Package: guix-patches;
Reported by: Nicolas Graves <ngraves <at> ngraves.fr>
Date: Fri, 7 Mar 2025 18:51:02 UTC
Severity: normal
Tags: patch
Done: Steve George <steve <at> futurile.net>
Bug is archived. No further changes may be made.
View this message in rfc822 format
From: Nicolas Graves <ngraves <at> ngraves.fr> To: 76835 <at> debbugs.gnu.org Cc: Nicolas Graves <ngraves <at> ngraves.fr> Subject: [bug#76835] [PATCH v3 38/40] gnu: snakemake-7: Move to (gnu packages python-science). Date: Mon, 10 Mar 2025 03:16:43 +0100
* gnu/packages/python-xyz.scm (snakemake-7): Move from here…
* gnu/packages/python-science.scm (snakemake-7): …to here.
Inherit from snakemake <at> 8.
---
gnu/packages/python-science.scm | 70 +++++++++++++++++++++
gnu/packages/python-xyz.scm | 104 --------------------------------
2 files changed, 70 insertions(+), 104 deletions(-)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 7ccd991478..5acead6523 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -4532,6 +4532,76 @@ (define-public snakemake
Python style, together with a fast and comfortable execution environment.")
(license license:expat)))
+(define-public snakemake-7
+ (package
+ (inherit snakemake)
+ (name "snakemake")
+ (version "7.7.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/snakemake/snakemake")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1qrqbmx4cbis0wxr6dl2rdjv9v627sbirsz6v5c31vlbqwkvs04q"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (substitute-keyword-arguments (package-arguments snakemake)
+ ((#:test-flags test-flags)
+ #~(list
+ ;; We don't care about lints.
+ "--ignore=tests/test_linting.py"
+ ;; These tests attempt to change S3 buckets on AWS and fail
+ ;; because there are no AWS credentials.
+ "--ignore=tests/test_tibanna.py"
+ ;; It's a similar story with this test, which requires access
+ ;; to the Google Storage service.
+ "--ignore=tests/test_google_lifesciences.py"))
+ ((#:phases phases)
+ #~(modify-phases #$phases
+ (delete 'avoid-assets-download)
+ ;; No longer needed with 7.15.2+
+ (add-after 'unpack 'tabulate-compatibility
+ (lambda _
+ (substitute* "snakemake/dag.py"
+ (("\"job\": rule,")
+ "\"job\": rule.name,"))))))))
+ (propagated-inputs
+ (list python-appdirs
+ python-configargparse
+ python-connection-pool
+ python-datrie
+ python-docutils
+ python-filelock
+ python-gitpython
+ python-jinja2
+ python-jsonschema
+ python-nbformat
+ python-networkx
+ python-psutil
+ python-pulp
+ python-pyyaml
+ python-py-tes
+ python-ratelimiter
+ python-requests
+ python-retry
+ python-smart-open
+ python-stopit
+ python-tabulate
+ python-toposort
+ python-wrapt
+ python-yte))
+ (native-inputs
+ (list git-minimal
+ python-wrapper
+ python-pytest
+ python-pandas
+ python-requests-mock
+ python-setuptools
+ python-wheel))))
+
;;;
;;; Avoid adding new packages to the end of this file. To reduce the chances
;;; of a merge conflict, place them above by existing packages with similar
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 81b8386049..740e6cfd33 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -15082,110 +15082,6 @@ (define-public snakemake-6
python-setuptools
python-wheel))))
-(define-public snakemake-7
- (package
- (inherit snakemake-6)
- (name "snakemake")
- (version "7.7.0")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/snakemake/snakemake")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32 "1qrqbmx4cbis0wxr6dl2rdjv9v627sbirsz6v5c31vlbqwkvs04q"))))
- (build-system pyproject-build-system)
- (arguments
- (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.
- (add-after 'unpack 'call-wrapper-not-wrapped-snakemake
- (lambda* (#:key outputs #:allow-other-keys)
- (substitute* "snakemake/executors/__init__.py"
- (("self\\.get_python_executable\\(\\),")
- "")
- (("\"-m snakemake\"")
- (string-append "\"" #$output
- "/bin/snakemake" "\""))
- ;; The snakemake command produced by format_job_exec contains
- ;; references to /gnu/store. Prior to patching above that's
- ;; just a reference to Python; after patching it's a reference
- ;; to the snakemake executable.
- ;;
- ;; In Tibanna execution mode Snakemake arranges for a certain
- ;; Docker image to be deployed to AWS. It then passes its own
- ;; command line to Tibanna. This is misguided because it only
- ;; ever works if the local Snakemake command was run inside
- ;; the same Docker image. In the case of using Guix this is
- ;; never correct, so we need to replace the store reference.
- (("tibanna_args.command = command")
- (string-append
- "tibanna_args.command = command.replace('"
- #$output "/bin/snakemake', 'python3 -m snakemake')")))))
- ;; No longer needed with 7.15.2+
- (add-after 'unpack 'tabulate-compatibility
- (lambda _
- (substitute* "snakemake/dag.py"
- (("\"job\": rule,")
- "\"job\": rule.name,"))))
- (add-after 'unpack 'patch-version
- (lambda _
- (substitute* "setup.py"
- (("version=versioneer.get_version\\(\\)")
- (format #f "version=~s" #$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")
- ;; It's a similar story with this test, which requires access
- ;; to the Google Storage service.
- (delete-file "tests/test_google_lifesciences.py")
- (invoke "pytest")))))))
- (propagated-inputs
- (list python-appdirs
- python-configargparse
- python-connection-pool
- python-datrie
- python-docutils
- python-filelock
- python-gitpython
- python-jinja2
- python-jsonschema
- python-nbformat
- python-networkx
- python-psutil
- python-pulp
- python-pyyaml
- python-py-tes
- python-ratelimiter
- python-requests
- python-retry
- python-smart-open
- python-stopit
- python-tabulate
- python-toposort
- python-wrapt
- python-yte))
- (native-inputs
- (list git-minimal
- python-wrapper
- python-pytest
- python-pandas
- python-requests-mock
- python-setuptools
- python-wheel))))
-
(define-public python-pyqrcode
(package
(name "python-pyqrcode")
--
2.48.1
GNU bug tracking system
Copyright (C) 1999 Darren O. Benham,
1997,2003 nCipher Corporation Ltd,
1994-97 Ian Jackson.