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-rw-r--r--gnu/packages/python-science.scm948
1 files changed, 691 insertions, 257 deletions
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 8065de0e99..2b4e74f9be 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -3,13 +3,13 @@
;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
-;;; Copyright © 2016, 2022, 2023 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2022-2024 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016-2020, 2022 Marius Bakke <marius@gnu.org>
;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; 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, 2023 Vinicius Monego <monego@posteo.net>
+;;; Copyright © 2020, 2021, 2022, 2023, 2024 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>
@@ -22,7 +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>
+;;; Copyright © 2023, 2024 Troy Figiel <troy@troyfigiel.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -47,9 +47,11 @@
#:use-module (gnu packages boost)
#:use-module (gnu packages build-tools)
#:use-module (gnu packages check)
+ #:use-module (gnu packages chemistry)
#:use-module (gnu packages cpp)
#:use-module (gnu packages crypto)
#:use-module (gnu packages databases)
+ #:use-module (gnu packages digest)
#:use-module (gnu packages gcc)
#:use-module (gnu packages geo)
#:use-module (gnu packages image)
@@ -84,21 +86,16 @@
(define-public python-scipy
(package
(name "python-scipy")
- (version "1.10.1")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "scipy" version))
(sha256
- (base32 "19gk88nvrxl050nasz25qpmmqvbdk247bkj09jx8jibv1awdzy9c"))))
+ (base32 "18rn15wg3lp58z204fbjjhy0h79c53yg3c4qqs9h3liniamspxab"))))
(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
@@ -140,8 +137,23 @@
(copy-recursively "build/html" html)))
(format #t "sphinx-build not found, skipping~%"))))))))
(propagated-inputs
- (list python-numpy python-matplotlib python-pyparsing python-pythran))
- (inputs (list openblas pybind11))
+ (append
+ (if (supported-package? python-jupytext) ; Depends on pandoc.
+ (list python-jupytext)
+ '())
+ (list python-matplotlib
+ python-mpmath
+ python-mypy
+ python-numpy
+ python-numpydoc
+ python-pydata-sphinx-theme
+ python-pydevtool
+ python-pythran
+ python-rich-click
+ python-sphinx
+ python-threadpoolctl
+ python-typing-extensions)))
+ (inputs (list openblas pybind11-2.10))
(native-inputs
(list gfortran
;; XXX: Adding gfortran shadows GCC headers, causing a compilation
@@ -149,10 +161,17 @@
gcc
meson-python
pkg-config
- python-cython
+ python-click
+ python-cython-0.29.35
+ python-doit
+ python-hypothesis
+ python-pooch
+ python-pycodestyle
+ python-pydevtool
python-pytest
- python-pytest-xdist
- python-threadpoolctl))
+ python-pytest-cov
+ python-pytest-timeout
+ python-pytest-xdist))
(home-page "https://scipy.org/")
(synopsis "The Scipy library provides efficient numerical routines")
(description "The SciPy library is one of the core packages that make up
@@ -214,7 +233,7 @@ genetic variation data.")
(define-public python-scikit-fem
(package
(name "python-scikit-fem")
- (version "8.1.0")
+ (version "9.0.1")
(source (origin
(method git-fetch) ; no tests in PyPI
(uri (git-reference
@@ -223,13 +242,14 @@ genetic variation data.")
(file-name (git-file-name name version))
(sha256
(base32
- "1zpn0wpsvls5nkrav5a43z77yg9nc09dpyy9ri0dpmpm2ndh2mhs"))))
+ "1r1c88rbaa7vjfnljbzx8paf36yzpy33bragl99ykn6i2srmjrd4"))))
(build-system pyproject-build-system)
- (arguments
- ;; Examples below require python-autograd and python-pyamg.
- (list #:test-flags #~(list "-k" "not TestEx32 and not TestEx45")))
(propagated-inputs (list python-meshio python-numpy python-scipy))
- (native-inputs (list python-pytest))
+ (native-inputs
+ (list python-autograd
+ python-pyamg
+ python-pytest
+ python-shapely))
(home-page "https://scikit-fem.readthedocs.io/en/latest/")
(synopsis "Library for performing finite element assembly")
(description
@@ -264,31 +284,31 @@ 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.
@@ -296,6 +316,7 @@ logic, also known as grey logic.")
(list python-cloudpickle
python-dask
python-imageio
+ python-lazy-loader
python-matplotlib
python-networkx
python-numpy
@@ -305,9 +326,13 @@ 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
@@ -331,7 +356,15 @@ 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
@@ -363,11 +396,6 @@ implements several methods for sequential model-based optimization.
(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?
@@ -385,31 +413,68 @@ of regular expressions from text data and automatic test generation.")
(define-public python-trimesh
(package
(name "python-trimesh")
- (version "3.23.5")
+ (version "4.0.10")
(source
(origin
- (method url-fetch)
- (uri (pypi-uri "trimesh" version))
+ (method git-fetch) ; no tests in PyPI
+ (uri (git-reference
+ (url "https://github.com/mikedh/trimesh")
+ (commit version)))
+ (file-name (git-file-name name version))
(sha256
- (base32 "08967axlnmfv98n05dhrkynyrmcc814hl8184gzzmcy4rjg6dzdx"))))
- (build-system python-build-system)
- (propagated-inputs
- (list python-numpy))
+ (base32 "0ry04qaw0pb3hkxv4gmna87jwk97aqangd21wbr2dr4xshmkbyyb"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:test-flags
+ #~(list "-k" (string-append
+ ;; XXX: When more optional modules are available review
+ ;; disabled tests once again.
+ ;;
+ ;; Disable tests requiring optional, not packed modules.
+ "not test_material_round"
+ " and not test_bezier_example"
+ " and not test_discrete"
+ " and not test_dxf"
+ " and not test_layer"
+ " and not test_multi_nodupe"
+ " and not test_obj_roundtrip"
+ " and not test_roundtrip"
+ " and not test_scene"
+ " and not test_slice_onplane"
+ " and not test_svg"
+ " and not test_svg"))
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'fix-build
+ (lambda _
+ (substitute* "trimesh/resources/templates/blender_boolean.py.tmpl"
+ (("\\$MESH_PRE")
+ "'$MESH_PRE'")))))))
(native-inputs
(list python-coveralls
python-pyinstrument
python-pytest
python-pytest-cov))
- (arguments
- `(;; TODO: Get tests to work.
- #:tests? #f
- #:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'fix-build
- (lambda _
- (substitute* "trimesh/resources/templates/blender_boolean.py.tmpl"
- (("\\$MESH_PRE")
- "'$MESH_PRE'")))))))
+ (propagated-inputs
+ (list python-chardet
+ python-colorlog
+ python-httpx
+ python-jsonschema
+ python-lxml
+ python-networkx
+ python-numpy
+ python-pillow
+ ;; python-pycollada ; not packed yet, optional
+ ;; python-pyglet ; not packed yet, optional
+ python-requests
+ python-rtree
+ python-scipy
+ python-setuptools
+ python-shapely
+ ;; python-svg-path ; not packed yet, optional
+ python-sympy
+ python-xxhash))
(home-page "https://github.com/mikedh/trimesh")
(synopsis "Python library for loading and using triangular meshes")
(description
@@ -445,6 +510,73 @@ volume computations for simple domains like regular polygons, disks,
spheres, cubes, etc.")
(license license:gpl3+)))
+(define-public python-pyamg
+ (package
+ (name "python-pyamg")
+ (version "5.0.1")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "pyamg" version))
+ (modules '((guix build utils)))
+ (snippet
+ ;; Delete autogenerated files, regenerate in a phase.
+ #~(begin
+ (for-each
+ (lambda (file)
+ (delete-file (string-append "pyamg/amg_core/" file)))
+ '("air_bind.cpp"
+ "evolution_strength_bind.cpp"
+ "graph_bind.cpp"
+ "krylov_bind.cpp"
+ "linalg_bind.cpp"
+ "relaxation_bind.cpp"
+ "ruge_stuben_bind.cpp"
+ "smoothed_aggregation_bind.cpp"
+ "tests/bind_examples_bind.cpp"))))
+ (sha256
+ (base32
+ "0l3dliwynxyjvbgpmi2k8jqvkkw6fc00c8w69h6swhrkfh0ql12z"))))
+ (arguments
+ (list
+ #:test-flags
+ ;; Test installed package in order to find C++ modules.
+ #~(list "--pyargs" "pyamg.tests")
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; Regenerate the autogenerated files.
+ (add-after 'unpack 'amg-core-bind-them
+ (lambda _
+ ;; bindthem.py heavily depends on location to produce *_bind.cpp
+ ;; file, make it available in tests as well.
+ (copy-file "pyamg/amg_core/bindthem.py"
+ "pyamg/amg_core/tests/bindthem.py")
+ (with-directory-excursion "pyamg/amg_core"
+ (substitute* "bindthem.py"
+ (("/usr/bin/env python3") (which "python3")))
+ (invoke "sh" "generate.sh"))
+ (with-directory-excursion "pyamg/amg_core/tests"
+ (invoke "python" "bindthem.py" "bind_examples.h")))))))
+ (build-system pyproject-build-system)
+ (native-inputs
+ (list pybind11
+ python-cppheaderparser
+ python-pytest
+ python-pyyaml
+ python-setuptools-scm))
+ (propagated-inputs (list python-numpy python-scipy))
+ (home-page "https://github.com/pyamg/pyamg")
+ (synopsis "Algebraic Multigrid Solvers in Python")
+ (description "PyAMG is a Python library of Algebraic Multigrid
+(AMG) solvers. It features implementations of:
+@itemize
+@item Ruge-Stuben (RS) or Classical AMG
+@item AMG based on Smoothed Aggregation (SA)
+@item Adaptive Smoothed Aggregation (αSA)
+@item Compatible Relaxation (CR)
+@item Krylov methods such as CG, GMRES, FGMRES, BiCGStab, MINRES, etc.
+@end itemize")
+ (license license:expat)))
+
(define-public python-tspex
(package
(name "python-tspex")
@@ -468,71 +600,73 @@ 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
@@ -542,7 +676,7 @@ 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
@@ -561,6 +695,247 @@ 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-pandarallel
+ (package
+ (name "python-pandarallel")
+ (version "1.6.5")
+ (source
+ (origin
+ (method git-fetch) ; no tests in PyPI
+ (uri (git-reference
+ (url "https://github.com/nalepae/pandarallel/")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0r2wlxlwp4wia0vm15k4cp421mwa20k4k5g2ml01inprj8bl1p0p"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:test-flags #~(list "-n" (number->string (parallel-job-count)))))
+ (propagated-inputs
+ (list python-dill
+ python-pandas
+ python-psutil))
+ (native-inputs
+ (list python-mkdocs-material
+ python-numpy
+ python-pytest
+ python-pytest-cov
+ python-pytest-xdist))
+ (home-page "https://nalepae.github.io/pandarallel/")
+ (synopsis "Tool to parallelize Pandas operations across CPUs")
+ (description
+ "@code{pandarallel} allows any Pandas user to take advantage of their
+multi-core computer, while Pandas uses only one core. @code{pandarallel} also
+offers nice progress bars (available on Notebook and terminal) to get an rough
+idea of the remaining amount of computation to be done.")
+ (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-pyjanitor
+ (package
+ (name "python-pyjanitor")
+ (version "0.26.0")
+ (source
+ (origin
+ ;; The build requires the mkdocs directory for the description in
+ ;; setup.py. This is not included in the PyPI tarball.
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/pyjanitor-devs/pyjanitor")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1f8xbl1k9l2z56bapp7v6bd3016zrk48igcaz6hb553r6yfl7vfx"))))
+ (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".
+ (arguments
+ (list
+ #:test-flags '(list
+ "-n" (number->string (parallel-job-count))
+ ;; Tries to connect to the internet.
+ "-k" "not test_is_connected"
+ ;; 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"))))))
+ (propagated-inputs (list python-multipledispatch
+ python-natsort
+ python-pandas-flavor
+ python-scipy
+ ;; Optional imports.
+ python-biopython ;biology submodule
+ python-unyt)) ;engineering submodule
+ (native-inputs (list python-pytest
+ python-pytest-xdist
+ ;; Optional imports. We do not propagate them due to
+ ;; their size.
+ python-numba ;speedup of joins
+ rdkit)) ;chemistry submodule
+ (home-page "https://github.com/pyjanitor-devs/pyjanitor")
+ (synopsis "Tools for cleaning and transforming pandas DataFrames")
+ (description
+ "@code{pyjanitor} provides a set of data cleaning routines for
+@code{pandas} DataFrames. These routines extend the method chaining API
+defined by @code{pandas} for a subset of its methods. Originally, this
+package was a port of the R package by the same name and it is inspired by the
+ease-of-use and expressiveness of the @code{dplyr} package.")
+ (license license:expat)))
+
(define-public python-pythran
(package
(name "python-pythran")
@@ -621,34 +996,16 @@ Python module with the same interface, but (hopefully) faster.")
(define-public python-pyts
(package
(name "python-pyts")
- (version "0.12.0")
+ (version "0.13.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "pyts" version))
(sha256
(base32
- "1cb5jwp8g52a3hxay6mxbfzk16ly6yj6rphq8cwbwk1k2jdf11dg"))))
- (build-system python-build-system)
- (arguments
- (list
- #:phases
- '(modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "pytest" "-v"
- ;; XXX: This test fails for unknown reasons
- ;; Expected:
- ;; (40, 9086)
- ;; Got:
- ;; (40, 9088)
- "-k"
- "not pyts.multivariate.transformation.weasel_muse.WEASELMUSE")))))))
+ "00pdzfkl0b4vhfdm8zas7b904jm2hhivdwv3wcmpik7l2p1yr85c"))))
+ (build-system pyproject-build-system)
(propagated-inputs
- (list python-joblib
- python-matplotlib
- python-numba
- python-numpy
+ (list python-joblib python-numba python-numpy
python-scikit-learn
python-scipy))
(native-inputs
@@ -817,18 +1174,21 @@ 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
@@ -844,7 +1204,7 @@ and visualization with these data structures.")
(define-public python-xarray-einstats
(package
(name "python-xarray-einstats")
- (version "0.5.1")
+ (version "0.7.0")
(source (origin
(method git-fetch) ; no tests in PyPI
(uri (git-reference
@@ -853,7 +1213,7 @@ and visualization with these data structures.")
(file-name (git-file-name name version))
(sha256
(base32
- "1gg7p2lq7zxic64nbr6a8ynizs8rjzb29fnqib7hw3lmp13wsfm0"))))
+ "14c424swpdginaz4pm3nmkizxy34x19q6xq3d4spx9s9031f6n3a"))))
(build-system pyproject-build-system)
(native-inputs (list python-einops python-flit-core python-numba
python-pytest))
@@ -1023,6 +1383,34 @@ automated with the minimum of fuss and the least effort.")
annotations on an existing boxplots and barplots generated by seaborn.")
(license license:expat)))
+(define-public python-unyt
+ (package
+ (name "python-unyt")
+ (version "3.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "unyt" version))
+ (sha256
+ (base32 "00900bw24rxgcgwgxp9xlx0l5im96r1n5hn0r3mxvbdgc3lyyq48"))))
+ (build-system pyproject-build-system)
+ ;; Astropy is an optional import, but we do not include it as it creates a
+ ;; module cycle: astronomy->python-science->astronomy.
+ (propagated-inputs (list python-h5py ; optional import
+ python-matplotlib ; optional import
+ python-numpy
+ python-sympy))
+ ;; Pint is optional, but we do not propagate it due to its size.
+ (native-inputs (list python-pint python-pytest))
+ (home-page "https://unyt.readthedocs.io")
+ (synopsis "Library for working with data that has physical units")
+ (description
+ "@code{unyt} is a Python library working with data that has physical
+units. It defines the @code{unyt.array.unyt_array} and
+@code{unyt.array.unyt_quantity} classess (subclasses of NumPy’s ndarray class)
+for handling arrays and scalars with units,respectively")
+ (license license:bsd-3)))
+
(define-public python-upsetplot
(package
(name "python-upsetplot")
@@ -1590,91 +1978,90 @@ 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"
+ '(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))
+ ;; 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
@@ -1924,7 +2311,7 @@ functions, convolutions, artificial neural networks etc.")
(define-public python-pydicom
(package
(name "python-pydicom")
- (version "2.3.0")
+ (version "2.4.4")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -1933,41 +2320,36 @@ functions, convolutions, artificial neural networks etc.")
(file-name (git-file-name name version))
(sha256
(base32
- "18l26s53yf5j9yh2zwq83n74qq4f2iq0cfblamsw4y9k35l1c108"))))
- (build-system python-build-system)
+ "0ksyyc1hbhyqy289a2frn84ss29fb7czirx3dkxx56f4ia33b4c8"))))
+ (build-system pyproject-build-system)
(arguments
(list
- #:phases
- #~(modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (chdir "pydicom/tests")
- (invoke "python3" "-m" "pytest" "-k" ;skip tests using web data
- (string-append
- "not test_jpeg_ls_pixel_data.py"
- " and not test_gdcm_pixel_data.py"
- " and not test_pillow_pixel_data.py"
- " and not test_rle_pixel_data.py"
- " and not Test_JPEG_LS_Lossless_transfer_syntax"
- " and not test_numpy_pixel_data.py"
- " and not test_data_manager.py"
- " and not test_handler_util.py"
- " and not test_overlay_np.py"
- " and not test_encoders_pydicom.py"
- " and not test_encaps.py"
- " and not test_reading_ds_with_known_tags_with_UN_VR"
- " and not TestDatasetOverlayArray"
- " and not TestReader"
- " and not test_filewriter.py"))))))))
+ #:test-flags
+ ;; Skip tests that require networking.
+ #~(list "-k" (string-append
+ "not test_jpeg_ls_pixel_data.py"
+ " and not test_gdcm_pixel_data.py"
+ " and not test_pillow_pixel_data.py"
+ " and not test_rle_pixel_data.py"
+ " and not Test_JPEG_LS_Lossless_transfer_syntax"
+ " and not test_numpy_pixel_data.py"
+ " and not test_data_manager.py"
+ " and not test_handler_util.py"
+ " and not test_overlay_np.py"
+ " and not test_encoders_pydicom.py"
+ " and not test_encaps.py"
+ " and not test_reading_ds_with_known_tags_with_UN_VR"
+ " and not TestDatasetOverlayArray"
+ " and not TestReader"
+ " and not test_filewriter.py"))))
(native-inputs (list python-pytest))
(inputs (list gdcm libjpeg-turbo))
(propagated-inputs (list python-numpy python-pillow))
(home-page "https://github.com/pydicom/pydicom")
(synopsis "Python library for reading and writing DICOM data")
(description "@code{python-pydicom} is a Python library for reading and
-writing DICOM medical imaging data. It lets developers read, modify and write
-DICOM data in a pythonic way.")
+writing DICOM medical imaging data. It can read, modify and write DICOM
+data.")
(license license:expat)))
(define-public python-deepdish
@@ -1981,7 +2363,20 @@ 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")
@@ -1992,7 +2387,7 @@ 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))
@@ -2166,6 +2561,45 @@ fractional factorial methods.")
NeuroML2 models.")
(license license:lgpl3)))
+(define-public python-pynetdicom
+ (package
+ (name "python-pynetdicom")
+ (version "2.0.2")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "pynetdicom" version))
+ (sha256
+ (base32
+ "0farmgviaarb3f4xn751card3v0lza57vwgl5azxxq65p7li44i3"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:test-flags
+ ;; Tests takes about 10-15min to complete.
+ ;; Skip tests that require networking.
+ #~(list "-k" (string-append
+ " not TestFindSCP"
+ " and not TestQRGetServiceClass"
+ " and not TestQRMoveServiceClass"
+ " and not TestStoreSCP"
+ " and not test_ae.py"
+ " and not test_echoscp.py"
+ " and not test_qrscp_echo.py"
+ " and not test_storescp.py"
+ " and not test_pr_level_patient"
+ " and not test_pr_level_series"
+ " and not test_scp_cancelled"))))
+ (native-inputs (list python-pyfakefs python-pytest))
+ (propagated-inputs (list python-pydicom python-sqlalchemy))
+ (home-page "https://github.com/pydicom/pynetdicom")
+ (synopsis "Python implementation of the DICOM networking protocol")
+ (description
+ "@code{pynetdicom} is a Python package that implements the DICOM
+networking protocol. It allows the easy creation of DICOM
+@acronym{SCUs,Service Class Users} and @acronym{SCPs,Service Class
+Providers}.")
+ (license license:expat)))
+
(define-public python-libneuroml
(package
(name "python-libneuroml")
generated by cgit v1.2.3 (git 2.50.1) at 2025-08-04 00:51:35 +0000