diff options
author | Ricardo Wurmus <rekado@elephly.net> | 2024-05-03 10:55:57 +0200 |
---|---|---|
committer | Ricardo Wurmus <rekado@elephly.net> | 2024-05-05 22:38:18 +0200 |
commit | cb9ec4c5c59d5a9b6d8d999acc7c84d5eff5e3b9 (patch) | |
tree | 6043d02404b1e684e36977ab820096cee727b62e | |
parent | 0e246350336f68bc03f27b709cb6e765b160c8d2 (diff) |
gnu: python-decoupler-py: Update to 1.6.0.
* gnu/packages/bioinformatics.scm (python-decoupler-py): Update to 1.6.0.
[arguments]: Do not disable test_plot_volcano test.
Change-Id: I44a31d30e8a03d2d1ffd86383c8bc6db79628def
-rw-r--r-- | gnu/packages/bioinformatics.scm | 119 |
1 files changed, 55 insertions, 64 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 78c71447d5..dff8ba4d87 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2026,71 +2026,62 @@ parsing of Variant Call Format (VCF) files.") (license license:expat))) (define-public python-decoupler-py - ;; This latest commit fixes a bug in test_omnip.py. - (let ((commit "459b235348ddd9135217a3722d9dd1caa9a14ace") - (revision "1")) - (package - (name "python-decoupler-py") - (version (git-version "1.5.0" revision commit)) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/saezlab/decoupler-py") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1c0xk006iilyffdaqar2d05qdhik22fbkny387zx0bndkgqifxhl")))) - (build-system pyproject-build-system) - (arguments - (list - #:test-flags - '(list "-k" - ;; These tests require internet access - (string-append "not test_get_resource" - " and not test_show_resources" - " and not test_get_dorothea" - " and not test_get_progeny" - " and not test_get_ksn_omnipath" - ;; XXX module 'omnipath.interactions' has no - ;; attribute 'CollecTRI' - " and not test_get_collectri" - ;; XXX This one fails because the "texts" list - ;; is empty, so there are no texts to adjust. - ;; It is not clear whether this a compatibility - ;; problem with our adjusttext package. - " and not test_plot_volcano")) - #:phases - '(modify-phases %standard-phases - (add-before 'check 'set-home - ;; Some tests require a home directory to be set. - (lambda _ (setenv "HOME" "/tmp"))) - ;; Numba needs a writable dir to cache functions. - (add-before 'build 'set-numba-cache-dir - (lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp")))))) - (propagated-inputs (list python-adjusttext - python-anndata - python-ipython - python-matplotlib - python-nbsphinx - python-numba - python-numpy - python-numpydoc - python-omnipath - python-scanpy - python-scikit-learn - python-scipy - python-skranger - python-tqdm - python-typing-extensions)) - (native-inputs (list python-pytest)) - (home-page "https://github.com/saezlab/decoupler-py") - (synopsis - "Framework for modeling, analyzing and interpreting single-cell RNA-seq data") - (description - "This package provides different statistical methods to extract + (package + (name "python-decoupler-py") + (version "1.6.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/saezlab/decoupler-py") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1mqkp0i8k5hzhfnka4nc2f0phmrs0k404ynbl1lqfjzywx25y75h")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + '(list "-k" + ;; These tests require internet access + (string-append "not test_get_resource" + " and not test_show_resources" + " and not test_get_dorothea" + " and not test_get_progeny" + " and not test_get_ksn_omnipath" + ;; This attempts to download things for Omnipath + " and not test_get_collectri")) + #:phases + '(modify-phases %standard-phases + (add-before 'check 'set-home + ;; Some tests require a home directory to be set. + (lambda _ (setenv "HOME" "/tmp"))) + ;; Numba needs a writable dir to cache functions. + (add-before 'build 'set-numba-cache-dir + (lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp")))))) + (propagated-inputs (list python-adjusttext + python-anndata + python-ipython + python-matplotlib + python-nbsphinx + python-numba + python-numpy + python-numpydoc + python-omnipath + python-scanpy + python-scikit-learn + python-scipy + python-skranger + python-tqdm + python-typing-extensions)) + (native-inputs (list python-pytest)) + (home-page "https://github.com/saezlab/decoupler-py") + (synopsis + "Framework for modeling, analyzing and interpreting single-cell RNA-seq data") + (description + "This package provides different statistical methods to extract biological activities from omics data within a unified framework.") - (license license:gpl3+)))) + (license license:gpl3+))) (define-public python-demuxem (package |