diff options
Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/cwl.scm | 61 | ||||
| -rw-r--r-- | gn/packages/python.scm | 7 |
2 files changed, 53 insertions, 15 deletions
diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm index 5a01dbf..245af84 100644 --- a/gn/packages/cwl.scm +++ b/gn/packages/cwl.scm @@ -4,6 +4,7 @@ #:use-module ((guix licenses) #:prefix license:) #: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 node) @@ -22,7 +23,7 @@ #:use-module (srfi srfi-1)) (define-public cwltool ; guix: needs work - (let ((commit "e12d36b6efbc5d4a6ff7b4fbfd7387bff8f72727")) + (let ((commit "15539fba76993f951af9eba913bea6d677c74005")) (package (name "cwltool") (version "1.0.20181012180214") @@ -35,12 +36,12 @@ ; ".tar.gz")) (method git-fetch) (uri (git-reference - (url "https://github.com/genenetwork/cwltool.git") + (url "https://github.com/genenetwork/cwltool.git") ;; my repo for Python 3.7 (commit commit))) - (file-name (git-file-name name version)) + (file-name (git-file-name name (string-append version "-" (string-take commit 7)))) (sha256 (base32 - "1zhba1hfizrw3bxfmhpjds92pj79hyyv5k7sglw24z52kg1in67p")))) + "1qwfa82car7477sy0cb5bj4964w7zq7dcw2bdcls6c2i9qdp0586")))) (build-system python-build-system) (propagated-inputs ; a lot of these are used for testing `(("git" ,git) @@ -66,7 +67,6 @@ ("python-schema-salad" ,python-schema-salad) ("python-html5lib" ,python-html5lib) ("python-rdflib-jsonld" ,python-rdflib-jsonld) - ("python-typing-extensions" ,python-typing-extensions) ("python-scandir" ,python-scandir) ("python-psutil" ,python-psutil) )) @@ -88,17 +88,56 @@ "Common workflow language reference implementation") (license license:asl2.0)))) +(define-public python-cachecontrol + (package + (name "python-cachecontrol") + (version "0.11.7") + (source + (origin + (method url-fetch) + ;; Pypi does not have tests. + (uri (string-append + "https://github.com/ionrock/cachecontrol/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1yfhwihx1b1xjsx0r19va2m0r2s91im03x4d7pwzp87368f2lkkp")))) + (build-system python-build-system) + (arguments + `(#:tests? #f)) ;; Recent version breaks on cherrypy + (native-inputs + `(("python-pytest" ,python-pytest) + ("python-redis" ,python-redis) + ("python-webtest" ,python-webtest) + ("python-mock" ,python-mock))) + (propagated-inputs + `(("python-requests" ,python-requests) + ("python-lockfile" ,python-lockfile))) + (home-page "https://github.com/ionrock/cachecontrol") + (synopsis "The httplib2 caching algorithms for use with requests") + (description "CacheControl is a port of the caching algorithms in +@code{httplib2} for use with @code{requests} session objects.") + (license license:asl2.0))) + + (define-public python-schema-salad + (let ((commit "eb85c3d49b99b7643e8a12248e2dc05504910c1e")) (package (name "python-schema-salad") (version "3.0.20181129082112") (source (origin - (method url-fetch) - (uri (pypi-uri "schema-salad" version)) - (sha256 - (base32 - "1xg70v82q053vz1sg8sc99alnkrm2kk05w6698vgmngl1767sk97")))) + ; (method url-fetch) + ; (uri (pypi-uri "schema-salad" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/genenetwork/schema_salad.git") ;; my repo for Python3.7 + (commit commit))) + (file-name (git-file-name name (string-append version "-" (string-take commit 7)))) + (sha256 + (base32 + "174f224zzjr0nbjlq3ypciyfijnibasysrgjswvx8yhan2dizlhr")))) (build-system python-build-system) (arguments `(#:tests? #f)) ;; CWL includes no tests. (inputs @@ -119,7 +158,7 @@ "Schema Annotations for Linked Avro Data (SALAD)") (description "Schema Annotations for Linked Avro Data (SALAD)") - (license license:asl2.0))) + (license license:asl2.0)))) ; (define-public python2-schema-salad ; (package-with-python2 python-schema-salad)) diff --git a/gn/packages/python.scm b/gn/packages/python.scm index 75f7cab..4cefe84 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -379,7 +379,7 @@ functions.") (define-public python-setuptools (package (name "python-setuptools") - (version "40.6.2") + (version "40.6.0") (source (origin (method url-fetch) @@ -753,9 +753,8 @@ the older versions.") (base32 "04h8brrbbx151dfa2cvvlnxgmb5wa00mhd2z7nd20s8kyibfkq1p")))) (build-system python-build-system) - (propagated-inputs - `(("python-version" ,python-version) - ("python-typing" ,python-typing))) + (inputs + `(("python-version" ,python-version))) (home-page "http://www.mypy-lang.org/") (synopsis "Experimental type system extensions for programs checked with the mypy typechecker.") |