diff options
Diffstat (limited to 'gnu/packages/python-science.scm')
| -rw-r--r-- | gnu/packages/python-science.scm | 99 |
1 files changed, 81 insertions, 18 deletions
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index b71f693538..f35795f922 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -253,28 +253,36 @@ possibility to differentiate functions that contain matrix functions as (define-public python-anndata (package (name "python-anndata") - (version "0.11.1") + (version "0.12.1") (source (origin ;; The tarball from PyPi doesn't include tests. (method git-fetch) (uri (git-reference - (url "https://github.com/theislab/anndata") - (commit version))) + (url "https://github.com/theislab/anndata") + (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 - "0skmjjvxk5gdsx6fkplszff92jsb4l45j23c6mhq1vdi3wqhqhcw")))) + (base32 "1pwqy1pxsiqf13kfshcbqah1a92x4044s6jyr94488ngpqkr275z")))) (build-system pyproject-build-system) (arguments (list #:test-flags - #~(list "-k" #$(string-append - ;; This one test seemingly freezes - "not test_read_lazy_h5_cluster" - ;; Fails with a numpy deprecation warning - ;; but not an actual failure - " and not test_read_write_X")) + #~(list "--numprocesses" (number->string (parallel-job-count)) + ;; XXX: AttributeError: module 'pyarrow.lib' has no attribute + ;; 'PyExtensionType + "--ignore=tests/test_awkward.py" + "-k" (string-join + ;; TypeError: read_text() takes from 1 to 2 positional + ;; arguments but 4 were given + (list "not test_read_csv" + ;; TypeError: _fix_co_filename() argument 2 must be + ;; str, not PosixPath + "test_hints" + ;; Failed: DID NOT WARN. No warnings of type (<class + ;; 'FutureWarning'>,) were emitted. + "test_readloom_deprecations") + " and not ")) #:phases #~(modify-phases %standard-phases ;; Doctests require scanpy from (gnu packages bioinformatics) @@ -293,15 +301,14 @@ possibility to differentiate functions that contain matrix functions as (setenv "NUMBA_CACHE_DIR" "/tmp")))))) (propagated-inputs (list python-array-api-compat - python-exceptiongroup ;only for Python <3.11 python-h5py python-importlib-metadata + python-legacy-api-wrap python-natsort - python-numcodecs python-packaging python-pandas - python-scipy python-scikit-learn + python-scipy python-setuptools ; For pkg_resources. python-zarr)) (native-inputs @@ -309,17 +316,14 @@ possibility to differentiate functions that contain matrix functions as python-boltons python-dask python-distributed - python-hatchling python-hatch-vcs + python-hatchling python-joblib python-loompy python-matplotlib python-pytest python-pytest-mock - python-pytest-doctestplus python-pytest-xdist - python-toml - python-flit python-setuptools-scm)) (home-page "https://github.com/theislab/anndata") (synopsis "Annotated data for data analysis pipelines") @@ -1540,6 +1544,32 @@ Features: @end itemize") (license license:bsd-2))) +(define-public python-legendkit + (package + (name "python-legendkit") + (version "0.3.6") + (source + (origin + (method git-fetch) ;no tests in PyPI archive + (uri (git-reference + (url "https://github.com/Marsilea-viz/legendkit") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "03xdhh95w4zydwa4ahp3gyfa6i60c9s5arfcj366knckb1bnpnn9")))) + (build-system pyproject-build-system) + (native-inputs + (list python-hatchling + python-pytest)) + (propagated-inputs + (list python-matplotlib)) + (home-page "https://github.com/Marsilea-viz/legendki") + (synopsis "Legend creation and manipulation for matplotlib") + (description + "This package implements a functionality to create and manipulate plot +legends for @code{matplotlib}.") + (license license:expat))) + (define-public python-libneuroml (package (name "python-libneuroml") @@ -1572,6 +1602,39 @@ Features: neuronal models") (license license:bsd-3))) +(define-public python-marsilea + (package + (name "python-marsilea") + (version "0.5.4") + (source + (origin + (method git-fetch) ;no tests in PyPI archive + (uri (git-reference + (url "https://github.com/Marsilea-viz/marsilea") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "09pyfx0gn46ypsp991d3n4a4xx6zlbpss078lw6yywnhl834v2i0")))) + (build-system pyproject-build-system) + (native-inputs + (list python-hatchling + python-pytest)) + (propagated-inputs + (list python-legendkit + python-matplotlib + python-numpy + python-pandas + python-platformdirs + python-scipy + python-seaborn)) + (home-page "https://github.com/Marsilea-viz/marsilea") + (synopsis "Declarative creation of composable visualizations") + (description + "Marsilea is a Python library for creating composable visualizations in a +declarative way. It is built on top of Matplotlib and provides a high-level +API for you to puzzle different visualizations together like logo.") + (license license:expat))) + (define-public python-meshzoo (package (name "python-meshzoo") |