uri (pypi-uri "GPy" version)) (sha256 (base32 - "1yx65ajrmqp02ykclhlb0n8s3bx5r0xj075swwwigiqaippr7dx2")))) + "1yx65ajrmqp02ykclhlb0n8s3bx5r0xj075swwwigiqaippr7dx2")) + (snippet + #~(begin (use-modules (guix build utils)) + (substitute* "GPy/models/state_space_main.py" + (("collections\\.Iterable") "collections.abc.Iterable")))))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases @@ -1833,6 +2061,31 @@ Python, from the Sheffield machine learning group. GPy implements a range of machine learning algorithms based on GPs.") (license license:bsd-3))) +(define-public python-pyfma + (package + (name "python-pyfma") + (version "0.1.6") + (source (origin + (method git-fetch) ;for tests + (uri (git-reference + (url "https://github.com/nschloe/pyfma") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "12i68jj9n1qj9phjnj6f0kmfhlsd3fqjlk9p6d4gs008azw5m8yn")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-numpy)) + (native-inputs (list pybind11 python-pytest)) + (home-page "https://github.com/nschloe/pyfma") + (synopsis "Fused multiply-add for Python") + (description "@code{pyfma} provides an implementation of fused +multiply-add which computes @code{(x*y) + z} with a single rounding. +This is useful for dot products, matrix multiplications, polynomial +evaluations (e.g., with Horner's rule), Newton's method for evaluating +functions, convolutions, artificial neural networks etc.") + (license license:expat))) + (define-public python-pydicom (package (name "python-pydicom") @@ -1893,7 +2146,20 @@ DICOM data in a pythonic way.") (base32 "1wqzwh3y0mjdyba5kfbvlamn561d3afz50zi712c7klkysz3mzva")))) (arguments - (list #:phases #~(modify-phases %standard-phases + ;; XXX: The project may no longer be compatible with the version of + ;; numpy packed in Guix. + ;; See: https://github.com/uchicago-cs/deepdish/issues/50. + ;; + ;; However, there is a maintained fork that appears to be a good + ;; replacement: https://github.com/portugueslab/flammkuchen. + ;; + ;; Disable few failing tests to pass the build. + (list #:test-flags + #~(list "-k" (string-append "not test_pad" + " and not test_pad_repeat_border" + " and not test_pad_repeat_border_corner" + " and not test_pad_to_size")) + #:phases #~(modify-phases %standard-phases (add-after 'unpack 'dont-vendor-six (lambda _ (delete-file "deepdish/six.py") @@ -1904,7 +2170,7 @@ DICOM data in a pythonic way.") "from deepdish import io, __version__ import six "))))))) - (build-system python-build-system) + (build-system pyproject-build-system) (native-inputs (list python-pandas)) (propagated-inputs (list python-numpy python-scipy python-six python-tables)) @@ -2005,6 +2271,7 @@ documentation for more information.") (propagated-inputs (list python-aplus python-blake3 + python-click ;XXX for dask python-cloudpickle python-dask python-filelock @@ -2030,6 +2297,33 @@ Out-of-Core DataFrames (similar to Pandas), to visualize and explore big tabular datasets. This package provides the core modules of Vaex.") (license license:expat))) +(define-public python-salib + (package + (name "python-salib") + (version "1.4.7") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/SALib/SALib") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "18xfyzircsx2q2lmfc9lxb6xvkxicnc83qzghd7df1jsprr5ymch")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-matplotlib + python-multiprocess + python-numpy + python-pandas + python-scipy)) + (native-inputs (list python-hatchling python-pytest python-pytest-cov)) + (home-page "https://salib.readthedocs.io/en/latest/") + (synopsis "Tools for global sensitivity analysis") + (description "SALib provides tools for global sensitivity analysis. It +contains Sobol', Morris, FAST, DGSM, PAWN, HDMR, Moment Independent and +fractional factorial methods.") + (license license:expat))) + (define-public python-pylems (package (name "python-pylems") |