diff options
Diffstat (limited to 'gnu/packages/python-science.scm')
| -rw-r--r-- | gnu/packages/python-science.scm | 730 |
1 files changed, 666 insertions, 64 deletions
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 862e101f6a..861badad2e 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -24,6 +24,7 @@ ;;; Copyright © 2022 jgart <jgart@dismail.de> ;;; Copyright © 2023, 2024 Troy Figiel <troy@troyfigiel.com> ;;; Copyright © 2024 Sharlatan Hellseher <sharlatanus@gmail.com> +;;; Copyright © 2024 Marco Baggio <marco.baggio@mdc-berlin.de> ;;; ;;; This file is part of GNU Guix. ;;; @@ -49,7 +50,9 @@ #:use-module (gnu packages build-tools) #:use-module (gnu packages check) #:use-module (gnu packages chemistry) + #:use-module (gnu packages cmake) #:use-module (gnu packages cpp) + #:use-module (gnu packages crates-io) #:use-module (gnu packages crypto) #:use-module (gnu packages databases) #:use-module (gnu packages digest) @@ -69,6 +72,7 @@ #:use-module (gnu packages python-check) #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) + #:use-module (gnu packages rust-apps) #:use-module (gnu packages simulation) #:use-module (gnu packages sphinx) #:use-module (gnu packages statistics) @@ -81,9 +85,134 @@ #:use-module (guix download) #:use-module (guix git-download) #:use-module (guix utils) + #:use-module (guix build-system cargo) #:use-module (guix build-system python) #:use-module (guix build-system pyproject)) +(define-public python-cvxpy + (package + (name "python-cvxpy") + (version "1.4.3") + (source + (origin + (method url-fetch) + (uri (pypi-uri "cvxpy" version)) + (sha256 + (base32 "0lyri9j5gyg6m1bvfy1a4q2sqdy3w45lp0bxiq9as8srq347ic5i")))) + (build-system pyproject-build-system) + ;; It's odd but cvxpy appears to need pybind11 at runtime according to its + ;; specification. Moving pybind11 to native-inputs would break downstream + ;; packages using cvxpy. + (propagated-inputs (list pybind11 + python-clarabel + python-ecos + python-numpy + python-osqp + python-scipy + python-scs)) + (native-inputs (list python-pytest python-setuptools)) + (home-page "https://github.com/cvxpy/cvxpy") + (synopsis "DSL for modeling convex optimization problems") + (description + "This package provides a domain-specific language for modeling convex +optimization problems in Python.") + (license license:asl2.0))) + +(define-public python-ecos + (package + (name "python-ecos") + (version "2.0.13") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/embotech/ecos-python") + (commit (string-append "v" version)) + (recursive? #true))) + (file-name (git-file-name name version)) + (sha256 + (base32 "16ljq8maflfkgbw16rldg6cy14vgz2pb3b2iga60i7yzkq2ikmyw")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-numpy python-scipy)) + (native-inputs (list python-pytest python-setuptools python-wheel)) + (home-page "https://github.com/embotech/ecos") + (synopsis "Embedded Cone Solver") + (description + "This is the Python package for ECOS: Embedded Cone Solver. ECOS is +numerical software for solving convex second-order cone programs (SOCPs).") + (license license:gpl3))) + +(define-public python-osqp + (package + (name "python-osqp") + (version "0.6.5") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/osqp/osqp-python") + (commit (string-append "v" version)) + (recursive? #true))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0s1nbzkfsi2h4ji3v0k14pfcrvinakrwy4xdbz320lbaq3yb0b65")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + ;; Some of these test failures are explained by + ;; https://github.com/osqp/osqp-python/issues/121. + ;; These tests require the module "vec_emosqp", which we don't have. + '(list "--ignore=src/osqp/tests/codegen_vectors_test.py" + ;; These tests need "mat_emosqp". + "--ignore=src/osqp/tests/codegen_matrices_test.py" + ;; These fail with accuracy differences + "--ignore=src/osqp/tests/update_matrices_test.py" + "--ignore=src/osqp/tests/feasibility_test.py" + "--ignore=src/osqp/tests/polishing_test.py" + ;; This requires the nonfree MKL. + "--ignore=src/osqp/tests/mkl_pardiso_test.py") + #:phases + #~(modify-phases %standard-phases + ;; It looks like the upgrade to scipy 1.12.0 only broke the test + ;; suite, not the features of this library. See + ;; https://github.com/osqp/osqp-python/issues/121. + (add-after 'unpack 'relax-requirements + (lambda _ + (substitute* "requirements.txt" + (("scipy.*1.12.0") "scipy <= 1.12.0")))) + (add-before 'build 'set-version + (lambda _ + (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)))))) + (propagated-inputs (list python-numpy python-qdldl python-scipy)) + ;; We need setuptools-scm only for the version number. Without it the + ;; version number will be "0.0.0" and downstream packages will complain. + (native-inputs (list cmake-minimal python-pytest python-setuptools-scm)) + (home-page "https://osqp.org/") + (synopsis "OSQP: operator splitting QP solver") + (description "The OSQP (Operator Splitting Quadratic Program) solver is a +numerical optimization package.") + (license license:asl2.0))) + +(define-public python-qdldl + (package + (name "python-qdldl") + (version "0.1.7.post2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "qdldl" version)) + (sha256 + (base32 "1lspam0k8gnw1yglqxvdv350fq00nkgdfmkizmx7bk0hxjjkj5ab")))) + (build-system pyproject-build-system) + (native-inputs (list cmake-minimal pybind11)) + (propagated-inputs (list python-numpy python-scipy)) + (home-page "https://github.com/oxfordcontrol/qdldl-python/") + (synopsis "QDLDL LDL factorization routine") + (description "This package provides a Python interface to the QDLDL LDL +factorization routine for quasi-definite linear system.") + (license license:asl2.0))) + (define-public python-scipy (package (name "python-scipy") @@ -231,6 +360,52 @@ routines such as routines for numerical integration and optimization.") genetic variation data.") (license license:expat))) +(define-public python-scikit-build-core + (package + (name "python-scikit-build-core") + (version "0.9.3") + (source + (origin + (method url-fetch) + (uri (pypi-uri "scikit_build_core" version)) + (sha256 + (base32 "146k3w3kcamyyqassmsmp6h4f5lb3cdqnbjjcbf0jm1s8wz1279l")))) + (build-system pyproject-build-system) + ;; Tests are aborted with the admonition: "setup.py install is + ;; deprecated. Use build and pip and other standards-based tools." + (arguments (list #:tests? #false)) + (propagated-inputs (list python-exceptiongroup + python-importlib-metadata + python-importlib-resources + python-packaging + python-pathspec + python-tomli + python-typing-extensions)) + (native-inputs (list pybind11 + python-pypa-build + python-cattrs + python-fastjsonschema + python-hatch-fancy-pypi-readme + python-hatch-vcs + python-hatchling + python-numpy + python-pip + python-pytest + python-rich + python-setuptools + python-setuptools-scm + python-virtualenv + python-wheel)) + (home-page "https://github.com/scikit-build/scikit-build-core") + (synopsis "Build backend for CMake based projects") + (description "Scikit-build-core is a build backend for Python that uses +CMake to build extension modules. It has a simple yet powerful static +configuration system in pyproject.toml, and supports almost unlimited +flexibility via CMake. It was initially developed to support the demanding +needs of scientific users, but can build any sort of package that uses +CMake.") + (license license:asl2.0))) + (define-public python-scikit-fem (package (name "python-scikit-fem") @@ -285,7 +460,7 @@ logic, also known as grey logic.") (define-public python-scikit-image (package (name "python-scikit-image") - (version "0.22.0") + (version "0.23.2") (source (origin (method git-fetch) @@ -294,7 +469,7 @@ logic, also known as grey logic.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "10fzyq2w1ldvfkmj374l375yrx33xrlw39xc9kmk8fxfi77jpykd")))) + (base32 "1bc8i57sjk44vd9k1ilr6fpvfq1zbq9yfi22lz22k26mzrlisym3")))) (build-system pyproject-build-system) (arguments (list @@ -351,7 +526,7 @@ logic, also known as grey logic.") (sha256 (base32 "0ycqizgsj7q57asc1bphzhf1fx9zqn0vx5rli7q541bas64hfqiy")))) (build-system pyproject-build-system) - (propagated-inputs (list python-numpy python-scipy)) + (propagated-inputs (list python-numpy python-pytorch python-scipy)) (home-page "https://github.com/guofei9987/scikit-opt") (synopsis "Swarm intelligence algorithms in Python") (description @@ -619,7 +794,7 @@ spheres, cubes, etc.") tissue-specificity metrics for gene expression.") (license license:gpl3+))) -(define-public python-pandas +(define-public python-pandas-1 (package (name "python-pandas") (version "1.5.3") @@ -717,13 +892,125 @@ 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-2 + (package + (name "python-pandas") + (version "2.1.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pandas-dev/pandas") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1v9j38bvw739csdfl98ga6fqjdm61q3p5a2l7h364kg925nbc9r1")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + #~(list "--pyargs" "pandas" + ;; "--exitfirst" + ;; FIXME "-n" (number->string (parallel-job-count)) + "-m" "not slow and not network and not db" + "-k" (string-append + "not test_git_version" + " and not test_show_versions_console" + ;; Not testing ~ expansion. + " and not test_expand_user" + " and not test_get_handle_with_path" + ;; 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] + " and 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" + " and not test_parsing_tzlocal_deprecated")) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'version-set-by-guix + (lambda _ + (with-output-to-file "_version.py" + (lambda _ + (display + (string-append "__version__ = \"" + #$(package-version this-package) + "\"")))))) + (add-before 'check 'prepare-x + (lambda _ + (system "Xvfb &") + (setenv "DISPLAY" ":0") + (setenv "HOME" ".") + ;; Skip tests that require lots of resources. + (setenv "PANDAS_CI" "1"))) + (add-after 'unpack 'patch-which + (lambda _ + (substitute* "pandas/io/clipboard/__init__.py" + (("^WHICH_CMD = .*") + (string-append "WHICH_CMD = \"" + #$(this-package-input "which") + "/bin/which\"\n"))))) + ;; The compiled libraries are only in the output at this point, + ;; but they are needed to run tests. + ;; FIXME: This should be handled by the pyargs pytest argument, + ;; but is not for some reason. + (add-before 'check 'pre-check + (lambda _ + (copy-recursively + (string-append #$output + "/lib/python3.10/site-packages/pandas/_libs") + "pandas/_libs")))))) + (propagated-inputs + (list python-dateutil + python-jinja2 + python-matplotlib + python-numpy + python-openpyxl + python-pytz + python-tzdata + python-xlrd + python-xlsxwriter)) + (inputs + (list which xclip xsel)) + (native-inputs + (list meson-python/newer + python-beautifulsoup4 + python-cython-0.29.35 + python-html5lib + python-lxml + python-matplotlib + python-openpyxl + python-pytest-asyncio + python-pytest-next + python-pytest-localserver + python-pytest-mock + python-pytest-xdist + python-versioneer + ;; Needed to test clipboard support. + xorg-server-for-tests)) + (home-page "https://pandas.pydata.org") + (synopsis "Data structures for data analysis, time series, and statistics") + (description + "Pandas is a Python package providing fast, flexible, and expressive data +structures designed to make working with structured (tabular, +multidimensional, potentially heterogeneous) and time series data both easy +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 python-pandas-2) + (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") + ;; python-pandas-stubs release. + (version "2.1.1.230928") (source (origin ;; No tests in the PyPI tarball. @@ -733,28 +1020,45 @@ doing practical, real world data analysis in Python.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1blwlq5053pxnmx721zdd6v8njiybz4azribx2ygq33jcpmknda6")))) + (base32 "13b6wcwf9ybxf492w1l8qqf2bcgch21xds5r88pfkmrvqhxwfpyr")))) (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. + ;; The python-pyarrow package in Guix is built + ;; with ORC integration, but these tests fail with + ;; an abort in ORC because a timezone file is not + ;; in the expected location: + ;; https://github.com/apache/arrow/issues/40633 "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))))))) + " and not test_orc_bytes" + " and not test_all_read_without_lxml_dtype_backend" + + ;; Apparently "numpy.bool_" is not the same as the + ;; expected "bool". + " and not test_timedelta_cmp" + " and not test_timedelta_cmp_rhs" + " and not test_timestamp_cmp" + " and not test_timestamp_eq_ne_rhs")) + #:phases + '(modify-phases %standard-phases + ;; We cannot yet upgrade numpy to 1.26 because numba needs numpy + ;; >1.24. + (add-after 'unpack 'relax-requirements + (lambda _ + (substitute* "pyproject.toml" + (("numpy = \\{ version = \">=1.26.0\", python = \"<3.13\" \\}") + "numpy = { version = \">=1.23.0\", python = \"<3.13\" }")))) + (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. @@ -905,7 +1209,7 @@ production-critical data pipelines or reproducible research settings. With (define-public python-pyjanitor (package (name "python-pyjanitor") - (version "0.26.0") + (version "0.27.0") (source (origin ;; The build requires the mkdocs directory for the description in @@ -916,7 +1220,7 @@ production-critical data pipelines or reproducible research settings. With (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1f8xbl1k9l2z56bapp7v6bd3016zrk48igcaz6hb553r6yfl7vfx")))) + (base32 "04vsg189msv8frx4zhpcg61djl7wsfvibmz0zmiih4rvkgly2cdr")))) (build-system pyproject-build-system) ;; Pyjanitor has an extensive test suite. For quick debugging, the tests ;; marked turtle can be skipped using "-m" "not turtle". @@ -925,16 +1229,29 @@ production-critical data pipelines or reproducible research settings. With #:test-flags '(list "-n" (number->string (parallel-job-count)) ;; Tries to connect to the internet. - "-k" "not test_is_connected" + "-k" (string-append "not test_is_connected" + ;; Test files are not included + " and not test_read_commandline_bad_cmd" + ;; This fails due to differences in accuracy + " and not test_jitter_results") + ;; Test files are not included + "--ignore=tests/io/test_read_csvs.py" ;; PySpark has not been packaged yet. "--ignore=tests/spark/functions/test_clean_names_spark.py" "--ignore=tests/spark/functions/test_update_where_spark.py") - #:phases #~(modify-phases %standard-phases - (add-before 'check 'set-env-ci - (lambda _ - ;; Some tests are skipped if the JANITOR_CI_MACHINE - ;; variable is not set. - (setenv "JANITOR_CI_MACHINE" "1")))))) + #:phases + #~(modify-phases %standard-phases + ;; Pandas 2.1.1 does not offer the BME frequency. + (add-after 'unpack 'pandas-compat + (lambda _ + (substitute* '("tests/functions/test_select_rows.py" + "tests/functions/test_select_columns.py") + (("freq=\"BME\"") "freq=\"BM\"")))) + (add-before 'check 'set-env-ci + (lambda _ + ;; Some tests are skipped if the JANITOR_CI_MACHINE + ;; variable is not set. + (setenv "JANITOR_CI_MACHINE" "1")))))) (propagated-inputs (list python-multipledispatch python-natsort python-pandas-flavor @@ -1116,6 +1433,26 @@ region of practical equivalence (rope), or that the second classifier has higher scores.") (license license:expat))) +(define-public python-fastcluster + (package + (name "python-fastcluster") + (version "1.2.6") + (source + (origin + (method url-fetch) + (uri (pypi-uri "fastcluster" version)) + (sha256 + (base32 "19labbgnq85p4r4jbli2p045lgh57larhi2g2anagfxnlzpqdf5a")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-numpy)) + (native-inputs (list python-scipy)) + (home-page "https://danifold.net/fastcluster.html") + (synopsis "Fast hierarchical clustering routines for R and Python") + (description "The fastcluster package implements seven common hierarchical +clustering schemes efficiently. The package is made with two interfaces to +standard software: R and Python.") + (license license:bsd-2))) + (define-public python-fbpca (package (name "python-fbpca") @@ -1205,8 +1542,14 @@ multiple deep learning frameworks.") "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"))) + (list + #:test-flags + ;; This needs a more recent version of python-hypothesis + '(list "--ignore=xarray/tests/test_strategies.py" + ;; These are known to fail with Pandas 2 + "-k" + (string-append "not test_datetime_conversion_warning" + " and not test_timedelta_conversion_warning")))) (native-inputs (list python-setuptools-scm python-pytest)) (propagated-inputs @@ -1223,6 +1566,54 @@ 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-dataclasses + (package + (name "python-xarray-dataclasses") + (version "1.7.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/astropenguin/xarray-dataclasses/") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "043lc1hadr5y0y16g682viiafy0hfsa7q18lqmndpyvnmcgm893z")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-numpy python-typing-extensions + python-xarray)) + (native-inputs (list python-pytest python-poetry-core)) + (home-page "https://github.com/astropenguin/xarray-dataclasses/") + (synopsis "xarray data creation made easy by dataclass") + (description "@code{xarray-dataclasses} is a Python package that makes it +easy to create @code{xarray}'s @code{DataArray} and @code{Datase} objects that +are \"typed\" (i.e. fixed dimensions, data type, coordinates, attributes, and +name) using the Python's @code{dataclass}.") + (license license:expat))) + +;; Note that this package will be folded into xarray eventually. See +;; https://github.com/pydata/xarray/issues/8572 for details. +(define-public python-xarray-datatree + (package + (name "python-xarray-datatree") + (version "0.0.14") + (source + (origin + (method url-fetch) + (uri (pypi-uri "xarray-datatree" version)) + (sha256 + (base32 "1x1s25s6dp1f2hck9qw8vl8hgkyy23rcwag2a9vd3w0dbgrrl5i6")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-packaging python-xarray)) + ;; We need setuptools-scm to correctly record the version string. + (native-inputs (list python-pytest python-setuptools-scm python-zarr)) + (home-page "https://github.com/xarray-contrib/datatree") + (synopsis "Hierarchical tree-like data structures for xarray") + (description "Datatree is a prototype implementation of a tree-like +hierarchical data structure for @code{xarray}. Datatree is in the process of +being merged upstream into @code{xarray}.") + (license license:asl2.0))) + (define-public python-xarray-einstats (package (name "python-xarray-einstats") @@ -1247,6 +1638,25 @@ and visualization with these data structures.") functions and around einops with an API and features adapted to xarray.") (license license:asl2.0))) +(define-public python-xarray-schema + (package + (name "python-xarray-schema") + (version "0.0.3") + (source + (origin + (method url-fetch) + (uri (pypi-uri "xarray-schema" version)) + (sha256 + (base32 "08194629696z98dkc74i6c9zmy1jicvd2ajb75q0lsf0i427cv4w")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-numpy python-xarray)) + (native-inputs (list python-pytest python-setuptools-scm)) + (home-page "https://github.com/carbonplan/xarray-schema") + (synopsis "Schema validation for Xarray objects") + (description "This package implements schema validation for Xarray +objects.") + (license license:expat))) + (define-public python-pytensor (package (name "python-pytensor") @@ -1382,6 +1792,33 @@ Python's native complex data types is also supported.") automated with the minimum of fuss and the least effort.") (license license:expat))) +(define-public python-scs + (package + (name "python-scs") + (version "3.2.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/bodono/scs-python") + (commit "3.2.4") + (recursive? #true))) + (file-name (git-file-name name version)) + (sha256 + (base32 "06wd8m3ri0gaddl7qq6243g25zjlnh3da915b73jnrfh7sg1nqsj")))) + (build-system pyproject-build-system) + (inputs (list meson-python openblas)) + (propagated-inputs (list python-numpy python-scipy)) + (native-inputs + (list pkg-config + python-meson-python + python-pytest)) + (home-page "https://github.com/bodono/scs-python") + (synopsis "Splitting conic solver") + (description "This package provides a Python interface for the +SCS (Splitting conic solver) library.") + (license license:expat))) + (define-public python-statannot (package (name "python-statannot") @@ -1554,7 +1991,7 @@ of Pandas (define-public python-pingouin (package (name "python-pingouin") - (version "0.5.2") + (version "0.5.4") (source ;; The PyPI tarball does not contain the tests. (origin @@ -1565,11 +2002,15 @@ of Pandas (file-name (git-file-name name version)) (sha256 (base32 - "0czy7cpn6xx9fs6wbz6rq2lpkb1a89bzxj1anf2f9in1m5qyrh83")))) - (build-system python-build-system) + "1j3qkgvyc31604ddl952h4hwza7schg8kwkycmxvpvx7xjj7nn68")))) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases + (list + #:test-flags + ;; This one fails due to minor differences in accuracy + '(list "-k" "not test_logistic_regression") + #:phases + '(modify-phases %standard-phases (add-after 'unpack 'loosen-requirements (lambda _ (substitute* '("requirements.txt" "setup.py") @@ -1587,10 +2028,11 @@ of Pandas (substitute* "pingouin/__init__.py" (("^from outdated[^\n]*") "") (("^warn_if_outdated[^\n]*") "")))) - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "pytest"))))))) + (add-after 'unpack 'sklearn-compatibility + (lambda _ + (substitute* "pingouin/regression.py" + (("kwargs\\[\"penalty\"\\] = \"none\"") + "kwargs[\"penalty\"] = None"))))))) (native-inputs (list python-pytest python-pytest-cov)) (propagated-inputs @@ -1654,10 +2096,61 @@ and more Mathematics (GLM) library to Python.") (license license:zlib))) +(define-public python-dask-expr + (package + (name "python-dask-expr") + (version "1.0.14") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/dask/dask-expr") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0c2q8w8wl5d2hycbjp9vavkl5f36kaz390wxlis2d8d43jnqhf0d")))) + (build-system pyproject-build-system) + (arguments + (list + #:tests? #false ;need python-distributed, which needs dask-expr. + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'versioneer + (lambda _ + ;; Our version of versioneer needs setup.cfg. This is adapted + ;; from pyproject.toml. + (with-output-to-file "setup.cfg" + (lambda () + (display "\ +[versioneer] +VCS = git +style = pep440 +versionfile_source = dask_expr/_version.py +versionfile_build = dask_expr/_version.py +tag_prefix = +parentdir_prefix = dask_expr- +"))) + (invoke "versioneer" "install") + (substitute* "setup.py" + (("versioneer.get_version\\(\\)") + (string-append "\"" #$version "\"")))))))) + (propagated-inputs (list python-pandas python-pyarrow)) + (native-inputs + ;; We use python-dask/bootstrap so that python-dask can propagate this + ;; package without creating a mutually recursive dependency. + (list python-dask/bootstrap + python-pytest + python-versioneer)) + (home-page "https://github.com/dask/dask-expr") + (synopsis "Dask DataFrames with query optimization") + (description "This is a rewrite of Dask DataFrame that includes query +optimization and generally improved organization.") + (license license:bsd-3))) + (define-public python-distributed (package (name "python-distributed") - (version "2023.7.0") + (version "2024.4.2") (source (origin ;; The test files are not included in the archive on pypi @@ -1668,12 +2161,12 @@ Mathematics (GLM) library to Python.") (file-name (git-file-name name version)) (sha256 (base32 - "0b93fpwz7kw31pkzfyihpkw8mzbqshzd6rw5vcwld7n3z2aaaxxb")))) + "0sy9mqa8qlxsagbz8xn304csrlxhxj4b6k84yrjxdcmkp9pkx166")))) (build-system pyproject-build-system) (arguments (list #:test-flags - '(list "-x" "-m" + '(list "-m" (string-append "not slow" " and not flaky" " and not gpu" @@ -1728,6 +2221,8 @@ Mathematics (GLM) library to Python.") "test_locked_comm_drop_in_replacement" "test_locked_comm_intercept_read" "test_locked_comm_intercept_write" + "test_messages_are_ordered_bsend" + "test_messages_are_ordered_raw" "test_mixing_clients_different_scheduler" "test_multiple_listeners" "test_no_dangling_asyncio_tasks" @@ -1736,6 +2231,7 @@ Mathematics (GLM) library to Python.") "test_plugin_multiple_exceptions" "test_ports" "test_preload_import_time" + "test_preload_manager_sequence" "test_queue_in_task" "test_quiet_client_close" "test_rebalance_sync" @@ -1775,9 +2271,12 @@ Mathematics (GLM) library to Python.") "test_variable_in_task" "test_worker_preload_text" "test_worker_uses_same_host_as_nanny" - "test_nanny_timeout") ; access to 127.0.0.1 + "test_nanny_timeout") ; access to 127.0.0.1 " and not ") + ;; This seems to want to use 64GB of memory. + " and not test_computation_object_code_dask_compute" + ;; These fail because it doesn't find dask[distributed] " and not test_quiet_close_process" @@ -1846,6 +2345,10 @@ parentdir_prefix = distributed- (add-before 'check 'pre-check (lambda _ (setenv "DISABLE_IPV6" "1") + ;; Disable job queueing + (setenv "DASK_DISTRIBUTED__SCHEDULER__WORKER_SATURATION" "inf") + ;; Do not use dask-expr + (setenv "DASK_DATAFRAME__QUERY_PLANNING" "False") ;; The integration tests are all problematic to some ;; degree. They either require network access or some ;; other setup. We only run the tests in @@ -1866,6 +2369,7 @@ parentdir_prefix = distributed- python-cloudpickle python-cryptography python-dask + python-dask-expr python-msgpack python-psutil python-pyyaml @@ -2038,6 +2542,10 @@ aggregated sum and more.") "test_stack_non_linear_scale" "test_uneven_num_of_lines" + ;; This triggers an unexpected but harmless + ;; warning. + "test_save_method" + ;; Missing optional modules "test_non_linear_smooth" "test_non_linear_smooth_no_ci") @@ -2070,6 +2578,7 @@ aggregated sum and more.") python-pandas python-pytest python-pytest-cov + python-setuptools-scm tzdata-for-tests)) (home-page "https://github.com/has2k1/plotnine") (synopsis "Grammar of Graphics for Python") @@ -2200,6 +2709,62 @@ build applications with traitlets in combination with the scipy stack.") specification and test suite in Python.") (license license:expat))) +(define-public python-clarabel + (package + (name "python-clarabel") + (version "0.7.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "clarabel" version)) + (sha256 + (base32 "15k32ynvh45n9q905bxwamh5w5cia9bxzmwz69wbribmyhsv22m3")) + (patches + (search-patches "python-clarabel-blas.patch")))) + (build-system cargo-build-system) + (arguments + (list + #:imported-modules `(,@%cargo-build-system-modules + ,@%pyproject-build-system-modules) + #:modules '((guix build cargo-build-system) + ((guix build pyproject-build-system) #:prefix py:) + (guix build utils)) + #:phases + #~(modify-phases %standard-phases + (add-after 'prepare-python-module 'build-python-module + (assoc-ref py:%standard-phases 'build)) + (add-after 'build-python-module 'install-python-module + (assoc-ref py:%standard-phases 'install))) + #:cargo-inputs + `(("rust-amd" ,rust-amd-0.2) + ("rust-blas" ,rust-blas-0.22) + ("rust-cfg-if" ,rust-cfg-if-1) + ("rust-derive-builder" ,rust-derive-builder-0.11) + ("rust-enum-dispatch" ,rust-enum-dispatch-0.3) ;0.3.8 + ("rust-itertools" ,rust-itertools-0.11) + ("rust-lapack" ,rust-lapack-0.19) + ("rust-lazy-static" ,rust-lazy-static-1) ;1.4 + ("rust-libc" ,rust-libc-0.2) + ("rust-num-derive" ,rust-num-derive-0.2) + ("rust-num-traits" ,rust-num-traits-0.2) + ("rust-pyo3" ,rust-pyo3-0.20) + ("rust-serde" ,rust-serde-1) + ("rust-serde-json" ,rust-serde-json-1) + ("rust-thiserror" ,rust-thiserror-1)) + #:features '(list "python") + #:install-source? #false)) + (inputs + (list maturin)) + (native-inputs + (list python-wrapper)) + (propagated-inputs (list python-numpy python-scipy)) + (home-page "https://github.com/oxfordcontrol/Clarabel.rs") + (synopsis "Interior-point solver for convex conic optimisation problems") + (description "Clarabel.rs is a Rust implementation of an interior point +numerical solver for convex optimization problems using a novel homogeneous +embedding.") + (license license:asl2.0))) + (define-public python-climin (package (name "python-climin") @@ -2224,16 +2789,20 @@ heavily biased to machine learning scenarios. It works on top of (define-public python-paramz (package (name "python-paramz") - (version "0.9.5") + (version "0.9.6") (source (origin - (method url-fetch) - (uri (pypi-uri "paramz" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/sods/paramz") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "16hbh97kj6b1c2gw22rqnr3w3nqkszh9gj8vgx738gq81wf225q9")))) - (build-system python-build-system) + "1ywc2jzj40m6wmq227j3snxvp4434s0m1xk1abg6v6mr87pv2sa9")))) + (build-system pyproject-build-system) (propagated-inputs (list python-decorator python-numpy python-scipy python-six)) + (native-inputs (list python-nose)) (home-page "https://github.com/sods/paramz") (synopsis "The Parameterization Framework") (description @@ -2258,27 +2827,35 @@ for parameterized model creation and handling. Its features include: (define-public python-gpy (package (name "python-gpy") - (version "1.10.0") + (version "1.13.1") (source (origin (method url-fetch) (uri (pypi-uri "GPy" version)) (sha256 (base32 - "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) + "05d1ry4jpp0srsrmp3qd6s0p2bjc4c0z99450pzdr79vagbfvlk4")))) + (build-system pyproject-build-system) (arguments - `(#:phases (modify-phases %standard-phases - (add-before 'check 'remove-plotting-tests - ;; These fail - (lambda _ - (delete-file "GPy/testing/plotting_tests.py")))))) - (native-inputs (list python-cython python-nose python-climin)) - (propagated-inputs (list python-numpy python-paramz python-scipy - python-six)) + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'compatibility + (lambda _ + ;; This file uses Python 2 statements + (delete-file "GPy/testing/mpi_test__.py") + (substitute* "setup.py" + (("scipy>=1.3.0,<1.12.0") + "scipy>=1.3.0,<=1.13.0")) + ;; Use numpy.exp because scipy.ext no longer exists + (substitute* "GPy/kern/src/sde_standard_periodic.py" + (("sp\\.exp") "np.exp")) + (substitute* "GPy/kern/src/sde_stationary.py" + (("sp\\.poly1d") "np.poly1d") + (("sp\\.roots") "np.roots"))))))) + (native-inputs + (list python-cython python-matplotlib python-pods python-pytest)) + (propagated-inputs + (list python-numpy python-paramz python-scipy python-six)) (home-page "https://sheffieldml.github.io/GPy/") (synopsis "The Gaussian Process Toolbox") (description @@ -2449,6 +3026,31 @@ interoperability offered by HDF5.") proportional-integral-derivative} controller.") (license license:expat))) +(define-public python-supersmoother + (package + (name "python-supersmoother") + (version "0.4") + (source + (origin + (method git-fetch) ; no package in PyPI + (uri (git-reference + (url "https://github.com/jakevdp/supersmoother") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1lkj8l2mpki6x2pxcwlrplx63lhi8h9v2rzxgjfb0cppsfr8m1wp")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-numpy)) + (native-inputs (list python-scipy)) + (home-page "http://github.com/jakevdp/supersmoother") + (synopsis "Python implementation of Friedman's Supersmoother") + (description + "This package provides an efficient implementation of +@url{https://www.slac.stanford.edu/pubs/slacpubs/3250/slac-pub-3477.pdf, +Friedman's SuperSmoother} based in Python. It makes use of numpy for fast +numerical computation.") + (license license:bsd-2))) + (define-public python-opt-einsum (package (name "python-opt-einsum") |