Merge pull request #37250 from dotlambda/python-fixes

Python fixes, cc #36453

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

@@ -0,0 +1,25 @@
+{ lib, buildPythonPackage, fetchPypi, six, pytest }:
+
+buildPythonPackage rec {
+  pname = "allpairspy";
+  version = "2.4.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "9fb7962ee523bd96c5098cd3c97ac1b8eb73021d3df9314657ee9de00f52e034";
+  };
+
+  propagatedBuildInputs = [ six ];
+
+  checkInputs = [ pytest ];
+
+  checkPhase = ''
+    py.test
+  '';
+
+  meta = with lib; {
+    description = "Pairwise test combinations generator";
+    homepage = https://github.com/thombashi/allpairspy;
+    license = licenses.mit;
+  };
+}

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

@@ -9,11 +9,11 @@
 
 buildPythonPackage rec {
   pname = "bleach";
-  version = "2.1.2";
+  version = "2.1.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "38fc8cbebea4e787d8db55d6f324820c7f74362b70db9142c1ac7920452d1a19";
+    sha256 = "eb7386f632349d10d9ce9d4a838b134d4731571851149f9cc2c05a9a837a9a44";
   };
 
   checkInputs = [ pytest pytestrunner ];
@@ -41,4 +41,4 @@ buildPythonPackage rec {
     license = lib.licenses.asl20;
     maintainers = with lib.maintainers; [ prikhi ];
   };
-}
+}

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

@@ -0,0 +1,21 @@
+{ lib, buildPythonPackage, fetchPypi
+, translationstring, iso8601 }:
+
+buildPythonPackage rec {
+  pname = "colander";
+  version = "1.4";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "e20e9acf190e5711cf96aa65a5405dac04b6e841028fc361d953a9923dbc4e72";
+  };
+
+  propagatedBuildInputs = [ translationstring iso8601 ];
+
+  meta = with lib; {
+    description = "A simple schema-based serialization and deserialization library";
+    homepage = https://docs.pylonsproject.org/projects/colander/en/latest/;
+    license = licenses.free; # http://repoze.org/LICENSE.txt
+    maintainers = with maintainers; [ garbas domenkozar ];
+  };
+}

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

@@ -0,0 +1,27 @@
+{ lib, buildPythonPackage, fetchPypi, isPy3k, glibcLocales, future }:
+
+buildPythonPackage rec {
+  pname = "CommonMark";
+  version = "0.7.5";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "4dfbbd1dbc669a9b71a015032b2bbe5c4b019ca8b6ca410d89cf7020de46d2c0";
+  };
+
+  preCheck = ''
+    export LC_ALL="en_US.UTF-8"
+  '';
+
+  # UnicodeEncodeError on Python 2
+  doCheck = isPy3k;
+
+  checkInputs = [  glibcLocales ];
+  propagatedBuildInputs = [ future ];
+
+  meta = with lib; {
+    description = "Python parser for the CommonMark Markdown spec";
+    homepage = https://github.com/rolandshoemaker/CommonMark-py;
+    license = licenses.bsd3;
+  };
+}

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

@@ -1,15 +1,20 @@
-{ stdenv, buildPythonPackage, fetchPypi, cryptography, boto3, pyyaml, docutils }:
+{ stdenv, buildPythonPackage, fetchPypi, fetchpatch, cryptography, boto3, pyyaml, docutils }:
 
 buildPythonPackage rec {
-  pname    = "credstash";
+  pname = "credstash";
   version = "1.14.0";
-  name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
     sha256 = "718b337f7a6fa001e014386071f05c59900525d0507009126d2fe8d75fe0761d";
   };
 
+  patches = fetchpatch {
+    url = https://github.com/fugue/credstash/pull/178.patch;
+    sha256 = "15ih4h5v63g7qfmqdl4zca147wkcrx8vnsh4ns33001dipcfb5sc";
+    excludes = [ ".travis.yml" ];
+  };
+
   propagatedBuildInputs = [ cryptography boto3 pyyaml docutils ];
 
   # No tests in archive

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

@@ -1,15 +1,24 @@
-{ lib, fetchurl, buildPythonPackage, flake8, nose }:
+{ lib, fetchPypi, buildPythonPackage, flake8, pycodestyle, pytestrunner, pytest }:
 
 buildPythonPackage rec {
   pname = "flake8-debugger";
-  name = "${pname}-${version}";
   version = "3.1.0";
-  src = fetchurl {
-    url = "mirror://pypi/f/flake8-debugger/${name}.tar.gz";
+
+  src = fetchPypi {
+    inherit pname version;
     sha256 = "be4fb88de3ee8f6dd5053a2d347e2c0a2b54bab6733a2280bb20ebd3c4ca1d97";
   };
-  buildInputs = [ nose ];
-  propagatedBuildInputs = [ flake8 ];
+
+  nativeBuildInputs = [ pytestrunner ];
+
+  propagatedBuildInputs = [ flake8 pycodestyle ];
+
+  checkInputs = [ pytest ];
+
+  # Tests not included in PyPI tarball
+  # FIXME: Remove when https://github.com/JBKahn/flake8-debugger/pull/15 is merged
+  doCheck = false;
+
   meta = {
     homepage = https://github.com/jbkahn/flake8-debugger;
     description = "ipdb/pdb statement checker plugin for flake8";

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

@@ -0,0 +1,22 @@
+{ lib, buildPythonPackage, fetchPypi, requests }:
+
+buildPythonPackage rec {
+  pname = "hvac";
+  version = "0.5.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "2c9308334301daee3b5c6d56a032ca2c81eeb97d2777b73d795e201e8d037687";
+  };
+
+  propagatedBuildInputs = [ requests ];
+
+  # Requires running a Vault server
+  doCheck = false;
+
+  meta = with lib; {
+    description = "HashiCorp Vault API client";
+    homepage = https://github.com/ianunruh/hvac;
+    license = licenses.asl20;
+  };
+}

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

@@ -1,13 +1,16 @@
-{ lib, buildPythonPackage, fetchurl, fetchpatch
+{ lib, buildPythonPackage, fetchurl, fetchpatch, isPy3k
 , pytest, werkzeug, pygments
 }:
 
 buildPythonPackage rec {
-  name = "moinmoin-${ver}";
-  ver = "1.9.9";
+  name = "moinmoin";
+  version = "1.9.9";
+
+  # SyntaxError in setup.py
+  disabled = isPy3k;
 
   src = fetchurl {
-    url = "http://static.moinmo.in/files/moin-${ver}.tar.gz";
+    url = "http://static.moinmo.in/files/moin-${version}.tar.gz";
     sha256 = "197ga41qghykmir80ik17f9hjpmixslv3zjgj7bj9qvs1dvdg5s3";
   };
 

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

@@ -37,5 +37,8 @@ buildPythonPackage rec {
     description = "Data migration utilities";
     license = lib.licenses.bsdOriginal;
     maintainers = with lib.maintainers; [ fridh ];
+    # incomaptible with Networkx 2
+    # see https://github.com/blaze/odo/pull/601
+    broken = true;
   };
-}
+}

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

@@ -0,0 +1,20 @@
+{ buildPythonPackage, fetchPypi
+, requests, six, pyopenssl }:
+
+buildPythonPackage rec {
+  pname = "paypalrestsdk";
+  version = "1.13.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "238713208031e8981bf70b3350b3d7f85ed64d34e0f21e4c1184444a546fee7f";
+  };
+
+  propagatedBuildInputs = [ requests six pyopenssl ];
+
+  meta = {
+    homepage = https://developer.paypal.com/;
+    description = "Python APIs to create, process and manage payment";
+    license = "PayPal SDK License";
+  };
+}

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

@@ -0,0 +1,27 @@
+{ lib, buildPythonPackage, fetchPypi
+, requests, websocket_client, python_magic
+, pytest, mock }:
+
+buildPythonPackage rec {
+  pname = "pushbullet.py";
+  version = "0.11.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "aa9dc7bb46e083e3497d46241154f12944a8f540e29d150330ca94db0b453b8d";
+  };
+
+  propagatedBuildInputs = [ requests websocket_client python_magic ];
+
+  checkInputs = [ pytest mock ];
+
+  checkPhase = ''
+    PUSHBULLET_API_KEY="" py.test -k "not test_e2e and not test_auth"
+  '';
+
+  meta = with lib; {
+    description = "A simple python client for pushbullet.com";
+    homepage = https://github.com/randomchars/pushbullet.py;
+    license = licenses.mit;
+  };
+}

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

@@ -1,10 +1,12 @@
-{ stdenv, fetchPypi, buildPythonPackage, defusedxml }:
+{ stdenv, fetchPypi, buildPythonPackage, isPy3k, defusedxml }:
 
 buildPythonPackage rec {
-  name = "${pname}-${version}";
   pname = "PyAMF";
   version = "0.8.0";
 
+  # according to setup.py
+  disabled = isPy3k;
+
   src = fetchPypi {
     inherit pname version;
     sha256 = "1r3lp9gkph48g9lijby5rs5daa3lhxs204r14zw4kvp3hf4xcm84";

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

@@ -14,6 +14,9 @@ buildPythonPackage rec {
     sha256 = "1g181x2mrhxcaswr6vi2m7if97wv4rf2g2pny60334sciga8njfz";
   };
 
+  # Unreliable timing: https://github.com/danielperna84/pyhomematic/issues/126
+  doCheck = false;
+
   meta = with stdenv.lib; {
     description = "Python 3 Interface to interact with Homematic devices";
     homepage = https://github.com/danielperna84/pyhomematic;

pkgs/development/python-modules/python-ctags3/default.nix

@@ -0,0 +1,17 @@
+{ lib, buildPythonPackage, fetchPypi }:
+
+buildPythonPackage rec {
+  pname = "python-ctags3";
+  version = "1.2.4";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "62e1d48a8cd88756767f3f5e3f1b1a81bc84deeb736f0c9480a5b5d066f63c3e";
+  };
+
+  meta = with lib; {
+    description = "Ctags indexing python bindings";
+    homepage = https://github.com/jonashaag/python-ctags3;
+    license = licenses.lgpl3Plus;
+  };
+}

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

@@ -2,6 +2,7 @@
 , buildPythonPackage
 , fetchPypi
 , pytest
+, CommonMark
 , bleach
 , docutils
 , pygments
@@ -10,18 +11,17 @@
 
 buildPythonPackage rec {
   pname = "readme_renderer";
-  version = "17.2";
-  name = "${pname}-${version}";
+  version = "17.4";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "9deab442963a63a71ab494bf581b1c844473995a2357f4b3228a1df1c8cba8da";
+    sha256 = "82d68175feec897af2a38fe8590778f14c3be5324cc62e3ce5752a9b1e4b60ab";
   };
 
   checkInputs = [ pytest ];
 
   propagatedBuildInputs = [
-    bleach docutils pygments six
+    CommonMark bleach docutils pygments six
   ];
 
   checkPhase = ''
@@ -33,4 +33,4 @@ buildPythonPackage rec {
     homepage = https://github.com/pypa/readme_renderer;
     license = lib.licenses.asl20;
   };
-}
+}

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

@@ -1,16 +1,15 @@
-{ stdenv, fetchurl, buildPythonPackage, pyparsing, argparse, robotframework }:
+{ stdenv, fetchPypi, buildPythonPackage, pyparsing, argparse, robotframework, allpairspy }:
 
 buildPythonPackage rec {
-  pname = "robomachine";
+  pname = "RoboMachine";
   version = "0.8.0";
-  name = pname + "-" + version;
 
-  src = fetchurl {
-    url = "mirror://pypi/R/RoboMachine/RoboMachine-0.6.tar.gz";
+  src = fetchPypi {
+    inherit pname version;
     sha256 = "242cfd9be0f7591138eaeba03c9c190f894ce045e1767ab7b90eca330259fc45";
   };
 
-  propagatedBuildInputs = [ pyparsing argparse robotframework ];
+  propagatedBuildInputs = [ pyparsing argparse robotframework allpairspy ];
 
   # Remove Windows .bat files
   postInstall = ''

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

@@ -21,8 +21,9 @@ buildPythonPackage rec {
   LC_ALL="en_US.UTF-8";
 
   # Disable doctests on OSX: https://github.com/scikit-learn/scikit-learn/issues/10213
+  # Disable doctests everywhere: https://github.com/NixOS/nixpkgs/issues/35436
   checkPhase = ''
-    HOME=$TMPDIR OMP_NUM_THREADS=1 nosetests ${stdenv.lib.optionalString stdenv.isDarwin "--doctest-options=+SKIP"} $out/${python.sitePackages}/sklearn/
+    HOME=$TMPDIR OMP_NUM_THREADS=1 nosetests --doctest-options=+SKIP $out/${python.sitePackages}/sklearn/
   '';
 
   meta = with stdenv.lib; {

pkgs/servers/web-apps/klaus/default.nix

@@ -0,0 +1,40 @@
+{ lib, python, fetchFromGitHub }:
+
+python.pkgs.buildPythonApplication rec {
+  pname = "klaus";
+  version = "1.2.2";
+
+  src = fetchFromGitHub {
+    owner = "jonashaag";
+    repo = pname;
+    rev = version;
+    sha256 = "0hkl1ycyd5ccijmknr3yfp3ga43y01m7390xnibqqgaisfvcm9wp";
+  };
+
+  prePatch = ''
+    substituteInPlace runtests.sh \
+      --replace "mkdir -p \$builddir" "mkdir -p \$builddir && pwd"
+  '';
+
+  propagatedBuildInputs = with python.pkgs; [
+    six flask pygments dulwich httpauth humanize
+  ];
+
+  checkInputs = with python.pkgs; [
+    pytest requests python-ctags3
+  ] ++ lib.optional (!isPy3k) mock;
+
+  checkPhase = ''
+    ./runtests.sh
+  '';
+
+  # Needs to set up some git repos
+  doCheck = false;
+
+  meta = with lib; {
+    description = "The first Git web viewer that Just Works";
+    homepage    = https://github.com/jonashaag/klaus;
+    license     = licenses.isc;
+    maintainers = with maintainers; [ matthiasbeyer ];
+  };
+}

pkgs/top-level/all-packages.nix

@@ -1280,6 +1280,8 @@ with pkgs;
 
   kisslicer = callPackage ../tools/misc/kisslicer { };
 
+  klaus = callPackage ../servers/web-apps/klaus { };
+
   lcdproc = callPackage ../servers/monitoring/lcdproc { };
 
   languagetool = callPackage ../tools/text/languagetool {  };

pkgs/top-level/python-packages.nix

@@ -456,6 +456,8 @@ in {
 
   alembic = callPackage ../development/python-modules/alembic {};
 
+  allpairspy = callPackage ../development/python-modules/allpairspy { };
+
   ansicolors = callPackage ../development/python-modules/ansicolors {};
 
   aniso8601 = callPackage ../development/python-modules/aniso8601 {};
@@ -1461,6 +1463,8 @@ in {
     inherit (pkgs.dlib) name src nativeBuildInputs meta;
 
     buildInputs = pkgs.dlib.buildInputs ++ [ self.boost ];
+
+    checkInputs = with self; [ pytest ];
   };
 
   datadog = buildPythonPackage rec {
@@ -2349,36 +2353,15 @@ in {
 
   colorlover = callPackage ../development/python-modules/colorlover { };
 
-  CommonMark = buildPythonPackage rec {
-    name = "CommonMark-${version}";
-    version = "0.6.3";
+  CommonMark = callPackage ../development/python-modules/commonmark { };
 
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/C/CommonMark/${name}.tar.gz";
-      sha256 = "ee5a88f23678794592efe3fc11033f17fc77b3296a85f5e1d5b715f8e110a773";
-    };
-
-    LC_ALL="en_US.UTF-8";
-
-    doCheck = false;
-
-    buildInputs = with self; [ flake8 pkgs.glibcLocales ];
-    propagatedBuildInputs = with self; [ future ];
-
-    meta = {
-      description = "Python parser for the CommonMark Markdown spec";
-      homepage = https://github.com/rolandshoemaker/CommonMark-py;
-      license = licenses.bsd3;
-    };
-  };
-
-  CommonMark_54 = self.CommonMark.override rec {
-    name = "CommonMark-0.5.4";
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/C/CommonMark/${name}.tar.gz";
+  CommonMark_54 = self.CommonMark.overridePythonAttrs (oldAttrs: rec {
+    version = "0.5.4";
+    src = oldAttrs.src.override {
+      inherit version;
       sha256 = "34d73ec8085923c023930dfc0bcd1c4286e28a2a82de094bb72fabcc0281cbe5";
     };
-  };
+  });
 
 
   coilmq = buildPythonPackage (rec {
@@ -2405,21 +2388,7 @@ in {
   });
 
 
-  colander = buildPythonPackage rec {
-    name = "colander-1.0";
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/c/colander/${name}.tar.gz";
-      sha256 = "7389413266b9e680c9529c16d56284edf87e0d5de557948e75f41d65683c23b3";
-    };
-
-    propagatedBuildInputs = with self; [ self.translationstring self.iso8601 ];
-
-    meta = {
-      maintainers = with maintainers; [ garbas domenkozar ];
-      platforms = platforms.all;
-    };
-  };
+  colander = callPackage ../development/python-modules/colander { };
 
   # Backported version of the ConfigParser library of Python 3.3
   configparser = if isPy3k then null else buildPythonPackage rec {
@@ -6115,6 +6084,8 @@ in {
     };
   };
 
+  python-ctags3 = callPackage ../development/python-modules/python-ctags3 { };
+
   junos-eznc = callPackage ../development/python-modules/junos-eznc {};
 
   raven = callPackage ../development/python-modules/raven { };
@@ -8397,17 +8368,7 @@ in {
     };
   };
 
-  hvac = buildPythonPackage rec {
-    name    = "hvac-${version}";
-    version = "0.2.15";
-
-    src = pkgs.fetchurl {
-      url    = "https://pypi.python.org/packages/11/ba/6101780891b9d55f6174fa78b47d462c8c1f0cde34072b45fc39f7f8a77c/hvac-0.2.15.tar.gz";
-      sha256 = "0qxa4g1ij1bj27mbp8l54lcr7d5krkb2rayisc6shkpf2b51ip4c";
-    };
-
-    propagatedBuildInputs = with self; [ requests ];
-  };
+  hvac = callPackage ../development/python-modules/hvac { };
 
   hypothesis = callPackage ../development/python-modules/hypothesis { };
 
@@ -8960,27 +8921,6 @@ in {
 
   keyutils = callPackage ../development/python-modules/keyutils { };
 
-  klaus = buildPythonPackage rec {
-    version = "0.9.1";
-    name = "klaus-${version}";
-
-    src = pkgs.fetchurl {
-      url = "https://github.com/jonashaag/klaus/archive/${version}.tar.gz";
-      sha256 = "0k3v3p56hq8alm083grrp98znxkz1zqx0pczm2lah8qddbyrdkgm";
-    };
-
-    propagatedBuildInputs = with self;
-      [ humanize httpauth dulwich pygments flask six ];
-
-    meta = {
-      description = "The first Git web viewer that Just Works";
-      homepage    = "https://github.com/jonashaag/klaus";
-      #license     = licenses.mit; # I'm not sure about the license
-      maintainers = with maintainers; [ matthiasbeyer ];
-      platforms   = platforms.linux; # Can only test linux
-    };
-  };
-
   klein = buildPythonPackage rec {
     name = "klein-15.3.1";
     src = pkgs.fetchurl {
@@ -11886,22 +11826,7 @@ in {
 
   pathpy = callPackage ../development/python-modules/path.py { };
 
-  paypalrestsdk = buildPythonPackage rec {
-    name = "paypalrestsdk-0.7.0";
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/p/paypalrestsdk/${name}.tar.gz";
-      sha256 = "117kfipzfahf9ysv414bh1mmm5cc9ck5zb6rhpslx1f8gk3frvd6";
-    };
-
-    propagatedBuildInputs = with self; [ httplib2 ];
-
-    meta = {
-      homepage = https://developer.paypal.com/;
-      description = "Python APIs to create, process and manage payment";
-      license = "PayPal SDK License";
-    };
-  };
+  paypalrestsdk = callPackage ../development/python-modules/paypalrestsdk { };
 
   pbr = callPackage ../development/python-modules/pbr { };
 
@@ -13915,23 +13840,6 @@ in {
     };
   };
 
-  pysphere = buildPythonPackage rec {
-    name = "pysphere-0.1.8";
-
-    src = pkgs.fetchurl {
-      url = "http://pysphere.googlecode.com/files/${name}.zip";
-      sha256 = "b3f9ba1f67afb17ac41725b01737cd42e8a39d9e745282dd9b692ae631af0add";
-    };
-
-    disabled = isPy3k;
-
-    meta = {
-      homepage    = "https://code.google.com/p/pysphere/";
-      license     = "BSD";
-      description = "Python API for interaction with the VMWare vSphere";
-    };
-  };
-
   pysqlite = buildPythonPackage rec {
     name = "pysqlite-2.8.3";
 
@@ -18727,17 +18635,7 @@ EOF
     };
   };
 
-  pushbullet = buildPythonPackage rec {
-    name = "pushbullet.py-${version}";
-    version = "0.10.0";
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/p/pushbullet.py/pushbullet.py-0.10.0.tar.gz";
-      sha256 = "537d3132e1dbc91e31ade4cccf4c7def6f9d48e904a67f341d35b8a54a9be74d";
-    };
-
-    propagatedBuildInputs = with self; [requests websocket_client python_magic ];
-  };
+  pushbullet = callPackage ../development/python-modules/pushbullet { };
 
   power = buildPythonPackage rec {
     name = "power-1.4";