Merge master into staging-next

pkgs/development/python-modules/ase/default.nix

@@ -1,5 +1,5 @@
 { lib
-, fetchurl
+, fetchPypi
 , buildPythonPackage
 , numpy
 , scipy
@@ -10,12 +10,12 @@
 }:
 
 buildPythonPackage rec {
-  version = "3.16.2";
   pname = "ase";
+  version = "3.17.0";
 
-  src = fetchurl {
-     url = "https://gitlab.com/${pname}/${pname}/-/archive/${version}/${pname}-${version}.tar.gz";
-     sha256 = "171j3f4a261cfnqjq98px5fldxql65i3jgf60wc945xvh0mbc8ds";
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1d4gxypaahby45zcpl0rffcn2z7n55dg9lcd8sv6jjsmbbf9vr4g";
   };
 
   propagatedBuildInputs = [ numpy scipy matplotlib flask pillow psycopg2 ];
@@ -27,10 +27,10 @@ buildPythonPackage rec {
   # tests just hang most likely due to something with subprocesses and cli
   doCheck = false;
 
-  meta = {
+  meta = with lib; {
     description = "Atomic Simulation Environment";
     homepage = https://wiki.fysik.dtu.dk/ase/;
-    license = lib.licenses.lgpl21Plus;
-    maintainers = with lib.maintainers; [ costrouc ];
+    license = licenses.lgpl21Plus;
+    maintainers = with maintainers; [ costrouc ];
   };
 }

pkgs/development/python-modules/fonttools/default.nix

@@ -8,11 +8,11 @@
 
 buildPythonPackage rec {
   pname = "fonttools";
-  version = "3.32.0";
+  version = "3.33.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "16cg5v50x905c0dr34wqk70b0n3mqzp41iir2rd73f31d1z9jndq";
+    sha256 = "196yl6m3fycrbsclcmg550821j18ga6dpghmk5nb1xi4j4yb62gq";
     extension = "zip";
   };
 

pkgs/development/python-modules/git-annex-adapter/default.nix

@@ -4,16 +4,16 @@
 
 buildPythonPackage rec {
   pname = "git-annex-adapter";
-  version = "0.2.0";
+  version = "0.2.1";
 
   disabled = !isPy3k;
 
-  # There is only a wheel on PyPI - build from source instead
+  # No tests in PyPI tarball
   src = fetchFromGitHub {
     owner = "alpernebbi";
     repo = pname;
     rev = "v${version}";
-    sha256 = "1sbgp4ivgw4m8nngrlb1f78xdnssh639c1khv4z98753w3sdsxdz";
+    sha256 = "146q1jhcfc7f96ajkhjffskkljk2xzivs5ih5clb8qx0sh7mj097";
   };
 
   prePatch = ''
@@ -22,38 +22,6 @@ buildPythonPackage rec {
       --replace "'git-annex'" "'${git-annex}/bin/git-annex'"
   '';
 
-  patches = [
-    # fixes the "not-a-git-repo" testcase where recent git versions expect a slightly different error.
-    ./not-a-git-repo-testcase.patch
-
-    # fixes the testcase which parses the output of `git-annex info` where several
-    # new lines are displayed that broke the test.
-    (fetchpatch {
-      url = "https://github.com/Ma27/git-annex-adapter/commit/39cb6da69c1aec3d57ea9f68c2dea5113ae1b764.patch";
-      sha256 = "0wyy2icqan3jpiw7dm50arfq3mgq4b5s3g91k82srap763r9hg5m";
-    })
-
-    # fixes the testcase which runs "git status" and complies with the
-    # slightly altered output.
-    (fetchpatch {
-      url = "https://github.com/alpernebbi/git-annex-adapter/commit/9f64c4b99cae7b681820c6c7382e1e40489f4d1e.patch";
-      sha256 = "0yh66gial6bx7kbl7s7lkzljnkpgvgr8yahqqcq9z76d0w752dir";
-    })
-
-    # fix test broken due to renaming of repository version 6 to 7
-    (fetchpatch {
-      url = https://github.com/alpernebbi/git-annex-adapter/commit/a72efea02ec9b2ed9c7aad0b222056d72eb0c143.patch;
-      sha256 = "0nv9ms01jnwp3qzwsla4w8pcpakq5lh7c77xdbhiidbrx0n1p4q7";
-    })
-  ] ++ stdenv.lib.optionals stdenv.isDarwin [
-    # `rev` is part of utillinux on NixOS which is not available on `nixpks` for darwin:
-    # https://logs.nix.ci/?key=nixos/nixpkgs.45061&attempt_id=271763ba-2ae7-4098-b469-b82b1d8edb9b
-    (fetchpatch {
-      url = "https://github.com/alpernebbi/git-annex-adapter/commit/0b60b4577528b309f6ac9d47b55a00dbda9850ea.patch";
-      sha256 = "0z608hpmyzv1mm01dxr7d6bi1hc77h4yafghkynmv99ijgnm1qk7";
-    })
-  ];
-
   checkInputs = [
     utillinux # `rev` is needed in tests/test_process.py
   ];

pkgs/development/python-modules/git-annex-adapter/not-a-git-repo-testcase.patch

@@ -1,13 +0,0 @@
-diff --git a/tests/test_process.py b/tests/test_process.py
-index 493fc8f..feb1833 100644
---- a/tests/test_process.py
-+++ b/tests/test_process.py
-@@ -126,7 +126,7 @@ class TestProcessOnEmptyDir(TempDirTestCase):
-         with self.assertRaises(subprocess.CalledProcessError) as cm:
-             runner('status', '-sb')
-         self.assertIn(
--            "fatal: Not a git repository",
-+            "fatal: not a git repository",
-             cm.exception.stderr,
-         )
- 

pkgs/development/python-modules/osc/default.nix

@@ -11,14 +11,14 @@
 
 buildPythonPackage {
   pname = "osc";
-  version = "0.162.0-55-gb730f88";
-  disabled = isPy3k;
+  version = "0.163.0-40-gb4b1ec7";
+  disabled = isPy3k;    # urlgrabber doesn't support python-3.x
 
   src = fetchFromGitHub {
     owner = "openSUSE";
     repo = "osc";
-    rev = "b730f880cfe85a8547f569355a21706f27ebfa78";
-    sha256 = "0hh9j5zd2kc0804d2jmf1q3w5xm9l9s69hhgysbncrv5fw0414lh";
+    rev = "b4b1ec7b64d4f9bb42f140754519221b810e232c";
+    sha256 = "01z1b15x9vzhd7j94f6n3g50h5br7lwz86akgic0wpp41zv37jad";
   };
 
   buildInputs = [ pkgs.bashInteractive ]; # needed for bash-completion helper

pkgs/development/python-modules/pygmo/default.nix

@@ -1,7 +1,6 @@
 { lib
 , fetchFromGitHub
 , buildPythonPackage
-, cmake
 , eigen
 , nlopt
 , ipopt
@@ -11,38 +10,44 @@
 , cloudpickle
 , ipyparallel
 , numba
+, python
 }:
 
-buildPythonPackage rec {
-  pname = "pygmo";
-  version = "2.8";
-
-  src = fetchFromGitHub {
-     owner = "esa";
-     repo = "pagmo2";
-     rev = "v${version}";
-     sha256 = "1xwxamcn3fkwr62jn6bkanrwy0cvsksf75hfwx4fvl56awnbz41z";
-  };
-
-  buildInputs = [ cmake eigen nlopt ipopt boost pagmo2 ];
+let
   propagatedBuildInputs = [ numpy cloudpickle ipyparallel numba ];
 
-  preBuild = ''
-    cp -v -r $src/* .
-    cmake -DCMAKE_INSTALL_PREFIX=$out -DPAGMO_BUILD_TESTS=no -DCMAKE_SYSTEM_NAME=Linux -DPagmo_DIR=${pagmo2} -DPAGMO_BUILD_PYGMO=yes -DPAGMO_BUILD_PAGMO=no -DPAGMO_WITH_EIGEN3=yes -DPAGMO_WITH_NLOPT=yes -DNLOPT_LIBRARY=${nlopt}/lib/libnlopt_cxx.so -DPAGMO_WITH_IPOPT=yes -DIPOPT=${ipopt}
+  pagmo2WithPython = pagmo2.overrideAttrs (oldAttrs: {
+    cmakeFlags = oldAttrs.cmakeFlags ++ [
+      "-DPAGMO_BUILD_PYGMO=yes"
+      "-DPAGMO_BUILD_PAGMO=no"
+      "-DPagmo_DIR=${pagmo2}"
+    ];
+    buildInputs = [ eigen nlopt ipopt boost pagmo2 ] ++ propagatedBuildInputs;
+    postInstall = ''
+      mv wheel $out
+    '';
+  });
 
-    make install
-    mv $out/lib/python*/site-packages/pygmo wheel
+in buildPythonPackage rec {
+  pname = "pygmo";
+  version = pagmo2WithPython.version;
+
+  inherit propagatedBuildInputs;
+
+  src = pagmo2WithPython;
+
+  preBuild = ''
+    mv ${python.sitePackages}/pygmo wheel
     cd wheel
   '';
 
   # dont do tests
   doCheck = false;
 
-  meta = {
+  meta = with lib; {
     description = "Parallel optimisation for Python";
     homepage = https://esa.github.io/pagmo2/;
-    license = lib.licenses.gpl3Plus;
-    maintainers = with lib.maintainers; [ costrouc ];
+    license = licenses.gpl3Plus;
+    maintainers = [ maintainers.costrouc ];
   };
 }