diff options
| -rw-r--r-- | gn/packages/genenetwork.scm | 144 |
1 files changed, 70 insertions, 74 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 91063b9..ce99066 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -130,50 +130,46 @@ (inputs (list python-click)) (native-inputs - `(("python-hypothesis" ,python-hypothesis) - ("python-mypy" ,python-mypy) - ("python-mypy-extensions" ,python-mypy-extensions) - ("python-pylint" ,python-pylint) - ("python-pytest" ,python-pytest) - ("python-pytest-mock" ,python-pytest-mock))) + (list python-hypothesis + python-mypy + python-mypy-extensions + python-pylint + python-pytest + python-pytest-mock)) (propagated-inputs - `(("gemma-wrapper" ,gemma-wrapper) - ("python-wrapper" ,python-wrapper) - ("csvdiff" ,csvdiff) - ("gn-rust-correlation" ,gn-rust-correlation) - ;; Replace use of bcrypt with argon below - ("python-bcrypt" ,python-bcrypt) - ("python-argon2-cffi" ,python-argon2-cffi) - ("python-flask" ,python-flask) - ("python-flask-cors" ,python-flask-cors) - ;; Not working in Python > 3.8 - ;; python-ipfshttpclient - ("python-lmdb" ,python-lmdb) - ("python-mysqlclient" ,python-mysqlclient) - ("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ;; python-pingouin << build failing - ("python-pingouin-without-tests" ,python-pingouin-without-tests) - ("python-plotly" ,python-plotly) - ("python-pyld" ,python-pyld) - ("python-scikit-learn" ,python-scikit-learn) - ("python-pymonad" ,python-pymonad) - ("python-redis" ,python-redis) - ("python-requests" ,python-requests) - ("python-scipy" ,python-scipy) - ("python-authlib" ,python-authlib) - ("python-sparqlwrapper" ,python-sparqlwrapper) - ("python-email-validator" ,python-email-validator) - ("python-xapian-bindings" ,python-xapian-bindings) - ("python-biopython" ,python-biopython) - ("r-optparse" ,r-optparse) - ("r-qtl" ,r-qtl) - ("r-rjson" ,r-rjson) - ("r-stringi" ,r-stringi) - ("r-wgcna" ,r-wgcna) - ("r-ctl" ,r-ctl) - ("rust-qtlreaper" ,rust-qtlreaper) - ("diffutils" ,diffutils))) + (list gemma-wrapper + python-wrapper + csvdiff + gn-rust-correlation + python-bcrypt ;; Replace use of bcrypt with argon below + python-argon2-cffi + python-flask + python-flask-cors + python-lmdb + python-mysqlclient + python-numpy + python-pandas + python-pingouin-without-tests + python-plotly + python-pyld + python-scikit-learn + python-pymonad + python-redis + python-requests + python-scipy + python-authlib + python-sparqlwrapper + python-email-validator + python-xapian-bindings + python-biopython + r-optparse + r-qtl + r-rjson + r-stringi + r-wgcna + r-ctl + rust-qtlreaper + diffutils)) (build-system python-build-system) (arguments (list #:phases @@ -273,7 +269,7 @@ javascript-plotly javascript-typeahead js-underscore - javascript-uikit + javascript-uikit js-smart-time-ago javascript-nouislider javascript-purescript-genome-browser @@ -288,7 +284,7 @@ javascript-datatables-buttons-styles javascript-shapiro-wilk javascript-underscore-string - javascript-htmx + javascript-htmx javascript-qtip2 javascript-d3js javascript-nvd3 @@ -297,8 +293,8 @@ javascript-zxcvbn javascript-jquery-ui javascript-jquery-cookie - javascript-linkify - javascript-linkify-html + javascript-linkify + javascript-linkify-html ; javascript-xterm -- disabled until we know what to do with it, not working on production ; javascript-xterm-style ; javascript-xterm-addon-fit @@ -363,7 +359,7 @@ (define-public gn-uploader (let ((commit "a4ed5d821921e43b73ecaf2ef802fab2b74d0b63") - (version "0.0.1")) + (version "0.0.1")) (package (name "gn-uploader") (version (string-append version "-" (string-take commit 8))) @@ -371,33 +367,33 @@ (origin (method git-fetch) (uri (git-reference - (url "https://git.genenetwork.org/gn-uploader") - (commit commit))) + (url "https://git.genenetwork.org/gn-uploader") + (commit commit))) (hash - (content-hash - (base32 - "01rlgdvmhxhibdw27rcjmjy0s39mv9y9nmxgn0l5p13vbib03iw5"))))) + (content-hash + (base32 + "01rlgdvmhxhibdw27rcjmjy0s39mv9y9nmxgn0l5p13vbib03iw5"))))) (build-system python-build-system) (arguments (list #:phases #~(modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "pytest" "-m" "unit_test"))))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-m" "unit_test"))))))) (native-inputs (list python-mypy - python-pylint - python-pytest - python-hypothesis)) + python-pylint + python-pytest + python-hypothesis)) (propagated-inputs (list gunicorn - python-redis - python-flask - python-pyyaml - python-jsonpickle - python-mysqlclient)) + python-redis + python-flask + python-pyyaml + python-jsonpickle + python-mysqlclient)) (synopsis "GeneNetwork Quality Control Application") (description "gn-uploader is a service allowing upload of new data into GeneNetwork, @@ -414,21 +410,21 @@ (origin (method git-fetch) (uri (git-reference - (url "https://github.com/genenetwork/gn-auth.git") - (commit "cd6eebd85d32feb289ccecd1aee45fb40b03d77f"))) + (url "https://github.com/genenetwork/gn-auth.git") + (commit "cd6eebd85d32feb289ccecd1aee45fb40b03d77f"))) (hash - (content-hash - (base32 - "06slj3z110mbc46qncdvyi29y85zkqxl76n89dxjp5wjfqxw0nsl"))))) + (content-hash + (base32 + "06slj3z110mbc46qncdvyi29y85zkqxl76n89dxjp5wjfqxw0nsl"))))) (build-system python-build-system) (arguments (list #:phases #~(modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "pytest" "-k" "unit_test"))))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-k" "unit_test"))))))) (native-inputs (list python-hypothesis python-mypy |