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authorEfraim Flashner2020-11-23 15:41:39 +0200
committerEfraim Flashner2020-11-23 15:41:39 +0200
commit4034fd9b19e6807d355c86726b33f6dc10a39664 (patch)
tree26ab62f567df2a27717139a46d4c69f846e01c26 /gn/packages/python.scm
parent8a66ab55cab786acb9cba38b387bbbc58fa35dfa (diff)
downloadguix-bioinformatics-4034fd9b19e6807d355c86726b33f6dc10a39664.tar.gz
upstream cwltools and dependant packages
Diffstat (limited to 'gn/packages/python.scm')
-rw-r--r--gn/packages/python.scm191
1 files changed, 0 insertions, 191 deletions
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")