From 793f831f84ab67081e57bc8ec58d9927c019feb5 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Thu, 25 Jun 2020 15:24:15 +0300
Subject: gn: Update bh20-seq-resource to 1.0-3.ae4cb3c.

---
 gn/packages/bioinformatics.scm | 21 ++++++++----
 gn/packages/python.scm         | 73 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 87 insertions(+), 7 deletions(-)

(limited to 'gn/packages')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index d4c6e00..fc2c923 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -1226,10 +1226,9 @@ runApp(launch.browser=0, port=4206)~%\n"
     "")
    (license #f)))
 
-;; Note this package is incomplete. Needs more to run properly.
 (define-public bh20-seq-resource
-  (let ((commit "bbca5ac9b2538e410efe3e09651f87e5573145de")
-        (revision "2"))
+  (let ((commit "ae4cb3c2cf7103bbc84f52618bb755d7ce25775b")
+        (revision "3"))
     (package
       (name "bh20-seq-resource")
       (version (git-version "1.0" revision commit))
@@ -1240,22 +1239,30 @@ runApp(launch.browser=0, port=4206)~%\n"
                        (commit commit)))
                 (file-name (git-file-name name version))
                 (sha256
-                 (base32 "1kkysjgmhp7kfb17470ik821p9djsidyqmkbjvv37jx2w9pvw31z"))))
+                 (base32 "1k0gsz4yc8l5znanzd094g2jp40ksbpa9667zr31ayrjx6labz02"))
+                (modules '((guix build utils)))
+                (snippet
+                 '(begin
+                    (substitute* "setup.py"
+                      (("py-dateutil") "python-dateutil"))
+                    #t))))
       (build-system python-build-system)
-      (inputs
+      (propagated-inputs
        `(("python-arvados-python-client" ,python-arvados-python-client)
+         ("python-dateutil" ,python-dateutil)
          ("python-flask" ,python-flask)
          ("python-magic" ,python-magic)
          ("python-pyyaml" ,python-pyyaml)
          ("python-pycurl" ,python-pycurl)
          ("python-pyshex" ,python-pyshex)
+         ("python-ruaml.yaml" ,python38-ruaml.yaml-0.15.76)
          ("clustalw" ,clustalw)
          ("python-schema-salad" ,python-schema-salad)))
       (native-inputs
        `(("git" ,(@ (gnu packages version-control) git))
          ("python-oauth2client" ,python-oauth2client)
-         ("python-pytest" ,python-pytest)
-         ("python-pytest-runner" ,python-pytest-runner)
+         ("python-pytest" ,python-pytest-4)
+         ("python-pytest-runner" ,python-pytest-runner-2)
          ("python-uritemplate" ,python-uritemplate)))
       (home-page "https://github.com/arvados/bh20-seq-resource")
       (synopsis
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 51efc4a..b181767 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -1588,3 +1588,76 @@ handles recursion and lists.")
     (synopsis "SPARQL Slurper for rdflib")
     (description "This package provides a SPARQL Slurper for rdflib.")
     (license license:asl2.0)))
+
+(define-public python38-ruaml.yaml-0.15.76
+  (package
+    (inherit python-ruamel.yaml)
+    (name "python-ruamel.yaml")
+    (version "0.15.76")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "ruamel.yaml" "0.15.78"))
+        (sha256
+         (base32
+          "0pwxgrma6k47kvsphqz5yrhwnfrhwsrhn6sjp8p21s91wdgkqyc5"))))
+    (arguments
+     `(#:tests? #f  ; suprise test failures
+       #:phases
+       (modify-phases %standard-phases
+         ;; For some unknown reason we need: ruamel.yaml<=0.15.77,>=0.15.54
+         ;; But 0.15.78 is the first which builds with python-3.8.
+         (add-after 'unpack 'patch-source
+           (lambda _
+             (substitute* "__init__.py"
+               (("0\\.15\\.78") "0.15.76")
+               (("15, 78") "15, 76"))
+             #t)))))))
+
+(define-public python2-ruamel.ordereddict
+  (package
+    (name "python2-ruamel.ordereddict")
+    (version "0.4.14")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "ruamel.ordereddict" version))
+        (sha256
+         (base32
+          "0jldrcanmz0284r2y6kbi82vslkaf5hf5q90v7rqxcdjdv952418"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+             (if tests?
+               (begin (add-installed-pythonpath inputs outputs)
+                      (invoke "python" "test/testordereddict.py"))
+               #t))))))
+    (home-page "https://sourceforge.net/projects/ruamel-ordereddict/")
+    (synopsis "Version of dict that keeps keys in insertion resp. sorted order")
+    (description
+     "This package provides a version of dict that keeps keys in insertion resp.
+sorted order.")
+    (license license:expat)))
+
+(define-public python-pytest-4
+  (package
+    (inherit python-pytest)
+    (version "4.6.11")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "pytest" version))
+        (sha256
+         (base32
+          "0ls3pqr86xgif6bphsb6wrww9r2vc7p7a2naq8zcq8115wwq5yjh"))))
+    (arguments
+     (substitute-keyword-arguments (package-arguments python-pytest)
+       ((#:tests? _ #f) #f)))
+    (native-inputs
+     `(("python-argcomplete" ,python-argcomplete)
+       ("python-requests" ,python-requests)
+       ,@(package-native-inputs python-pytest)))))
-- 
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