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-rw-r--r--gn/packages/cwl.scm22
-rw-r--r--gn/packages/python.scm54
2 files changed, 69 insertions, 7 deletions
diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm
index 9b75c2b..2642f90 100644
--- a/gn/packages/cwl.scm
+++ b/gn/packages/cwl.scm
@@ -7,6 +7,7 @@
#:use-module (gnu packages python)
#:use-module (gnu packages python-web)
#:use-module (gnu packages rdf)
+ #:use-module (gnu packages serialization)
#:use-module (gn packages python)
#:use-module (guix download)
#:use-module (guix packages)
@@ -17,9 +18,9 @@
; #:use-module (guix build-system trivial)
#:use-module (srfi srfi-1))
-(define-public python-cwltool ; guix: needs work
+(define-public cwltool ; guix: needs work
(package
- (name "python-cwltool")
+ (name "cwltool")
(version "1.0.20181012180214")
(source
(origin
@@ -36,18 +37,30 @@
`(("python-bagit" ,python-bagit)
("python-setuptools" ,python-setuptools)
("python-pytest-cov" ,python-pytest-cov)
+ ("python-prov" ,python-prov)
("python-pytest-runner" ,python-pytest-runner)
("python-rdflib" ,python-rdflib)
("python-typing-extensions" ,python-typing-extensions)
("python-pyparsing" ,python-pyparsing)
("python-subprocess32" ,python-subprocess32)
+ ("python-ruamel.yaml" ,python-ruamel.yaml)
+ ("python-cachecontrol" ,python-cachecontrol)
+ ("python-mypy-extensions" ,python-mypy-extensions)
))
(propagated-inputs
`(("python-schema-salad" ,python-schema-salad)
- ("python-prov" ,python-prov)
("python-html5lib" ,python-html5lib)
))
; (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
+
(home-page
"https://github.com/common-workflow-language/common-workflow-language")
(synopsis
@@ -56,9 +69,6 @@
"Common workflow language reference implementation")
(license license:asl2.0)))
-(define-public python2-cwltool
- (package-with-python2 python-cwltool))
-
(define-public python-schema-salad
(package
(name "python-schema-salad")
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index ef30812..808eb9d 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -146,7 +146,7 @@ functions.")
"1m6y04qmig0b5hzb35lnaw3d2yfydb7alyr1579yblvgs3da6j7j"))))
(build-system python-build-system)
(inputs
- `(("python-setuptools-scm" ,python-setuptools-scm)
+ `(("python-setuptools-scm" ,python-setuptools-scm)
("python-coverage" ,python-coverage)
("python-mock" ,python-mock)
))
@@ -711,3 +711,55 @@ the older versions.")
(description "This is a python library for generating html from classes.")
(home-page "https://github.com/srittau/python-htmlgen")
(license license:expat)))
+
+(define-public python-version
+(let ((commit "e5aadc720bb74c535f29e5a2de5cd9697efe8d7c"))
+(package
+ (name "python-version")
+ (version "0.1.2")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ ; (url "https://github.com/genenetwork/pylmm.git")
+ (url "https://github.com/keleshev/version.git") ; version not in pypi
+ (commit commit)))
+ (file-name (string-append name "-" commit))
+ (sha256
+ (base32
+ "1rc8kf72v180qlygkh1y0jwv2fxqpx7n97bqfhbwgnn31iwai9g3"))))
+ (build-system python-build-system)
+ (build-system python-build-system)
+ (propagated-inputs
+ `(
+ ("python-more-itertools" ,python-more-itertools)
+ ("python-pytest" ,python-pytest)))
+ (home-page "http://github.com/halst/version")
+ (synopsis "Implementation of semantic version")
+ (description
+ "Implementation of semantic version")
+ (license license:expat)
+)))
+
+(define-public python-mypy-extensions
+(package
+ (name "python-mypy-extensions")
+ (version "0.4.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "mypy_extensions" version))
+ (sha256
+ (base32
+ "04h8brrbbx151dfa2cvvlnxgmb5wa00mhd2z7nd20s8kyibfkq1p"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-version" ,python-version)
+ ("python-typing" ,python-typing)))
+ (home-page "http://www.mypy-lang.org/")
+ (synopsis
+ "Experimental type system extensions for programs checked with the mypy typechecker.")
+ (description
+ "Experimental type system extensions for programs checked with the mypy typechecker.")
+ (license #f))
+)