diff options
Diffstat (limited to 'gn/packages/genenetwork.scm')
| -rw-r--r-- | gn/packages/genenetwork.scm | 52 |
1 files changed, 39 insertions, 13 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 18b77e4..36d3ae6 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -27,8 +27,10 @@ #:use-module (gnu packages golang) #:use-module (gnu packages graph) #:use-module (gnu packages graphviz) + #:use-module (gnu packages machine-learning) #:use-module (gnu packages parallel) #:use-module (gnu packages python) + #:use-module (gnu packages python-build) #:use-module (gnu packages python-check) #:use-module (gnu packages python-crypto) #:use-module (gnu packages python-science) @@ -41,9 +43,7 @@ #:use-module (gnu packages statistics) #:use-module (gnu packages textutils) #:use-module (gnu packages version-control) - ; #:use-module (gnu packages vim) #:use-module (gnu packages web) - ; #:use-module (gnu packages wget) #:use-module (gnu packages xml) #:use-module (gn packages bioinformatics) #:use-module (gn packages crates-io) @@ -51,8 +51,8 @@ #:use-module (gn packages javascript) #:use-module (gn packages python) #:use-module (gn packages statistics) - #:use-module (gn packages twint) #:use-module (gn packages web) + #:use-module (gn packages python-web) #:use-module (srfi srfi-1)) @@ -100,11 +100,20 @@ (description "Reimplementation of genenetwork/QTLReaper in Rust") (license #f)))) +; Tests on the upstream python-pengouin package are broken. So, we +; create this temporary workaround. +(define python-pingouin-without-tests + (package + (inherit python-pingouin) + (arguments + (substitute-keyword-arguments (package-arguments python-pingouin) + ((#:tests? _ #f) #f))))) + (define-public genenetwork3 - (let ((commit "fe1b8be86b65346724f8f78ab9e5d897e0c480b0")) + (let ((commit "f52247c15f3694f3dd5fd0fd79c3e15376137e07")) (package (name "genenetwork3") - (version (git-version "0.1.0" "2" commit)) + (version (git-version "0.1.0" "3" commit)) (source (origin (method git-fetch) @@ -114,7 +123,9 @@ (file-name (git-file-name name version)) (sha256 (base32 - "1i7g2c3irp5rr2b8vb7xm9v1hjb5vssc92s2lq910qszd53pdzgn")))) + "0ac0dr8dny65x4xvm8gw6ap3g8g0j933ipy9116idcws31rk2adk")))) + (inputs + (list python-click)) (native-inputs (list python-hypothesis python-mypy @@ -127,7 +138,8 @@ python-wrapper csvdiff gn-rust-correlation - python-bcrypt + python-bcrypt ;; Replace use of bcrypt with argon below + python-argon2-cffi python-flask python-flask-cors ;; Not working in Python > 3.8 @@ -136,12 +148,18 @@ python-mysqlclient python-numpy python-pandas - python-pingouin + ;; python-pingouin << build failing + python-pingouin-without-tests python-plotly + python-scikit-learn + python-pymonad python-redis python-requests python-scipy + python-authlib python-sparqlwrapper + python-email-validator + python-xapian-bindings r-optparse r-qtl r-rjson @@ -149,15 +167,23 @@ r-wgcna r-ctl rust-qtlreaper - diffutils)) + diffutils + yoyo-migrations)) (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"))))))) (home-page "https://github.com/genenetwork/genenetwork3") (synopsis "GeneNetwork3 API for data science and machine learning.") (description "GeneNetwork3 API for data science and machine learning.") (license license:agpl3+)))) (define-public genenetwork2 - (let ((commit "13289325fb22c4bc10b52414fb9755e7911795f3")) + (let ((commit "bfe557dc1e537dc78a82a30817ecf2ca3004d978")) (package (name "genenetwork2") (version (git-version "3.11" "2" commit)) @@ -169,7 +195,7 @@ (file-name (string-append name "-" version)) (sha256 (base32 - "1ny0ix9h7r52lb2qhf2hpfqijckhkw4jr1wp53qfzrd84lf4pii4")))) + "1bn0j0fpk4hcicgfird62x5wq2n6lj4rs1ggw69dcxyf4qdxbk5d")))) (native-inputs (list graphviz)) (propagated-inputs @@ -221,13 +247,13 @@ ("python-simplejson" ,python-simplejson) ("python-markdown" ,python-markdown) ("python-rdflib" ,python-rdflib) - ("python-twint" ,python-twint) + ("python-authlib" ,python-authlib) + ("python-flask-session" ,python-flask-session) ;; TODO: Get rid of Python R bindings ("python-rpy2" ,python-rpy2) ("python-beautifulsoup4" ,python-beautifulsoup4) ;; Disable for now. Build fails on Penguin2 ;; ("python-flask-socketio" ,python-flask-socketio) - ("python-xapian-bindings" ,python-xapian-bindings) ("python-xlsxwriter" ,python-xlsxwriter) ;; All the external js dependencies ("javascript-twitter-post-fetcher" ,javascript-twitter-post-fetcher) |