ryan77627/guix
1
0
Fork 0
mirror of https://git.in.rschanz.org/ryan77627/guix.git synced 2024-11-07 15:36:20 -05:00
Code Issues Projects Releases Packages Wiki Activity Actions

gnu: snakemake-6: Fix version reporting.

Browse source 
* gnu/packages/python-xyz.scm (snakemake-6)[arguments]: Add phase
'patch-version and use G-exp.
[build-system]: Use pyproject-build-system.
This commit is contained in:
Ricardo Wurmus 2023-08-01 08:17:27 +02:00
parent a3f4ccfebd
commit 896b40d2ca
No known key found for this signature in database
GPG key ID: 197A5888235FACAC
1 changed files with 30 additions and 22 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

52
gnu/packages/python-xyz.scm
View file

@ -11443,30 +11443,38 @@ (define-public snakemake-6
(file-name (git-file-name name version))
(sha256
(base32 "09yrpi9f86r9yvcm2dfjs5zy87c4j31bxama77kfd6y8yfrrjlai"))))
(build-system python-build-system)
(build-system pyproject-build-system)
(arguments
'(#:phases
(modify-phases %standard-phases
;; For cluster execution Snakemake will call Python. Since there is
;; no suitable GUIX_PYTHONPATH set, cluster execution will fail. We
;; fix this by calling the snakemake wrapper instead.
(list
#:phases
#~(modify-phases %standard-phases
;; For cluster execution Snakemake will call Python. Since there is
;; no suitable GUIX_PYTHONPATH set, cluster execution will fail. We
;; fix this by calling the snakemake wrapper instead.
;; XXX: There is another instance of sys.executable on line 692, but
;; it is not clear how to patch it.
(add-after 'unpack 'call-wrapper-not-wrapped-snakemake
(lambda* (#:key outputs #:allow-other-keys)
(substitute* "snakemake/executors/__init__.py"
(("\\{sys.executable\\} -m snakemake")
(string-append (assoc-ref outputs "out")
"/bin/snakemake")))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(setenv "HOME" "/tmp")
;; This test attempts to change S3 buckets on AWS and fails
;; because there are no AWS credentials.
(delete-file "tests/test_tibanna.py")
(invoke "pytest")))))))
;; XXX: There is another instance of sys.executable on line 692, but
;; it is not clear how to patch it.
(add-after 'unpack 'call-wrapper-not-wrapped-snakemake
(lambda* (#:key outputs #:allow-other-keys)
(substitute* "snakemake/executors/__init__.py"
(("\\{sys.executable\\} -m snakemake")
(string-append #$output "/bin/snakemake")))))
(add-after 'unpack 'patch-version
(lambda _
(substitute* "setup.py"
(("version=versioneer.get_version\\(\\)")
(format #f "version=~s" #$version)))
(substitute* '("snakemake/_version.py"
"versioneer.py")
(("0\\+unknown") #$version))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(setenv "HOME" "/tmp")
;; This test attempts to change S3 buckets on AWS and fails
;; because there are no AWS credentials.
(delete-file "tests/test_tibanna.py")
(invoke "pytest")))))))
(propagated-inputs
(list python-appdirs
python-configargparse