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authorEfraim Flashner2020-07-19 04:22:08 -0500
committerEfraim Flashner2020-07-19 04:22:08 -0500
commit632dfa25516ce98026cbad3e7b66ed4360b9e0c1 (patch)
tree68dbff2bb29fb7db0c8c3052c021d27dacdc17e8
parent22af6bde5aa62b7f022fc1e76b413f3d7a2f3bc2 (diff)
downloadguix-bioinformatics-632dfa25516ce98026cbad3e7b66ed4360b9e0c1.tar.gz
gn: Update cwltool to 3.0.20200710214758
-rw-r--r--gn/packages/cwl.scm126
-rw-r--r--gn/packages/python.scm23
2 files changed, 85 insertions, 64 deletions
diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm
index be531f6..938cbe3 100644
--- a/gn/packages/cwl.scm
+++ b/gn/packages/cwl.scm
@@ -1,91 +1,89 @@
-;; Experimental packaging for the Common Workflow Language (started by Bruno)
-
(define-module (gn packages cwl)
#:use-module ((guix licenses) #:prefix license:)
+ #:use-module (gn packages python)
+ #:use-module (guix download)
+ #:use-module (guix packages)
+ #:use-module (guix build-system python)
#:use-module (gnu packages)
#:use-module (gnu packages check)
- #:use-module (gnu packages databases)
- #:use-module (gnu packages python)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages node)
#:use-module (gnu packages rdf)
#:use-module (gnu packages serialization)
#:use-module (gnu packages time)
- #:use-module (gnu packages version-control)
- #:use-module (gnu packages xml)
- #:use-module (gn packages python)
- #:use-module (guix download)
- #:use-module (guix packages)
- #:use-module (guix git-download)
- #:use-module (guix utils)
- ; #:use-module (guix build-system gnu)
- #:use-module (guix build-system python)
- ; #:use-module (guix build-system trivial)
- #:use-module (srfi srfi-1))
+ #:use-module (gnu packages xml))
-(define-public cwltool ; guix: needs work
- (let ((commit "15539fba76993f951af9eba913bea6d677c74005"))
+(define-public cwltool
(package
(name "cwltool")
- (version "1.0.20181012180214")
+ (version "3.0.20200710214758")
(source
(origin
- ; (method url-fetch)
- ; (uri (string-append
- ; "https://pypi.python.org/packages/source/c/cwltool/cwltool-"
- ; version
- ; ".tar.gz"))
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/genenetwork/cwltool.git") ;; my repo for Python 3.7
- (commit commit)))
- (file-name (git-file-name name (string-append version "-" (string-take commit 7))))
+ (method url-fetch)
+ (uri (pypi-uri "cwltool" version))
(sha256
- (base32
- "1qwfa82car7477sy0cb5bj4964w7zq7dcw2bdcls6c2i9qdp0586"))))
+ (base32
+ "1qbqkhinkhzg98jf24d5gnafsw23kng76rbi2hfvzl18bdsp1zz5"))))
(build-system python-build-system)
- (propagated-inputs ; a lot of these are used for testing
- `(("git" ,git)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'loosen-version-restrictions
+ (lambda _
+ (substitute* "setup.py"
+ (("== 1.5.1") ">=1.5.1"))
+ #t))
+ (add-after 'unpack 'modify-tests
+ (lambda _
+ ;; Tries to connect to the internet.
+ (delete-file "tests/test_udocker.py")
+ (substitute* "tests/test_http_input.py"
+ (("https://raw.githubusercontent.com/common-workflow-language/cwltool/main")
+ "."))
+ (substitute* "tests/test_load_tool.py"
+ (("def test_load_graph_fragment_from_packed")
+ "@pytest.mark.skip(reason=\"Disabled by Guix\")\ndef test_load_graph_fragment_from_packed"))
+ (substitute* "tests/test_examples.py"
+ (("def test_env_filtering")
+ "@pytest.mark.skip(reason=\"Disabled by Guix\")\ndef test_env_filtering"))
+ ;; Tries to use cwl-runners.
+ (substitute* "tests/test_examples.py"
+ (("def test_v1_0_arg_empty_prefix_separate_false")
+ "@pytest.mark.skip(reason=\"Disabled by Guix\")\ndef test_v1_0_arg_empty_prefix_separate_false"))
+ #t)))))
+ (propagated-inputs
+ `(;; does this need to be proagated?
("node" ,node)
+
("python-bagit" ,python-bagit)
- ("python-arcp" ,python-arcp)
- ("python-setuptools" ,python-setuptools)
- ("python-dateutil" ,python-dateutil)
- ("python-pytest-cov" ,python-pytest-cov)
+ ("python-coloredlogs" ,python-coloredlogs)
+ ("python-mypy-extensions" ,python-mypy-extensions)
("python-prov" ,python-prov)
- ("python-pytest-runner" ,python-pytest-runner)
+ ("python-psutil" ,python-psutil)
("python-rdflib" ,python-rdflib)
- ("python-pyparsing" ,python-pyparsing)
- ("python-pytest-mock" ,python-pytest-mock)
- ("python-mock" ,python-mock)
- ("python-subprocess32" ,python-subprocess32)
+ ("python-requests" ,python-requests)
("python-ruamel.yaml" ,python-ruamel.yaml)
+ ("python-schema-salad" ,python-schema-salad-7)
+ ("python-setuptools" ,python-setuptools)
+ ("python-shellescape" ,python-shellescape)
+ ("python-typing-extensions" ,python-typing-extensions)))
+ (native-inputs
+ `(("python-arcp" ,python-arcp)
("python-cachecontrol" ,python-cachecontrol-0.11)
+ ("python-dateutil" ,python-dateutil)
+ ("python-humanfriendly" ,python-humanfriendly)
("python-lxml" ,python-lxml)
- ("python-mypy-extensions" ,python-mypy-extensions)
- ("python-mistune" ,python-mistune)
+ ("python-mock" ,python-mock)
("python-networkx" ,python-networkx)
- ("python-schema-salad" ,python-schema-salad)
- ("python-html5lib" ,python-html5lib)
- ("python-rdflib-jsonld" ,python-rdflib-jsonld)
- ("python-scandir" ,python-scandir)
- ("python-psutil" ,python-psutil)
- ))
- ; (arguments `(#:tests? #f)) ;; CWL includes no tests.
- (arguments
- `(;#:phases
- ; (modify-phases %standard-phases
- ; (replace 'check
- ; (lambda* (#:key inputs outputs #:allow-other-keys)
- ; (invoke "python" "-m" "pytest")
- ; )))
- #:tests? #f)) ; Disable for now
-
+ ("python-pytest" ,python-pytest)
+ ("python-pytest-cov" ,python-pytest-cov)
+ ("python-pytest-mock" ,python-pytest-mock)
+ ("python-pytest-runner" ,python-pytest-runner)
+ ("python-rdflib-jsonld" ,python-rdflib-jsonld)))
(home-page
- "https://github.com/common-workflow-language/common-workflow-language")
- (synopsis
- "Common workflow language reference implementation")
+ "https://github.com/common-workflow-language/common-workflow-language")
+ (synopsis "Common workflow language reference implementation")
(description
- "Common workflow language reference implementation")
- (license license:asl2.0))))
+ "Common workflow language reference implementation.")
+ (license license:asl2.0)))
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 7be6b4f..3e6b60e 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -1176,6 +1176,29 @@ generation, and transformation to RDF. Salad provides a bridge between document
and record oriented data modeling and the Semantic Web.")
(license license:asl2.0)))
+(define-public python-schema-salad-7
+ (package
+ (inherit python-schema-salad)
+ (name "python-schema-salad")
+ (version "7.0.20200612160654")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "schema-salad" version))
+ (sha256
+ (base32
+ "15ma3lb6fkfc6sj75hnmmg0jj8q3pc5yrlyx15lpdd4dcp2jc39s"))))
+ (propagated-inputs
+ `(("python-cachecontrol" ,python-cachecontrol)
+ ("python-lockfile" ,python-lockfile)
+ ("python-mistune" ,python-mistune)
+ ("python-rdflib" ,python-rdflib)
+ ("python-rdflib-jsonld" ,python-rdflib-jsonld)
+ ("python-requests" ,python-requests)
+ ("python-ruamel.yaml" ,python-ruamel.yaml)
+ ("python-setuptools" ,python-setuptools)
+ ("python-typing-extensions" ,python-typing-extensions)))))
+
(define-public python-cfgraph
(package
(name "python-cfgraph")