summaryrefslogtreecommitdiff
path: root/gnu/packages/python-xyz.scm
diff options
context:
space:
mode:
Diffstat (limited to 'gnu/packages/python-xyz.scm')
-rw-r--r--gnu/packages/python-xyz.scm271
1 files changed, 0 insertions, 271 deletions
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 2e8ff4b297..8e3b5e0046 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -15179,277 +15179,6 @@ approach.")
"This is a Python package for easy throttling with asyncio support.")
(license license:expat)))
-(define-public snakemake-5
- (package
- (name "snakemake")
- (version "5.32.2")
- (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 "0nxp4z81vykv07kv2b6zrwk7ns8s10zqsb7vcignp8695yq3nlcm"))))
- (build-system pyproject-build-system)
- (arguments
- (list
- #:test-flags
- '(list
- ;; We have no TES support.
- "--ignore=tests/test_tes.py"
- ;; This test attempts to change S3 buckets on AWS and fails
- ;; 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"
- ;; Unclear failure.
- "-k" "not test_lint[long_run-positive]")
- #:phases
- #~(modify-phases %standard-phases
- (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))))
- ;; For cluster execution Snakemake will call Python. Since there is
- ;; no suitable PYTHONPATH set, cluster execution will fail. We fix
- ;; this by calling the snakemake wrapper instead.
- (add-after 'unpack 'call-wrapper-not-wrapped-snakemake
- (lambda _
- (substitute* "snakemake/executors/__init__.py"
- (("\\{sys.executable\\} -m snakemake")
- (string-append #$output "/bin/snakemake")))))
- (add-before 'check 'pre-check
- (lambda _ (setenv "HOME" "/tmp"))))))
- (propagated-inputs
- (list python-appdirs
- python-configargparse
- python-datrie
- python-docutils
- python-gitpython
- python-jinja2
- python-jsonschema
- python-nbformat
- python-networkx
- python-psutil
- python-pulp
- python-pyyaml
- python-ratelimiter
- python-requests
- python-toposort
- python-wrapt))
- (native-inputs
- (list git-minimal
- python-wrapper
- python-pytest
- python-pandas
- python-requests-mock
- python-setuptools
- python-wheel))
- (home-page "https://snakemake.readthedocs.io")
- (synopsis "Python-based execution environment for make-like workflows")
- (description
- "Snakemake aims to reduce the complexity of creating workflows by
-providing a clean and modern domain specific specification language (DSL) in
-Python style, together with a fast and comfortable execution environment.")
- (license license:expat)))
-
-(define-public snakemake-6
- (package
- (inherit snakemake-5)
- (name "snakemake")
- (version "6.15.5")
- (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 "09yrpi9f86r9yvcm2dfjs5zy87c4j31bxama77kfd6y8yfrrjlai"))))
- (build-system pyproject-build-system)
- (arguments
- (list
- #:test-flags
- '(list
- ;; This test attempts to change S3 buckets on AWS and fails
- ;; because there are no AWS credentials.
- "--ignore=tests/test_tibanna.py"
- ;; Unclear failure.
- "-k" "not test_lint[long_run-positive]")
- #: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 #$output "/bin/snakemake")))))
- (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))))
- (add-before 'check 'pre-check
- (lambda _ (setenv "HOME" "/tmp"))))))
- (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-smart-open
- python-stopit
- python-tabulate
- python-toposort
- python-wrapt))
- (native-inputs
- (list git-minimal
- python-wrapper
- python-pytest
- python-pandas
- python-requests-mock
- python-setuptools
- python-wheel))))
-
-(define-public snakemake-7
- (package
- (inherit snakemake-6)
- (name "snakemake")
- (version "7.32.4")
- (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 "1d5hizai89k1glfqfkvf1ghj0l7wm8il6gl5pfwk2gkza87yka6d"))))
- (build-system pyproject-build-system)
- (arguments
- (list
- #:test-flags
- ;; This test attempts to change S3 buckets on AWS and fails
- ;; because there are no AWS credentials.
- '(list "--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"
- "--ignore-glob=tests/test_conda_python_3_7_script/*"
- ;; We don't have a slurm installation in the build environment
- "--ignore=tests/test_slurm.py")
- #: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')")))))
- (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))))
- (add-before 'check 'pre-check
- (lambda _ (setenv "HOME" "/tmp"))))))
- (propagated-inputs
- (list python-appdirs
- python-configargparse
- python-connection-pool
- python-datrie
- python-docutils
- python-filelock
- python-gitpython
- python-humanfriendly
- python-jinja2
- python-jsonschema
- python-nbformat
- python-networkx
- python-psutil
- python-pulp
- python-pyyaml
- python-py-tes
- python-requests
- python-retry
- python-reretry
- python-smart-open
- python-stopit
- python-tabulate
- python-throttler
- 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")
generated by cgit v1.2.3 (git 2.50.1) at 2025-11-18 03:13:18 +0000