diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 75 | ||||
| -rw-r--r-- | gn/packages/cwl.scm | 77 | ||||
| -rw-r--r-- | gn/packages/python.scm | 75 |
3 files changed, 76 insertions, 151 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 5a33929..02ac1e8 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -1266,78 +1266,3 @@ COVID-19 Virtual Biohackathon's Public Sequence Resource project. You can use it to upload the genomes of SARS-CoV-2 samples to make them publicly and freely available to other researchers.") (license license:asl2.0)))) - -(define-public python-arvados-python-client - (package - (name "python-arvados-python-client") - (version "2.0.2") - (source - (origin - (method url-fetch) - (uri (pypi-uri "arvados-python-client" version)) - (sha256 - (base32 - "19l4w6m5426x5k2kick630dh2jx26j16ycs2nhbfgr4cd43d29y4")))) - (build-system python-build-system) - (arguments - `(#:tests? #f)) ; tests not included? - (propagated-inputs - `(("python-ciso8601" ,python-ciso8601) - ("python-future" ,python-future) - ;("python-google-api-python-client" ,python-google-api-python-client) - ("python-google-api-client" ,python-google-api-client) - ("python-httplib2" ,python-httplib2) - ("python-pycurl" ,python-pycurl) - ("python-ruamel.yaml" ,python-ruamel.yaml-0.15) - ("python-setuptools" ,python-setuptools) - ("python-ws4py" ,python-ws4py))) - (native-inputs - `(("python-mock" ,python-mock) - ("python-oauth2client" ,python-oauth2client) - ("python-pbr" ,python-pbr-1.6.0) - ("python-pyyaml" ,python-pyyaml) - ("python-uritemplate" ,python-uritemplate))) - (home-page "https://arvados.org") - (synopsis "Arvados client library") - (description "This package provides the arvados module, an API client for -Arvados. It also includes higher-level functions to help you write Crunch -scripts, and command-line tools to store and retrieve data in the Keep storage -server.") - (license license:asl2.0))) - -(define-public python-schema-salad - (package - (name "python-schema-salad") - (version "5.0.20200416112825") - (source - (origin - (method url-fetch) - (uri (pypi-uri "schema-salad" version)) - (sha256 - (base32 - "1pm6q266qrw4r0w0vnzhsvqgk5j8b3q61hxg99awhgpjsmcvkmsz")))) - (build-system python-build-system) - (propagated-inputs - `(("python-cachecontrol" ,python-cachecontrol-0.11) - ("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))) - (native-inputs - `(("python-pytest" ,python-pytest) - ("python-pytest-runner" ,python-pytest-runner))) - (home-page "https://github.com/common-workflow-language/schema_salad") - (synopsis "Schema Annotations for Linked Avro Data (SALAD)") - (description - "Salad is a schema language for describing JSON or YAML structured linked -data documents. Salad schema describes rules for preprocessing, structural -validation, and hyperlink checking for documents described by a Salad schema. -Salad supports rich data modeling with inheritance, template specialization, -object identifiers, object references, documentation generation, code -generation, and transformation to RDF. Salad provides a bridge between document -and record oriented data modeling and the Semantic Web.") - (license license:asl2.0))) diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm index 6e0c909..be531f6 100644 --- a/gn/packages/cwl.scm +++ b/gn/packages/cwl.scm @@ -61,7 +61,7 @@ ("python-mock" ,python-mock) ("python-subprocess32" ,python-subprocess32) ("python-ruamel.yaml" ,python-ruamel.yaml) - ("python-cachecontrol" ,python-cachecontrol) + ("python-cachecontrol" ,python-cachecontrol-0.11) ("python-lxml" ,python-lxml) ("python-mypy-extensions" ,python-mypy-extensions) ("python-mistune" ,python-mistune) @@ -89,78 +89,3 @@ (description "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)) - (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 - `(("python-cython" ,python-cython) - ("python-setuptools" ,python-setuptools) - ("python-rdflib-jsonld" ,python-rdflib-jsonld) - ("python-mistune" ,python-mistune))) - (propagated-inputs - `(("python-rdflib" ,python-rdflib) - ("python-avro" ,python-avro) - ("python-pyyaml" ,python-pyyaml) - ("python-requests" ,python-requests) - ("python-shellescape" ,python-shellescape) - )) - (home-page - "https://github.com/common-workflow-language/common-workflow-language") - (synopsis - "Schema Annotations for Linked Avro Data (SALAD)") - (description - "Schema Annotations for Linked Avro Data (SALAD)") - (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 c343815..46122ce 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -1134,3 +1134,78 @@ spreadsheets without the need for COM objects.") (sha256 (base32 "1lg1klrczvzfan89y3bl9ykrknl3nb01vvai37fkww24apzyibjf")))))) + +(define-public python-arvados-python-client + (package + (name "python-arvados-python-client") + (version "2.0.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "arvados-python-client" version)) + (sha256 + (base32 + "19l4w6m5426x5k2kick630dh2jx26j16ycs2nhbfgr4cd43d29y4")))) + (build-system python-build-system) + (arguments + `(#:tests? #f)) ; tests not included? + (propagated-inputs + `(("python-ciso8601" ,python-ciso8601) + ("python-future" ,python-future) + ;("python-google-api-python-client" ,python-google-api-python-client) + ("python-google-api-client" ,python-google-api-client) + ("python-httplib2" ,python-httplib2) + ("python-pycurl" ,python-pycurl) + ("python-ruamel.yaml" ,python-ruamel.yaml-0.15) + ("python-setuptools" ,python-setuptools) + ("python-ws4py" ,python-ws4py))) + (native-inputs + `(("python-mock" ,python-mock) + ("python-oauth2client" ,python-oauth2client) + ("python-pbr" ,python-pbr-1.6.0) + ("python-pyyaml" ,python-pyyaml) + ("python-uritemplate" ,python-uritemplate))) + (home-page "https://arvados.org") + (synopsis "Arvados client library") + (description "This package provides the arvados module, an API client for +Arvados. It also includes higher-level functions to help you write Crunch +scripts, and command-line tools to store and retrieve data in the Keep storage +server.") + (license license:asl2.0))) + +(define-public python-schema-salad + (package + (name "python-schema-salad") + (version "5.0.20200416112825") + (source + (origin + (method url-fetch) + (uri (pypi-uri "schema-salad" version)) + (sha256 + (base32 + "1pm6q266qrw4r0w0vnzhsvqgk5j8b3q61hxg99awhgpjsmcvkmsz")))) + (build-system python-build-system) + (propagated-inputs + `(("python-cachecontrol" ,python-cachecontrol-0.11) + ("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))) + (native-inputs + `(("python-pytest" ,python-pytest) + ("python-pytest-runner" ,python-pytest-runner))) + (home-page "https://github.com/common-workflow-language/schema_salad") + (synopsis "Schema Annotations for Linked Avro Data (SALAD)") + (description + "Salad is a schema language for describing JSON or YAML structured linked +data documents. Salad schema describes rules for preprocessing, structural +validation, and hyperlink checking for documents described by a Salad schema. +Salad supports rich data modeling with inheritance, template specialization, +object identifiers, object references, documentation generation, code +generation, and transformation to RDF. Salad provides a bridge between document +and record oriented data modeling and the Semantic Web.") + (license license:asl2.0))) |