Inherit from `gnqc-py` in `guix-bioinformatics`.

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