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-rw-r--r--gn/packages/bioinformatics.scm6
-rw-r--r--gn/packages/check.scm61
-rw-r--r--gn/packages/crates-io.scm6
-rw-r--r--gn/packages/dlang.scm2
-rw-r--r--gn/packages/edash.scm5
-rw-r--r--gn/packages/fpga.scm2
-rw-r--r--gn/packages/genecup.scm2
-rw-r--r--gn/packages/genenetwork.scm14
-rw-r--r--gn/packages/machine-learning.scm11
-rw-r--r--gn/packages/pangenome.scm2
-rw-r--r--gn/packages/patches/python-unittest2-python3-compat.patch46
-rw-r--r--gn/packages/patches/python-unittest2-remove-argparse.patch11
-rw-r--r--gn/packages/python.scm5
-rw-r--r--gn/packages/virtualization.scm3
-rw-r--r--gn/packages/yaj.scm3
15 files changed, 147 insertions, 32 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 1815bed..e6ca5db 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -41,9 +41,7 @@
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cpp)
   #:use-module (gnu packages cran)
-  #:use-module (gnu packages crates-compression)
-  #:use-module (gnu packages crates-io)
-  #:use-module (gnu packages crates-graphics)
+  #:use-module (past-crates packages crates-io)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages datastructures)
@@ -76,7 +74,7 @@
   #:use-module (gnu packages python-build)
   #:use-module (gnu packages python-science)
   #:use-module (gnu packages python-web)
-  #:use-module ((gnu packages python-xyz) #:hide (python2-six))
+  #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages python-check)
   #:use-module (gnu packages rdf)
   #:use-module (gnu packages readline)
diff --git a/gn/packages/check.scm b/gn/packages/check.scm
new file mode 100644
index 0000000..960e78e
--- /dev/null
+++ b/gn/packages/check.scm
@@ -0,0 +1,61 @@
+(define-module (gn packages check)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix build-system python)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (gnu packages check)
+  #:use-module (gnu packages python-xyz)
+  #:use-module (past packages python27))
+
+(define-public python-nosexcover
+  (package
+    (name "python-nosexcover")
+    (version "1.0.11")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "nosexcover" version))
+              (sha256
+               (base32
+                "10xqr12qv62k2flxwqhh8cr00cjhn7sfjrm6p35gd1x5bmjkr319"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     (list python-coverage python-nose))
+    (home-page "https://github.com/cmheisel/nose-xcover")
+    (synopsis "Extends nose.plugins.cover to add Cobertura-style XML reports")
+    (description "Nose-xcover is a companion to the built-in
+@code{nose.plugins.cover}.  This plugin will write out an XML coverage report
+to a file named coverage.xml.
+
+It will honor all the options you pass to the Nose coverage plugin,
+especially -cover-package.")
+    (license license:expat)))
+
+(define-public python-unittest2
+  (package
+    (name "python-unittest2")
+    (version "1.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "unittest2" version))
+       (patches
+        (search-patches "python-unittest2-python3-compat.patch"
+                        "python-unittest2-remove-argparse.patch"))
+       (sha256
+        (base32
+         "0y855kmx7a8rnf81d3lh5lyxai1908xjp0laf4glwa4c8472m212"))))
+    (build-system python-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda _
+             (zero? (system* "python" "-m" "unittest2" "discover" "--verbose")))))))
+    (propagated-inputs
+     (list python-six python-traceback2))
+    (home-page "https://pypi.org/project/unittest2/")
+    (synopsis "Python unit testing library")
+    (description
+     "Unittest2 is a replacement for the unittest module in the Python
+standard library.")
+    (license license:psfl)))
diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm
index 92969fd..23182a2 100644
--- a/gn/packages/crates-io.scm
+++ b/gn/packages/crates-io.scm
@@ -5,11 +5,7 @@
   #:use-module (guix download)
   #:use-module (guix git-download)
   #:use-module (guix build-system cargo)
-  #:use-module (gnu packages crates-check)
-  #:use-module (gnu packages crates-compression)
-  #:use-module (gnu packages crates-graphics)
-  #:use-module (gnu packages crates-io)
-  #:use-module (gnu packages crates-windows)
+  #:use-module (past-crates packages crates-io)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages python))
 
diff --git a/gn/packages/dlang.scm b/gn/packages/dlang.scm
index 5cab985..a7d76a2 100644
--- a/gn/packages/dlang.scm
+++ b/gn/packages/dlang.scm
@@ -103,7 +103,7 @@ std.algorithm.endsWith(tzName, \"/leapseconds\"))")))))))
        ("tzdata" ,tzdata)
        ("zlib" ,zlib)))
     (native-inputs
-     `(("llvm" ,llvm-6)
+     `(("llvm" ,llvm-12)
        ("python-wrapper" ,python-wrapper)
        ("unzip" ,unzip)
        ("phobos-src"
diff --git a/gn/packages/edash.scm b/gn/packages/edash.scm
index f75ec88..42da046 100644
--- a/gn/packages/edash.scm
+++ b/gn/packages/edash.scm
@@ -18,7 +18,8 @@
   #:use-module (gnu packages check)
   #:use-module (gn packages web)
   #:use-module (gnu packages sqlite)
-  #:use-module (gn packages python))
+  #:use-module (gn packages python)
+  #:use-module (past packages python27))
 
 (define-public python-s3transfer-0.1.13
   (package
@@ -272,7 +273,6 @@ necessary.")
        ("python-pytest-cov" ,python-pytest-cov)
        ("python-jsonschema" ,python-jsonschema)
        ("python-pytest-pycodestyle" ,python-pytest-pycodestyle)
-       ("python-pytest-cache" ,python-pytest-cache)
 ;;       ("python-pytest-flakes" ,python-pytest-flakes)
        ))
     (arguments `(#:tests? #f))
@@ -304,7 +304,6 @@ with the Specification.")
        ("python-flake8" ,python-flake8)
        ("python-pytest-cov" ,python-pytest-cov)
        ("python-pytest-pycodestyle" ,python-pytest-pycodestyle)
-       ("python-pytest-cache" ,python-pytest-cache)
 ;;       ("python-pytest-flakes" ,python-pytest-flakes)
        ))
     (arguments `(#:tests? #f))
diff --git a/gn/packages/fpga.scm b/gn/packages/fpga.scm
index 654b71d..b8c3537 100644
--- a/gn/packages/fpga.scm
+++ b/gn/packages/fpga.scm
@@ -1,5 +1,5 @@
 (define-module (gn packages fpga)
-  #:use-module (gnu packages fpga)
+  #:use-module (gnu packages electronics)
   #:use-module (guix git-download)
   #:use-module (guix packages))
 
diff --git a/gn/packages/genecup.scm b/gn/packages/genecup.scm
index d761826..88e0879 100644
--- a/gn/packages/genecup.scm
+++ b/gn/packages/genecup.scm
@@ -237,7 +237,7 @@ if __name__ == '__main__':
        ("python-nltk" ,python-nltk)
        ("python-pandas" ,python-pandas)
        ("python-regex" ,python-regex)
-       ("tensorflow" ,tensorflow)))
+       ("tensorflow" ,tensorflow-lite)))
     (native-inputs
      `(("bootstrap" ,web-bootstrap)
        ("cytoscape" ,javascript-cytoscape-3.17)
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 745cb18..4c35f86 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -25,7 +25,7 @@
   #:use-module (gnu packages bioinformatics)
   #:use-module (gnu packages check)
   #:use-module (gnu packages cran)
-  #:use-module (gnu packages crates-io)
+  #:use-module (past-crates packages crates-io)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages ghostscript)
@@ -118,7 +118,7 @@
       ((#:tests? _ #f) #f)))))
 
 (define-public genenetwork3
-  (let ((commit "082d585fcb7e1f488831faf71785480d20173c5e")
+  (let ((commit "d24ffc9afa92c7d938813ee6745f8d43ac88a0a8")
         (revision "5"))
     (package
       (name "genenetwork3")
@@ -132,7 +132,7 @@
          (file-name (git-file-name name version))
          (sha256
           (base32
-           "1hky4ya4x8i9kidlxdsm71lpp987zxf90jlr4czi6agpaa9ir2id"))))
+           "19lnwrb30hz3wp2nh09fvvpd75jig5gy5vjfzw3m9k9bvd6ac9f4"))))
       (inputs
        (list python-click))
       (native-inputs
@@ -227,7 +227,7 @@ storage.")
     (license license:bsd-3)))
 
 (define-public genenetwork2
-  (let ((commit "2881fd0657cf632e003e4666e7ff301b96f47ceb")
+  (let ((commit "e00d5adc4534d07fe97e20f491d33b3ad843ca72")
         (revision "4"))
     (package
       (name "genenetwork2")
@@ -240,7 +240,7 @@ storage.")
                 (file-name (string-append name "-" version))
                 (sha256
                  (base32
-                  "0cbjq7l2wpw78zankz9hpdln1nn1b8qzf5hsn7g8wcxp7ikacfnl"))))
+                  "17hrsznb0ph2agsw1rin41pry96w4kpk3zzr5c2pfasgmsai219g"))))
       (native-inputs
        (list graphviz))
       (propagated-inputs
@@ -533,7 +533,7 @@ storage.")
      (license license:agpl3+))))
 
 (define-public gn-auth
-  (let ((commit "33418d9f428c8ea5dc14f2accc15f4abbf275ab2")
+  (let ((commit "9839e5bf35bd7be158b35fa98a734f7a3473688d")
         (revision "01"))
     (package
       (name "gn-auth")
@@ -548,7 +548,7 @@ storage.")
          (hash
           (content-hash
            (base32
-            "0ljwhcdm65z33b352skg84c4b04qsg76k1ing43y6sw427rxjany")))))
+            "1lsi7z8hvpdqgcsx3zc5ip701xka9s75c7r4pjlby2ryjc0gw83d")))))
       (build-system python-build-system)
       (arguments
        (list
diff --git a/gn/packages/machine-learning.scm b/gn/packages/machine-learning.scm
index ebb89e2..541b3b6 100644
--- a/gn/packages/machine-learning.scm
+++ b/gn/packages/machine-learning.scm
@@ -11,14 +11,15 @@
   #:use-module (gnu packages check)
   #:use-module (gnu packages python-check)
   #:use-module (gnu packages sphinx)
-  #:use-module (gnu packages python-web))
+  #:use-module (gnu packages python-web)
+  #:use-module (past packages python27))
 
 (define-public tensorflow-native
   (package
-    (inherit tensorflow)
+    (inherit tensorflow-lite)
     (name "tensorflow-native")
     (arguments
-     (substitute-keyword-arguments (package-arguments tensorflow)
+     (substitute-keyword-arguments (package-arguments tensorflow-lite)
        ((#:substitutable? _ #f) #f)
        ((#:configure-flags flags)
         `(cons
@@ -77,7 +78,7 @@ models for use with the Keras deep learning framework.")
            python-pytest
            python-pytest-cov
            python-pytest-xdist
-           tensorflow))
+           tensorflow-lite))
     (home-page "https://github.com/keras-team/keras-preprocessing/")
     (synopsis "Data preprocessing and augmentation for deep learning models")
     (description
@@ -161,7 +162,7 @@ with image data, text data, and sequence data.")
            python-pyyaml
            python-scipy
            python-six
-           tensorflow
+           tensorflow-lite
            graphviz))
     (native-inputs
      (list python-flaky
diff --git a/gn/packages/pangenome.scm b/gn/packages/pangenome.scm
index c66b594..5c5ef00 100644
--- a/gn/packages/pangenome.scm
+++ b/gn/packages/pangenome.scm
@@ -5,7 +5,7 @@
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix build-system cargo)
-  #:use-module (gnu packages crates-io)
+  #:use-module (past-crates packages crates-io)
   #:use-module (gn packages crates-io))
 
 
diff --git a/gn/packages/patches/python-unittest2-python3-compat.patch b/gn/packages/patches/python-unittest2-python3-compat.patch
new file mode 100644
index 0000000..68fbcca
--- /dev/null
+++ b/gn/packages/patches/python-unittest2-python3-compat.patch
@@ -0,0 +1,46 @@
+Skip tests that fail with newer versions of Python.
+
+Patch copied from Gentoo:
+
+https://gitweb.gentoo.org/repo/gentoo.git/tree/dev-python/unittest2/files/unittest2-1.1.0-python3.5-test.patch
+
+diff --git a/unittest2/test/test_loader.py b/unittest2/test/test_loader.py
+index 683f662..347eea5 100644
+--- a/unittest2/test/test_loader.py
++++ b/unittest2/test/test_loader.py
+@@ -509,6 +509,7 @@ class Test_TestLoader(unittest2.TestCase):
+     #
+     # What happens when an impossible name is given, relative to the provided
+     # `module`?
++    @unittest.skipIf(sys.version_info[:2] >= (3, 5), "python 3.5 has problems here")
+     def test_loadTestsFromName__relative_malformed_name(self):
+         loader = unittest.TestLoader()
+ 
+@@ -811,6 +812,7 @@ class Test_TestLoader(unittest2.TestCase):
+     # TestCase or TestSuite instance."
+     #
+     # What happens when presented with an impossible module name?
++    @unittest.skipIf(sys.version_info[:2] >= (3, 5), "python 3.5 has problems here")
+     def test_loadTestsFromNames__malformed_name(self):
+         loader = unittest2.TestLoader()
+ 
+@@ -918,6 +920,7 @@ class Test_TestLoader(unittest2.TestCase):
+     # "The method optionally resolves name relative to the given module"
+     #
+     # What happens when presented with an impossible attribute name?
++    @unittest.skipIf(sys.version_info[:2] >= (3, 5), "python 3.5 has problems here")
+     def test_loadTestsFromNames__relative_malformed_name(self):
+         loader = unittest.TestLoader()
+ 
+diff --git a/unittest2/compatibility.py b/unittest2/compatibility.py
+index 9e5f1a5..2d20c19 100644
+--- a/unittest2/compatibility.py
++++ b/unittest2/compatibility.py
+@@ -140,6 +140,6 @@ except ImportError:
+ ###  ChainMap (helper for configparser and string.Template)
+ ########################################################################
+ 
+-class ChainMap(collections.MutableMapping):
++class ChainMap(collections.abc.MutableMapping):
+     ''' A ChainMap groups multiple dicts (or other mappings) together
+     to create a single, updateable view.
diff --git a/gn/packages/patches/python-unittest2-remove-argparse.patch b/gn/packages/patches/python-unittest2-remove-argparse.patch
new file mode 100644
index 0000000..c967387
--- /dev/null
+++ b/gn/packages/patches/python-unittest2-remove-argparse.patch
@@ -0,0 +1,11 @@
+--- a/setup.py	2017-09-12 01:22:06.273997788 +0200
++++ b/setup.py	2017-09-12 01:22:14.297918757 +0200
+@@ -57,7 +57,7 @@
+ # Both install and setup requires - because we read VERSION from within the
+ # package, and the package also exports all the APIs.
+ # six for compat helpers
+-REQUIRES = ['argparse', 'six>=1.4', 'traceback2'],
++REQUIRES = ['six>=1.4', 'traceback2'],
+ 
+ params = dict(
+     name=NAME,
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 9dd6edd..54d45a4 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -26,7 +26,7 @@
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages jupyter)
   #:use-module (gnu packages cran)
-  #:use-module ((gnu packages python-xyz) #:hide (python2-six))
+  #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages rdf)
   #:use-module (gnu packages readline)
   #:use-module (gnu packages serialization)
@@ -42,7 +42,8 @@
   #:use-module (guix utils)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system python)
-  #:use-module (srfi srfi-1))
+  #:use-module (srfi srfi-1)
+  #:use-module (gn packages check))
 
 (define-public python-rpy2-2.9
   (package
diff --git a/gn/packages/virtualization.scm b/gn/packages/virtualization.scm
index e0eb016..22753f8 100644
--- a/gn/packages/virtualization.scm
+++ b/gn/packages/virtualization.scm
@@ -16,7 +16,8 @@
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages protobuf)
   #:use-module (gnu packages python)
-  #:use-module (gnu packages python-xyz))
+  #:use-module (gnu packages python-xyz)
+  #:use-module (past packages python27))
 
 (define-public gem5
   (package
diff --git a/gn/packages/yaj.scm b/gn/packages/yaj.scm
index c36a6cc..bdd417d 100644
--- a/gn/packages/yaj.scm
+++ b/gn/packages/yaj.scm
@@ -12,7 +12,8 @@
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages web)
-  #:use-module (gn packages web))
+  #:use-module (gn packages web)
+  #:use-module (gn packages check))
 
 (define-public python-elasticsearch
   (package
generated by cgit-pink 1.4.1 (git 2.36.1) at 2025-10-06 21:16:57 +0000