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gnu: Move all snakemake variants to python-science.

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* gnu/packages/python-xyz.scm (snakemake-5, snakemake-6, snakemake-7):
Move from here ...
* gnu/packages/python-science.scm: ... to here.

Change-Id: Ia771b316049f375183025e7617e6d0ddf06f99ff
This commit is contained in:
Sharlatan Hellseher 2025-05-26 17:36:37 +01:00
parent 127f232d1d
commit 74d1cf2583
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2 changed files with 271 additions and 271 deletions
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271
gnu/packages/python-science.scm
View file

@ -5004,6 +5004,277 @@ 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-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))))
;;;
;;; 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

271
gnu/packages/python-xyz.scm
View file

@ -15155,277 +15155,6 @@ 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")