GNU bug report logs - #64801
[PATCH 1/2] gnu: Add python-liana-py.

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
Subject: bug#64801: closed ([PATCH 1/2] gnu: Add python-liana-py.)
Date: Mon, 31 Jul 2023 10:23:02 +0000

[Message part 1 (text/plain, inline)]

Your bug report

#64801: [PATCH 1/2] gnu: Add python-liana-py.

which was filed against the guix-patches package, has been closed.

The explanation is attached below, along with your original report.
If you require more details, please reply to 64801 <at> debbugs.gnu.org.

-- 
64801: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=64801
GNU Bug Tracking System
Contact help-debbugs <at> gnu.org with problems

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From: Ricardo Wurmus <rekado <at> elephly.net>
To: 64801-done <at> debbugs.gnu.org
Subject: [PATCH 1/2] gnu: Add python-liana-py.
Date: Mon, 31 Jul 2023 12:22:19 +0200

Thank you for the patch!  I pushed it with minor adjustments.

-- 
Ricardo

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From: Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Subject: [PATCH 1/2] gnu: Add python-liana-py.
Date: Sun, 23 Jul 2023 12:41:46 +0200

* gnu/packages/bioinformatics.scm (python-liana-py): New variable.
---
 gnu/packages/bioinformatics.scm | 58 +++++++++++++++++++++++++++++++++
 1 file changed, 58 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 864c200707..a0ae298a2c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1863,6 +1863,64 @@ (define-public python-htsget
 servers supporting the protocol.")
    (license license:asl2.0)))
 
+(define-public python-liana-py
+  (package
+    (name "python-liana-py")
+    (version "0.1.9")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/saezlab/liana-py")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "00lqrmi38wmdpjlcafgmrnkwsbp0yvm2rya6qs8y6jfizww9ff8i"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list #:test-flags '(list "-k"
+                               ;; These tests require internet access.
+                               (string-append "not test_generate_lr_resource"
+                                " and not test_generate_nondefault_lr_resource"))
+           #:phases '(modify-phases %standard-phases
+                       (add-before 'check 'set-home
+                         ;; Some tests require home directory to be set.
+                         (lambda _
+                           (setenv "HOME" "/tmp")))
+                       ;; Numba needs a writable directory to cache functions.
+                       (add-before 'build 'set-numba-cache-dir
+                         (lambda _
+                           (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
+    (propagated-inputs (list python-anndata
+                             python-black
+                             python-cell2cell
+                             python-decoupler-py
+                             python-hypothesis
+                             python-ipykernel
+                             python-ipython
+                             python-mofax
+                             python-mudata
+                             python-nbconvert
+                             python-nbsphinx
+                             python-numpydoc
+                             python-omnipath
+                             python-pandas
+                             python-plotnine
+                             python-pypandoc
+                             python-scipy
+                             python-requests
+                             python-scanpy
+                             python-statsmodels
+                             python-tqdm
+                             tzdata))
+    (native-inputs (list python-pytest python-pytest-cov python-numpy))
+    (home-page "https://github.com/saezlab/liana-py")
+    (synopsis "LIANA is a ligand-receptor analysis framework")
+    (description "This is a Ligand-Receptor inference framework.
+The framework enables the use of any LR method
+with any resources.")
+    (license license:gpl3+)))
+
 (define-public python-logomaker
   (package
     (name "python-logomaker")

base-commit: 445a0359083388b5ee686e6e855f94a3aac5f79c
-- 
2.34.1

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