diff options
| author | Sharlatan Hellseher <sharlatanus@gmail.com> | 2025-10-01 15:00:33 +0100 |
|---|---|---|
| committer | Sharlatan Hellseher <sharlatanus@gmail.com> | 2025-10-01 15:02:06 +0100 |
| commit | e5579dc5de77fe1b3d595ac514c09cf86d4310cb (patch) | |
| tree | d99b376e0be0792fe804ffcabfff3fa66a727ce5 /gnu | |
| parent | 2605ef607e707be2158868e994b065bc8ae2a6dc (diff) | |
gnu: umi-tools: Fix tests.
* gnu/packages/bioinformatics.scm (umi-tools)[arguments] <test-flags>:
Skip style and broken test files.
<phases>: Add 'fix-bash-path and 'build-extensions.
[native-inputs]: Remove python-wheel; add python-cython, python-pyaml,
and python-pytest.
Change-Id: I96da9eaed696bc94999e41cffe88a47500542754
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 25 |
1 files changed, 22 insertions, 3 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3cd2c838bf..9ba3e900a0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -21816,16 +21816,32 @@ throughput chromatin profiles. Typical use cases include: (package (name "umi-tools") (version "1.1.6") + ;; TODO: Delete generated Cython C files. (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/CGATOxford/UMI-tools") - (commit (string-append "v" version)))) + (url "https://github.com/CGATOxford/UMI-tools") + (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "1liykfj4msvcgk8an5qq802jcxwlijqxrvijipqj1pwpxqzl9qnh")))) (build-system pyproject-build-system) + (arguments + (list + #:test-flags + #~(list "--ignore=tests/test_style.py" + "--ignore=step1_unit_test.py") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-bash-path + (lambda _ + (substitute* "tests/test_umi_tools.py" + (("/bin/bash") + (which "sh"))))) + (add-before 'check 'build-extensions + (lambda _ + (invoke "python" "setup.py" "build_ext" "--inplace")))))) (inputs (list python-pandas python-future @@ -21836,7 +21852,10 @@ throughput chromatin profiles. Typical use cases include: python-scipy python-pysam)) (native-inputs - (list python-setuptools python-wheel)) + (list python-cython + python-pyaml + python-pytest + python-setuptools)) (home-page "https://github.com/CGATOxford/UMI-tools") (synopsis "Tools for analyzing unique modular identifiers") (description "This package provides tools for dealing with @dfn{Unique |