Merge branch 'staging-next' into staging

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

@@ -0,0 +1,28 @@
+{ stdenv
+, buildPythonPackage
+, fetchPypi
+, pyvcf
+}:
+
+buildPythonPackage rec {
+  pname = "ACEBinf";
+  version = "1.0.2";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1168pny671l6zfm2vv1pwspnflmzi7f4v8yldjl7zlz0b9cm5zlz";
+  };
+
+  buildInputs = [ pyvcf ];
+
+  # no tests
+  doCheck = false;
+  pythonImportsCheck = [ "acebinf" ];
+
+  meta = with stdenv.lib; {
+    homepage = "https://github.com/ACEnglish/acebinf";
+    description = "Collection of simple utilities used when building bioinformatics tools";
+    license = licenses.unlicense;
+    maintainers = with maintainers; [ ris ];
+  };
+}

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

@@ -0,0 +1,42 @@
+{ stdenv
+, buildPythonPackage
+, pythonOlder
+, fetchPypi
+, bwa
+, cffi
+, zlib
+}:
+
+buildPythonPackage rec {
+  pname = "bwapy";
+  version = "0.1.4";
+  disabled = pythonOlder "3.6";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "090qwx3vl729zn3a7sksbviyg04kc71gpbm3nd8dalqp673x1npw";
+  };
+  postPatch = ''
+    # replace bundled bwa
+    rm -r bwa/*
+    cp ${bwa}/lib/*.a ${bwa}/include/*.h bwa/
+
+    substituteInPlace setup.py \
+      --replace 'setuptools>=49.2.0' 'setuptools'
+  '';
+
+  buildInputs = [ zlib bwa ];
+
+  propagatedBuildInputs = [ cffi ];
+
+  # no tests
+  doCheck = false;
+  pythonImportsCheck = [ "bwapy" ];
+
+  meta = with stdenv.lib; {
+    homepage = "https://github.com/ACEnglish/acebinf";
+    description = "Python bindings to bwa mem aligner";
+    license = licenses.mpl20;
+    maintainers = with maintainers; [ ris ];
+  };
+}

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

@@ -0,0 +1,53 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, isPy27
+, attrs
+, colorlog
+, csvw
+, dateutil
+, tabulate
+, mock
+, postgresql
+, pytestCheckHook
+, pytest-mock
+}:
+
+buildPythonPackage rec {
+  pname = "clldutils";
+  version = "3.5.2";
+  disabled = isPy27;
+
+  src = fetchFromGitHub {
+    owner = "clld";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "0qlqp9yq4lbi9ik2psgw0svxlb7raadqaxdh2dgkn85d7h20y4nd";
+  };
+
+  patchPhase = ''
+    substituteInPlace setup.cfg --replace "--cov" ""
+  '';
+
+  propagatedBuildInputs = [
+    dateutil
+    tabulate
+    colorlog
+    attrs
+    csvw
+  ];
+
+  checkInputs = [
+    mock
+    postgresql
+    pytestCheckHook
+    pytest-mock
+  ];
+
+  meta = with lib; {
+    description = "CSV on the Web";
+    homepage = "https://github.com/cldf/csvw";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ hexa ];
+  };
+}

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

@@ -4,6 +4,7 @@
 buildPythonPackage {
   pname = "cozy";
   version = "2.0a1";
+  disabled = !isPy3k;
 
   propagatedBuildInputs = [
     z3 ply python-igraph oset ordered-set dictionaries
@@ -18,18 +19,18 @@ buildPythonPackage {
 
   # Yoink the Z3 dependency name, because our Z3 package doesn't provide it.
   postPatch = ''
-    sed -i -e '/z3-solver/d' requirements.txt
+    sed -i -e '/z3-solver/d' -e 's/^dictionaries.*$/dictionaries/' requirements.txt
   '';
 
   # Tests are not correctly set up in the source tree.
   doCheck = false;
+  pythonImportsCheck = [ "cozy" ];
 
   # There is some first-time-run codegen that we will force to happen.
   postInstall = ''
     $out/bin/cozy --help
   '';
 
-  disabled = !isPy3k;
 
   meta = {
     description = "The collection synthesizer";

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

@@ -0,0 +1,51 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, isPy27
+, attrs
+, isodate
+, dateutil
+, rfc3986
+, uritemplate
+, mock
+, pytestCheckHook
+, pytest-mock
+}:
+
+buildPythonPackage rec {
+  pname = "csvw";
+  version = "1.8.0";
+  disabled = isPy27;
+
+  src = fetchFromGitHub {
+    owner = "cldf";
+    repo = "csvw";
+    rev = "v${version}";
+    sha256 = "0maxrsiv9i9hkg627hwqyq8g6jg3g8iv8gdqaxz4aysjd9xddydd";
+  };
+
+  patchPhase = ''
+    substituteInPlace setup.cfg --replace "--cov" ""
+  '';
+
+  propagatedBuildInputs = [
+    attrs
+    isodate
+    dateutil
+    rfc3986
+    uritemplate
+  ];
+
+  checkInputs = [
+    mock
+    pytestCheckHook
+    pytest-mock
+  ];
+
+  meta = with lib; {
+    description = "CSV on the Web";
+    homepage = "https://github.com/cldf/csvw";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ hexa ];
+  };
+}

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

@@ -23,6 +23,7 @@
 , singledispatch
 , mpi4py
 , bokeh
+, pythonOlder
 }:
 
 buildPythonPackage rec {
@@ -35,11 +36,13 @@ buildPythonPackage rec {
     sha256 = "469e505fd7ce75f600188bdb69a95641899d5b372f74246c8f308376b6929e9c";
   };
 
+  disabled = pythonOlder "3.6";
+
   checkInputs = [ pytest pytest-repeat pytest-timeout mock joblib ];
   propagatedBuildInputs = [
       click cloudpickle dask msgpack psutil six
       sortedcontainers tblib toolz tornado zict pyyaml mpi4py bokeh
-  ] ++ lib.optionals (!isPy3k) [ futures singledispatch ];
+  ];
 
   # tests take about 10-15 minutes
   # ignore 5 cli tests out of 1000 total tests that fail due to subprocesses

pkgs/development/python-modules/google-api-python-client/default.nix

@@ -4,11 +4,11 @@
 
 buildPythonPackage rec {
   pname = "google-api-python-client";
-  version = "1.12.1";
+  version = "1.12.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "ddadc243ce627512c2a27e11d369f5ddf658ef80dbffb247787499486ef1ea98";
+    sha256 = "54a7d330833a2e7b0587446d7e4ae6d0244925a9a8e1dfe878f3f7e06cdedb62";
   };
 
   # No tests included in archive

pkgs/development/python-modules/google-crc32c/default.nix

@@ -0,0 +1,31 @@
+{ lib, buildPythonPackage, isPy3k, fetchFromGitHub, cffi, crc32c, pytestCheckHook }:
+
+buildPythonPackage rec {
+  pname = "google-crc32c";
+  version = "1.0.0";
+
+  disabled = !isPy3k;
+
+  src = fetchFromGitHub {
+    owner = "googleapis";
+    repo = "python-crc32c";
+    rev = "v${version}";
+    sha256 = "0n3ggsxmk1fhq0kz6p5rcj4gypfb05i26fcn7lsawakgl7fzxqyl";
+  };
+
+  buildInputs = [ crc32c  ];
+  propagatedBuildInputs = [ cffi ];
+
+  LDFLAGS = "-L${crc32c}/lib";
+  CFLAGS = "-I${crc32c}/include";
+
+  checkInputs = [ pytestCheckHook crc32c ];
+  pythonImportsCheck = [ "google_crc32c" ];
+
+  meta = with lib; {
+    homepage = "https://github.com/googleapis/python-crc32c";
+    description = "Wrapper the google/crc32c hardware-based implementation of the CRC32C hashing algorithm";
+    license = with licenses; [ asl20 ];
+    maintainers = with maintainers; [ freezeboy ];
+  };
+}

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

@@ -1,30 +1,35 @@
-{ stdenv
+{ lib
 , buildPythonPackage
+, isPy3k
 , fetchPypi
 , six
 , requests
 , setuptools
 , pytest
 , mock
+, crcmod
+, google-crc32c
 }:
 
 buildPythonPackage rec {
   pname = "google-resumable-media";
-  version = "0.7.1";
+  version = "1.0.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "57841f5e65fb285c01071f439724745b2549a72eb75e5fd979198eb518608ed0";
+    sha256 = "FzrMa63hSApSn6KcbCcXVDri3AnULpRh/bhvOVAu/PI=";
   };
 
   checkInputs = [ pytest mock ];
-  propagatedBuildInputs = [ requests setuptools six ];
+  propagatedBuildInputs = [ requests setuptools six ]
+    ++ lib.optional isPy3k google-crc32c
+    ++ lib.optional (!isPy3k) crcmod;
 
   checkPhase = ''
     py.test tests/unit
   '';
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     description = "Utilities for Google Media Downloads and Resumable Uploads";
     homepage = "https://github.com/GoogleCloudPlatform/google-resumable-media-python";
     license = licenses.asl20;

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

@@ -1,14 +1,13 @@
 { stdenv
 , lib
 , buildPythonPackage
+, pythonOlder
 , fetchFromGitHub
 , six
-, enum34
 , decorator
 , nose
 , krb5Full
 , darwin
-, isPy27
 , parameterized
 , shouldbe
 , cython
@@ -18,13 +17,14 @@
 
 buildPythonPackage rec {
   pname = "gssapi";
-  version = "1.6.2";
+  version = "1.6.9";
+  disabled = pythonOlder "3.6";
 
   src = fetchFromGitHub {
     owner = "pythongssapi";
     repo = "python-${pname}";
     rev = "v${version}";
-    sha256 = "195x3zqzyv491i9hf7l4asmic5pb2w3l1r7bps89651wkb3mrz1l";
+    sha256 = "1shm3pc0l2r91qadkpq4bx45my0165nw3kdcp0gw4lk50z215hag";
   };
 
   # It's used to locate headers
@@ -41,7 +41,7 @@ buildPythonPackage rec {
   propagatedBuildInputs =  [
     decorator
     six
-  ] ++ lib.optional isPy27 enum34;
+  ];
 
   buildInputs = lib.optionals stdenv.isDarwin [
     darwin.apple_sdk.frameworks.GSS
@@ -55,12 +55,21 @@ buildPythonPackage rec {
     six
   ];
 
-  doCheck = !stdenv.isDarwin; # many failures on darwin
+  doCheck = pythonOlder "3.8"  # `shouldbe` not available
+    && !stdenv.isDarwin;  # many failures on darwin
 
+  # skip tests which fail possibly due to be an upstream issue (see
+  # https://github.com/pythongssapi/python-gssapi/issues/220)
   checkPhase = ''
+    # some tests don't respond to being disabled through nosetests -x
+    echo $'\ndel CredsTestCase.test_add_with_impersonate' >> gssapi/tests/test_high_level.py
+    echo $'\ndel TestBaseUtilities.test_acquire_creds_impersonate_name' >> gssapi/tests/test_raw.py
+    echo $'\ndel TestBaseUtilities.test_add_cred_impersonate_name' >> gssapi/tests/test_raw.py
+
     export PYTHONPATH="$out/${python.sitePackages}:$PYTHONPATH"
-    ${python.interpreter} setup.py nosetests
+    ${python.interpreter} setup.py nosetests -e 'ext_test_\d.*'
   '';
+  pythonImportsCheck = [ "gssapi" ];
 
   meta = with lib; {
     homepage = "https://pypi.python.org/pypi/gssapi";

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

@@ -28,12 +28,12 @@
 
 buildPythonPackage rec {
   pname = "notebook";
-  version = "6.1.3";
+  version = "6.1.4";
   disabled = !isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "9990d51b9931a31e681635899aeb198b4c4b41586a9e87fbfaaed1a71d0a05b6";
+    sha256 = "0cnyi4zd3byh7zixdj2q71axm31xgjiyfklh1c63c87acgwh2zb8";
   };
 
   LC_ALL = "en_US.utf8";
@@ -67,6 +67,9 @@ buildPythonPackage rec {
     "TestInstallServerExtension"
     "launch_socket"
     "sock_server"
+  ] ++ lib.optional stdenv.isDarwin [
+    "test_delete"
+    "test_checkpoints_follow_file"
   ];
 
   # Some of the tests use localhost networking.

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

@@ -9,12 +9,12 @@
 }:
 
 buildPythonPackage rec {
-  version = "3.0.1";
+  version = "2.3.0";
   pname = "pamqp";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0a9b49bde3f554ec49b47ebdb789133979985f24d5f4698935ed589a2d4392a4";
+    sha256 = "1s4lwbsiikz3czqad7jarb7k303q0wamla0rirghvwl9bslgbl2w";
   };
 
   buildInputs = [ mock nose pep8 pylint mccabe ];

pkgs/development/python-modules/pysdl2/PySDL2-dll.patch

@@ -1,119 +1,100 @@
-diff -ru PySDL2-0.9.6-old/sdl2/dll.py PySDL2-0.9.6/sdl2/dll.py
---- PySDL2-0.9.6-old/sdl2/dll.py	2018-03-08 10:18:37.583471745 +0100
-+++ PySDL2-0.9.6/sdl2/dll.py	2018-03-08 10:20:06.705517520 +0100
-@@ -45,29 +45,31 @@
+diff -ru PySDL2-0.9.7-old/sdl2/dll.py PySDL2-0.9.7/sdl2/dll.py
+--- PySDL2-0.9.7-old/sdl2/dll.py	2020-02-15 09:36:29.000000000 +0100
++++ PySDL2-0.9.7/sdl2/dll.py	2020-09-23 20:24:09.365497270 +0200
+@@ -94,15 +94,16 @@
      """Function wrapper around the different DLL functions. Do not use or
      instantiate this one directly from your user code.
      """
 -    def __init__(self, libinfo, libnames, path=None):
--        self._dll = None
++    def __init__(self, libinfo, libfile):
+         self._dll = None
+         self._libname = libinfo
+         self._version = None
 -        foundlibs = _findlib(libnames, path)
 -        dllmsg = "PYSDL2_DLL_PATH: %s" % (os.getenv("PYSDL2_DLL_PATH") or "unset")
 -        if len(foundlibs) == 0:
 -            raise RuntimeError("could not find any library for %s (%s)" %
 -                               (libinfo, dllmsg))
--        for libfile in foundlibs:
--            try:
--                self._dll = CDLL(libfile)
--                self._libfile = libfile
--                break
--            except Exception as exc:
--                # Could not load the DLL, move to the next, but inform the user
--                # about something weird going on - this may become noisy, but
--                # is better than confusing the users with the RuntimeError below
--                warnings.warn(repr(exc), DLLWarning)
--        if self._dll is None:
--            raise RuntimeError("found %s, but it's not usable for the library %s" %
--                               (foundlibs, libinfo))
++        #foundlibs = _findlib(libnames, path)
++        #dllmsg = "PYSDL2_DLL_PATH: %s" % (os.getenv("PYSDL2_DLL_PATH") or "unset")
++        #if len(foundlibs) == 0:
++        #    raise RuntimeError("could not find any library for %s (%s)" %
++        #                       (libinfo, dllmsg))
++        foundlibs = [ libfile ]
+         for libfile in foundlibs:
+             try:
+                 self._dll = CDLL(libfile)
+@@ -117,9 +118,9 @@
+         if self._dll is None:
+             raise RuntimeError("found %s, but it's not usable for the library %s" %
+                                (foundlibs, libinfo))
 -        if path is not None and sys.platform in ("win32",) and \
 -            path in self._libfile:
 -            os.environ["PATH"] = "%s;%s" % (path, os.environ["PATH"])
-+    def __init__(self, libfile):
-+        self._dll = CDLL(libfile)
-+        self._libfile = libfile
-+        # self._dll = None
-+        # foundlibs = _findlib(libnames, path)
-+        # dllmsg = "PYSDL2_DLL_PATH: %s" % (os.getenv("PYSDL2_DLL_PATH") or "unset")
-+        # if len(foundlibs) == 0:
-+        #     raise RuntimeError("could not find any library for %s (%s)" %
-+        #                        (libinfo, dllmsg))
-+        # for libfile in foundlibs:
-+        #     try:
-+        #         self._dll = CDLL(libfile)
-+        #         self._libfile = libfile
-+        #         break
-+        #     except Exception as exc:
-+        #         # Could not load the DLL, move to the next, but inform the user
-+        #         # about something weird going on - this may become noisy, but
-+        #         # is better than confusing the users with the RuntimeError below
-+        #         warnings.warn(repr(exc), DLLWarning)
-+        # if self._dll is None:
-+        #     raise RuntimeError("found %s, but it's not usable for the library %s" %
-+        #                        (foundlibs, libinfo))
-+        # if path is not None and sys.platform in ("win32",) and \
-+        #     path in self._libfile:
-+        #     os.environ["PATH"] = "%s;%s" % (path, os.environ["PATH"])
++        #if path is not None and sys.platform in ("win32",) and \
++        #    path in self._libfile:
++        #    os.environ["PATH"] = "%s;%s" % (path, os.environ["PATH"])
  
-     def bind_function(self, funcname, args=None, returns=None, optfunc=None):
+     def bind_function(self, funcname, args=None, returns=None, added=None):
          """Binds the passed argument and return value types to the specified
-@@ -110,7 +112,7 @@
+@@ -220,7 +221,7 @@
      return
  
  try:
 -    dll = DLL("SDL2", ["SDL2", "SDL2-2.0"], os.getenv("PYSDL2_DLL_PATH"))
-+    dll = DLL("SDL2")
++    dll = DLL("SDL2", "@sdl2@")
  except RuntimeError as exc:
      raise ImportError(exc)
  
-diff -ru PySDL2-0.9.6-old/sdl2/sdlgfx.py PySDL2-0.9.6/sdl2/sdlgfx.py
---- PySDL2-0.9.6-old/sdl2/sdlgfx.py	2018-03-08 10:18:37.585471769 +0100
-+++ PySDL2-0.9.6/sdl2/sdlgfx.py	2018-03-08 10:20:06.705517520 +0100
-@@ -34,8 +34,7 @@
+diff -ru PySDL2-0.9.7-old/sdl2/sdlgfx.py PySDL2-0.9.7/sdl2/sdlgfx.py
+--- PySDL2-0.9.7-old/sdl2/sdlgfx.py	2020-02-02 11:07:00.000000000 +0100
++++ PySDL2-0.9.7/sdl2/sdlgfx.py	2020-09-23 20:23:56.997419129 +0200
+@@ -39,8 +39,7 @@
             ]
  
  try:
 -    dll = DLL("SDL2_gfx", ["SDL2_gfx", "SDL2_gfx-1.0"],
 -              os.getenv("PYSDL2_DLL_PATH"))
-+    dll = DLL("SDL2_gfx")
++    dll = DLL("SDL2_gfx", "@sdl2_gfx@")
  except RuntimeError as exc:
      raise ImportError(exc)
  
-diff -ru PySDL2-0.9.6-old/sdl2/sdlimage.py PySDL2-0.9.6/sdl2/sdlimage.py
---- PySDL2-0.9.6-old/sdl2/sdlimage.py	2018-03-08 10:18:37.585471769 +0100
-+++ PySDL2-0.9.6/sdl2/sdlimage.py	2018-03-08 10:20:06.705517520 +0100
-@@ -26,8 +26,7 @@
+diff -ru PySDL2-0.9.7-old/sdl2/sdlimage.py PySDL2-0.9.7/sdl2/sdlimage.py
+--- PySDL2-0.9.7-old/sdl2/sdlimage.py	2020-02-02 11:07:00.000000000 +0100
++++ PySDL2-0.9.7/sdl2/sdlimage.py	2020-09-23 20:23:50.085375658 +0200
+@@ -27,8 +27,7 @@
             ]
  
  try:
 -    dll = DLL("SDL2_image", ["SDL2_image", "SDL2_image-2.0"],
 -              os.getenv("PYSDL2_DLL_PATH"))
-+    dll = DLL("SDL2_image")
++    dll = DLL("SDL2_image", "@sdl2_image@")
  except RuntimeError as exc:
      raise ImportError(exc)
  
-diff -ru PySDL2-0.9.6-old/sdl2/sdlmixer.py PySDL2-0.9.6/sdl2/sdlmixer.py
---- PySDL2-0.9.6-old/sdl2/sdlmixer.py	2018-03-08 10:18:37.585471769 +0100
-+++ PySDL2-0.9.6/sdl2/sdlmixer.py	2018-03-08 10:20:27.415758478 +0100
-@@ -50,8 +50,7 @@
+diff -ru PySDL2-0.9.7-old/sdl2/sdlmixer.py PySDL2-0.9.7/sdl2/sdlmixer.py
+--- PySDL2-0.9.7-old/sdl2/sdlmixer.py	2020-02-02 11:07:00.000000000 +0100
++++ PySDL2-0.9.7/sdl2/sdlmixer.py	2020-09-23 20:23:46.117350771 +0200
+@@ -53,8 +53,7 @@
            ]
  
  try:
 -    dll = DLL("SDL2_mixer", ["SDL2_mixer", "SDL2_mixer-2.0"],
 -              os.getenv("PYSDL2_DLL_PATH"))
-+    dll = DLL("SDL2_mixer")
++    dll = DLL("SDL2_mixer", "@sdl2_mixer@")
  except RuntimeError as exc:
      raise ImportError(exc)
  
-diff -ru PySDL2-0.9.6-old/sdl2/sdlttf.py PySDL2-0.9.6/sdl2/sdlttf.py
---- PySDL2-0.9.6-old/sdl2/sdlttf.py	2018-03-08 10:18:37.585471769 +0100
-+++ PySDL2-0.9.6/sdl2/sdlttf.py	2018-03-08 10:20:06.705517520 +0100
-@@ -38,8 +38,7 @@
+diff -ru PySDL2-0.9.7-old/sdl2/sdlttf.py PySDL2-0.9.7/sdl2/sdlttf.py
+--- PySDL2-0.9.7-old/sdl2/sdlttf.py	2020-02-02 11:07:00.000000000 +0100
++++ PySDL2-0.9.7/sdl2/sdlttf.py	2020-09-23 20:23:40.069312931 +0200
+@@ -39,8 +39,7 @@
            ]
  
  try:
 -    dll = DLL("SDL2_ttf", ["SDL2_ttf", "SDL2_ttf-2.0"],
 -              os.getenv("PYSDL2_DLL_PATH"))
-+    dll = DLL("SDL2_ttf")
++    dll = DLL("SDL2_ttf", "@sdl2_ttf@")
  except RuntimeError as exc:
      raise ImportError(exc)
  

pkgs/development/python-modules/pysdl2/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, lib, fetchPypi, buildPythonPackage, SDL2, SDL2_ttf, SDL2_image, SDL2_gfx, SDL2_mixer }:
+{ stdenv, lib, substituteAll, fetchPypi, buildPythonPackage, SDL2, SDL2_ttf, SDL2_image, SDL2_gfx, SDL2_mixer }:
 
 buildPythonPackage rec {
   pname = "PySDL2";
@@ -18,19 +18,18 @@ buildPythonPackage rec {
   # which library they want to include.
   buildInputs = [ SDL2_ttf SDL2_image SDL2_gfx SDL2_mixer ];
   propagatedBuildInputs = [ SDL2 ];
-  patches = [ ./PySDL2-dll.patch ];
-  postPatch = ''
-    substituteInPlace sdl2/dll.py --replace \
-      "DLL(\"SDL2\")" "DLL('${SDL2}/lib/libSDL2${stdenv.hostPlatform.extensions.sharedLibrary}')"
-    substituteInPlace sdl2/sdlttf.py --replace \
-      "DLL(\"SDL2_ttf\")" "DLL('${SDL2_ttf}/lib/libSDL2_ttf${stdenv.hostPlatform.extensions.sharedLibrary}')"
-    substituteInPlace sdl2/sdlimage.py --replace \
-      "DLL(\"SDL2_image\")" "DLL('${SDL2_image}/lib/libSDL2_image${stdenv.hostPlatform.extensions.sharedLibrary}')"
-    substituteInPlace sdl2/sdlgfx.py --replace \
-     "DLL(\"SDL2_gfx\")" "DLL('${SDL2_gfx}/lib/libSDL2_gfx${stdenv.hostPlatform.extensions.sharedLibrary}')"
-    substituteInPlace sdl2/sdlmixer.py --replace \
-     "DLL(\"SDL2_mixer\")" "DLL('${SDL2_mixer}/lib/libSDL2_mixer${stdenv.hostPlatform.extensions.sharedLibrary}')"
-  '';
+  patches = [
+    (substituteAll ({
+      src = ./PySDL2-dll.patch;
+    } // builtins.mapAttrs (_: pkg: "${pkg}/lib/lib${pkg.pname}${stdenv.hostPlatform.extensions.sharedLibrary}") {
+      # substituteAll keys must start lowercase
+      sdl2 = SDL2;
+      sdl2_ttf = SDL2_ttf;
+      sdl2_image = SDL2_image;
+      sdl2_gfx = SDL2_gfx;
+      sdl2_mixer = SDL2_mixer;
+    }))
+  ];
 
   meta = {
     description = "A wrapper around the SDL2 library and as such similar to the discontinued PySDL project";

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

@@ -0,0 +1,32 @@
+{ stdenv
+, buildPythonPackage
+, isPy3k
+, fetchPypi
+, zlib
+}:
+
+buildPythonPackage rec {
+  pname = "pytabix";
+  version = "0.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1ldp5r4ggskji6qx4bp2qxy2vrvb3fam03ksn0gq2hdxgrlg2x07";
+  };
+
+  buildInputs = [ zlib ];
+
+  doCheck = !isPy3k;
+  preCheck = ''
+    substituteInPlace test/test.py \
+      --replace 'test_remote_file' 'dont_test_remote_file'
+  '';
+  pythonImportsCheck = [ "tabix" ];
+
+  meta = with stdenv.lib; {
+    homepage = "https://github.com/slowkow/pytabix";
+    description = "Python interface for tabix";
+    license = licenses.mit;
+    maintainers = with maintainers; [ ris ];
+  };
+}

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

@@ -7,7 +7,7 @@
 }:
 
 buildPythonPackage rec {
-  version = "1.0.0";
+  version = "2.0.1";
   pname = "rabbitpy";
 
   # No tests in the pypi tarball, so we directly fetch from git
@@ -15,7 +15,7 @@ buildPythonPackage rec {
     owner = "gmr";
     repo = pname;
     rev = version;
-    sha256 = "0fd80zlr4p2sh77rxyyfi9l0h2zqi2csgadr0rhnpgpqsy10qck6";
+    sha256 = "0m5z3i3d5adrz1wh6y35xjlls3cq6p4y9p1mzghw3k7hdvg26cck";
   };
 
   propagatedBuildInputs = [ pamqp ];
@@ -31,7 +31,7 @@ buildPythonPackage rec {
   postPatch = ''
     # See: https://github.com/gmr/rabbitpy/issues/118
     substituteInPlace setup.py \
-      --replace 'pamqp>=1.6.1,<2.0' 'pamqp'
+      --replace 'pamqp>=2,<3' 'pamqp'
   '';
 
   meta = with stdenv.lib; {

pkgs/development/python-modules/scikits-odes/default.nix

@@ -49,7 +49,7 @@ buildPythonPackage rec {
     description = "A scikit offering extra ode/dae solvers, as an extension to what is available in scipy";
     homepage = "https://github.com/bmcage/odes";
     license = licenses.bsd3;
-    maintainers = with maintainers; [ flokli idontgetoutmuch ];
+    maintainers = with maintainers; [ idontgetoutmuch ];
     platforms = [ "aarch64-linux" "x86_64-linux" "x86_64-darwin" ];
   };
 }

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

@@ -0,0 +1,47 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, isPy27
+, regex
+, csvw
+, clldutils
+, mock
+, pytestCheckHook
+, pytest-mock
+}:
+
+buildPythonPackage rec {
+  pname = "segments";
+  version = "2.1.3";
+  disabled = isPy27;
+
+  src = fetchFromGitHub {
+    owner = "cldf";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "12lnpk834r3y7hw5x7nvswa60ddh69ylvr44k46gqcfba160hhb0";
+  };
+
+  patchPhase = ''
+    substituteInPlace setup.cfg --replace "--cov" ""
+  '';
+
+  propagatedBuildInputs = [
+    regex
+    csvw
+    clldutils
+  ];
+
+  checkInputs = [
+    mock
+    pytestCheckHook
+    pytest-mock
+  ];
+
+  meta = with lib; {
+    description = "Unicode Standard tokenization routines and orthography profile segmentation";
+    homepage = "https://github.com/cldf/segments";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ hexa ];
+  };
+}

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

@@ -10,6 +10,7 @@
 , toolz
 , tornado
 , zict
+, pythonOlder
 }:
 
 buildPythonPackage rec {
@@ -38,6 +39,8 @@ buildPythonPackage rec {
     requests
   ];
 
+  disabled = pythonOlder "3.6";
+
   # Disable test_tcp_async because fails on sandbox build
   # disable kafka tests
   checkPhase = ''

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

@@ -6,6 +6,7 @@
 , regex
 , requests
 , numpy
+, parameterized
 , sacremoses
 , sentencepiece
 , timeout-decorator
@@ -16,13 +17,13 @@
 
 buildPythonPackage rec {
   pname = "transformers";
-  version = "3.1.0";
+  version = "3.2.0";
 
   src = fetchFromGitHub {
     owner = "huggingface";
     repo = pname;
     rev = "v${version}";
-    sha256 = "0wg36qrcljmpsyhjaxpqw3s1r6276yg8cq0bjrf52l4zlc5k4xzk";
+    sha256 = "0jj94153kgdyklra30xcszxv11hwzfigzy82fgvgzvbwlxv3a1j5";
   };
 
   propagatedBuildInputs = [
@@ -38,6 +39,7 @@ buildPythonPackage rec {
   ];
 
   checkInputs = [
+    parameterized
     pytestCheckHook
     timeout-decorator
   ];
@@ -49,14 +51,17 @@ buildPythonPackage rec {
 
   preCheck = ''
     export HOME="$TMPDIR"
-    cd tests
 
     # This test requires the nlp module, which we haven't
     # packaged yet. However, nlp is optional for transformers
     # itself
-    rm test_trainer.py
+    rm tests/test_trainer.py
   '';
 
+  # We have to run from the main directory for the tests. However,
+  # letting pytest discover tests leads to errors.
+  pytestFlagsArray = [ "tests" ];
+
   # Disable tests that require network access.
   disabledTests = [
     "PegasusTokenizationTest"
@@ -76,6 +81,7 @@ buildPythonPackage rec {
     "test_tokenizer_from_model_type"
     "test_tokenizer_from_model_type"
     "test_tokenizer_from_pretrained"
+    "test_tokenizer_from_tokenizer_class"
     "test_tokenizer_identifier_with_correct_config"
   ];
 

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

@@ -1,5 +1,5 @@
 { stdenv, buildPythonPackage, fetchPypi
-, pytest, heapdict }:
+, pytest, heapdict, pythonOlder }:
 
 buildPythonPackage rec {
   pname = "zict";
@@ -10,6 +10,8 @@ buildPythonPackage rec {
     sha256 = "8e2969797627c8a663575c2fc6fcb53a05e37cdb83ee65f341fc6e0c3d0ced16";
   };
 
+  disabled = pythonOlder "3.6";
+
   buildInputs = [ pytest ];
   propagatedBuildInputs = [ heapdict ];