Merge master into staging-next

pkgs/development/python-modules/azure-mgmt-policyinsights/default.nix

@@ -10,12 +10,12 @@
 
 buildPythonPackage rec {
   pname = "azure-mgmt-policyinsights";
-  version = "0.5.0";
+  version = "0.6.0";
 
   src = fetchPypi {
     inherit pname version;
     extension = "zip";
-    sha256 = "ed229e3845c477e88dde413825d4fba0d38b3a5ffab4e694c7d0da995f3db0f3";
+    sha256 = "2c64533f6eab08dc16450fc5d7c7651557fc0edc8ef1278dda336333d648a7c4";
   };
 
   propagatedBuildInputs = [

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

@@ -12,11 +12,11 @@
 
 buildPythonPackage rec {
   pname = "bpython";
-  version = "0.20";
+  version = "0.20.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "fec7d97be9912a50d8f5b34ca10d70715c99a33f0cd0b9e4977c1b0f617fa913";
+    sha256 = "6e7738806013b469be57b0117082b9c4557ed7c92c70ceb79f96d674d89c7503";
   };
 
   patches = [ (substituteAll {

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

@@ -8,7 +8,7 @@
 
 buildPythonPackage rec {
   pname = "casbin";
-  version = "0.9.0";
+  version = "0.10.0";
 
   disabled = isPy27;
 
@@ -16,7 +16,7 @@ buildPythonPackage rec {
     owner = pname;
     repo = "pycasbin";
     rev = "v${version}";
-    sha256 = "16bqa2f5l2cns2izc4siy8jw23q9vrqm9wnyp696fj83y77nkp75";
+    sha256 = "13r8alja25yd5gk5124y1v6frwphmz6wl5z5gz1fafb5nv2zgqw9";
   };
 
   propagatedBuildInputs = [

pkgs/development/python-modules/cmd2/default.nix

@@ -6,11 +6,11 @@
 }:
 buildPythonPackage rec {
   pname = "cmd2";
-  version = "1.3.11";
+  version = "1.4.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "826a288ee6d9c4ec1184e64e9566c09d3b73be8f4283c1898fa4332f1daf8dbf";
+    sha256 = "e59fa932418603af4e046a96c8985812b05af8a73bfd9d7a386cd1b02c6ab687";
   };
 
   LC_ALL="en_US.UTF-8";

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

@@ -3,6 +3,7 @@
 , fetchFromGitHub
 , dill
 , filelock
+, multiprocess
 , numpy
 , pandas
 , pyarrow
@@ -13,18 +14,19 @@
 
 buildPythonPackage rec {
   pname = "datasets";
-  version = "1.0.1";
+  version = "1.1.2";
 
   src = fetchFromGitHub {
     owner = "huggingface";
     repo = pname;
     rev = version;
-    sha256 = "14f7847b8md5kf631zl8x2f53wy8zbzxypq4wdgzvwsjz4k7v4jn";
+    hash = "sha256-upXZ2rOfmjnJbDo6RMGeHv/fe10RQAf/zwDWWKdt6SA=";
   };
 
   propagatedBuildInputs = [
     dill
     filelock
+    multiprocess
     numpy
     pandas
     pyarrow

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

@@ -9,11 +9,12 @@
 , scipy
 , h5py
 , nibabel
+, tqdm
 }:
 
 buildPythonPackage rec {
   pname = "dipy";
-  version = "1.2.0";
+  version = "1.3.0";
 
   disabled = isPy27;
 
@@ -21,7 +22,7 @@ buildPythonPackage rec {
     owner  = "dipy";
     repo   = pname;
     rev    = version;
-    sha256 = "0x49lph400ndlvk419nd2g9ss4jg75xr7xh88ggv5d2ama19v7py";
+    sha256 = "0555abx0fwqmk6dc3im7r45d9j7r9xh6gm9mbwfwvlf7laf8h098";
   };
 
   nativeBuildInputs = [ cython packaging ];
@@ -30,6 +31,7 @@ buildPythonPackage rec {
     scipy
     h5py
     nibabel
+    tqdm
   ];
 
   checkInputs = [ pytest ];

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

@@ -3,11 +3,11 @@
 
 buildPythonPackage rec {
   pname = "dropbox";
-  version = "10.8.0";
+  version = "10.10.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "2312a0314d7698f6aa6944bf6d73a756f4ff7d7d90fa26c323a418a84dc3b533";
+    sha256 = "df43e9e0bdcae6d610dd754a5ec72f2f91a311bbc2c8a28d076df69695b18398";
   };
 
   # Set DROPBOX_TOKEN environment variable to a valid token.

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

@@ -15,13 +15,13 @@
 
 buildPythonPackage rec {
   pname = "gtts";
-  version = "2.1.1";
+  version = "2.1.2";
 
   src = fetchFromGitHub {
     owner = "pndurette";
     repo = "gTTS";
     rev = "v${version}";
-    sha256 = "1d0r6dnb8xvgyvxz7nfj4q4xqmpmvcwcsjghxrh76m6p364lh1hj";
+    sha256 = "1vcsxzqzl61h50lm934hd7q5nl7l10wwymgq1mcynmqxbm1s4rnl";
   };
 
   propagatedBuildInputs = [

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

@@ -5,11 +5,11 @@
 
 buildPythonPackage rec {
   pname = "hyperopt";
-  version = "0.1.2";
+  version = "0.2.5";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "34xIpivBYUvcN/XMVwBkqTpLgaFlWWIduazuP2U2tlg=";
+    sha256 = "bc6047d50f956ae64eebcb34b1fd40f186a93e214957f20e87af2f10195295cc";
   };
 
   propagatedBuildInputs = [ future cloudpickle numpy networkx six tqdm scipy pymongo ];

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

@@ -19,11 +19,11 @@
 
 buildPythonPackage rec {
   pname = "internetarchive";
-  version = "1.9.5";
+  version = "1.9.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "759053685c75e6e969d690043b82643c4016500abcbbc44e4daf52ec097a9a15";
+    sha256 = "0e9b24577086283280a5089b3e65086640b4e42d61ca4af913639f45b02b9e4c";
   };
 
   propagatedBuildInputs = [

pkgs/development/python-modules/notmuch/2.nix

@@ -0,0 +1,22 @@
+{ stdenv
+, buildPythonPackage
+, notmuch
+, python
+, cffi
+}:
+
+buildPythonPackage {
+  pname = "notmuch2";
+  inherit (notmuch) version src;
+
+  sourceRoot = "${notmuch.src.name}/bindings/python-cffi";
+
+  buildInputs = [ python notmuch cffi ];
+
+  meta = with stdenv.lib; {
+    description = "Pythonic bindings for the notmuch mail database using CFFI";
+    homepage = "https://notmuchmail.org/";
+    license = licenses.gpl3;
+    maintainers = with maintainers; [ teto ];
+  };
+}

pkgs/development/python-modules/phonemizer/backend-paths.patch

@@ -0,0 +1,29 @@
+diff --git a/phonemizer/backend/espeak.py b/phonemizer/backend/espeak.py
+index 387c11c..ceb5e7e 100644
+--- a/phonemizer/backend/espeak.py
++++ b/phonemizer/backend/espeak.py
+@@ -81,10 +81,7 @@ class BaseEspeakBackend(BaseBackend):
+         if _ESPEAK_DEFAULT_PATH:
+             return _ESPEAK_DEFAULT_PATH
+ 
+-        espeak = distutils.spawn.find_executable('espeak-ng')
+-        if not espeak:  # pragma: nocover
+-            espeak = distutils.spawn.find_executable('espeak')
+-        return espeak
++        return "@espeak@"
+ 
+     @classmethod
+     def is_available(cls):
+diff --git a/phonemizer/backend/festival.py b/phonemizer/backend/festival.py
+index b5bc56d..0833160 100644
+--- a/phonemizer/backend/festival.py
++++ b/phonemizer/backend/festival.py
+@@ -78,7 +78,7 @@ class FestivalBackend(BaseBackend):
+         if _FESTIVAL_DEFAULT_PATH:
+             return _FESTIVAL_DEFAULT_PATH
+ 
+-        return distutils.spawn.find_executable('festival')
++        return "@festival@"
+ 
+     @classmethod
+     def is_available(cls):

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

@@ -0,0 +1,73 @@
+{ lib
+, substituteAll
+, buildPythonApplication
+, fetchPypi
+, python3Packages
+, pkgs
+, joblib
+, segments
+, attrs
+, espeak-ng
+, pytestCheckHook
+, pytestrunner
+, pytestcov
+}:
+
+buildPythonApplication rec {
+  pname = "phonemizer";
+  version = "2.2.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "127n4f10zxq60qd8xvlc1amji4wbghqb90rfp25rzdk716kvgwab";
+  };
+
+  postPatch = ''
+    sed -i -e '/\'pytest-runner\'/d setup.py
+  '';
+
+  patches = [
+    (substituteAll {
+      src = ./backend-paths.patch;
+      espeak = "${lib.getBin espeak-ng}/bin/espeak";
+      # override festival path should you try to integrate it
+      festival = "";
+    })
+    ./remove-intertwined-festival-test.patch
+  ];
+
+  propagatedBuildInputs = [
+    joblib
+    segments
+    attrs
+  ];
+
+  preCheck = ''
+    export HOME=$TMPDIR
+  '';
+
+  checkInputs = [
+    pytestCheckHook
+    pytestcov
+  ];
+
+  # We tried to package festvial, but were unable to get the backend running,
+  # so let's disable related tests.
+  pytestFlagsArray = [
+    "--ignore=test/test_festival.py"
+  ];
+
+  disabledTests = [
+    "test_festival"
+    "test_relative"
+    "test_absolute"
+    "test_readme_festival_syll"
+  ];
+
+  meta = with lib; {
+    homepage = "https://github.com/bootphon/phonemizer";
+    description = "Simple text to phones converter for multiple languages";
+    license = licenses.gpl3;
+    maintainers = with maintainers; [ hexa ];
+  };
+}

pkgs/development/python-modules/phonemizer/drop-readme-festival-test.patch

@@ -0,0 +1,12 @@
+diff --git a/test/test_main.py b/test/test_main.py
+index 71d605a..d137cd7 100644
+--- a/test/test_main.py
++++ b/test/test_main.py
+@@ -63,7 +63,6 @@ def test_readme():
+     _test(u'hello world', u'həloʊ wɜːld ')
+     _test(u'hello world', u'həloʊ wɜːld ', '--verbose')
+     _test(u'hello world', u'həloʊ wɜːld ', '--quiet')
+-    _test(u'hello world', u'hhaxlow werld', '-b festival --strip')
+     _test(u'hello world', u'həloʊ wɜːld ', '-l en-us')
+     _test(u'bonjour le monde', u'bɔ̃ʒuʁ lə mɔ̃d ', '-l fr-fr')
+     _test(u'bonjour le monde', u'b ɔ̃ ʒ u ʁ ;eword l ə ;eword m ɔ̃ d ;eword ',

pkgs/development/python-modules/phonemizer/remove-intertwined-festival-test.patch

@@ -0,0 +1,22 @@
+diff --git a/test/test_main.py b/test/test_main.py
+index 71d605a..0ea3c74 100644
+--- a/test/test_main.py
++++ b/test/test_main.py
+@@ -63,17 +63,12 @@ def test_readme():
+     _test(u'hello world', u'həloʊ wɜːld ')
+     _test(u'hello world', u'həloʊ wɜːld ', '--verbose')
+     _test(u'hello world', u'həloʊ wɜːld ', '--quiet')
+-    _test(u'hello world', u'hhaxlow werld', '-b festival --strip')
+     _test(u'hello world', u'həloʊ wɜːld ', '-l en-us')
+     _test(u'bonjour le monde', u'bɔ̃ʒuʁ lə mɔ̃d ', '-l fr-fr')
+     _test(u'bonjour le monde', u'b ɔ̃ ʒ u ʁ ;eword l ə ;eword m ɔ̃ d ;eword ',
+           '-l fr-fr -p " " -w ";eword "')
+ 
+ 
+-@pytest.mark.skipif(
+-    '2.1' in backend.FestivalBackend.version(),
+-    reason='festival-2.1 gives different results than further versions '
+-    'for syllable boundaries')
+ def test_readme_festival_syll():
+     _test(u'hello world',
+           u'hh ax ;esyll l ow ;esyll ;eword w er l d ;esyll ;eword ',

pkgs/development/python-modules/python-jsonrpc-server/default.nix

@@ -16,7 +16,7 @@ buildPythonPackage rec {
   };
 
   postPatch = ''
-    sed -i 's/version=versioneer.get_version(),/version="${version}",/g' setup.py
+    sed -i "s/version=versioneer.get_version(),/version=\"$version\",/g" setup.py
     # https://github.com/palantir/python-jsonrpc-server/issues/36
     sed -iEe "s!'ujson.*\$!'ujson',!" setup.py
   '';

pkgs/development/python-modules/pytorch-metric-learning/default.nix

@@ -4,6 +4,7 @@
 , isPy27
 , numpy
 , scikitlearn
+, pytestCheckHook
 , pytorch
 , torchvision
 , tqdm
@@ -11,15 +12,15 @@
 
 buildPythonPackage rec {
   pname   = "pytorch-metric-learning";
-  version = "0.9.81";
+  version = "0.9.94";
 
   disabled = isPy27;
 
   src = fetchFromGitHub {
     owner = "KevinMusgrave";
     repo = pname;
-    rev = "cb23328aba64f7f4658374cc2920ef5d56cda5c8";  # no version tag
-    sha256 = "0c2dyi4qi7clln43481xq66f6r4fadrz84jphjc5phz97bp33ds8";
+    rev = "v${version}";
+    sha256 = "1i2m651isa6xk3zj8dhzdbmd1bdzl51bh6rxifx6gg22hfa5dj9a";
   };
 
   propagatedBuildInputs = [
@@ -30,6 +31,22 @@ buildPythonPackage rec {
     tqdm
   ];
 
+  preCheck = ''
+    export HOME=$TMP
+    export TEST_DEVICE=cpu
+    export TEST_DTYPES=float32,float64  # half-precision tests fail on CPU
+  '';
+  # package only requires `unittest`, but use `pytest` to exclude tests
+  checkInputs = [ pytestCheckHook ];
+  disabledTests = [
+    # requires FAISS (not in Nixpkgs)
+    "test_accuracy_calculator_and_faiss"
+    # require network access:
+    "test_get_nearest_neighbors"
+    "test_tuplestoweights_sampler"
+    "test_untrained_indexer"
+  ];
+
   meta = {
     description = "Metric learning library for PyTorch";
     homepage = "https://github.com/KevinMusgrave/pytorch-metric-learning";

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

@@ -3,11 +3,11 @@
 
 buildPythonPackage rec {
   pname = "pyvips";
-  version = "2.1.12";
+  version = "2.1.13";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0pg0dxhxgi2m7bb5bi5wpx9hgnbi8ws1bz6w2dldbhi52pizghl4";
+    sha256 = "4f1f6fa19893048bf6b950eb7eb2d4cdfeb8b940a9defaca5d4f79e5acd5085f";
   };
 
   nativeBuildInputs = [ pytestrunner pkgconfig pkg-config ];

pkgs/development/python-modules/sphinxcontrib-katex/default.nix

@@ -2,7 +2,7 @@
 
 buildPythonPackage rec {
   pname = "sphinxcontrib-katex";
-  version = "0.6.1";
+  version = "0.7.1";
 
   # pkgutil namespaces are broken in nixpkgs (because they can't scan multiple
   # directories). But python2 is EOL, so not supporting it should be ok.
@@ -10,7 +10,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "88320b2780f350d67f84a5424973ce24aee65701e8e163a7f5856c5df3353188";
+    sha256 = "fa80aba8af9d78f70a0a255815d44e33e8aca8e806ca6101e0eb18b2b7243246";
   };
 
   propagatedBuildInputs = [ sphinx ];

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

@@ -1,14 +1,14 @@
-{ stdenv, buildPythonPackage, fetchPypi }:
+{ stdenv, buildPythonPackage, fetchPypi, isPy27 }:
 
 
 buildPythonPackage rec {
-
   pname = "versioneer";
-  version = "0.18";
+  version = "0.19";
+  disabled = isPy27;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0dgkzg1r7mjg91xp81sv9z4mabyxl39pkd11jlc1200md20zglga";
+    sha256 = "a4fed39bbebcbd2d07f8a86084773f303cb442709491955a0e6754858e47afae";
   };
 
   # Couldn't get tests to work because, for instance, they used virtualenv and

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

@@ -15,11 +15,11 @@
 
 buildPythonPackage rec {
   pname = "vowpalwabbit";
-  version = "8.8.1";
+  version = "8.9.0";
 
   src = fetchPypi{
     inherit pname version;
-    sha256 = "17fw1g4ka9jppd41srw39zbp2b8h81izc71bbggxgf2r0xbdpga6";
+    sha256 = "37fb7a400f3a7923a04df9921b3eef1bbe96117424ef083dcfed0e4eea77fa08";
   };
 
   nativeBuildInputs = [

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

@@ -10,7 +10,6 @@
 , flake8
 , jq
 , pytest
-, unixtools
 , toml
 }:
 
@@ -23,6 +22,10 @@ buildPythonPackage rec {
     sha256 = "1q4rky0a6n4izmq7slb91a54g8swry1xrbfqxwc8lkd3hhvlxxkl";
   };
 
+  postPatch = ''
+    substituteInPlace test/test.py --replace "expect_exit_codes={0} if sys.stdin.isatty() else {2}" "expect_exit_codes={0}"
+  '';
+
   propagatedBuildInputs = [
     pyyaml
     xmltodict
@@ -32,7 +35,6 @@ buildPythonPackage rec {
   doCheck = true;
 
   checkInputs = [
-   unixtools.script
    pytest
    coverage
    flake8
@@ -40,8 +42,7 @@ buildPythonPackage rec {
    toml
   ];
 
-  # tests fails if stdin is not a tty
-  checkPhase = "echo | script -c 'pytest ./test/test.py'";
+  checkPhase = "pytest ./test/test.py";
 
   pythonImportsCheck = [ "yq" ];