From f65893ba096bc4b190d9101cca8fe490af80109e Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Tue, 11 Dec 2018 21:50:50 -0600 Subject: CWL: updating --- gn/packages/cwl.scm | 26 +++++++++++++++----------- 1 file changed, 15 insertions(+), 11 deletions(-) (limited to 'gn/packages/cwl.scm') diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm index 4f04f41..6980bb8 100644 --- a/gn/packages/cwl.scm +++ b/gn/packages/cwl.scm @@ -3,6 +3,7 @@ (define-module (gn packages cwl) #:use-module ((guix licenses) #:prefix license:) #:use-module (gnu packages) + #:use-module (gnu packages check) #:use-module (gnu packages python) #:use-module (gnu packages python-web) #:use-module (gnu packages rdf) @@ -19,7 +20,7 @@ (define-public python-cwltool ; guix: needs work (package (name "python-cwltool") - (version "1.0.20150916041152") + (version "1.0.20181012180214") (source (origin (method url-fetch) @@ -29,17 +30,23 @@ ".tar.gz")) (sha256 (base32 - "1kqxc6nvq4nr8qdv39ycdi6fhzaipgjpmbghsz94ij6jhf5r3dq2")))) + "0pk0jlac2vl6vfihdq07agzz9dasw84yjz5ladcbwnmzzl022cg7")))) (build-system python-build-system) (inputs - `(("python-setuptools" ,python-setuptools) + `(("python-bagit" ,python-bagit) + ("python-setuptools" ,python-setuptools) + ("python-pytest-cov" ,python-pytest-cov) + ("python-pytest-runner" ,python-pytest-runner) + ("python-typing-extensions" ,python-typing-extensions) + ("python-prov" ,python-prov) ("python-pyparsing" ,python-pyparsing) + ("python-subprocess32" ,python-subprocess32) )) (propagated-inputs `(("python-schema-salad" ,python-schema-salad) ("python-html5lib" ,python-html5lib) )) - (arguments `(#:tests? #f)) ;; CWL includes no tests. + ; (arguments `(#:tests? #f)) ;; CWL includes no tests. (home-page "https://github.com/common-workflow-language/common-workflow-language") (synopsis @@ -54,17 +61,14 @@ (define-public python-schema-salad (package (name "python-schema-salad") - (version "1.0.2") + (version "3.0.20181129082112") (source (origin (method url-fetch) - (uri (string-append - "https://pypi.python.org/packages/source/s/schema-salad/schema-salad-" - version - ".tar.gz")) + (uri (pypi-uri "schema-salad" version)) (sha256 (base32 - "09axiiirq73s1cs21n8mkdslaca2gxc2mlayyl6yiaq98cfgfh37")))) + "1xg70v82q053vz1sg8sc99alnkrm2kk05w6698vgmngl1767sk97")))) (build-system python-build-system) (arguments `(#:tests? #f)) ;; CWL includes no tests. (inputs @@ -73,7 +77,7 @@ ("python-rdflib-jsonld" ,python-rdflib-jsonld) ("python-mistune" ,python-mistune))) (propagated-inputs - `(("python-rdflib-4.2" ,python-rdflib-4.2) + `(("python-rdflib" ,python-rdflib) ("python-avro" ,python-avro) ("python-pyyaml" ,python-pyyaml) ("python-requests" ,python-requests) -- cgit v1.2.3 From 7cdcccfd9cf87915969e0706042673114d2b1d91 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 12 Dec 2018 04:00:26 -0600 Subject: CWL --- gn/packages/cwl.scm | 3 ++- gn/packages/python.scm | 9 +++++++++ 2 files changed, 11 insertions(+), 1 deletion(-) (limited to 'gn/packages/cwl.scm') diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm index 6980bb8..9b75c2b 100644 --- a/gn/packages/cwl.scm +++ b/gn/packages/cwl.scm @@ -37,13 +37,14 @@ ("python-setuptools" ,python-setuptools) ("python-pytest-cov" ,python-pytest-cov) ("python-pytest-runner" ,python-pytest-runner) + ("python-rdflib" ,python-rdflib) ("python-typing-extensions" ,python-typing-extensions) - ("python-prov" ,python-prov) ("python-pyparsing" ,python-pyparsing) ("python-subprocess32" ,python-subprocess32) )) (propagated-inputs `(("python-schema-salad" ,python-schema-salad) + ("python-prov" ,python-prov) ("python-html5lib" ,python-html5lib) )) ; (arguments `(#:tests? #f)) ;; CWL includes no tests. diff --git a/gn/packages/python.scm b/gn/packages/python.scm index fa9696f..ef30812 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -11,6 +11,7 @@ #: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) @@ -170,6 +171,14 @@ functions.") (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)") -- cgit v1.2.3 From 792c615b32c8eef93a8da7993b1cda32b3e3a0b8 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 12 Dec 2018 20:07:54 -0600 Subject: CWL builds --- gn/packages/cwl.scm | 22 ++++++++++++++------ gn/packages/python.scm | 54 +++++++++++++++++++++++++++++++++++++++++++++++++- 2 files changed, 69 insertions(+), 7 deletions(-) (limited to 'gn/packages/cwl.scm') diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm index 9b75c2b..2642f90 100644 --- a/gn/packages/cwl.scm +++ b/gn/packages/cwl.scm @@ -7,6 +7,7 @@ #:use-module (gnu packages python) #:use-module (gnu packages python-web) #:use-module (gnu packages rdf) + #:use-module (gnu packages serialization) #:use-module (gn packages python) #:use-module (guix download) #:use-module (guix packages) @@ -17,9 +18,9 @@ ; #:use-module (guix build-system trivial) #:use-module (srfi srfi-1)) -(define-public python-cwltool ; guix: needs work +(define-public cwltool ; guix: needs work (package - (name "python-cwltool") + (name "cwltool") (version "1.0.20181012180214") (source (origin @@ -36,18 +37,30 @@ `(("python-bagit" ,python-bagit) ("python-setuptools" ,python-setuptools) ("python-pytest-cov" ,python-pytest-cov) + ("python-prov" ,python-prov) ("python-pytest-runner" ,python-pytest-runner) ("python-rdflib" ,python-rdflib) ("python-typing-extensions" ,python-typing-extensions) ("python-pyparsing" ,python-pyparsing) ("python-subprocess32" ,python-subprocess32) + ("python-ruamel.yaml" ,python-ruamel.yaml) + ("python-cachecontrol" ,python-cachecontrol) + ("python-mypy-extensions" ,python-mypy-extensions) )) (propagated-inputs `(("python-schema-salad" ,python-schema-salad) - ("python-prov" ,python-prov) ("python-html5lib" ,python-html5lib) )) ; (arguments `(#:tests? #f)) ;; CWL includes no tests. + (arguments + `(;#:phases + ; (modify-phases %standard-phases + ; (replace 'check + ; (lambda* (#:key inputs outputs #:allow-other-keys) + ; (invoke "python" "-m" "pytest") + ; ))) + #:tests? #f)) ; Disable for now + (home-page "https://github.com/common-workflow-language/common-workflow-language") (synopsis @@ -56,9 +69,6 @@ "Common workflow language reference implementation") (license license:asl2.0))) -(define-public python2-cwltool - (package-with-python2 python-cwltool)) - (define-public python-schema-salad (package (name "python-schema-salad") diff --git a/gn/packages/python.scm b/gn/packages/python.scm index ef30812..808eb9d 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -146,7 +146,7 @@ functions.") "1m6y04qmig0b5hzb35lnaw3d2yfydb7alyr1579yblvgs3da6j7j")))) (build-system python-build-system) (inputs - `(("python-setuptools-scm" ,python-setuptools-scm) + `(("python-setuptools-scm" ,python-setuptools-scm) ("python-coverage" ,python-coverage) ("python-mock" ,python-mock) )) @@ -711,3 +711,55 @@ the older versions.") (description "This is a python library for generating html from classes.") (home-page "https://github.com/srittau/python-htmlgen") (license license:expat))) + +(define-public python-version +(let ((commit "e5aadc720bb74c535f29e5a2de5cd9697efe8d7c")) +(package + (name "python-version") + (version "0.1.2") + (source + (origin + (method git-fetch) + (uri (git-reference + ; (url "https://github.com/genenetwork/pylmm.git") + (url "https://github.com/keleshev/version.git") ; version not in pypi + (commit commit))) + (file-name (string-append name "-" commit)) + (sha256 + (base32 + "1rc8kf72v180qlygkh1y0jwv2fxqpx7n97bqfhbwgnn31iwai9g3")))) + (build-system python-build-system) + (build-system python-build-system) + (propagated-inputs + `( + ("python-more-itertools" ,python-more-itertools) + ("python-pytest" ,python-pytest))) + (home-page "http://github.com/halst/version") + (synopsis "Implementation of semantic version") + (description + "Implementation of semantic version") + (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) + (propagated-inputs + `(("python-version" ,python-version) + ("python-typing" ,python-typing))) + (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)) +) -- cgit v1.2.3 From 2372ecc00bb08b033bba48316edd17ef9a6e974b Mon Sep 17 00:00:00 2001 From: pjotrp Date: Fri, 14 Dec 2018 04:38:50 +0000 Subject: CWL final packages - tests pass in principle (except for some networking) --- gn/packages/cwl.scm | 29 +++++++++++++++++++++-------- gn/packages/python.scm | 21 +++++++++++++++++++++ 2 files changed, 42 insertions(+), 8 deletions(-) (limited to 'gn/packages/cwl.scm') diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm index 2642f90..785a6ed 100644 --- a/gn/packages/cwl.scm +++ b/gn/packages/cwl.scm @@ -6,8 +6,11 @@ #:use-module (gnu packages check) #:use-module (gnu packages python) #:use-module (gnu packages python-web) + #: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 (gn packages python) #:use-module (guix download) #:use-module (guix packages) @@ -33,23 +36,33 @@ (base32 "0pk0jlac2vl6vfihdq07agzz9dasw84yjz5ladcbwnmzzl022cg7")))) (build-system python-build-system) - (inputs - `(("python-bagit" ,python-bagit) + (propagated-inputs ; a lot of these are used for testing + `(("git" ,git) + ("node" ,node) + ("python-bagit" ,python-bagit) + ("python-arcp" ,python-arcp) ("python-setuptools" ,python-setuptools) + ("python-dateutil" ,python-dateutil) ("python-pytest-cov" ,python-pytest-cov) ("python-prov" ,python-prov) ("python-pytest-runner" ,python-pytest-runner) ("python-rdflib" ,python-rdflib) - ("python-typing-extensions" ,python-typing-extensions) ("python-pyparsing" ,python-pyparsing) + ("python-pytest-mock" ,python-pytest-mock) + ("python-mock" ,python-mock) ("python-subprocess32" ,python-subprocess32) ("python-ruamel.yaml" ,python-ruamel.yaml) ("python-cachecontrol" ,python-cachecontrol) + ("python-lxml" ,python-lxml) ("python-mypy-extensions" ,python-mypy-extensions) - )) - (propagated-inputs - `(("python-schema-salad" ,python-schema-salad) + ("python-mistune" ,python-mistune) + ("python-networkx" ,python-networkx) + ("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) )) ; (arguments `(#:tests? #f)) ;; CWL includes no tests. (arguments @@ -102,5 +115,5 @@ "Schema Annotations for Linked Avro Data (SALAD)") (license license:asl2.0))) -(define-public python2-schema-salad - (package-with-python2 python-schema-salad)) +; (define-public python2-schema-salad +; (package-with-python2 python-schema-salad)) diff --git a/gn/packages/python.scm b/gn/packages/python.scm index 808eb9d..75f7cab 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -763,3 +763,24 @@ the older versions.") "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)) +) -- cgit v1.2.3 From 9e84151973674af3cc31e0cbe5e6e1a9eeaa6ed4 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Fri, 14 Dec 2018 04:58:44 +0000 Subject: CWL: fetching from git repo to get the latest --- gn/packages/cwl.scm | 20 +++++++++++++------- 1 file changed, 13 insertions(+), 7 deletions(-) (limited to 'gn/packages/cwl.scm') diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm index 785a6ed..5a01dbf 100644 --- a/gn/packages/cwl.scm +++ b/gn/packages/cwl.scm @@ -22,19 +22,25 @@ #:use-module (srfi srfi-1)) (define-public cwltool ; guix: needs work + (let ((commit "e12d36b6efbc5d4a6ff7b4fbfd7387bff8f72727")) (package (name "cwltool") (version "1.0.20181012180214") (source (origin - (method url-fetch) - (uri (string-append - "https://pypi.python.org/packages/source/c/cwltool/cwltool-" - version - ".tar.gz")) + ; (method url-fetch) + ; (uri (string-append + ; "https://pypi.python.org/packages/source/c/cwltool/cwltool-" + ; version + ; ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/genenetwork/cwltool.git") + (commit commit))) + (file-name (git-file-name name version)) (sha256 (base32 - "0pk0jlac2vl6vfihdq07agzz9dasw84yjz5ladcbwnmzzl022cg7")))) + "1zhba1hfizrw3bxfmhpjds92pj79hyyv5k7sglw24z52kg1in67p")))) (build-system python-build-system) (propagated-inputs ; a lot of these are used for testing `(("git" ,git) @@ -80,7 +86,7 @@ "Common workflow language reference implementation") (description "Common workflow language reference implementation") - (license license:asl2.0))) + (license license:asl2.0)))) (define-public python-schema-salad (package -- cgit v1.2.3