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charset=utf-8 Content-Transfer-Encoding: quoted-printable Message-ID: <171887347750.7.17381680002823190276.359657180@mawumag.com> X-SimpleLogin-Type: Reply X-SimpleLogin-EmailLog-ID: 359657180 X-SimpleLogin-Want-Signing: yes X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Reply-to: guix@mawumag.com X-ACL-Warn: , guix--- via Guix-patches From: guix--- via Guix-patches via Errors-To: guix-patches-bounces+larch=yhetil.org@gnu.org Sender: guix-patches-bounces+larch=yhetil.org@gnu.org X-Migadu-Country: US X-Migadu-Flow: FLOW_IN X-Spam-Score: -5.86 X-Migadu-Queue-Id: B640989B2 X-Migadu-Scanner: mx10.migadu.com X-Migadu-Spam-Score: -5.86 X-TUID: mQDPe2xnNOqV Change-Id: I21431b089d1f404828b78d79124d96e7d36d5a2d --- gnu/packages/bioinformatics.scm | 55 +++++++++++++++++++++++++++++++++ 1 file changed, 55 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.= scm index 37fa1727cb..b3fe67cae7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4481,6 +4481,61 @@ (define-public python-mofapy2 (description "Multi-omics factor analysis.") (license license:lgpl3))) =20 +(define-public python-muon + (package + (name "python-muon") + (version "0.1.6") + (source + (origin + ;; The tarball from PyPi doesn't include tests. + (method git-fetch) + (uri (git-reference + (url "https://github.com/scverse/muon") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1kd3flgy41dc0sc71wfnirh8vk1psxgyjxkbx1zx9yskkh6anbgw")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; Numba needs a writable dir to cache functions. + (add-before 'build 'set-numba-cache-dir + (lambda _ + (setenv "NUMBA_CACHE_DIR" "/tmp"))) + (add-before 'check 'disable-failing-tests + (lambda _ + ;; even providing a random seed, scipy.sparse.rand + ;; produces inconsistent results across scipy versions + (substitute* "tests/test_atac_preproc.py" + (("^class TestTFIDFSparse.*" m) + (string-append "@unittest.skip(reason=3D\"\")\n" m)))))))) + (propagated-inputs (list python-anndata + python-h5py + python-matplotlib + python-mofapy2 + python-mudata + python-numba + python-numpy + python-pandas + python-protobuf + python-pybedtools + python-pysam + python-scanpy + python-scikit-learn + python-seaborn + python-tqdm + python-umap-learn)) + (native-inputs (list python-flit-core-bootstrap + python-pytest + python-pytest-flake8)) + (home-page "https://github.com/scverse/muon") + (synopsis "Multimodal omics analysis framework") + (description "Multimodal omics analysis framework.") + (license license:bsd-3))) + (define-public python-pyega3 (deprecated-package "python-pyega3" python-ega-download-client)) =20 --=20 2.45.1