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gnu: python-liana-py: Update to 1.6.0.

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* gnu/packages/bioinformatics.scm (python-liana-py): Update to 1.6.0.
  [arguments] <test-flags>: Skip more problematic tests. Adjust pathe
  for "--ignore" option.
  <phases>: Remove 'relax-requirements.
  [propagated-inputs]: Remove python-decoupler-py; add python-decoupler.
  [native-inputs]: Remove python-black, python-poetry-core, and
  python-pytest-cov; add python-hatchling.

Change-Id: Icfec6a217f828b5e68cccde88fc889b2ee3e32f3
This commit is contained in:
Sharlatan Hellseher 2025-08-07 17:07:25 +01:00
parent 962948f2a4
commit 702b64e41e
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1 changed files with 19 additions and 18 deletions
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@ -3139,16 +3139,16 @@ servers supporting the protocol.")
(define-public python-liana-py (define-public python-liana-py
(package (package
(name "python-liana-py") (name "python-liana-py")
(version "1.4.0") (version "1.6.0")
(source (origin (source (origin
(method git-fetch) (method git-fetch)
(uri (git-reference (uri (git-reference
(url "https://github.com/saezlab/liana-py") (url "https://github.com/saezlab/liana-py")
(commit version))) (commit (string-append "v" version))))
(file-name (git-file-name name version)) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"1kwbhfmsjhfc6m4kcp4zc2xgzg1qf16ywfkdamn868anwwrvjxzb")))) "1k6l371wd00m95l5pb2jsmzzxh5nc5v21fg2v0cslr9761q151r9"))))
(build-system pyproject-build-system) (build-system pyproject-build-system)
(arguments (arguments
(list (list
@ -3179,27 +3179,30 @@ servers supporting the protocol.")
" and not test_bivar_product" " and not test_bivar_product"
;; XXX unclear failure: large difference in data ;; XXX unclear failure: large difference in data
;; frames. ;; frames.
" and not test_aggregate_res") " and not test_aggregate_res"
;; XXX: ValueError: Only CSR and CSC matrices are
;; supported.
" and not test_bivar_nondefault"
" and not test_masked_spearman"
" and not test_vectorized_spearman"
" and not test_basic_interpolation"
" and not test_different_methods"
" and not test_fill_value"
" and not test_use_raw_layer_parameters")
;; These need the optional squidpy, which we don't have yet. ;; These need the optional squidpy, which we don't have yet.
"--ignore=liana/tests/test_misty.py" "--ignore=tests/test_misty.py"
;; These need the optional corneto. ;; These need the optional corneto.
"--ignore=liana/tests/test_causalnet.py" "--ignore=tests/test_causalnet.py"
;; Needs internet access. ;; Needs internet access.
"--ignore=liana/tests/test_orthology.py") "--ignore=tests/test_orthology.py")
#:phases #:phases
'(modify-phases %standard-phases '(modify-phases %standard-phases
(add-after 'unpack 'relax-requirements
(lambda _
;; Don't fail the sanity check when these optional inputs aren't
;; available.
(substitute* "pyproject.toml"
(("^pre-commit =.*") ""))))
;; Numba needs a writable directory to cache functions. ;; Numba needs a writable directory to cache functions.
(add-before 'build 'set-numba-cache-dir (add-before 'build 'set-numba-cache-dir
(lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp")))))) (lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
(propagated-inputs (list python-anndata (propagated-inputs (list python-anndata
python-cell2cell python-cell2cell
python-decoupler-py python-decoupler
python-hypothesis python-hypothesis
python-ipykernel python-ipykernel
python-ipython python-ipython
@ -3219,10 +3222,8 @@ servers supporting the protocol.")
python-tqdm python-tqdm
tzdata)) tzdata))
(native-inputs (native-inputs
(list python-black (list python-hatchling
python-poetry-core python-pytest))
python-pytest
python-pytest-cov))
(home-page "https://github.com/saezlab/liana-py") (home-page "https://github.com/saezlab/liana-py")
(synopsis "LIANA is a ligand-receptor analysis framework") (synopsis "LIANA is a ligand-receptor analysis framework")
(description "This is a Ligand-Receptor inference framework. The (description "This is a Ligand-Receptor inference framework. The