* [bug#64801] [PATCH 1/2] gnu: Add python-liana-py.
@ 2023-07-23 10:41 Navid Afkhami
2023-07-23 10:41 ` [bug#64802] [PATCH 2/2] gnu: python-decoupler-py: Update to (git-version 1.5.0 revision commit) Navid Afkhami
2023-07-31 10:22 ` bug#64801: [PATCH 1/2] gnu: Add python-liana-py Ricardo Wurmus
0 siblings, 2 replies; 4+ messages in thread
From: Navid Afkhami @ 2023-07-23 10:41 UTC (permalink / raw)
To: 64801
* 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
^ permalink raw reply related [flat|nested] 4+ messages in thread* [bug#64802] [PATCH 2/2] gnu: python-decoupler-py: Update to (git-version 1.5.0 revision commit).
2023-07-23 10:41 [bug#64801] [PATCH 1/2] gnu: Add python-liana-py Navid Afkhami
@ 2023-07-23 10:41 ` Navid Afkhami
2023-07-31 10:22 ` bug#64802: " Ricardo Wurmus
2023-07-31 10:22 ` bug#64801: [PATCH 1/2] gnu: Add python-liana-py Ricardo Wurmus
1 sibling, 1 reply; 4+ messages in thread
From: Navid Afkhami @ 2023-07-23 10:41 UTC (permalink / raw)
To: 64802
* 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
^ permalink raw reply related [flat|nested] 4+ messages in thread* bug#64801: [PATCH 1/2] gnu: Add python-liana-py.
2023-07-23 10:41 [bug#64801] [PATCH 1/2] gnu: Add python-liana-py Navid Afkhami
2023-07-23 10:41 ` [bug#64802] [PATCH 2/2] gnu: python-decoupler-py: Update to (git-version 1.5.0 revision commit) Navid Afkhami
@ 2023-07-31 10:22 ` Ricardo Wurmus
1 sibling, 0 replies; 4+ messages in thread
From: Ricardo Wurmus @ 2023-07-31 10:22 UTC (permalink / raw)
To: 64801-done
Thank you for the patch! I pushed it with minor adjustments.
--
Ricardo
^ permalink raw reply [flat|nested] 4+ messages in thread
end of thread, other threads:[~2023-07-31 10:24 UTC | newest]
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2023-07-23 10:41 [bug#64801] [PATCH 1/2] gnu: Add python-liana-py Navid Afkhami
2023-07-23 10:41 ` [bug#64802] [PATCH 2/2] gnu: python-decoupler-py: Update to (git-version 1.5.0 revision commit) Navid Afkhami
2023-07-31 10:22 ` bug#64802: " Ricardo Wurmus
2023-07-31 10:22 ` bug#64801: [PATCH 1/2] gnu: Add python-liana-py Ricardo Wurmus
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