GNU bug report logs - #71670
[PATCH 0/2] bioinformatics: Add python-muon

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: guix <at> mawumag.com
To: guix-patches <at> gnu.org
Cc: tanguy <at> bioneland.org, me <at> bonfacemunyoki.com, lars <at> 6xq.net,
 Ricardo Wurmus <rekado <at> elephly.net>, jgart <at> dismail.de, marius <at> gnu.org,
 sharlatanus <at> gmail.com
Subject: [PATCH 0/2] bioinformatics: Add python-muon
Date: Thu, 20 Jun 2024 08:45:24 +0000

I am adding the packages python-muon and python-mofapy2 (as a muon
dependency).

Muon is a multi-omics analysis framework and is part of the scverse.

I had to modify a couple of tests slightly (explained in the comments).

Marco Baggio (2):
  bioinformatics: Add python-mofapy2
  bioinformatics: Add python-muon

 gnu/packages/bioinformatics.scm | 93 +++++++++++++++++++++++++++++++++
 1 file changed, 93 insertions(+)


base-commit: e32e3d0a03dc17c4c54a91aad053c9036998b601
--
2.45.1

Message #8 received at 71670 <at> debbugs.gnu.org (full text, mbox):

From: guix <at> mawumag.com
To: 71670 <at> debbugs.gnu.org
Cc: tanguy <at> bioneland.org, me <at> bonfacemunyoki.com, lars <at> 6xq.net,
 Ricardo Wurmus <rekado <at> elephly.net>, jgart <at> dismail.de, marius <at> gnu.org,
 sharlatanus <at> gmail.com
Subject: [PATCH 1/2] bioinformatics: Add python-mofapy2
Date: Thu, 20 Jun 2024 08:50:03 +0000

Change-Id: Ide92878258511b3daf4e56d5faa94d190fdee62f
---
 gnu/packages/bioinformatics.scm | 38 +++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index cdda029809..37fa1727cb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4443,6 +4443,44 @@ (define-public python-mudata
 omics data.")
     (license license:bsd-3)))
 
+(define-public python-mofapy2
+  (package
+    (name "python-mofapy2")
+    (version "0.7.1")
+    (source
+     (origin
+       ;; The tarball from PyPi doesn't include tests.
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/bioFAM/mofapy2")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0ahhnqk6gjrhyq286mrd5n7mxcv8l6040ffsawbjx9maqx8wbam0"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'disable-failing-tests
+            (lambda _
+              ;; cupy is an optional dependency, which
+              ;; itself has nonfree dependencies (CUDA)
+              (delete-file "mofapy2/notebooks/test_cupy.py"))))))
+    (propagated-inputs (list python-anndata
+                             python-pandas
+                             python-scipy
+                             python-numpy
+                             python-scikit-learn
+                             python-h5py))
+    (native-inputs (list python-poetry-core
+                         python-pytest))
+    (home-page "https:/biofam.github.io/MOFA2/")
+    (synopsis "Multi-omics factor analysis")
+    (description "Multi-omics factor analysis.")
+    (license license:lgpl3)))
+
 (define-public python-pyega3
   (deprecated-package "python-pyega3" python-ega-download-client))
 
-- 
2.45.1

Message #11 received at 71670 <at> debbugs.gnu.org (full text, mbox):

From: guix <at> mawumag.com
To: 71670 <at> debbugs.gnu.org
Cc: sharlatanus <at> gmail.com, me <at> bonfacemunyoki.com, lars <at> 6xq.net,
 Ricardo Wurmus <rekado <at> elephly.net>, jgart <at> dismail.de, marius <at> gnu.org,
 tanguy <at> bioneland.org
Subject: [PATCH 2/2] bioinformatics: Add python-muon
Date: Thu, 20 Jun 2024 08:51:12 +0000

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)))
 
+(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=\"\")\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))
 
-- 
2.45.1

Message #16 received at 71670-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: guix <at> mawumag.com
Cc: tanguy <at> bioneland.org, me <at> bonfacemunyoki.com, lars <at> 6xq.net, jgart <at> dismail.de,
 marius <at> gnu.org, sharlatanus <at> gmail.com, 71670-done <at> debbugs.gnu.org
Subject: Re: [PATCH 2/2] bioinformatics: Add python-muon
Date: Mon, 01 Jul 2024 16:21:18 +0200

guix <at> mawumag.com writes:

> +(define-public python-muon

Thank you for the patches!  I've applied them with minor changes.
(Commit ddce6b2303dc6064ca50b4fbd53389e50faa115d.)

-- 
Ricardo

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