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-rw-r--r--.guix/modules/gnqc-py.scm69
1 files changed, 29 insertions, 40 deletions
diff --git a/.guix/modules/gnqc-py.scm b/.guix/modules/gnqc-py.scm
index 4ff86b5..848b29d 100644
--- a/.guix/modules/gnqc-py.scm
+++ b/.guix/modules/gnqc-py.scm
@@ -1,16 +1,13 @@
(define-module (gnqc-py)
- #:use-module (guix)
#:use-module (guix gexp)
+ #:use-module (guix utils)
#:use-module (guix packages)
#:use-module (guix git-download)
- #:use-module ((guix licenses) #:prefix license:)
- #:use-module (gnu packages check)
- #:use-module (gnu packages databases)
- #:use-module (gnu packages python-xyz)
- #:use-module (gnu packages python-web)
- #:use-module (guix build-system python)
- #:use-module (gnu packages python-check))
+ #:use-module ((gnu packages check) #:select (python-pylint))
+ #:use-module ((gnu packages python-check) #:select (python-mypy))
+
+ #:use-module ((gn packages genenetwork) #:select (gnqc-py) #:prefix gn:))
(define %source-dir (dirname (dirname (current-source-directory))))
@@ -18,40 +15,32 @@
(or (git-predicate %source-dir)
(const #t)))
-(define gnqc-py
+(define-public gnqc-py
+ (package
+ (inherit gn:gnqc-py)
+ (source
+ (local-file "../.."
+ "gnqc-py-checkout"
+ #:recursive? #t
+ #:select? vcs-file?))))
+
+(define-public gnqc-py-all-tests
(package
- (name "gnqc-py")
- (version "0.0.1")
- (source (local-file "../.."
- "gnqc-py-checkout"
- #:recursive? #t
- #:select? vcs-file?))
- (build-system python-build-system)
+ (inherit gnqc-py)
(arguments
- (list
- #:phases
- #~(modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "pytest" "-k" "unit_test")))))))
+ (substitute-keyword-arguments (package-arguments gnqc-py)
+ ((#:phases #~%standard-phases)
+ #~(modify-phases #$phases
+ (add-before 'build 'pylint
+ (lambda _
+ (invoke "pylint" "setup.py" "wsgi.py" "tests" "quality_control"
+ "qc_app" "r_qtl" "scripts")))
+ (add-after 'pylint 'mypy
+ (lambda _
+ (invoke "mypy" ".")))))))
(native-inputs
- (list python-mypy
- python-pylint
- python-pytest
- python-hypothesis))
- (propagated-inputs
- (list gunicorn
- python-redis
- python-flask
- python-pyyaml
- python-jsonpickle
- python-mysqlclient))
- (synopsis "GeneNetwork Quality Control Application")
- (description
- "GeneNetwork qc is a quality control application for the data files that
- eventually are used to add to the data in the GeneNetwork project.")
- (home-page "https://gitlab.com/fredmanglis/gnqc_py")
- (license license:agpl3+)))
+ (modify-inputs (package-native-inputs gnqc-py)
+ (prepend python-mypy)
+ (prepend python-pylint)))))
gnqc-py