diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 21 | ||||
| -rw-r--r-- | gn/packages/python.scm | 73 |
2 files changed, 87 insertions, 7 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index d4c6e00..fc2c923 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -1226,10 +1226,9 @@ runApp(launch.browser=0, port=4206)~%\n" "") (license #f))) -;; Note this package is incomplete. Needs more to run properly. (define-public bh20-seq-resource - (let ((commit "bbca5ac9b2538e410efe3e09651f87e5573145de") - (revision "2")) + (let ((commit "ae4cb3c2cf7103bbc84f52618bb755d7ce25775b") + (revision "3")) (package (name "bh20-seq-resource") (version (git-version "1.0" revision commit)) @@ -1240,22 +1239,30 @@ runApp(launch.browser=0, port=4206)~%\n" (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 "1kkysjgmhp7kfb17470ik821p9djsidyqmkbjvv37jx2w9pvw31z")))) + (base32 "1k0gsz4yc8l5znanzd094g2jp40ksbpa9667zr31ayrjx6labz02")) + (modules '((guix build utils))) + (snippet + '(begin + (substitute* "setup.py" + (("py-dateutil") "python-dateutil")) + #t)))) (build-system python-build-system) - (inputs + (propagated-inputs `(("python-arvados-python-client" ,python-arvados-python-client) + ("python-dateutil" ,python-dateutil) ("python-flask" ,python-flask) ("python-magic" ,python-magic) ("python-pyyaml" ,python-pyyaml) ("python-pycurl" ,python-pycurl) ("python-pyshex" ,python-pyshex) + ("python-ruaml.yaml" ,python38-ruaml.yaml-0.15.76) ("clustalw" ,clustalw) ("python-schema-salad" ,python-schema-salad))) (native-inputs `(("git" ,(@ (gnu packages version-control) git)) ("python-oauth2client" ,python-oauth2client) - ("python-pytest" ,python-pytest) - ("python-pytest-runner" ,python-pytest-runner) + ("python-pytest" ,python-pytest-4) + ("python-pytest-runner" ,python-pytest-runner-2) ("python-uritemplate" ,python-uritemplate))) (home-page "https://github.com/arvados/bh20-seq-resource") (synopsis diff --git a/gn/packages/python.scm b/gn/packages/python.scm index 51efc4a..b181767 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -1588,3 +1588,76 @@ handles recursion and lists.") (synopsis "SPARQL Slurper for rdflib") (description "This package provides a SPARQL Slurper for rdflib.") (license license:asl2.0))) + +(define-public python38-ruaml.yaml-0.15.76 + (package + (inherit python-ruamel.yaml) + (name "python-ruamel.yaml") + (version "0.15.76") + (source + (origin + (method url-fetch) + (uri (pypi-uri "ruamel.yaml" "0.15.78")) + (sha256 + (base32 + "0pwxgrma6k47kvsphqz5yrhwnfrhwsrhn6sjp8p21s91wdgkqyc5")))) + (arguments + `(#:tests? #f ; suprise test failures + #:phases + (modify-phases %standard-phases + ;; For some unknown reason we need: ruamel.yaml<=0.15.77,>=0.15.54 + ;; But 0.15.78 is the first which builds with python-3.8. + (add-after 'unpack 'patch-source + (lambda _ + (substitute* "__init__.py" + (("0\\.15\\.78") "0.15.76") + (("15, 78") "15, 76")) + #t))))))) + +(define-public python2-ruamel.ordereddict + (package + (name "python2-ruamel.ordereddict") + (version "0.4.14") + (source + (origin + (method url-fetch) + (uri (pypi-uri "ruamel.ordereddict" version)) + (sha256 + (base32 + "0jldrcanmz0284r2y6kbi82vslkaf5hf5q90v7rqxcdjdv952418")))) + (build-system python-build-system) + (arguments + `(#:python ,python-2 + #:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key inputs outputs tests? #:allow-other-keys) + (if tests? + (begin (add-installed-pythonpath inputs outputs) + (invoke "python" "test/testordereddict.py")) + #t)))))) + (home-page "https://sourceforge.net/projects/ruamel-ordereddict/") + (synopsis "Version of dict that keeps keys in insertion resp. sorted order") + (description + "This package provides a version of dict that keeps keys in insertion resp. +sorted order.") + (license license:expat))) + +(define-public python-pytest-4 + (package + (inherit python-pytest) + (version "4.6.11") + (source + (origin + (method url-fetch) + (uri (pypi-uri "pytest" version)) + (sha256 + (base32 + "0ls3pqr86xgif6bphsb6wrww9r2vc7p7a2naq8zcq8115wwq5yjh")))) + (arguments + (substitute-keyword-arguments (package-arguments python-pytest) + ((#:tests? _ #f) #f))) + (native-inputs + `(("python-argcomplete" ,python-argcomplete) + ("python-requests" ,python-requests) + ,@(package-native-inputs python-pytest))))) |