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

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

[Navid Afkhami]

* 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

[bug#64802] [PATCH 2/2] gnu: python-decoupler-py: Update to (git-version 1.5.0 revision commit).

[Navid Afkhami]

* gnu/packages/bioinformatics.scm (python-decoupler-py): Update to (git-version 1.5.0 revision commit).
---
 gnu/packages/bioinformatics.scm | 49 +++++++++++++++++----------------
 1 file changed, 25 insertions(+), 24 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a0ae298a2c..d39a47d694 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1680,11 +1680,11 @@ (define-public python-cmseq
 
 (define-public python-decoupler-py
   ;; This latest commit fixes a bug in test_omnip.py.
-  (let ((commit "b84c524ec4a9280a56c0db963e2c7b010316ce8f")
+  (let ((commit "459b235348ddd9135217a3722d9dd1caa9a14ace")
         (revision "1"))
     (package
       (name "python-decoupler-py")
-      (version (git-version "1.3.1" revision commit))
+      (version (git-version "1.5.0" revision commit))
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
@@ -1693,30 +1693,31 @@ (define-public python-decoupler-py
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "0d74yr5jqc52vcxaca84kxqw7m5rbazpmvnrcp2y4xxrj6yr1sfc"))))
+                  "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"
-                              ;; 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"))))))
+       (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_collectri"
+                                  " and not test_get_ksn_omnipath"
+                                  ;; 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
-- 
2.34.1

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

[Ricardo Wurmus]

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

-- 
Ricardo

bug#64802: [PATCH 2/2] gnu: python-decoupler-py: Update to (git-version 1.5.0 revision commit).

[Ricardo Wurmus]

Thank you for the patch!  I pushed it with minor changes to the
formatting and the git commit message.

-- 
Ricardo