diff options
Diffstat (limited to 'gnu/packages/python-xyz.scm')
| -rw-r--r-- | gnu/packages/python-xyz.scm | 356 |
1 files changed, 315 insertions, 41 deletions
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 87963f9f19..8591423116 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -131,6 +131,7 @@ ;;; Copyright © 2022 Mathieu Laparie <mlaparie@disr.it> ;;; Copyright © 2022 Garek Dyszel <garekdyszel@disroot.org> ;;; Copyright © 2022 Baptiste Strazzulla <bstrazzull@hotmail.fr> +;;; Copyright © 2022 Nicolas Graves <ngraves@ngraves.fr> ;;; ;;; This file is part of GNU Guix. ;;; @@ -159,9 +160,11 @@ #:use-module (gnu packages check) #:use-module (gnu packages cmake) #:use-module (gnu packages compression) + #:use-module (gnu packages cpp) #:use-module (gnu packages crypto) #:use-module (gnu packages databases) #:use-module (gnu packages dbm) + #:use-module (gnu packages digest) #:use-module (gnu packages django) #:use-module (gnu packages djvu) #:use-module (gnu packages docker) @@ -562,6 +565,24 @@ and variables you'll need already imported and created. (home-page "https://github.com/google/python-fire") (license license:asl2.0))) +(define-public python-fit-nbinom + (package + (name "python-fit-nbinom") + (version "1.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "fit_nbinom" version)) + (sha256 + (base32 + "12v8l5i35vjbpvh5i4lw29ys6vpr3z7pysyrx33hxaq09zr015mx")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-numpy python-scipy)) + (home-page "https://github.com/joachimwolff/fit_nbinom") + (synopsis "Negative binomial maximum likelihood estimator") + (description "This package provides an implementation in Python using +scipy and numpy of negative binomial maximum likelihood estimation.") + (license license:gpl3+))) + (define-public python-dotmap (package (name "python-dotmap") @@ -898,6 +919,24 @@ template") variables into the markdown template") (license license:expat))) +(define-public python-py4j + (package + (name "python-py4j") + (version "0.10.9.7") + (source (origin + (method url-fetch) + (uri (pypi-uri "py4j" version)) + (sha256 + (base32 + "1fwdx92cdaiviradksfyygg05g1fpc3x2lf65bv5rnispcam6vhb")))) + (build-system python-build-system) + (home-page "https://www.py4j.org/") + (synopsis "Dynamically access arbitrary Java objects from Python") + (description + "This package enables Python programs to dynamically access arbitrary +Java objects.") + (license license:bsd-3))) + (define-public python-pymdown-extensions (package (name "python-pymdown-extensions") @@ -921,6 +960,36 @@ variables into the markdown template") Markdown. All extensions are found under the module namespace of pymdownx.") (license license:expat))) +(define-public python-pint + (package + (name "python-pint") + (version "0.19.2") + (source (origin + (method url-fetch) + (uri (pypi-uri "Pint" version)) + (sha256 + (base32 + "1bsbiikm9i4saqc6mc3minkmrgnsgcg734agsvd7icqhyngrim71")))) + (build-system python-build-system) + (native-inputs + (list python-pytest + python-pytest-cov + python-pytest-mpl + python-pytest-subtests + python-setuptools-scm + python-sparse + python-dask + python-xarray + python-distributed)) + (home-page "https://github.com/hgrecco/pint") + (synopsis "Physical quantities module") + (description + "Pint is a Python package to define, operate and manipulate physical +quantities: the product of a numerical value and a unit of measurement. It +allows arithmetic operations between them and conversions from and to +different units.") + (license license:bsd-3))) + (define-public python-plotille (package (name "python-plotille") @@ -3008,6 +3077,29 @@ the optional C extension for speedups. Simplejson is also supported on Python 3.3+.") (license license:x11))) +(define-public python-simple-rlp + (package + (name "python-simple-rlp") + (version "0.1.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/SamuelHaidu/simple-rlp") + ;; Upstream doesn't tag the git repo. + (commit "342ea269d84da1ddc4a7630cdebc90159261391c"))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1nv92sphpkyrncak4qgj50qmgkmj4ycl2szbnv9c7ihgl5df4div")))) + (build-system python-build-system) + (home-page "https://github.com/SamuelHaidu/simple-rlp") + (synopsis + "Python implementation of RLP (Recursive Length Prefix) encoding") + (description + "@code{simple-rlp} is a python implementation of RLP (Recursive Length \ +Prefix) - Encode and decode data structures.") + (license license:expat))) (define-public python-pyicu (package @@ -3228,6 +3320,46 @@ existing ones.") a certain expected condition.") (license license:expat))) +(define-public python-pomegranate + (package + (name "python-pomegranate") + (version "0.14.8") + (source (origin + (method url-fetch) + (uri (pypi-uri "pomegranate" version)) + (sha256 + (base32 + "0gb9srkbxzlkjyfizvxkw5y0bvnfcyiaxapz0hrdaba8j096b5i2")) + (modules '((guix build utils))) + ;; Delete generated Cython C files. + (snippet + '(for-each delete-file (find-files "." "\\.c$"))))) + (build-system python-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python" "setup.py" "test"))))))) + (propagated-inputs + (list python-joblib + python-networkx + python-numpy + python-pyyaml + python-scipy)) + (native-inputs + (list python-cython + python-nose + python-pandas)) + (home-page "https://pypi.python.org/pypi/pomegranate/") + (synopsis "Graphical models library for Python") + (description + "Pomegranate is a graphical models library for Python, implemented in +Cython for speed.") + (license license:expat))) + (define-public python-poyo (package (name "python-poyo") @@ -3668,18 +3800,6 @@ with sensible defaults out of the box.") (base32 "06kbzd6sjfkqan3miwj9wqyddfxc2b6hi7p5s4dvqjb3gif2bdfj")))) (arguments `()))) -(define-public python-click-5 - (package (inherit python-click) - (name "python-click") - (version "5.1") - (source - (origin - (method url-fetch) - (uri (pypi-uri "click" version)) - (sha256 - (base32 "0njsm0wn31l21bi118g5825ma5sa3rwn7v2x4wjd7yiiahkri337")))) - (arguments `()))) - (define-public python-cligj (package (name "python-cligj") @@ -4634,6 +4754,73 @@ accessible for novices, as well as a scripting interface offering the full flexibility and power of the Python language.") (license license:gpl3+))) +(define-public python-dm-tree + (package + (name "python-dm-tree") + (version "0.1.7") + (source (origin + (method url-fetch) + (uri (pypi-uri "dm-tree" version)) + (sha256 + (base32 "0apxfxgmqh22qpk92zmmf3acqkavhwxz78lnwz026a5rlnncizih")))) + (build-system python-build-system) + (inputs (list pybind11 abseil-cpp python)) + (propagated-inputs (list python-wheel + python-absl-py + python-attrs + python-numpy + python-wrapt)) + (arguments + (list #:tests? #f + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'build-shared-lib + (lambda _ + (let* ((pybind11 #$(this-package-input "pybind11")) + (python #$(this-package-input "python")) + (version (python-version python)) + (abseil-cpp #$(this-package-input "abseil-cpp"))) + ;; Delete default cmake build. + (substitute* "setup.py" + (("ext_modules.*") "") + (("cmdclass.*") "")) + ;; Actual build phase. + (mkdir-p "build/temp/tree/") + (invoke + "gcc" "-pthread" "-Wno-unused-result" "-Wsign-compare" + "-DNDEBUG" "-g" "-fwrapv" "-O3" "-Wall" + "-fno-semantic-interposition" "-fPIC" + "-I" (string-append pybind11 + "/lib/python" version + "/site-packages/pybind11/include") + "-I" (string-append python "/include/python" + version) + "-I" (string-append abseil-cpp "/include") + "-c" "tree/tree.cc" + "-o" "build/temp/tree/tree.o" + "-fvisibility=hidden" "-g0") + (mkdir-p "build/lib/tree") + (invoke + "g++" "-pthread" "-shared" + (string-append "-Wl," "-rpath=" python "/lib") + "-fno-semantic-interposition" + "build/temp/tree/tree.o" + "-L" (string-append python "/lib") + "-L" (string-append abseil-cpp "/lib") + "-l" "absl_int128" + "-l" "absl_raw_hash_set" + "-l" "absl_raw_logging_internal" + "-l" "absl_strings" + "-l" "absl_throw_delegate" + "-o" "build/lib/tree/_tree.so"))))))) + (home-page "https://github.com/deepmind/tree") + (synopsis "Work with nested data structures in Python") + (description "Tree is a python library for working with nested data +structures. In a way, @code{tree} generalizes the builtin @code{map} function +which only supports flat sequences, and allows you to apply a function to each +leaf preserving the overall structure.") + (license license:asl2.0))) + (define-public python-docutils (package (name "python-docutils") @@ -4831,6 +5018,23 @@ text styles of documentation.") (description "This package installs Github custom lexers to Pygments.") (license license:bsd-3))) +(define-public python-pygtrie + (package + (name "python-pygtrie") + (version "2.5.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "pygtrie" version)) + (sha256 + (base32 + "1qm4xdmzd4q5pc9h5gjdpr5m7lg06k8dvqnjn7d07d3fhani8d90")))) + (build-system pyproject-build-system) + (home-page "https://github.com/mina86/pygtrie") + (synopsis "Pure Python trie data structure implementation") + (description + "This package provides a pure Python trie data structure implementation.") + (license license:asl2.0))) + (define-public python-bump2version (package (name "python-bump2version") @@ -10169,40 +10373,37 @@ SVG, EPS, PNG and terminal output.") (define-public python-seaborn (package (name "python-seaborn") - (version "0.11.2") + (version "0.12.0") (source (origin (method url-fetch) (uri (pypi-uri "seaborn" version)) (sha256 (base32 - "1xpl3zb945sihsiwm9q1yyx84sakk1phcg0fprj6i0j0dllfjifg")) - (patches (search-patches "python-seaborn-kde-test.patch" - "python-seaborn-2690.patch")))) + "08vvnp4ps86857imxz2l5xi2vir5xdcdp3apq4badb4b5llifgw9")))) (build-system python-build-system) (arguments - `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'patch-more-tests - (lambda _ - (substitute* "seaborn/tests/test_distributions.py" - (("get_contour_color\\(ax\\.collections\\[0\\]\\)") - "get_contour_color(ax.collections[0])") - (("c\\.get_color\\(\\)") "get_contour_color(c)") - (("def test_hue_ignores_cmap") - "def skip_test_hue_ignores_cmap") - (("def test_fill_artists") - "def skip_test_fill_artists") - (("def test_with_rug") "def skip_test_with_rug")))) - (add-before 'check 'start-xserver - (lambda _ - (system "Xvfb :1 &") - (setenv "DISPLAY" ":1"))) - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "pytest" "seaborn"))))))) + (list #:modules '((guix build python-build-system) + (guix build utils) + (ice-9 match)) + #:phases #~(modify-phases %standard-phases + (replace 'build + (lambda _ + (invoke "python" "-m" "build" "--wheel" + "--no-isolation" "."))) + (replace 'install + (lambda _ + (match (find-files "dist" "\\.whl$") + ((wheel _ ...) + (invoke "python" "-m" "pip" "install" + (string-append "--prefix=" #$output) + wheel))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-vv"))))))) (propagated-inputs (list python-pandas python-matplotlib python-numpy python-scipy)) - (native-inputs (list python-pytest xorg-server-for-tests)) + (native-inputs (list python-flit-core python-pypa-build python-pytest)) (home-page "https://seaborn.pydata.org/") (synopsis "Statistical data visualization") (description @@ -14709,7 +14910,7 @@ with a new public API, and RPython support.") (define-public python-hy (package (name "python-hy") - (version "0.24.0") + (version "0.25.0") (source (origin (method git-fetch) ; no tests in PyPI release @@ -14718,7 +14919,7 @@ with a new public API, and RPython support.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1s458ymd9g3s8k2ccc300jr4w66c7q3vhmhs9z3d3a4qg0xdhs9y")))) + (base32 "1am6z9m0s9svysj0wrfz069rpvbqqimphqll3912q4bvdlz6vrjp")))) (build-system python-build-system) (arguments '(#:phases @@ -20831,6 +21032,34 @@ while only declaring the test-specific fields.") as Swagger.") (license license:expat))) +(define-public python-apispec-webframeworks + (package + (name "python-apispec-webframeworks") + (version "0.5.2") + (source (origin + (method url-fetch) + (uri (pypi-uri "apispec-webframeworks" version)) + (sha256 + (base32 + "1wyw30402xq2a8icrsjmy9v43jyvawcjd85ccb2zicqlg4k5pcqd")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-apispec)) + (native-inputs + (list python-bottle + python-flake8 + python-flake8-bugbear + python-flask + python-mock + python-pre-commit + python-pytest + python-tornado + python-tox)) + (home-page "https://github.com/marshmallow-code/apispec-webframeworks") + (synopsis "Web framework plugins for apispec") + (description "This package provides plugins for using @code{apispec} with +web frameworks.") + (license license:expat))) + (define-public python-flasgger (package (name "python-flasgger") @@ -22364,6 +22593,25 @@ working with iterables.") (description "Lexer and codec to work with LaTeX code in Python.") (license license:expat))) +(define-public python-pybloom-live + (package + (name "python-pybloom-live") + (version "4.0.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "pybloom_live" version)) + (sha256 + (base32 + "040i6bjqvl33j30v865shsk30s3h7f16pqwiaj5kig857dfmqm4r")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-bitarray python-xxhash)) + (native-inputs (list python-pytest)) + (home-page "https://github.com/joseph-fox/python-bloomfilter") + (synopsis "Bloom filter") + (description "This package provides a scalable Bloom filter implemented in +Python.") + (license license:expat))) + (define-public python-pybtex (package (name "python-pybtex") @@ -23082,6 +23330,32 @@ environments.") "PyNamecheap is a Namecheap API client in Python.") (license license:expat))) +(define-public python-pynixutil + (package + (name "python-pynixutil") + (version "0.5.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/nix-community/pynixutil") + (commit version))) + (file-name (git-file-name name version)) + ;; Derivation test uses nix. + (modules '((guix build utils))) + (snippet '(delete-file "tests/test_drv.py")) + (sha256 + (base32 + "1lnspcai7mqpv73bbd8kgyw63fxwgkwvfkl09b2bl5y2g2v7np6m")))) + (build-system pyproject-build-system) + (native-inputs (list poetry python-pytest)) + (home-page "https://github.com/nix-community/pynixutil") + (synopsis "Utility functions for working with data from Nix in Python") + (description + "@code{pynixutil} provides functions for base32 encoding/decoding and +derivation parsing, namingly @code{b32decode()}, @code{b32encode()} and +@code{drvparse()}.") + (license license:expat))) + (define-public python-dns-lexicon (package (name "python-dns-lexicon") @@ -25429,7 +25703,7 @@ scripts to load entry points more quickly.") (define-public python-funcparserlib (package (name "python-funcparserlib") - (version "1.0.0") + (version "1.0.1") (source (origin ;; Source tarball on PyPi lacks tests. @@ -25439,7 +25713,7 @@ scripts to load entry points more quickly.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "00pswdys5c4hpqpvfcy5zqv30gyjvjvagi12811jizw57hxrm1cs")))) + (base32 "0dw3i4fyf3j9h1l7xfgs99fc2w2axk6xqk0sdag43k444ss4hkrc")))) (build-system pyproject-build-system) (arguments '(#:phases |