diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 3 | ||||
| -rw-r--r-- | gn/packages/cwl.scm | 115 | ||||
| -rw-r--r-- | gn/packages/python.scm | 191 |
3 files changed, 1 insertions, 308 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 9784aca..25aece9 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -17,7 +17,6 @@ #:use-module (gn packages python) #:use-module (gn packages twint) #:use-module (gnu packages algebra) - #:use-module (gnu packages autotools) #:use-module (gnu packages base) #:use-module (gnu packages bash) #:use-module (gnu packages bioconductor) @@ -32,7 +31,6 @@ #:use-module (gnu packages elf) #:use-module (gnu packages fontutils) #:use-module (gnu packages gcc) - #:use-module (gnu packages graphviz) #:use-module (gnu packages gtk) #:use-module (gnu packages imagemagick) #:use-module (gnu packages jemalloc) @@ -51,7 +49,6 @@ #:use-module (gnu packages rdf) #:use-module (gnu packages readline) #:use-module (gnu packages ruby) - #:use-module (gnu packages serialization) #:use-module (gnu packages statistics) #:use-module (gnu packages time) #:use-module (gnu packages web)) diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm index 9871ed9..a327187 100644 --- a/gn/packages/cwl.scm +++ b/gn/packages/cwl.scm @@ -1,124 +1,11 @@ (define-module (gn packages cwl) #:use-module ((guix licenses) #:prefix license:) - #:use-module (gn packages python) #:use-module (guix download) - #:use-module (guix git-download) #:use-module (guix packages) #:use-module (guix build-system python) #:use-module (gnu packages) - #:use-module (gnu packages check) - #:use-module (gnu packages graphviz) - #:use-module (gnu packages python-web) - #:use-module (gnu packages python-xyz) - #:use-module (gnu packages node) - #:use-module (gnu packages rdf) - #:use-module (gnu packages serialization) - #:use-module (gnu packages time) - #:use-module (gnu packages version-control) - #:use-module (gnu packages xml)) + #:use-module (gnu packages bioinformatics)) -(define-public python-pydot ;; can be updated in GNU Guix - this is a copy - (package - (name "python-pydot") - (version "1.4.1") - (source - (origin - (method url-fetch) - (uri (pypi-uri "pydot" version)) - (sha256 - (base32 - "00az4cbf8bv447lkk9xi6pjm7gcc7ia33y4pm71fwfwis56rv76l")))) - (build-system python-build-system) - (native-inputs - ;; For tests. - `(("python-chardet" ,python-chardet))) - (propagated-inputs - `(("python-pyparsing" ,python-pyparsing))) - (home-page "https://github.com/erocarrera/pydot") - (synopsis "Python interface to Graphviz's DOT language") - (description - "Pydot provides an interface to create, handle, modify and process -graphs in Graphviz's DOT language, written in pure Python.") - (license license:expat))) - - -(define-public cwltool - (let ((commit "78fe9d41ee5a44f8725dfbd7028e4a5ee42949cf") - (revision "1")) - (package - (name "cwltool") - (version "3.0.20201117141248") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/common-workflow-language/cwltool.git") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1awf99n7aglxc5zszrlrv6jxp355jp45ws7wpsgjlgcdv7advn0w")))) - (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'loosen-version-restrictions - (lambda _ - (substitute* "setup.py" - (("== 1.5.1") ">=1.5.1")) - #t)) - (add-after 'unpack 'modify-tests - (lambda _ - ;; Tries to connect to the internet. - (delete-file "tests/test_udocker.py") - (delete-file "tests/test_http_input.py") - (substitute* "tests/test_load_tool.py" - (("def test_load_graph_fragment_from_packed") - "@pytest.mark.skip(reason=\"Disabled by Guix\")\ndef test_load_graph_fragment_from_packed")) - (substitute* "tests/test_examples.py" - (("def test_env_filtering") - "@pytest.mark.skip(reason=\"Disabled by Guix\")\ndef test_env_filtering")) - ;; Tries to use cwl-runners. - (substitute* "tests/test_examples.py" - (("def test_v1_0_arg_empty_prefix_separate_false") - "@pytest.mark.skip(reason=\"Disabled by Guix\")\ndef test_v1_0_arg_empty_prefix_separate_false")) - #t))))) - (propagated-inputs - `(("git" ,git) - ("python-argcomplete" ,python-argcomplete) - ("python-bagit" ,python-bagit) - ("python-coloredlogs" ,python-coloredlogs) - ("python-mypy-extensions" ,python-mypy-extensions) - ("python-prov" ,python-prov) - ("python-pydot" ,python-pydot) - ("python-psutil" ,python-psutil) - ("python-rdflib" ,python-rdflib) - ("python-requests" ,python-requests) - ("python-ruamel.yaml" ,python-ruamel.yaml) - ("python-schema-salad" ,python-schema-salad) - ("python-setuptools" ,python-setuptools) - ("python-shellescape" ,python-shellescape) - ("python-typing-extensions" ,python-typing-extensions) - ;; Not listed as needed but seems to be necessary: - ("node" ,node) - ("python-cachecontrol" ,python-cachecontrol-0.11) - ("python-dateutil" ,python-dateutil) - ("python-lxml" ,python-lxml) - ("python-networkx" ,python-networkx))) - (native-inputs - `(("python-arcp" ,python-arcp) - ("python-humanfriendly" ,python-humanfriendly) - ("python-mock" ,python-mock) - ("python-pytest" ,python-pytest) - ("python-pytest-cov" ,python-pytest-cov) - ("python-pytest-mock" ,python-pytest-mock) - ("python-pytest-runner" ,python-pytest-runner) - ("python-rdflib-jsonld" ,python-rdflib-jsonld))) - (home-page - "https://github.com/common-workflow-language/common-workflow-language") - (synopsis "Common workflow language reference implementation") - (description - "Common workflow language reference implementation.") - (license license:asl2.0)))) (define-public cwl-runner (package 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") |