From 4034fd9b19e6807d355c86726b33f6dc10a39664 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 23 Nov 2020 15:41:39 +0200 Subject: upstream cwltools and dependant packages --- gn/packages/python.scm | 191 ------------------------------------------------- 1 file changed, 191 deletions(-) (limited to 'gn/packages/python.scm') diff --git a/gn/packages/python.scm b/gn/packages/python.scm index a9c2770..c8892be 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -1,31 +1,16 @@ (define-module (gn packages python) #:use-module ((guix licenses) #:prefix license:) #:use-module (gnu packages) - #:use-module (gnu packages attr) - #:use-module (gnu packages base) - #:use-module (gnu packages bioinformatics) #:use-module (gnu packages check) #:use-module (gnu packages compression) - #:use-module (gnu packages databases) #:use-module (gnu packages fontutils) - #:use-module (gnu packages gcc) #:use-module (gnu packages ghostscript) - #:use-module (gnu packages glib) - #:use-module (gnu packages gnupg) #:use-module (gnu packages graphviz) - #:use-module (gnu packages gtk) #:use-module (gnu packages icu4c) #:use-module (gnu packages image) - #:use-module (gnu packages imagemagick) #:use-module (gnu packages libffi) #:use-module (gnu packages linux) - #:use-module (gnu packages maths) - #:use-module (gnu packages multiprecision) - #:use-module (gnu packages networking) - #:use-module (gnu packages ncurses) #:use-module (gnu packages pcre) - #:use-module (gnu packages perl) - #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) #:use-module (gnu packages python-compression) #:use-module (gnu packages python-crypto) @@ -37,20 +22,12 @@ #:use-module (gnu packages serialization) #:use-module (gnu packages statistics) #:use-module (gnu packages tcl) - #:use-module (gnu packages tex) - #:use-module (gnu packages texinfo) #:use-module (gnu packages time) - #:use-module (gnu packages tls) - #:use-module (gnu packages web) - #:use-module (gnu packages xml) - #:use-module (gnu packages xorg) #:use-module (guix packages) #:use-module (guix download) #: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)) (define-public python-pyvcf @@ -172,56 +149,6 @@ functions.") (define-public python2-plotly-3.2.1 (package-with-python2 python-plotly-3.2.1)) -(define-public python-bagit; guix candidate - (package - (name "python-bagit") - (version "1.7.0") - (source - (origin - (method url-fetch) - (uri (pypi-uri "bagit" version)) - (sha256 - (base32 - "1m6y04qmig0b5hzb35lnaw3d2yfydb7alyr1579yblvgs3da6j7j")))) - (build-system python-build-system) - (inputs - `(("python-setuptools-scm" ,python-setuptools-scm) - ("python-coverage" ,python-coverage) - ("python-mock" ,python-mock))) - (arguments `(#:tests? #f)) ;; No tests. - (home-page "https://pypi.python.org/pypi/bagit") - (synopsis "Create and validate BagIt packages") - (description - "Create and validate BagIt packages") - (license license:gpl2))) - -(define-public python-prov ; guix candidate -(package - (name "python-prov") - (version "1.5.3") - (source - (origin - (method url-fetch) - (uri (pypi-uri "prov" version)) - (sha256 - (base32 - "1a9h406laclxalmdny37m0yyw7y17n359akclbahimdggq853jd0")))) - (build-system python-build-system) - (inputs - `(("python-rdflib" ,python-rdflib) - ("python-lxml" ,python-lxml) - ("python-networkx" ,python-networkx) - ("python-dateutil" ,python-dateutil) - ("python-pydot" ,python-pydot) - ("graphviz" ,graphviz) ; for testing - )) - (home-page "https://github.com/trungdong/prov") - (synopsis - "A library for W3C Provenance Data Model supporting PROV-JSON, PROV-XML and PROV-O (RDF)") - (description - "A library for W3C Provenance Data Model supporting PROV-JSON, PROV-XML and PROV-O (RDF)") - (license license:expat))) - (define-public python-subprocess32 ; guix candidate (package (name "python-subprocess32") @@ -398,30 +325,6 @@ Python 3 support.") (define-public python2-avro (package-with-python2 python-avro)) -(define-public python-shellescape ; guix ready - (package - (name "python-shellescape") - (version "3.4.1") - (source - (origin - (method url-fetch) - (uri (pypi-uri "shellescape" version)) - (sha256 - (base32 - "0n5ky1b2vw2y0d4xl3qybyp2rk0gq5frjs8nr8ak6mgj2fyb4676")))) - (build-system python-build-system) - (native-inputs - `(("python-setuptools" ,python-setuptools))) - (home-page "https://github.com/chrissimpkins/shellescape") - (synopsis - "Shell escape a string to safely use it as a token in a shell command (backport of Python shlex.quote for Python versions 2.x & < 3.3)") - (description - "Shell escape a string to safely use it as a token in a shell command (backport of Python shlex.quote for Python versions 2.x & < 3.3)") - (license license:expat))) - -(define-public python2-shellescape - (package-with-python2 python-shellescape)) - ; env IPFS_PATH=/export/ipfs/ ipfs add -r htmlgen/ ; added QmUD9LMJTE8q5wYkUyAwLdz2QCGXWt457iFnyYQAGfsN3j htmlgen/htmlgen-2.2.2-gn.tar.gz @@ -829,49 +732,6 @@ the older versions.") (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) - (inputs - `(("python-version" ,python-version))) - (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)) -) - - -(define-public python-arcp -(package - (name "python-arcp") - (version "0.2.0") - (source - (origin - (method url-fetch) - (uri (pypi-uri "arcp" version)) - (sha256 - (base32 - "0h8sn0mlb6vb8wqqnqc4pxdklrkyx3p72afdhm7b9kyalrqzd7dd")))) - (build-system python-build-system) - (home-page "http://arcp.readthedocs.io/") - (synopsis - "arcp (Archive and Package) URI parser and generator") - (description - "arcp (Archive and Package) URI parser and generator") - (license license:asl2.0)) -) - (define-public python2-pp (package (name "python2-pp") @@ -1032,19 +892,6 @@ spreadsheets without the need for COM objects.") (define-public python2-admiral (package-with-python2 python-admiral)) -(define-public python-cachecontrol-0.11 - (package - (inherit python-cachecontrol) - (name "python-cachecontrol") - (version "0.11.7") - (source - (origin - (method url-fetch) - (uri (pypi-uri "CacheControl" version)) - (sha256 - (base32 - "07jsfhlbcwgqg6ayz8nznzaqg5rmxqblbzxz1qvg5wc44pcjjy4g")))))) - (define-public python-pbr-1.6.0 (package (inherit python-pbr) @@ -1097,44 +944,6 @@ 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 "7.0.20200811075006") - (source - (origin - (method url-fetch) - (uri (pypi-uri "schema-salad" version)) - (sha256 - (base32 - "0wanbwmqb189x1m0vacnhpivfsr8rwbqknngivzxxs8j46yj80bg")))) - (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) - ;; This needs to be fixed before upstreaming - fixed? - ("python-ruamel.yaml" ,python-ruamel.yaml) - ("python-setuptools" ,python-setuptools) - ("python-typing-extensions" ,python-typing-extensions))) - (native-inputs - `(("python-pytest" ,python-pytest-4) - ("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))) - (define-public python-pyshex (package (name "python-pyshex") -- cgit v1.2.3