diff options
| -rw-r--r-- | gn/packages/cwl.scm | 61 | ||||
| -rw-r--r-- | gn/packages/edash.scm | 37 | ||||
| -rw-r--r-- | gn/packages/python.scm | 8 |
3 files changed, 88 insertions, 18 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/edash.scm b/gn/packages/edash.scm index 6324d3a..8d23a08 100644 --- a/gn/packages/edash.scm +++ b/gn/packages/edash.scm @@ -5,14 +5,17 @@ #:use-module (guix build-system trivial) #:use-module (guix build-system python) #:use-module (gnu packages web) + #:use-module (gnu packages base) #:use-module (gnu packages python) #:use-module (gnu packages python-web) + #:use-module (gnu packages python-xyz) #:use-module (gnu packages python-crypto) #:use-module (gnu packages compression) #:use-module (gnu packages time) #:use-module (gnu packages databases) #:use-module (gnu packages check) #:use-module (gn packages web) + #:use-module (gnu packages sqlite) #:use-module (gn packages python)) (define-public python-s3transfer-0.1.13 @@ -442,6 +445,30 @@ with the Specification.") "Connexion - API first applications with OpenAPI/Swagger and Flask") (license license:asl2.0))) +(define-public python-flask-cors + (package + (name "python-flask-cors") + (version "3.0.7") + (source + (origin + (method url-fetch) + (uri (pypi-uri "Flask-Cors" version)) + (sha256 + (base32 + "1v6gq4vjgyxi8q8lxawpdfhq01adb4bznnabp08ks5nzbwibz43y")))) + (build-system python-build-system) + (inputs + `(("python-flask" ,python-flask) + ("python-six" ,python-six) + ("python-nose" ,python-nose))) + (home-page + "https://github.com/corydolphin/flask-cors") + (synopsis + "A Flask extension adding a decorator for CORS support") + (description + "A Flask extension adding a decorator for CORS support") + (license license:expat))) + (define-public edash (let ((md5 "93e745e9c")) (package @@ -460,6 +487,7 @@ with the Specification.") ;;(inputs `(("sassc" ,sassc))) (propagated-inputs `(("python" ,python) + ("glibc-locales" ,glibc-locales) ("gunicorn" ,gunicorn) ("python-wrapper" ,python-wrapper) ("python-elasticsearch" ,python-elasticsearch) @@ -467,7 +495,7 @@ with the Specification.") ("python-jinja2" ,python-jinja2) ("python-markdown" ,python-markdown) ("python-misaka" ,python-misaka) - ("python-pygit2" ,python-pygit2) + ;; ("python-pygit2" ,python-pygit2) ("web-bootstrap" ,web-bootstrap) ;;("sassc" ,sassc) ("python-boto3" ,python-boto3) @@ -480,8 +508,11 @@ with the Specification.") ("python-flask-mail" ,python-flask-mail) ("python-flask-wtf" ,python-flask-wtf) ("sqlite" ,sqlite) - ("python-ipython" ,python-ipython) - )) + ;; ("python-ipython" ,python-ipython) + ("python-swagger-ui-bundle" ,python-swagger-ui-bundle) + ("python-connexion" ,python-connexion) + ("python-schedule" ,python-schedule) + ("python-flask-cors" ,python-flask-cors))) (arguments `(#:modules ((guix build utils)) #:builder diff --git a/gn/packages/python.scm b/gn/packages/python.scm index 75f7cab..651a635 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -37,6 +37,7 @@ #:use-module (gnu packages web) #:use-module (gnu packages xml) #:use-module (gnu packages xorg) + #:use-module (gnu packages python-xyz) #:use-module (guix packages) #:use-module (guix download) #:use-module (guix git-download) @@ -379,7 +380,7 @@ functions.") (define-public python-setuptools (package (name "python-setuptools") - (version "40.6.2") + (version "40.6.0") (source (origin (method url-fetch) @@ -753,9 +754,8 @@ 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.") |