rekado pushed a commit to branch master
in repository guix.
commit bbbbfe5751881bec1e0d664ecbf1e9d5d1579cde
Author: Ricardo Wurmus <[email protected]>
AuthorDate: Sun Jan 12 12:52:34 2025 +0100
gnu: instrain: Update to 1.9.0.
* gnu/packages/bioinformatics.scm (instrain): Update to 1.9.0.
[source]: Fetch git repository.
[build-system]: Use pyproject-build-system.
[arguments]: Disable tests.
[inputs]: Move all from here...
[propagated-inputs]: ...to here; remove python-boto3, python-numba,
python-scikit-learn, and python-drep.
[native-inputs]: Add python-boto3, python-setuptools, and python-wheel.
Change-Id: Ied1e909a6b22518908b95a43b8db5f35bd6c6ac6
---
gnu/packages/bioinformatics.scm | 40 +++++++++++++++++++++++++---------------
1 file changed, 25 insertions(+), 15 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2ad3fb87a4..72bb057a1a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -19055,44 +19055,54 @@ set.")
(define-public instrain
(package
(name "instrain")
- (version "1.5.4")
+ (version "1.9.0")
(source
(origin
- (method url-fetch)
- (uri (pypi-uri "inStrain" version))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/MrOlm/instrain";)
+ ;; There are no tags.
+ (commit "168f3f777b45139a9f6099f68974105b45e2d8ba")))
+ (file-name (git-file-name name version))
(sha256
(base32
- "05w1lw75x4lwkzg4qpi055g7hdjp9rnc4ksbxg2hfgksq9djk0hx"))))
- (build-system python-build-system)
+ "1wc69ggyiacm1slb678239lqmf1g5dlb4alwsbp14gi6393gj9fg"))))
+ (build-system pyproject-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
+ (list
+ ;; Tests assume that test files exist (they don't) and are located in
+ ;; the developer's home directory.
+ #:tests? #false
+ #:phases
+ '(modify-phases %standard-phases
(add-after 'unpack 'patch-relative-imports
(lambda _
+ (substitute* (find-files "test/tests" "test_.*\\.py")
+ (("from test_utils import BTO")
+ "from .test_utils import BTO")
+ (("import test_utils") "from . import test_utils"))
(substitute* "docker/run_instrain.py"
(("from s3_utils")
"from .s3_utils")
(("from job_utils")
"from .job_utils")))))))
- (inputs
+ (propagated-inputs
(list python-biopython-1.73
- python-boto3
python-h5py
python-lmfit
python-matplotlib
python-networkx
- python-numba
python-numpy
python-pandas
python-psutil
python-pysam
- python-scikit-learn
python-seaborn
- python-tqdm
- ;; drep is needed for deprecated plot utilities
- python-drep))
+ python-tqdm))
(native-inputs
- (list python-pytest))
+ (list python-boto3
+ python-pytest
+ python-setuptools
+ python-wheel))
(home-page "https://github.com/MrOlm/inStrain";)
(synopsis "Calculation of strain-level metrics")
(description
