Merge branch 'staging-next' into staging

doc/languages-frameworks/python.section.md

@@ -605,7 +605,7 @@ All parameters from `stdenv.mkDerivation` function are still supported. The foll
 * `disabled` ? false: If `true`, package is not build for the particular Python interpreter version.
 * `dontWrapPythonPrograms ? false`: Skip wrapping of python programs.
 * `installFlags ? []`: A list of strings. Arguments to be passed to `pip install`. To pass options to `python setup.py install`, use `--install-option`. E.g., `installFlags=["--install-option='--cpp_implementation'"]`.
-* `format ? "setuptools"`: Format of the source. Valid options are `"setuptools"`, `"flit"`, `"wheel"`, and `"other"`. `"setuptools"` is for when the source has a `setup.py` and `setuptools` is used to build a wheel, `flit`, in case `flit` should be used to build a wheel, and `wheel` in case a wheel is provided. Use `other` when a custom `buildPhase` and/or `installPhase` is needed.
+* `format ? "setuptools"`: Format of the source. Valid options are `"setuptools"`, `"pyproject"`, `"flit"`, `"wheel"`, and `"other"`. `"setuptools"` is for when the source has a `setup.py` and `setuptools` is used to build a wheel, `flit`, in case `flit` should be used to build a wheel, and `wheel` in case a wheel is provided. Use `other` when a custom `buildPhase` and/or `installPhase` is needed.
 * `makeWrapperArgs ? []`: A list of strings. Arguments to be passed to `makeWrapper`, which wraps generated binaries. By default, the arguments to `makeWrapper` set `PATH` and `PYTHONPATH` environment variables before calling the binary. Additional arguments here can allow a developer to set environment variables which will be available when the binary is run. For example, `makeWrapperArgs = ["--set FOO BAR" "--set BAZ QUX"]`.
 * `namePrefix`: Prepends text to `${name}` parameter. In case of libraries, this defaults to `"python3.5-"` for Python 3.5, etc., and in case of applications to `""`.
 * `pythonPath ? []`: List of packages to be added into `$PYTHONPATH`. Packages in `pythonPath` are not propagated (contrary to `propagatedBuildInputs`).
@@ -881,7 +881,6 @@ example of such a situation is when `py.test` is used.
     '';
   }
   ```
-- Unicode issues can typically be fixed by including `glibcLocales` in `buildInputs` and exporting `LC_ALL=en_US.utf-8`.
 - Tests that attempt to access `$HOME` can be fixed by using the following work-around before running tests (e.g. `preCheck`): `export HOME=$(mktemp -d)`
 
 ## FAQ

nixos/doc/manual/release-notes/rl-1903.xml

@@ -167,12 +167,18 @@
    </listitem>
    <listitem>
     <para>
-      The <varname>buildPythonPackage</varname> now sets <varname>strictDeps = true</varname>
+      The <varname>buildPythonPackage</varname> function now sets <varname>strictDeps = true</varname>
       to help distinguish between native and non-native dependencies in order to
       improve cross-compilation compatibility. Note however that this may break
       user expressions.
     </para>
    </listitem>
+   <listitem>
+    <para>
+      The <varname>buildPythonPackage</varname> function now sets <varname>LANG = C.UTF-8</varname>
+      to enable Unicode support. The <varname>glibcLocales</varname> package is no longer needed as a build input.
+    </para>
+   </listitem>
    <listitem>
     <para>
       The Syncthing state and configuration data has been moved from

pkgs/development/interpreters/python/build-python-package-pyproject.nix

@@ -0,0 +1,53 @@
+# This function provides specific bits for building a setuptools-based Python package.
+
+{ lib
+, python
+}:
+
+{
+# passed to "python setup.py build_ext"
+# https://github.com/pypa/pip/issues/881
+# Rename to `buildOptions` because it is not setuptools specific?
+  setupPyBuildFlags ? []
+# Execute before shell hook
+, preShellHook ? ""
+# Execute after shell hook
+, postShellHook ? ""
+, ... } @ attrs:
+
+let
+  options = lib.concatMapStringsSep " " (option: "--global-option ${option}") setupPyBuildFlags;
+in attrs // {
+  buildPhase = attrs.buildPhase or ''
+    runHook preBuild
+    mkdir -p dist
+    echo "Creating a wheel..."
+    ${python.pythonForBuild.interpreter} -m pip wheel --no-index --no-deps --no-clean --no-build-isolation --wheel-dir dist ${options} .
+    echo "Finished creating a wheel..."
+    runHook postBuild
+  '';
+
+  installCheckPhase = ''
+    runHook preCheck
+    echo "No checkPhase defined. Either provide a checkPhase or disable tests in case tests are not available."; exit 1
+    runHook postCheck
+  '';
+
+  # With Python it's a common idiom to run the tests
+  # after the software has been installed.
+  doCheck = attrs.doCheck or true;
+
+  shellHook = attrs.shellHook or ''
+    ${preShellHook}
+    # Long-term setup.py should be dropped.
+    if [ -e pyproject.toml ]; then
+      tmp_path=$(mktemp -d)
+      export PATH="$tmp_path/bin:$PATH"
+      export PYTHONPATH="$tmp_path/${python.pythonForBuild.sitePackages}:$PYTHONPATH"
+      mkdir -p $tmp_path/${python.pythonForBuild.sitePackages}
+      ${python.pythonForBuild.pkgs.bootstrapped-pip}/bin/pip install -e . --prefix $tmp_path >&2
+    fi
+    ${postShellHook}
+  '';
+
+}

pkgs/development/interpreters/python/build-python-package.nix

@@ -17,6 +17,7 @@
 
 let
   setuptools-specific = import ./build-python-package-setuptools.nix { inherit lib python; };
+  pyproject-specific = import ./build-python-package-pyproject.nix { inherit lib python; };
   flit-specific = import ./build-python-package-flit.nix { inherit python flit; };
   wheel-specific = import ./build-python-package-wheel.nix { };
   common = import ./build-python-package-common.nix { inherit python; };
@@ -37,7 +38,8 @@ format ? "setuptools"
 
 let
   formatspecific =
-    if format == "setuptools" then common (setuptools-specific attrs)
+    if format == "pyproject" then common (pyproject-specific attrs)
+    else if format == "setuptools" then common (setuptools-specific attrs)
     else if format == "flit" then common (flit-specific attrs)
     else if format == "wheel" then common (wheel-specific attrs)
     else if format == "other" then {}

pkgs/development/interpreters/python/mk-python-derivation.nix

@@ -90,6 +90,8 @@ let self = toPythonModule (python.stdenv.mkDerivation (builtins.removeAttrs attr
   # Enabled to detect some (native)BuildInputs mistakes
   strictDeps = true;
 
+  LANG = "${if python.stdenv.isDarwin then "en_US" else "C"}.UTF-8";
+
   # Python packages don't have a checkPhase, only an installCheckPhase
   doCheck = false;
   doInstallCheck = doCheck;

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

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "XlsxWriter";
-  version = "1.1.4";
+  version = "1.1.5";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "07e38c73b687e2f867151adce821e43e02856c4d8c6e482807b6ea7f4ac9506c";
+    sha256 = "de9ef46088489915eaaee00c7088cff93cf613e9990b46b933c98eb46f21b47f";
   };
 
   meta = {

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

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "aiohue";
-  version = "1.9.0";
+  version = "1.9.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "3b6cb87652cf1ffc904443b9c5514873c331e159953f2ebf77a051444b350594";
+    sha256 = "3c23aed8e82f398b732279f5f7ee7ed00949ff2db7009f7a2dc705f7c2d16783";
   };
 
   propagatedBuildInputs = [ aiohttp ];

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

@@ -4,11 +4,11 @@
 
 buildPythonPackage rec {
   pname = "alerta-server";
-  version = "6.7.4";
+  version = "6.7.5";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "5ca2783f6e9211fdebd433b9eae83fbcf75ed127dc87946257d101a7d7a465db";
+    sha256 = "e8dc3428248a5b20c4fe8da76c2d353b715d515bd4879928c499671d4360a90f";
   };
 
   propagatedBuildInputs = [ python-dateutil requests pymongo raven bcrypt flask pyjwt flask-cors psycopg2 pytz flask-compress jinja2 pyyaml];

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

@@ -2,12 +2,12 @@
   asn1crypto, click, pydot, ipython, pyqt5, pyperclip }:
 
 buildPythonPackage rec {
-  version = "3.3.4";
+  version = "3.3.5";
   pname = "androguard";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1hinfbvha7f1py1jnvxih7lx0p4z2nyaiq9bvg8v3bykwrd9jff2";
+    sha256 = "f0655ca3a5add74c550951e79bd0bebbd1c5b239178393d30d8db0bd3202cda2";
   };
 
   propagatedBuildInputs = [

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

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "atom";
-  version = "0.4.2";
+  version = "0.4.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "5b1c15599681398e343fcfcf2c00d26071964f5305a403fc590c45388bacdf16";
+    sha256 = "ce96fb50326a3bfa084463dbde1cf2e02c92735e5bc324d836355c25af87e0ae";
   };
 
   propagatedBuildInputs = [ future ];

pkgs/development/python-modules/bootstrapped-pip/default.nix

@@ -3,9 +3,9 @@
 let
   wheel_source = fetchPypi {
     pname = "wheel";
-    version = "0.33.0";
+    version = "0.33.1";
     format = "wheel";
-    sha256 = "b79ffea026bc0dbd940868347ae9eee36789b6496b6623bd2dec7c7c540a8f99";
+    sha256 = "8eb4a788b3aec8abf5ff68d4165441bc57420c9f64ca5f471f58c3969fe08668";
   };
   setuptools_source = fetchPypi {
     pname = "setuptools";
@@ -16,13 +16,13 @@ let
 
 in stdenv.mkDerivation rec {
   pname = "pip";
-  version = "19.0.2";
+  version = "19.0.3";
   name = "${python.libPrefix}-bootstrapped-${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
     format = "wheel";
-    sha256 = "6a59f1083a63851aeef60c7d68b119b46af11d9d803ddc1cf927b58edcd0b312";
+    sha256 = "bd812612bbd8ba84159d9ddc0266b7fbce712fc9bc98c82dee5750546ec8ec64";
   };
 
   unpackPhase = ''

pkgs/development/python-modules/boto3/default.nix

@@ -13,11 +13,11 @@
 
 buildPythonPackage rec {
   pname =  "boto3";
-  version = "1.9.96"; # N.B: if you change this, change botocore too
+  version = "1.9.101"; # N.B: if you change this, change botocore too
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "c103241394d396ee08548b03d5d1f0f89a7ad1dfa7ccca88a47131f329cca093";
+    sha256 = "bc25b83405cede6025fd7de0240fa8ade910f445da46f267c1dd13409d19ad64";
   };
 
   propagatedBuildInputs = [ botocore jmespath s3transfer ] ++ lib.optionals (!isPy3k) [ futures ];

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

@@ -12,11 +12,11 @@
 
 buildPythonPackage rec {
   pname = "botocore";
-  version = "1.12.96"; # N.B: if you change this, change boto3 and awscli to a matching version
+  version = "1.12.101"; # N.B: if you change this, change boto3 and awscli to a matching version
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "55c1594041e6716847d5a8b38181e3cc44e245edbf4598ae2b99e3040073b2cf";
+    sha256 = "46e4daaa7c8cb29237802b63699c16a116f96f301ad2fcfef800574333b58b98";
   };
 
   propagatedBuildInputs = [

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

@@ -2,11 +2,11 @@
 
 if isPyPy then null else buildPythonPackage rec {
   pname = "cffi";
-  version = "1.12.0";
+  version = "1.12.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "08090454ff236239e583a9119d0502a6b9817594c0a3714dd1d8593f2350ba11";
+    sha256 = "9b6f7ba4e78c52c1a291d0c0c0bd745d19adde1a9e1c03cb899f0c6efd6f8033";
   };
 
   outputs = [ "out" "dev" ];

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

@@ -41,7 +41,10 @@ in buildPythonPackage rec {
 
   checkPhase = ''
     # 3 out of 5 SignalHandlingTests need network access
-    LANG=en_US.UTF-8 pytest -k "not SignalHandlingTests and not test_4_Autoreload"
+    # test_2_File_Concurrency also fails upstream: https://github.com/cherrypy/cherrypy/issues/1306
+    # ...and skipping it makes 2 other tests fail
+    LANG=en_US.UTF-8 pytest -k "not SignalHandlingTests and not test_4_Autoreload \
+                            and not test_2_File_Concurrency and not test_3_Redirect and not test_4_File_deletion"
   '';
 
   meta = with lib; {

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

@@ -6,11 +6,11 @@
 }:
 buildPythonPackage rec {
   pname = "cmd2";
-  version = "0.9.8";
+  version = "0.9.10";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "22c3461af56769e74225e3aeecab0e98ef86ab8d9b4ded29ba84722449fe7608";
+    sha256 = "00d68374abe02363a417160e5836022be5c8f8bdac1da5dd101fadb6f8e96619";
   };
 
   LC_ALL="en_US.UTF-8";

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

@@ -2,18 +2,18 @@
 
 buildPythonPackage rec {
   pname = "configparser";
-  version = "3.7.1";
+  version = "3.7.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "5bd5fa2a491dc3cfe920a3f2a107510d65eceae10e9c6e547b90261a4710df32";
+    sha256 = "27594cf4fc279f321974061ac69164aaebd2749af962ac8686b20503ac0bcf2d";
   };
 
   # No tests available
   doCheck = false;
 
   preConfigure = ''
-    export LC_ALL=C.UTF-8
+    export LC_ALL=${if stdenv.isDarwin then "en_US" else "C"}.UTF-8
   '';
 
   meta = with stdenv.lib; {

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

@@ -2,13 +2,13 @@
 
 buildPythonPackage rec {
   pname = "cx_Oracle";
-  version = "7.1.0";
+  version = "7.1.1";
 
   buildInputs = [ odpic ];
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "57f084bbd7d28af4deff22ef358188c06dec885c818df92fb74e093ab22fdd8f";
+    sha256 = "17d760bdf89e364fc7c964c5640c1b38cbb22ab49b53830883f21fda92c59131";
   };
 
   preConfigure = ''

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

@@ -6,11 +6,11 @@
 
 buildPythonPackage rec {
   pname = "django-contrib-comments";
-  version = "1.9.0";
+  version = "1.9.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "689f3f80ff7ea8ab9f712ae5fe17ffa2ee8babbf8d75229ee8acc7bad461dfef";
+    sha256 = "61b051d7bc3ff593e86b41a1ed5e969423cf55cc92768598af3315e2528e0890";
   };
 
   propagatedBuildInputs = [ django ];

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

@@ -1,6 +1,7 @@
-{ stdenv, buildPythonPackage, fetchPypi,
-  six, cligj, munch, click-plugins, enum34, pytest, nose,
-  gdal
+{ stdenv, buildPythonPackage, fetchPypi, isPy3k
+, attrs, click, cligj, click-plugins, six, munch, enum34
+, pytest, boto3
+, gdal
 }:
 
 buildPythonPackage rec {
@@ -14,24 +15,35 @@ buildPythonPackage rec {
 
   CXXFLAGS = stdenv.lib.optionalString stdenv.cc.isClang "-std=c++11";
 
+  nativeBuildInputs = [
+    gdal # for gdal-config
+  ];
+
   buildInputs = [
     gdal
   ];
 
   propagatedBuildInputs = [
-    six
+    attrs
+    click
     cligj
-    munch
     click-plugins
-    enum34
-  ];
+    six
+    munch
+  ] ++ stdenv.lib.optional (!isPy3k) enum34;
 
   checkInputs = [
     pytest
-    nose
+    boto3
   ];
 
-  doCheck = false;
+  checkPhase = ''
+    rm -r fiona # prevent importing local fiona
+    # Some tests access network, others test packaging
+    pytest -k "not test_*_http \
+           and not test_*_https \
+           and not test_*_wheel"
+  '';
 
   meta = with stdenv.lib; {
     description = "OGR's neat, nimble, no-nonsense API for Python";

pkgs/development/python-modules/flake8/default.nix

@@ -5,11 +5,11 @@
 
 buildPythonPackage rec {
   pname = "flake8";
-  version = "3.7.5";
+  version = "3.7.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "fd9ddf503110bf3d8b1d270e8c673aab29ccb3dd6abf29bae1f54e5116ab4a91";
+    sha256 = "6d8c66a65635d46d54de59b027a1dda40abbe2275b3164b634835ac9c13fd048";
   };
 
   checkInputs = [ pytest mock pytestrunner ];

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/globus-sdk/default.nix

@@ -10,11 +10,11 @@
 
 buildPythonPackage rec {
   pname = "globus-sdk";
-  version = "1.7.0";
+  version = "1.7.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "b8adcbe355c2baf610e9f5751967d7e910fa48604b39d6d2f083750a7a805a64";
+    sha256 = "d96f7ed1887c8f55f2bc8d493cd8ec73ff9f3361f0a134203e34e2e57bedd964";
   };
 
   checkPhase = ''

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

@@ -3,11 +3,11 @@
 
 buildPythonPackage rec {
   pname = "google-auth";
-  version = "1.6.2";
+  version = "1.6.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "e8d64e9bc8cb6f0fc5360c693f86dc9ee6964081ee702e3b5ddc937f99efc950";
+    sha256 = "0f7c6a64927d34c1a474da92cfc59e552a5d3b940d3266606c6a28b72888b9e4";
   };
 
   checkInputs = [ pytest mock oauth2client flask requests urllib3 pytest-localserver ];

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/hypothesis/default.nix

@@ -9,7 +9,7 @@ buildPythonPackage rec {
   # pytz fake_factory django numpy pytest
   # If you need these, you can just add them to your environment.
 
-  version = "3.79.3";
+  version = "3.88.3";
   pname = "hypothesis";
 
   # Use github tarballs that includes tests
@@ -17,7 +17,7 @@ buildPythonPackage rec {
     owner = "HypothesisWorks";
     repo = "hypothesis-python";
     rev = "hypothesis-python-${version}";
-    sha256 = "1ay0kwh5315scv7yz9xxrr7shynyx6flgplc1qzbz3j21cyx3yn7";
+    sha256 = "03l4hp0p7i2k04arnqkav0ygc23ml46dy3cfrlwviasrj7yzk5hc";
   };
 
   postUnpack = "sourceRoot=$sourceRoot/hypothesis-python";

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

@@ -4,11 +4,11 @@
 
 buildPythonPackage rec {
   pname = "ledgerblue";
-  version = "0.1.22";
+  version = "0.1.23";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "15206e92220d96512b357a9a740bc91b8b33b42b9164fe3b56c4c3aedf882cdc";
+    sha256 = "476a1d1f6d9e7f72befff0ea4e631461882c9c1c620b92878503bf46383c8d20";
   };
 
   propagatedBuildInputs = [

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

@@ -1,29 +1,38 @@
-{ 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
@@ -35,4 +44,3 @@ buildPythonPackage rec {
     maintainers = with maintainers; [ psyanticy ];
   };
 }
-

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

@@ -6,11 +6,11 @@
 
 buildPythonPackage rec {
   pname = "murmurhash";
-  version = "1.0.1";
+  version = "1.0.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "02wbyjixvzd6l1mljpm1ci7x835zhk3nqxgy7kvbi4jimvairs9q";
+    sha256 = "c7a646f6b07b033642b4f52ae2e45efd8b80780b3b90e8092a0cec935fbf81e2";
   };
 
   postPatch = ''

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

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "phonenumbers";
-  version = "8.10.5";
+  version = "8.10.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "aed1483d6d97fe5176715b87fa2b8a572b8695ba9d27b810ad618320198529b3";
+    sha256 = "2fe47dbf947cc74643ef1a49411466483d1165ced2b62578a14b513dd09642a9";
   };
 
   meta = {

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/pip/default.nix

@@ -10,11 +10,11 @@
 
 buildPythonPackage rec {
   pname = "pip";
-  version = "19.0.2";
+  version = "19.0.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "f851133f8b58283fa50d8c78675eb88d4ff4cde29b6c41205cd938b06338e0e5";
+    sha256 = "6e6f197a1abfb45118dbb878b5c859a0edbdd33fd250100bc015b67fded4b9f2";
   };
 
   # pip detects that we already have bootstrapped_pip "installed", so we need

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

@@ -1,12 +1,12 @@
 { lib, buildPythonPackage, fetchPypi, requests, pytest }:
 
 buildPythonPackage rec {
-  version = "2.4.0";
+  version = "2.4.1";
   pname = "plaid-python";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "734fe8328b7fc9a52f8e204b4cce99dd475fe5add784a57fdf0f0cb99eb752a0";
+    sha256 = "2b7832f9fe0c6cd23dfdb805bcfc52e2ff06fca6604e5782b7518904c1dad6bb";
   };
 
   checkInputs = [ pytest ];

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

@@ -8,11 +8,11 @@
 
 buildPythonPackage rec {
   pname = "prompt_toolkit";
-  version = "2.0.8";
+  version = "2.0.9";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "c6655a12e9b08edb8cf5aeab4815fd1e1bdea4ad73d3bbf269cf2e0c4eb75d5e";
+    sha256 = "2519ad1d8038fd5fc8e770362237ad0364d16a7650fb5724af6997ed5515e3c1";
   };
   checkPhase = ''
     py.test -k 'not test_pathcompleter_can_expanduser'

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

@@ -1,26 +1,18 @@
 { stdenv
 , buildPythonPackage
-, fetchPypi, fetchpatch
+, fetchPypi
 , darwin
 }:
 
 buildPythonPackage rec {
   pname = "psutil";
-  version = "5.4.8";
+  version = "5.5.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "6e265c8f3da00b015d24b842bfeb111f856b13d24f2c57036582568dc650d6c3";
+    sha256 = "045qaqvn6k90bj5bcy259yrwcd2afgznaav3sfhphy9b8ambzkkj";
   };
 
-  patches = [
-    (fetchpatch {
-      name = "disk_io_counters_fails.patch";
-      url = "https://github.com/giampaolo/psutil/commit/8f99f3782663959062ee868bbfdbc336307a3a4d.diff";
-      sha256 = "0j7wdgq8y20k27wcpmbgc1chd0vmbkxy8j0zwni1s4i7hyk64hmk";
-    })
-  ];
-
   # No tests in archive
   doCheck = false;
 

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

@@ -8,11 +8,11 @@
 
 buildPythonPackage rec {
   pname = "py_stringmatching";
-  version = "0.4.0";
+  version = "0.4.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0rjsx7iipn6svki21lmsza7b0dz9vkgmix696zryiv7gkhblqyb4";
+    sha256 = "c46db1e855cef596dfbbe1bd48fcabb30736479eff602c2bf88af10f998f1532";
   };
 
   checkInputs = [ nose ];

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

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "PyChromecast";
-  version = "2.5.1";
+  version = "2.5.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "936672df42f25f271c806569ee4fb7abbc0d6c17e15deba5d6c9f1128ff6974e";
+    sha256 = "7ce4eeb398a73c26bd65870739c94845da60f4527ebe2f104826ee32d70d035c";
   };
 
   disabled = !isPy3k;

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

@@ -5,11 +5,11 @@
 
 buildPythonPackage rec {
   pname   = "pykeepass";
-  version = "3.0.2";
+  version = "3.0.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1kfnh42nimsbdpwpny2c9df82b2n4fb5fagh54ck06f3x483vd90";
+    sha256 = "2c9e2ddb03ee696ed8aa72c2cddfb81280614864e003226141d68b975aa56f6f";
   };
 
   propagatedBuildInputs = [

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

@@ -9,7 +9,7 @@ buildPythonPackage rec {
     sha256 = "0v47p840myqgc7hr4lir72xshcfpa0w8j9n077h3njpqyn6wlbag";
   };
 
-  buildInputs = [ krb5 ];
+  nativeBuildInputs = [ krb5 ];
 
   # there are no tests
   doCheck = false;

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/pyrsistent/default.nix

@@ -9,11 +9,11 @@
 
 buildPythonPackage rec {
   pname = "pyrsistent";
-  version = "0.14.10";
+  version = "0.14.11";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "07f7ae71291af8b0dbad8c2ab630d8223e4a8c4e10fc37badda158c02e753acf";
+    sha256 = "3ca82748918eb65e2d89f222b702277099aca77e34843c5eb9d52451173970e2";
   };
 
   propagatedBuildInputs = [ six ];

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

@@ -21,7 +21,6 @@ buildPythonPackage rec {
     description = "LGPL-licensed Python bindings for the Qt cross-platform application and UI framework";
     license = lib.licenses.lgpl21;
     homepage = http://www.pyside.org;
-    maintainers = [ ];
     broken = true;
   };
 }

pkgs/development/python-modules/pytest-server-fixtures/default.nix

@@ -4,11 +4,11 @@
 
 buildPythonPackage rec {
   pname = "pytest-server-fixtures";
-  version = "1.6.1";
+  version = "1.6.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "cf4a6aff42f620fe556c175e8f493f086c9690a492059cf23521a10d3ac5db1a";
+    sha256 = "c89f9532f62cf851489082ece1ec692b6ed5b0f88f20823bea25e2a963ebee8f";
   };
 
   buildInputs = [ pytest ];

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

@@ -3,11 +3,11 @@
 
 buildPythonPackage rec {
   pname = "pyupdate";
-  version = "0.2.26";
+  version = "0.2.29";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "8d30f5b011c6be41886741e31bc87cadc9762d60800faf3ce419fa52132de35c";
+    sha256 = "0096bde03f43b67c068914ebcb756265641a6d2a5888d4bc81636347c22bf0aa";
   };
 
   propagatedBuildInputs = [ requests ];

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

@@ -9,11 +9,11 @@
 
 buildPythonPackage rec {
   pname = "pyzmq";
-  version = "17.1.2";
+  version = "17.1.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "a72b82ac1910f2cf61a49139f4974f994984475f771b0faa730839607eeedddf";
+    sha256 = "83722236bd6ae6a07dec0cb728906785040e91826c7575709a258b4e21d0f812";
   };
 
   checkInputs = [  pytest tornado ];

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

@@ -21,13 +21,13 @@
 
 buildPythonPackage rec {
   pname = "qiskit";
-  version = "0.7.2";
+  version = "0.7.3";
 
   disabled = !isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "08c7f7ccd32a5cb0c0a0c4f63d6ff068d659c9c0b51e2df6f2054e586e8bfa19";
+    sha256 = "63e7a7c3033fe955d715cc825b3fb61d27c25ad66e1761493ca2243b5dbfb4f9";
   };
 
   buildInputs = [ cmake ]

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

@@ -7,11 +7,11 @@
 
 buildPythonPackage rec {
   pname = "quantities";
-  version = "0.12.2";
+  version = "0.12.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "92e8397938516483f4fd1855097ec11953ab10dd0bf3293954559226679f76f0";
+    sha256 = "582f3c7aeba897846761e966615e01202a5e5d06add304492931b05085d19883";
   };
 
   propagatedBuildInputs = [ numpy ];

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

@@ -7,11 +7,11 @@
 
 buildPythonPackage rec {
   pname = "regex";
-  version = "2019.02.07";
+  version = "2019.02.21";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "4a1a1d963f462c13722b34ef1f82c4707091b0a3fb9b5fd79b6670c38b734095";
+    sha256 = "587bd4cad11c7294f89799c45778abca271d7c6668a0e85c41a6dbfa8096f9bb";
   };
 
   postCheck = ''
@@ -19,6 +19,9 @@ buildPythonPackage rec {
     ${python.interpreter} -c 'import test_regex; test_regex.test_main();'
   '';
 
+  # No tests in archive
+  doCheck = false;
+
   meta = {
     description = "Alternative regular expression module, to replace re";
     homepage = https://bitbucket.org/mrabarnett/mrab-regex;

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

@@ -14,5 +14,6 @@ buildPythonPackage rec {
 
   builder = ./builder.sh;
 
-  buildInputs = [ rpmextract python wirelesstools gettext ];
+  nativeBuildInputs = [ rpmextract  gettext ];
+  buildInputs = [ wirelesstools ];
 }

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():

pkgs/development/python-modules/spectral-cube/default.nix

@@ -7,13 +7,13 @@
 
 buildPythonPackage rec {
   pname = "spectral-cube";
-  version = "0.4.3";
+  version = "0.4.4";
 
   doCheck = false; # the tests requires several pytest plugins that are not in nixpkgs
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "057g3mzlg5cy4wg2hh3p6gssn93rs6i7pswzhldvcq4k8m8hsl3b";
+    sha256 = "9051ede204b1e25b6358b5e0e573b624ec0e208c24eb03a7ed4925b745c93b5e";
   };
 
   propagatedBuildInputs = [ astropy radio_beam pytest ];

pkgs/development/python-modules/telethon-session-sqlalchemy/default.nix

@@ -2,13 +2,13 @@
 
 buildPythonPackage rec {
   pname = "telethon-session-sqlalchemy";
-  version = "0.2.8";
+  version = "0.2.9.post1";
 
   disabled = !isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "5097b4fe103e377b719f1840e121d14dbae38c4b7c72634c7ba1f0ec05b20533";
+    sha256 = "bbe6a8ca32dd42aa1830b91f08f0458d728dc9eedca0ca27814a34c0b566100e";
   };
 
   propagatedBuildInputs = [

pkgs/development/python-modules/uproot-methods/default.nix

@@ -6,12 +6,12 @@
 }:
 
 buildPythonPackage rec {
-  version = "0.4.2";
+  version = "0.4.3";
   pname = "uproot-methods";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "dcb72692067cfc4c5ccfa859fe737b2cd47661692a0cc0b42c75d13dbb1eb040";
+    sha256 = "f90d91a613a875ebdf214f0f6f3fd0f8beea9125fc35e54f334d6104fe47c87d";
   };
 
   propagatedBuildInputs = [ numpy awkward ];

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

@@ -15,11 +15,11 @@
 
 buildPythonPackage rec {
   pname = "uproot";
-  version = "3.4.5";
+  version = "3.4.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "46a99b590c062ad01f2721af04e6262986f0b53e51dfedf68bf4049bb015c12f";
+    sha256 = "1fafe476c26252e4dbd399456323778e76d23dc2f43cf6581a707d1647978610";
   };
 
   buildInputs = [ pytestrunner ];

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

@@ -6,11 +6,11 @@
 
 buildPythonPackage rec {
   pname = "virtualenv";
-  version = "16.4.0";
+  version = "16.4.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "cceab52aa7d4df1e1871a70236eb2b89fcfe29b6b43510d9738689787c513261";
+    sha256 = "5a3ecdfbde67a4a3b3111301c4d64a5b71cf862c8c42958d30cf3253df1f29dd";
   };
 
   # Doubt this is needed - FRidh 2017-07-07

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

@@ -9,11 +9,11 @@
 
 buildPythonPackage rec {
   pname = "wheel";
-  version = "0.33.0";
+  version = "0.33.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "12363e6df5678ecf9daf8429f06f97e7106e701405898f24318ce7f0b79c611a";
+    sha256 = "66a8fd76f28977bb664b098372daef2b27f60dc4d1688cfab7b37a09448f0e9d";
   };
 
   checkInputs = [ pytest pytestcov coverage ];

pkgs/development/python-modules/zope_i18n/default.nix

@@ -7,11 +7,11 @@
 
 buildPythonPackage rec {
   pname = "zope.i18n";
-  version = "4.6.1";
+  version = "4.6.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "14f7339f6d4fed5e94882a7f1b2e40fd90ad00b3c28a7f4353762101395e3304";
+    sha256 = "229de41f751dae36b1ef9fa284bc548ef40169234bf0d2199e41581e16304621";
   };
 
   propagatedBuildInputs = [ pytz zope_component ];

pkgs/development/tools/build-managers/cmake/application-services.patch

@@ -1,6 +1,24 @@
-diff -ur cmake-3.12.1/Source/cmGlobalXCodeGenerator.cxx cmake-3.12.1-patched/Source/cmGlobalXCodeGenerator.cxx
---- cmake-3.12.1/Source/cmGlobalXCodeGenerator.cxx	2018-08-09 21:14:08.000000000 +0900
-+++ cmake-3.12.1-patched/Source/cmGlobalXCodeGenerator.cxx	2018-08-12 02:47:28.719691934 +0900
+diff --git a/Source/CMakeLists.txt b/Source/CMakeLists.txt
+index 8aff8f6..af1852d 100644
+--- a/Source/CMakeLists.txt
++++ b/Source/CMakeLists.txt
+@@ -791,12 +791,6 @@ if(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND CMAKE_SYSTEM_PROCESSOR MATCHES "sparc"
+   endif()
+ endif()
+ 
+-# On Apple we need CoreFoundation and CoreServices
+-if(APPLE)
+-  target_link_libraries(CMakeLib "-framework CoreFoundation")
+-  target_link_libraries(CMakeLib "-framework CoreServices")
+-endif()
+-
+ if(WIN32 AND NOT UNIX)
+   # We need the rpcrt4 library on Windows.
+   # We need the crypt32 library on Windows for crypto/cert APIs.
+diff --git a/Source/cmGlobalXCodeGenerator.cxx b/Source/cmGlobalXCodeGenerator.cxx
+index e353a37..b06f842 100644
+--- a/Source/cmGlobalXCodeGenerator.cxx
++++ b/Source/cmGlobalXCodeGenerator.cxx
 @@ -35,11 +35,6 @@
  
  struct cmLinkImplementation;
@@ -13,3 +31,19 @@ diff -ur cmake-3.12.1/Source/cmGlobalXCodeGenerator.cxx cmake-3.12.1-patched/Sou
  #if defined(CMAKE_BUILD_WITH_CMAKE)
  #  include "cmXMLParser.h"
  
+diff --git a/Utilities/cmlibarchive/CMakeLists.txt b/Utilities/cmlibarchive/CMakeLists.txt
+index d7af6e2..d4808fc 100644
+--- a/Utilities/cmlibarchive/CMakeLists.txt
++++ b/Utilities/cmlibarchive/CMakeLists.txt
+@@ -1662,11 +1662,6 @@ IF(MSVC)
+   ADD_DEFINITIONS(-D_CRT_SECURE_NO_DEPRECATE)
+ ENDIF(MSVC)
+ 
+-# We need CoreServices on Mac OS.
+-IF(APPLE)
+-  LIST(APPEND ADDITIONAL_LIBS "-framework CoreServices")
+-ENDIF(APPLE)
+-
+ add_subdirectory(libarchive)
+ 
+ install(FILES COPYING DESTINATION ${CMAKE_DOC_DIR}/cmlibarchive)

pkgs/development/tools/build-managers/cmake/default.nix

@@ -2,7 +2,7 @@
 , bzip2, curl, expat, libarchive, xz, zlib, libuv, rhash
 , buildPackages
 # darwin attributes
-, ps
+, cf-private, ps
 , isBootstrap ? false
 , useSharedLibraries ? (!isBootstrap && !stdenv.isCygwin)
 , useNcurses ? false, ncurses
@@ -34,11 +34,6 @@ stdenv.mkDerivation rec {
     inherit sha256;
   };
 
-  prePatch = optionalString (!useSharedLibraries) ''
-    substituteInPlace Utilities/cmlibarchive/CMakeLists.txt \
-      --replace '"-framework CoreServices"' '""'
-  '';
-
   patches = [
     # Don't search in non-Nix locations such as /usr, but do search in our libc.
     ./search-path.patch
@@ -57,6 +52,7 @@ stdenv.mkDerivation rec {
 
   buildInputs =
     [ setupHook pkgconfig ]
+    ++ optional stdenv.isDarwin cf-private  # needed for CFBundleCopyExecutableURL
     ++ optionals useSharedLibraries [ bzip2 curl expat libarchive xz zlib libuv rhash ]
     ++ optional useNcurses ncurses
     ++ optional useQt4 qt4

pkgs/tools/compression/xar/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, libxml2, openssl, zlib, bzip2, fts }:
+{ stdenv, fetchurl, libxml2, lzma, openssl, zlib, bzip2, fts }:
 
 stdenv.mkDerivation rec {
   version = "1.6.1";
@@ -9,7 +9,7 @@ stdenv.mkDerivation rec {
     sha256 = "0ghmsbs6xwg1092v7pjcibmk5wkyifwxw6ygp08gfz25d2chhipf";
   };
 
-  buildInputs = [ libxml2 openssl zlib bzip2 fts ];
+  buildInputs = [ libxml2 lzma openssl zlib bzip2 fts ];
 
   meta = {
     homepage    = https://mackyle.github.io/xar/;

pkgs/tools/misc/vdirsyncer/default.nix

@@ -49,6 +49,12 @@ python3Packages.buildPythonApplication rec {
   ];
 
   postPatch = ''
+    # Invalid argument: 'perform_health_check' is not a valid setting
+    substituteInPlace tests/conftest.py \
+      --replace "perform_health_check=False" ""
+    substituteInPlace tests/unit/test_repair.py \
+      --replace $'@settings(perform_health_check=False)  # Using the random module for UIDs\n' ""
+
     # for setuptools_scm:
     echo 'Version: ${version}' >PKG-INFO
 

pkgs/top-level/all-packages.nix

@@ -8516,7 +8516,9 @@ in
 
   cmake_2_8 = callPackage ../development/tools/build-managers/cmake/2.8.nix { };
 
-  cmake = libsForQt5.callPackage ../development/tools/build-managers/cmake { };
+  cmake = libsForQt5.callPackage ../development/tools/build-managers/cmake {
+    inherit (darwin) cf-private;
+  };
 
   cmakeCurses = cmake.override { useNcurses = true; };