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-rw-r--r--gn/packages/genenetwork.scm52
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)