From 792c615b32c8eef93a8da7993b1cda32b3e3a0b8 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Wed, 12 Dec 2018 20:07:54 -0600
Subject: CWL builds

---
 gn/packages/cwl.scm    | 22 ++++++++++++++------
 gn/packages/python.scm | 54 +++++++++++++++++++++++++++++++++++++++++++++++++-
 2 files changed, 69 insertions(+), 7 deletions(-)

diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm
index 9b75c2b..2642f90 100644
--- a/gn/packages/cwl.scm
+++ b/gn/packages/cwl.scm
@@ -7,6 +7,7 @@
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages rdf)
+  #:use-module (gnu packages serialization)
   #:use-module (gn packages python)
   #:use-module (guix download)
   #:use-module (guix packages)
@@ -17,9 +18,9 @@
   ; #:use-module (guix build-system trivial)
   #:use-module (srfi srfi-1))
 
-(define-public python-cwltool ; guix: needs work
+(define-public cwltool ; guix: needs work
   (package
-    (name "python-cwltool")
+    (name "cwltool")
     (version "1.0.20181012180214")
     (source
       (origin
@@ -36,18 +37,30 @@
      `(("python-bagit" ,python-bagit)
        ("python-setuptools" ,python-setuptools)
        ("python-pytest-cov" ,python-pytest-cov)
+       ("python-prov" ,python-prov)
        ("python-pytest-runner" ,python-pytest-runner)
        ("python-rdflib" ,python-rdflib)
        ("python-typing-extensions" ,python-typing-extensions)
        ("python-pyparsing" ,python-pyparsing)
        ("python-subprocess32" ,python-subprocess32)
+       ("python-ruamel.yaml" ,python-ruamel.yaml)
+       ("python-cachecontrol" ,python-cachecontrol)
+       ("python-mypy-extensions" ,python-mypy-extensions)
        ))
     (propagated-inputs
      `(("python-schema-salad" ,python-schema-salad)
-       ("python-prov" ,python-prov)
        ("python-html5lib" ,python-html5lib)
        ))
     ; (arguments `(#:tests? #f)) ;; CWL includes no tests.
+    (arguments
+     `(;#:phases
+       ; (modify-phases %standard-phases
+       ;   (replace 'check
+       ;     (lambda* (#:key inputs outputs #:allow-other-keys)
+       ;       (invoke "python" "-m" "pytest")
+       ;       )))
+       #:tests? #f))   ; Disable for now
+
     (home-page
       "https://github.com/common-workflow-language/common-workflow-language")
     (synopsis
@@ -56,9 +69,6 @@
       "Common workflow language reference implementation")
     (license license:asl2.0)))
 
-(define-public python2-cwltool
-  (package-with-python2 python-cwltool))
-
 (define-public python-schema-salad
   (package
     (name "python-schema-salad")
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index ef30812..808eb9d 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -146,7 +146,7 @@ functions.")
           "1m6y04qmig0b5hzb35lnaw3d2yfydb7alyr1579yblvgs3da6j7j"))))
   (build-system python-build-system)
   (inputs
-      `(("python-setuptools-scm" ,python-setuptools-scm)
+     `(("python-setuptools-scm" ,python-setuptools-scm)
       ("python-coverage" ,python-coverage)
       ("python-mock" ,python-mock)
       ))
@@ -711,3 +711,55 @@ the older versions.")
     (description "This is a python library for generating html from classes.")
     (home-page "https://github.com/srittau/python-htmlgen")
     (license license:expat)))
+
+(define-public python-version
+(let ((commit "e5aadc720bb74c535f29e5a2de5cd9697efe8d7c"))
+(package
+  (name "python-version")
+  (version "0.1.2")
+  (source
+    (origin
+      (method git-fetch)
+      (uri (git-reference
+      ; (url "https://github.com/genenetwork/pylmm.git")
+        (url "https://github.com/keleshev/version.git") ; version not in pypi
+        (commit commit)))
+      (file-name (string-append name "-" commit))
+      (sha256
+        (base32
+          "1rc8kf72v180qlygkh1y0jwv2fxqpx7n97bqfhbwgnn31iwai9g3"))))
+  (build-system python-build-system)
+  (build-system python-build-system)
+  (propagated-inputs
+    `(
+    ("python-more-itertools" ,python-more-itertools)
+    ("python-pytest" ,python-pytest)))
+  (home-page "http://github.com/halst/version")
+  (synopsis "Implementation of semantic version")
+  (description
+    "Implementation of semantic version")
+  (license license:expat)
+)))
+
+(define-public python-mypy-extensions
+(package
+  (name "python-mypy-extensions")
+  (version "0.4.1")
+  (source
+    (origin
+      (method url-fetch)
+      (uri (pypi-uri "mypy_extensions" version))
+      (sha256
+        (base32
+          "04h8brrbbx151dfa2cvvlnxgmb5wa00mhd2z7nd20s8kyibfkq1p"))))
+  (build-system python-build-system)
+  (propagated-inputs
+    `(("python-version" ,python-version)
+      ("python-typing" ,python-typing)))
+  (home-page "http://www.mypy-lang.org/")
+  (synopsis
+    "Experimental type system extensions for programs checked with the mypy typechecker.")
+  (description
+    "Experimental type system extensions for programs checked with the mypy typechecker.")
+  (license #f))
+)
-- 
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