diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 29edb649852..9770e73f52e 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -265,6 +265,108 @@ can be imported from spreadsheets, text files and database sources and it can be output in text, PostScript, PDF or HTML.") (license license:gpl3+))) +(define-public python-altair + (package + (name "python-altair") + (version "5.3.0") + (source (origin + (method git-fetch) ; no tests in PyPI + (uri (git-reference + (url "https://github.com/altair-viz/altair") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1lx3pkphi36pljns6jjxhyn9fbrana8f1y6gcg4yca48nvwlfssl")))) + (build-system pyproject-build-system) + (arguments + (list #:test-flags + ;; XXX: This test file requires hard to package python-anywidgets. + #~(list "--ignore=tests/test_jupyter_chart.py" + "-k" (string-join + (list + ;; these tests open an external connection. + "not test_from_and_to_json_roundtrip" + "test_render_examples_to_chart" + ;; introduces a circular dependency on altair-viewer. + "not test_save_html" + ;; these tests require the vl-convert vega compiler + "test_vegalite_compiler" + "test_to_dict_with_format_vega" + "test_to_json_with_format_vega" + "test_to_url" + "test_renderer_with_none_embed_options" + "test_jupyter_renderer_mimetype") + " and not ")))) + (propagated-inputs (list python-jinja2 + python-jsonschema + python-numpy + python-pandas + python-setuptools + python-toolz + python-typing-extensions)) + (native-inputs (list python-black + python-hatchling + python-ipython + python-pytest + python-vega-datasets)) + (home-page "https://altair-viz.github.io/") + (synopsis "Declarative statistical visualization library for Python") + (description + "Vega-Altair is a declarative statistical visualization library for Python.") + (license license:expat))) + +(define-public python-arviz + (package + (name "python-arviz") + (version "0.21.0") + (source (origin + (method git-fetch) ; PyPI misses some test files + (uri (git-reference + (url "https://github.com/arviz-devs/arviz") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "02bqpl61gzn65vhwspi6gx9ln2wlwh8xm418i8vhmls44rvszcxf")))) + (build-system pyproject-build-system) + (arguments + ;; FIXME: matplotlib tests fail because of the "--save" test flag. + (list #:test-flags #~'("--ignore" + "arviz/tests/base_tests/test_plots_matplotlib.py") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'remove-radon + (lambda _ + (delete-file + ;; This dataset is loaded remotely, it's not supposed to + ;; be copied locally. + "arviz/data/example_data/code/radon/radon.json"))) + (add-before 'check 'write-permission + (lambda _ + ;; 3 tests require write permission. + (setenv "HOME" "/tmp")))))) + (native-inputs (list python-cloudpickle python-pytest)) + (propagated-inputs (list python-dm-tree + python-h5netcdf + python-matplotlib + python-numpy + python-packaging + python-pandas + python-scipy + python-typing-extensions + python-xarray + python-xarray-einstats + python-setuptools + python-wheel)) + (home-page "https://github.com/arviz-devs/arviz") + (synopsis "Exploratory analysis of Bayesian models") + (description + "ArviZ is a Python package for exploratory analysis of Bayesian models. +It includes functions for posterior analysis, data storage, model checking, +comparison and diagnostics.") + (license license:asl2.0))) + ;; Update this package together with the set of recommended packages: r-boot, ;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice, ;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival. @@ -908,57 +1010,6 @@ Keizer et al. (2013) , and Jonsson et al. and Vega-Lite examples.") (license license:expat))) -(define-public python-altair - (package - (name "python-altair") - (version "5.3.0") - (source (origin - (method git-fetch) ; no tests in PyPI - (uri (git-reference - (url "https://github.com/altair-viz/altair") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1lx3pkphi36pljns6jjxhyn9fbrana8f1y6gcg4yca48nvwlfssl")))) - (build-system pyproject-build-system) - (arguments - (list #:test-flags - ;; XXX: This test file requires hard to package python-anywidgets. - #~(list "--ignore=tests/test_jupyter_chart.py" - "-k" (string-join - (list - ;; these tests open an external connection. - "not test_from_and_to_json_roundtrip" - "test_render_examples_to_chart" - ;; introduces a circular dependency on altair-viewer. - "not test_save_html" - ;; these tests require the vl-convert vega compiler - "test_vegalite_compiler" - "test_to_dict_with_format_vega" - "test_to_json_with_format_vega" - "test_to_url" - "test_renderer_with_none_embed_options" - "test_jupyter_renderer_mimetype") - " and not ")))) - (propagated-inputs (list python-jinja2 - python-jsonschema - python-numpy - python-pandas - python-setuptools - python-toolz - python-typing-extensions)) - (native-inputs (list python-black - python-hatchling - python-ipython - python-pytest - python-vega-datasets)) - (home-page "https://altair-viz.github.io/") - (synopsis "Declarative statistical visualization library for Python") - (description - "Vega-Altair is a declarative statistical visualization library for Python.") - (license license:expat))) - (define-public python-emcee (package (name "python-emcee") @@ -1142,57 +1193,6 @@ is widely used in many areas of astrophysical research.") algorithms for evaluating Bayesian evidence.") (license license:expat))) -(define-public python-arviz - (package - (name "python-arviz") - (version "0.21.0") - (source (origin - (method git-fetch) ; PyPI misses some test files - (uri (git-reference - (url "https://github.com/arviz-devs/arviz") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "02bqpl61gzn65vhwspi6gx9ln2wlwh8xm418i8vhmls44rvszcxf")))) - (build-system pyproject-build-system) - (arguments - ;; FIXME: matplotlib tests fail because of the "--save" test flag. - (list #:test-flags #~'("--ignore" - "arviz/tests/base_tests/test_plots_matplotlib.py") - #:phases - #~(modify-phases %standard-phases - (add-after 'unpack 'remove-radon - (lambda _ - (delete-file - ;; This dataset is loaded remotely, it's not supposed to - ;; be copied locally. - "arviz/data/example_data/code/radon/radon.json"))) - (add-before 'check 'write-permission - (lambda _ - ;; 3 tests require write permission. - (setenv "HOME" "/tmp")))))) - (native-inputs (list python-cloudpickle python-pytest)) - (propagated-inputs (list python-dm-tree - python-h5netcdf - python-matplotlib - python-numpy - python-packaging - python-pandas - python-scipy - python-typing-extensions - python-xarray - python-xarray-einstats - python-setuptools - python-wheel)) - (home-page "https://github.com/arviz-devs/arviz") - (synopsis "Exploratory analysis of Bayesian models") - (description - "ArviZ is a Python package for exploratory analysis of Bayesian models. -It includes functions for posterior analysis, data storage, model checking, -comparison and diagnostics.") - (license license:asl2.0))) - (define-public python-pymc (package (name "python-pymc")