Merge pull request #56312 from costrouc/python-unstable

Fixes several broken python packages for python-unstable

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

@@ -1,4 +1,4 @@
-{ stdenv
+{ lib
 , buildPythonPackage
 , fetchPypi
 , pythonOlder
@@ -15,24 +15,28 @@
 
 buildPythonPackage rec {
   pname = "gidgethub";
-  version = "3.0.0";
-  format = "flit";
+  version = "3.1.0";
 
   disabled = pythonOlder "3.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1ebe79cf80ad64cb78c880efc7f30ac664e18b80dfd18ee201bf8685cf029628";
+    sha256 = "52119435ba73ddd5e697dae7bec8b93a048bc738720b81691ebd4b4d81d2d762";
   };
 
-  buildInputs = [ setuptools pytestrunner ];
+  nativeBuildInputs = [ setuptools pytestrunner ];
   checkInputs = [ pytest pytest-asyncio twisted treq tornado aiohttp ];
   propagatedBuildInputs = [ uritemplate ];
 
+  postPatch = ''
+    substituteInPlace setup.py \
+      --replace "extras_require=extras_require," "extras_require=None,"
+  '';
+
   # requires network (reqests github.com)
   doCheck = false;
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     description = "An async GitHub API library";
     homepage = https://github.com/brettcannon/gidgethub;
     license = licenses.asl20;

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

@@ -1,5 +1,12 @@
-{ stdenv, buildPythonPackage, fetchPypi
-, six, requests-cache, pygments, pyquery }:
+{ lib
+, buildPythonPackage
+, fetchPypi
+, six
+, requests-cache
+, pygments
+, pyquery
+, python
+}:
 
 buildPythonPackage rec {
   pname = "howdoi";
@@ -12,9 +19,14 @@ buildPythonPackage rec {
 
   propagatedBuildInputs = [ six requests-cache pygments pyquery ];
 
-  meta = with stdenv.lib; {
+  preCheck = ''
+    export HOME=$(mktemp -d)
+  '';
+
+  meta = with lib; {
     description = "Instant coding answers via the command line";
     homepage = https://pypi.python.org/pypi/howdoi;
     license = licenses.mit;
+    maintainers = [ maintainers.costrouc ];
   };
 }

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

@@ -1,33 +1,42 @@
-{ stdenv, buildPythonPackage, fetchFromGitHub, nose, numpy, six, ruamel_yaml, msgpack-python, coverage, coveralls, pymongo, lsof }:
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, nose
+, numpy
+, six
+, ruamel_yaml
+, msgpack-python
+, coverage
+, coveralls
+, pymongo
+, lsof
+}:
 
 buildPythonPackage rec {
   pname = "monty";
-  version = "1.0.2";
+  version = "1.0.4";
 
   # No tests in Pypi
   src = fetchFromGitHub {
     owner = "materialsvirtuallab";
     repo = pname;
     rev = "v${version}";
-    sha256 = "0ss70fanavqdpj56yymj06lacgnknb4ap39m2q28v9lz32cs6xdg";
+    sha256 = "0vqaaz0dw0ypl6sfwbycpb0qs3ap04c4ghbggklxih66spdlggh6";
   };
 
-  propagatedBuildInputs = [ nose numpy six ruamel_yaml msgpack-python coverage coveralls pymongo lsof ];
-  
+  checkInputs = [ lsof nose numpy msgpack-python coverage coveralls pymongo];
+  propagatedBuildInputs = [ six ruamel_yaml ];
+
   preCheck = ''
     substituteInPlace tests/test_os.py \
-      --replace 'def test_which(self):' '#' \
-      --replace 'py = which("python")' '#' \
-      --replace 'self.assertEqual(os.path.basename(py), "python")' '#' \
-      --replace 'self.assertEqual("/usr/bin/find", which("/usr/bin/find"))' '#' \
-      --replace 'self.assertIs(which("non_existent_exe"), None)' '#' \
+      --replace 'self.assertEqual("/usr/bin/find", which("/usr/bin/find"))' '#'
   '';
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     description = "Serves as a complement to the Python standard library by providing a suite of tools to solve many common problems";
     longDescription = "
-      Monty implements supplementary useful functions for Python that are not part of the 
-      standard library. Examples include useful utilities like transparent support for zipped files, useful design 
+      Monty implements supplementary useful functions for Python that are not part of the
+      standard library. Examples include useful utilities like transparent support for zipped files, useful design
       patterns such as singleton and cached_class, and many more.
     ";
     homepage = https://github.com/materialsvirtuallab/monty;
@@ -35,4 +44,3 @@ buildPythonPackage rec {
     maintainers = with maintainers; [ psyanticy ];
   };
 }
-

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

@@ -1,6 +1,8 @@
-{ stdenv
+{ lib
 , buildPythonPackage
 , fetchPypi
+, isPy27
+, funcsigs
 }:
 
 buildPythonPackage rec {
@@ -8,14 +10,18 @@ buildPythonPackage rec {
   version = "0.9";
 
   src = fetchPypi {
-    inherit pname version;
+    inherit version;
+    pname = "Pint";
     sha256 = "32d8a9a9d63f4f81194c0014b3b742679dce81a26d45127d9810a68a561fe4e2";
   };
 
-  meta = with stdenv.lib; {
+  propagatedBuildInputs = lib.optional isPy27 funcsigs;
+
+  meta = with lib; {
     description = "Physical quantities module";
     license = licenses.bsd3;
     homepage = "https://github.com/hgrecco/pint/";
+    maintainers = [ maintainers.costrouc ];
   };
 
 }

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

@@ -1,21 +1,36 @@
-{ stdenv, buildPythonPackage, fetchFromGitHub, pytest, libsodium, cffi, six, hypothesis}:
+{ stdenv
+, buildPythonPackage
+, fetchPypi
+, pytest
+, libsodium
+, cffi
+, six
+, hypothesis
+}:
 
 buildPythonPackage rec {
   pname = "pynacl";
   version = "1.3.0";
 
-  src = fetchFromGitHub {
-    owner = "pyca";
-    repo = pname;
-    rev = version;
-    sha256 = "0ac00d5bfdmz1x428h2scq5b34llp61yhxradl94qjwz7ikqv052";
+  src = fetchPypi {
+    inherit version;
+    pname = "PyNaCl";
+    sha256 = "0c6100edd16fefd1557da078c7a31e7b7d7a52ce39fdca2bec29d4f7b6e7600c";
   };
 
   checkInputs = [ pytest hypothesis ];
-  propagatedBuildInputs = [ libsodium cffi six ];
+  buildInputs = [ libsodium ];
+  propagatedBuildInputs = [ cffi six ];
 
   SODIUM_INSTALL = "system";
 
+  # fixed in next release 1.3.0+
+  # https://github.com/pyca/pynacl/pull/480
+  postPatch = ''
+    substituteInPlace tests/test_bindings.py \
+      --replace "average_size=128," ""
+  '';
+
   checkPhase = ''
     py.test
   '';

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

@@ -1,5 +1,5 @@
-{ stdenv, buildPythonPackage, fetchPypi
-, geos, glibcLocales, pytest, cython
+{ stdenv, buildPythonPackage, fetchPypi, substituteAll
+, geos, pytest, cython
 , numpy
 }:
 
@@ -12,26 +12,31 @@ buildPythonPackage rec {
     sha256 = "c4b87bb61fc3de59fc1f85e71a79b0c709dc68364d9584473697aad4aa13240f";
   };
 
-  buildInputs = [ geos glibcLocales cython ];
+  nativeBuildInputs = [
+    geos # for geos-config
+    cython
+  ];
 
   checkInputs = [ pytest ];
 
   propagatedBuildInputs = [ numpy ];
 
-  preConfigure = ''
-    export LANG="en_US.UTF-8";
-  '';
+  # environment variable used in shapely/_buildcfg.py
+  GEOS_LIBRARY_PATH = "${geos}/lib/libgeos_c${stdenv.hostPlatform.extensions.sharedLibrary}";
 
-  patchPhase = let
-    libc = if stdenv.isDarwin then "libc.dylib" else "libc.so.6";
-  in ''
-    sed -i "s|_lgeos = load_dll('geos_c', fallbacks=.*)|_lgeos = load_dll('geos_c', fallbacks=['${geos}/lib/libgeos_c${stdenv.hostPlatform.extensions.sharedLibrary}'])|" shapely/geos.py
-    sed -i "s|free = load_dll('c').free|free = load_dll('c', fallbacks=['${stdenv.cc.libc}/lib/${libc}']).free|" shapely/geos.py
-  '';
+  patches = [
+    (substituteAll {
+      src = ./library-paths.patch;
+      libgeos_c = GEOS_LIBRARY_PATH;
+      libc = "${stdenv.cc.libc}/lib/libc${stdenv.hostPlatform.extensions.sharedLibrary}"
+               + stdenv.lib.optionalString (!stdenv.isDarwin) ".6";
+    })
+  ];
 
   # Disable the tests that improperly try to use the built extensions
   checkPhase = ''
-    py.test -k 'not test_vectorized and not test_fallbacks' tests
+    rm -r shapely # prevent import of local shapely
+    py.test tests
   '';
 
   meta = with stdenv.lib; {

pkgs/development/python-modules/shapely/library-paths.patch

@@ -0,0 +1,109 @@
+diff --git a/shapely/geos.py b/shapely/geos.py
+index 09bf1ab..837aa98 100644
+--- a/shapely/geos.py
++++ b/shapely/geos.py
+@@ -55,100 +55,10 @@ def load_dll(libname, fallbacks=None, mode=DEFAULT_MODE):
+             "Could not find lib {0} or load any of its variants {1}.".format(
+                 libname, fallbacks or []))
+ 
+-_lgeos = None
+-
+-if sys.platform.startswith('linux'):
+-    # Test to see if we have a wheel repaired by 'auditwheel' containing its
+-    # own libgeos_c
+-    geos_whl_so = glob.glob(os.path.abspath(os.path.join(os.path.dirname(
+-        __file__), '.libs/libgeos_c-*.so.*')))
+-    if len(geos_whl_so) == 1:
+-        _lgeos = CDLL(geos_whl_so[0])
+-        LOG.debug("Found GEOS DLL: %r, using it.", _lgeos)
+-    else:
+-        alt_paths = [
+-            'libgeos_c.so.1',
+-            'libgeos_c.so',
+-            # anaconda
+-            os.path.join(sys.prefix, "lib", "libgeos_c.so"),
+-        ]
+-        _lgeos = load_dll('geos_c', fallbacks=alt_paths)
+-    free = load_dll('c').free
+-    free.argtypes = [c_void_p]
+-    free.restype = None
+-
+-elif sys.platform == 'darwin':
+-    # Test to see if we have a delocated wheel with a GEOS dylib.
+-    geos_whl_dylib = os.path.abspath(os.path.join(os.path.dirname(
+-        __file__), '.dylibs/libgeos_c.1.dylib'))
+-    if os.path.exists(geos_whl_dylib):
+-        _lgeos = CDLL(geos_whl_dylib)
+-        LOG.debug("Found GEOS DLL: %r, using it.", _lgeos)
+-
+-    else:
+-        if hasattr(sys, 'frozen'):
+-            try:
+-                # .app file from py2app
+-                alt_paths = [os.path.join(
+-                    os.environ['RESOURCEPATH'], '..', 'Frameworks',
+-                    'libgeos_c.dylib')]
+-            except KeyError:
+-                # binary from pyinstaller
+-                alt_paths = [
+-                    os.path.join(sys.executable, 'libgeos_c.dylib')]
+-                if hasattr(sys, '_MEIPASS'):
+-                    alt_paths.append(
+-                        os.path.join(sys._MEIPASS, 'libgeos_c.1.dylib'))
+-        else:
+-            alt_paths = [
+-                # anaconda
+-                os.path.join(sys.prefix, "lib", "libgeos_c.dylib"),
+-                # The Framework build from Kyng Chaos
+-                "/Library/Frameworks/GEOS.framework/Versions/Current/GEOS",
+-                # macports
+-                '/opt/local/lib/libgeos_c.dylib',
+-            ]
+-        _lgeos = load_dll('geos_c', fallbacks=alt_paths)
+-
+-    free = load_dll('c').free
+-    free.argtypes = [c_void_p]
+-    free.restype = None
+-
+-elif sys.platform == 'win32':
+-    try:
+-        egg_dlls = os.path.abspath(
+-            os.path.join(os.path.dirname(__file__), 'DLLs'))
+-        if hasattr(sys, "frozen"):
+-            wininst_dlls = os.path.normpath(
+-                os.path.abspath(sys.executable + '../../DLLS'))
+-        else:
+-            wininst_dlls = os.path.abspath(os.__file__ + "../../../DLLs")
+-        original_path = os.environ['PATH']
+-        os.environ['PATH'] = "%s;%s;%s" % \
+-            (egg_dlls, wininst_dlls, original_path)
+-        _lgeos = load_dll("geos_c.dll", fallbacks=[
+-            os.path.join(sys.prefix, "Library", "lib", "geos_c.dll"),
+-        ])
+-    except (ImportError, WindowsError, OSError):
+-        raise
+-
+-    def free(m):
+-        try:
+-            cdll.msvcrt.free(m)
+-        except WindowsError:
+-            # XXX: See http://trac.gispython.org/projects/PCL/ticket/149
+-            pass
+-
+-elif sys.platform == 'sunos5':
+-    _lgeos = load_dll('geos_c', fallbacks=['libgeos_c.so.1', 'libgeos_c.so'])
+-    free = CDLL('libc.so.1').free
+-    free.argtypes = [c_void_p]
+-    free.restype = None
+-else:  # other *nix systems
+-    _lgeos = load_dll('geos_c', fallbacks=['libgeos_c.so.1', 'libgeos_c.so'])
+-    free = load_dll('c', fallbacks=['libc.so.6']).free
+-    free.argtypes = [c_void_p]
+-    free.restype = None
++_lgeos = CDLL('@libgeos_c@')
++free = CDLL('@libc@').free
++free.argtypes = [c_void_p]
++free.restype = None
+ 
+ 
+ def _geos_version():