Merge remote-tracking branch 'upstream/release-20.03' into add-tensorflow-2

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

@@ -3,14 +3,14 @@
 
 buildPythonPackage rec {
   pname = "acoustics";
-  version = "0.2.3";
+  version = "0.2.4";
 
   checkInputs = [ pytest ];
   propagatedBuildInputs = [ numpy scipy matplotlib pandas tabulate ];
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "ca663059d61fbd2899aed4e3cedbc3f983aa67afd3ae1617db3c59b724206fb3";
+    sha256 = "8ccb68ac258ba81a0b9064523e85eae013f9bfce7244d01db42d7d2d21d712cc";
   };
 
   checkPhase = ''

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

@@ -1,4 +1,5 @@
 { lib
+, stdenv
 , buildPythonPackage
 , fetchPypi
 , pythonOlder
@@ -54,6 +55,7 @@ buildPythonPackage rec {
                and not handle_keepalive_on_closed_connection \
                and not proxy_https_bad_response \
                and not partially_applied_handler \
+               ${lib.optionalString stdenv.is32bit "and not test_cookiejar"} \
                and not middleware" \
       --ignore=test_connector.py
   '';

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

@@ -1,4 +1,4 @@
-{ stdenv, lib, buildPythonPackage, python, fetchFromGitHub, isPy3k
+{ stdenv, lib, buildPythonPackage, python, fetchFromGitHub, fetchpatch, isPy3k
 , notmuch, urwid, urwidtrees, twisted, python_magic, configobj, mock, file, gpgme
 , service-identity
 , gnupg ? null, sphinx, awk ? null, procps ? null, future ? null
@@ -19,6 +19,15 @@ buildPythonPackage rec {
     sha256 = "sha256-WUwOJcq8JE7YO8sFeZwYikCRhpufO0pL6MKu54ZYsHI=";
   };
 
+  patches = [
+    # can't compose email if signature is set: https://github.com/pazz/alot/issues/1468
+    (fetchpatch {
+      name = "envelope-body.patch";
+      url = "https://github.com/pazz/alot/commit/28a4296c7f556c251d71d9502681980d46d9fa55.patch";
+      sha256 = "1iwvmjyz4mh1g08vr85ywhah2xarcqg8dazagygk19icgsn45w06";
+    })
+  ];
+
   nativeBuildInputs = lib.optional withManpage sphinx;
 
   propagatedBuildInputs = [

pkgs/development/python-modules/apache-airflow/default.nix

@@ -137,6 +137,8 @@ buildPythonPackage rec {
 
    substituteInPlace setup.py \
      --replace "flask>=1.1.0, <2.0" "flask" \
+     --replace "jinja2>=2.10.1, <2.11.0" "jinja2" \
+     --replace "pandas>=0.17.1, <1.0.0" "pandas" \
      --replace "flask-caching>=1.3.3, <1.4.0" "flask-caching" \
      --replace "flask-appbuilder>=1.12.5, <2.0.0" "flask-appbuilder" \
      --replace "pendulum==1.4.4" "pendulum" \
@@ -156,7 +158,7 @@ buildPythonPackage rec {
      --replace "sqlalchemy~=1.3" "sqlalchemy" \
      --replace "gunicorn>=19.5.0, <20.0" "gunicorn" \
      --replace "werkzeug>=0.14.1, <0.15.0" "werkzeug"
- 
+
   # dumb-init is only needed for CI and Docker, not relevant for NixOS.
   substituteInPlace setup.py \
      --replace "'dumb-init>=1.2.2'," ""

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

@@ -9,21 +9,26 @@
 , pytest
 , pytest-astropy
 , astropy-helpers
+, isPy3k
 }:
 
 buildPythonPackage rec {
   pname = "astroquery";
-  version = "0.3.10";
+  version = "0.4";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1ce57a8792c7d5d74206d797d379de6da35d56be433ea5840c41a49f202e2fab";
+    sha256 = "1ddwnj9vpvxkrfb45c4pwv5f5za9kn2q0040dpw2ymj2bwlpl61h";
   };
 
+  disabled = !isPy3k;
+
   propagatedBuildInputs = [ astropy requests keyring beautifulsoup4 html5lib ];
 
   nativeBuildInputs = [ astropy-helpers ];
 
+  # Tests disabled until pytest-astropy has been updated to include pytest-astropy-header
+  doCheck = false;
   checkInputs = [ pytest pytest-astropy ];
 
   # Disable automatic update of the astropy-helper module

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

@@ -3,7 +3,7 @@
   sqlalchemy_migrate, dateutil, txaio, autobahn, pyjwt, pyyaml, treq,
   txrequests, pyjade, boto3, moto, mock, python-lz4, setuptoolsTrial,
   isort, pylint, flake8, buildbot-worker, buildbot-pkg, buildbot-plugins,
-  parameterized, git, openssh, glibcLocales }:
+  parameterized, git, openssh, glibcLocales, nixosTests }:
 
 let
   withPlugins = plugins: buildPythonPackage {
@@ -25,11 +25,11 @@ let
 
   package = buildPythonPackage rec {
     pname = "buildbot";
-    version = "2.6.0";
+    version = "2.7.0";
 
     src = fetchPypi {
       inherit pname version;
-      sha256 = "1l3ajhy68jddbgbizaa5hq65lgqkll6389hss4p2j36cbxbn7hiv";
+      sha256 = "0jj8fh611n7xc3vsfbgpqsllp38cfj3spkr2kz3ara2x7jvh3406";
     };
 
     propagatedBuildInputs = [
@@ -91,6 +91,7 @@ let
 
     passthru = {
       inherit withPlugins;
+      tests.buildbot = nixosTests.buildbot;
     };
 
     meta = with lib; {

pkgs/development/python-modules/buildbot/pkg.nix

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "buildbot-pkg";
-  version = "2.6.0";
+  version = "2.7.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "07ynk46c9h47ibbdm93h15xbrzflsl4llm0jr4c8pm6krs6byb4z";
+    sha256 = "03zb09r8w8dvd9qas7h6gdwlqc7q482ikph6h3708lpnkn72xdkb";
   };
 
   postPatch = ''

pkgs/development/python-modules/buildbot/plugins.nix

@@ -7,14 +7,12 @@
 
     src = fetchPypi {
       inherit pname version;
-      sha256 = "0njix8g6g1dgfviick55p9calm82nnkhhgkikh7a5yvqk524cprg";
+      sha256 = "1d8xdk4rq4p3fw03cvz7d1pmpjjbyrnzzjifzv46q88vk7jakgxi";
     };
 
     # Remove unneccessary circular dependency on buildbot
     postPatch = ''
-      sed -i setup.py \
-        -e "/import buildbot/d" \
-        -e "s/'buildbot',//"
+      sed -i "s/'buildbot'//" setup.py
     '';
 
     buildInputs = [ buildbot-pkg mock ];
@@ -36,7 +34,7 @@
 
     src = fetchPypi {
       inherit pname version;
-      sha256 = "1wmay9bbb1wwf0zh9rw95swmdc7bxabgvx2n6dyyzs4p8k92px10";
+      sha256 = "03pl75avi6cmmhjvfn0a0b4drn35yv37kvgn04zjdwa3m6p3haa8";
     };
 
     buildInputs = [ buildbot-pkg ];
@@ -58,7 +56,7 @@
 
     src = fetchPypi {
       inherit pname version;
-      sha256 = "14b28vpkk68yk6zmdd64n7izb1r3barb7y711n4g37skqd13jygb";
+      sha256 = "0rzjk3qmlvid8qag3r00zaszchncl1nl8l2yapvc1zqh2dqlln58";
     };
 
     buildInputs = [ buildbot-pkg ];
@@ -80,7 +78,7 @@
 
     src = fetchPypi {
       inherit pname version;
-      sha256 = "1m8kbycjq7jsl72xbrzjj48hb65r53lfxx78yvlnhc2f9ian5vnh";
+      sha256 = "1n4j73y9kwfqk7dz1fh1bpan68vlpnbz7idxpmsphyay8w8y9dd4";
     };
 
     buildInputs = [ buildbot-pkg ];
@@ -102,7 +100,7 @@
 
     src = fetchPypi {
       inherit pname version;
-      sha256 = "1sbp13qimv8kc7dp0xz1pmda1x1n4948zgrz2pc45rwlbbn5h69r";
+      sha256 = "1babkcgxczs6zfk2b6jmsy2vwbrgdydrp2px1mfwa3wmv8fwlssg";
     };
 
     buildInputs = [ buildbot-pkg ];

pkgs/development/python-modules/buildbot/worker.nix

@@ -3,11 +3,11 @@
 
 buildPythonPackage (rec {
   pname = "buildbot-worker";
-  version = "2.6.0";
+  version = "2.7.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0hr42fp3sw6c59qahihm9440618z7prwsy4z0ax553zvw47pc22l";
+    sha256 = "1vwy46acvczgk1hhpsqdwpcw55j4hm5pkw6j01f92axiga8r5jk6";
   };
 
   propagatedBuildInputs = [ twisted future ];

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

@@ -1,5 +1,6 @@
 { lib
 , buildPythonPackage
+, fetchpatch
 , fetchPypi
 }:
 
@@ -12,9 +13,12 @@ buildPythonPackage rec {
     sha256 = "54c38050039232e1db4ad7375cfce6748d7b41c29e95a081c8a6d2c30364a2ce";
   };
 
-  postPatch = ''
-    substituteInPlace src/tests/test.py --replace "DocumentationTestCase" "NoDocumentation"
-  '';
+  patches = [
+    (fetchpatch {
+      url = https://github.com/micheles/decorator/commit/3265f2755d16c0a3dfc9f1feee39722ddc11ee80.patch;
+      sha256 = "1q5nmff30vccqq5swf2ivm8cn7x3lhz8c9qpj0zddgs2y7fw8syz";
+    })
+  ];
 
   meta = with lib; {
     homepage = https://pypi.python.org/pypi/decorator;

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

@@ -3,7 +3,6 @@
 , fetchPypi
 , pytest
 , pytest-repeat
-, pytest-faulthandler
 , pytest-timeout
 , mock
 , joblib
@@ -36,7 +35,7 @@ buildPythonPackage rec {
     sha256 = "d37a5c5be992f3b16db24b54d2801cbe370990fbc63089c6e7ef40d6f03cf5dd";
   };
 
-  checkInputs = [ pytest pytest-repeat pytest-faulthandler pytest-timeout mock joblib ];
+  checkInputs = [ pytest pytest-repeat pytest-timeout mock joblib ];
   propagatedBuildInputs = [
       click cloudpickle dask msgpack psutil six
       sortedcontainers tblib toolz tornado zict pyyaml mpi4py bokeh
@@ -54,7 +53,7 @@ buildPythonPackage rec {
 
   meta = {
     description = "Distributed computation in Python.";
-    homepage = https://distributed.readthedocs.io/en/latest/;
+    homepage = "https://distributed.readthedocs.io/en/latest/";
     license = lib.licenses.bsd3;
     platforms = lib.platforms.x86; # fails on aarch64
     maintainers = with lib.maintainers; [ teh costrouc ];

pkgs/development/python-modules/django-compat/default.nix

@@ -1,9 +1,7 @@
 { stdenv, buildPythonPackage, fetchFromGitHub, python,
   django, six
 }:
-if stdenv.lib.versionAtLeast django.version "2.0"
-then throw "django-compat requires django < 2.0"
-else
+
 buildPythonPackage rec {
   pname = "django-compat";
   version = "1.0.15";
@@ -16,6 +14,10 @@ buildPythonPackage rec {
     sha256 = "1pr6v38ahrsvxlgmcx69s4b5q5082f44gzi4h3c32sccdc4pwqxp";
   };
 
+  patches = [
+    ./fix-tests.diff
+  ];
+
   checkPhase = ''
     runHook preCheck
 

pkgs/development/python-modules/django-compat/fix-tests.diff

@@ -0,0 +1,56 @@
+diff -ur a/compat/tests/settings.py b/compat/tests/settings.py
+--- a/compat/tests/settings.py	2020-03-06 15:32:07.548482597 +0100
++++ b/compat/tests/settings.py	2020-03-06 22:19:25.422934249 +0100
+@@ -16,11 +16,12 @@
+     'django.contrib.admin',
+     'django.contrib.auth',
+     'django.contrib.contenttypes',
++    'django.contrib.messages',
+     'compat',
+     'compat.tests.test_app',
+ ]
+ 
+-MIDDLEWARE_CLASSES = (
++MIDDLEWARE = (
+     'django.contrib.sessions.middleware.SessionMiddleware',
+     'django.middleware.common.CommonMiddleware',
+     'django.middleware.csrf.CsrfViewMiddleware',
+@@ -43,6 +44,7 @@
+                 'django.template.context_processors.i18n',
+                 'django.template.context_processors.tz',
+                 'django.template.context_processors.request',
++                'django.contrib.messages.context_processors.messages',
+             ],
+             'loaders': [
+                 'django.template.loaders.filesystem.Loader',
+diff -ur a/compat/tests/test_compat.py b/compat/tests/test_compat.py
+--- a/compat/tests/test_compat.py	2020-03-06 15:32:07.548482597 +0100
++++ b/compat/tests/test_compat.py	2020-03-06 15:37:39.202835075 +0100
+@@ -9,7 +9,7 @@
+ from django.core.serializers.json import DjangoJSONEncoder
+ from django.test import TestCase, SimpleTestCase
+ from django.test.client import RequestFactory
+-from django.contrib.auth.views import logout
++from django.contrib.auth.views import auth_logout
+ try:
+     from django.urls import NoReverseMatch
+ except ImportError:
+@@ -103,7 +103,7 @@
+         Tests that passing a view name to ``resolve_url`` will result in the
+         URL path mapping to that view name.
+         """
+-        resolved_url = resolve_url(logout)
++        resolved_url = resolve_url(auth_logout)
+         self.assertEqual('/accounts/logout/', resolved_url)
+ 
+     '''
+diff -ur a/compat/tests/urls.py b/compat/tests/urls.py
+--- a/compat/tests/urls.py	2020-03-06 15:32:07.548482597 +0100
++++ b/compat/tests/urls.py	2020-03-06 15:34:25.962377799 +0100
+@@ -2,5 +2,5 @@
+ from django.contrib.auth import views
+ 
+ urlpatterns = [
+-    url(r'^accounts/logout/$', views.logout, name='logout'),
++    url(r'^accounts/logout/$', views.auth_logout, name='logout'),
+ ]

pkgs/development/python-modules/django-gravatar2/default.nix

@@ -2,18 +2,18 @@
 
 buildPythonPackage rec {
   pname = "django-gravatar2";
-  version = "1.4.2";
+  version = "1.4.4";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1qsv40xywbqsf4mkrmsswrpzqd7nfljxpfiim9an2z3dykn5rka6";
+    sha256 = "1vn921fb6jjx7rf5dzhy66rkb71nwmh9ydd0xs9ys72icw4jh4y8";
   };
 
   doCheck = false;
 
   meta = with stdenv.lib; {
     description = "Essential Gravatar support for Django";
-    homepage = https://github.com/twaddington/django-gravatar;
+    homepage = "https://github.com/twaddington/django-gravatar";
     license = licenses.mit;
   };
 }

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

@@ -1,33 +1,40 @@
 { buildPythonPackage
 , fetchPypi
 , lib
+, isPy3k
 , six
 , attrs
 , pytest
 , testtools
 }:
+
 buildPythonPackage rec {
   version = "1.1.0";
   pname = "effect";
+  disabled = (!isPy3k);
 
   src = fetchPypi {
     inherit pname version;
     sha256 = "7affb603707c648b07b11781ebb793a4b9aee8acf1ac5764c3ed2112adf0c9ea";
   };
+
   checkInputs = [
     pytest
     testtools
   ];
+
   propagatedBuildInputs = [
     six
     attrs
   ];
+
   checkPhase = ''
     pytest
   '';
+
   meta = with lib; {
     description = "Pure effects for Python";
-    homepage = https://github.com/python-effect/effect;
+    homepage = "https://github.com/python-effect/effect";
     license = licenses.mit;
   };
 }

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

@@ -1,6 +1,7 @@
 { lib
 , buildPythonPackage
 , fetchFromGitHub
+, fetchurl
 , uvicorn
 , starlette
 , pydantic
@@ -10,11 +11,12 @@
 , pyjwt
 , passlib
 , aiosqlite
+, peewee
 }:
 
 buildPythonPackage rec {
   pname = "fastapi";
-  version = "0.45.0";
+  version = "0.49.0";
   format = "flit";
   disabled = !isPy3k;
 
@@ -22,7 +24,7 @@ buildPythonPackage rec {
     owner = "tiangolo";
     repo = "fastapi";
     rev = version;
-    sha256 = "1qwh382ny6qa3zi64micdq4j7dc64zv4rfd8g91j0digd4rhs6i1";
+    sha256 = "1dw5f2xvn0fqqsy29ypba8v3444cy7dvc7gkpmnhshky0rmfni3n";
   };
 
   propagatedBuildInputs = [
@@ -37,16 +39,9 @@ buildPythonPackage rec {
     pyjwt
     passlib
     aiosqlite
+    peewee
   ];
 
-  # starlette pinning kept in place due to 0.12.9 being a hard
-  # dependency luckily fastapi is currently the only dependent on
-  # starlette. Please remove pinning when possible
-  postPatch = ''
-    substituteInPlace pyproject.toml \
-      --replace "pydantic >=0.32.2,<=0.32.2" "pydantic"
-  '';
-
   checkPhase = ''
     pytest --ignore=tests/test_default_response_class.py
   '';

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

@@ -3,13 +3,13 @@ thrift, pytest, python-snappy, lz4 }:
 
 buildPythonPackage rec {
   pname = "fastparquet";
-  version = "0.3.2";
+  version = "0.3.3";
 
   src = fetchFromGitHub {
     owner = "dask";
     repo = pname;
     rev = version;
-    sha256 = "142kmyddaq6mvmca23abwns1csn8f3lk9c8mbxwxrg4wa1dh0lb4";
+    sha256 = "1vnxr4r0bia2zi9csjw342l507nic6an4hr5xb3a36ggqlbaa0g5";
   };
 
   postPatch = ''

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

@@ -1,18 +1,27 @@
-{ stdenv, fetchPypi, buildPythonPackage }:
+{ lib, fetchPypi, buildPythonPackage }:
 
 buildPythonPackage rec {
   pname = "faulthandler";
-  version = "3.1";
+  version = "3.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "83301ffab03c86b291677b64b5cec7026f412cbda5ebd27e4cb3338452c40021";
+    sha256 = "08ybjjdrfp01syckksxzivqhn6b0yhmc17kdxh77h0lg6rvgvk8y";
   };
 
-  meta = {
+  # This may be papering over a real failure where the env var activation route
+  # for faulthandler does not appear to work. That said, since all other tests
+  # pass and since this module is python 2 only (it was upstreamed into the
+  # interpreter itself as of python 3.3 and is disabled ) this just disables the
+  # test to fix the build. From inspecting Hydra logs and git bisect, the commit
+  # that broke it is this one:
+  # https://github.com/NixOS/nixpkgs/commit/90be4c2c7875c9487508d95b5c638d97e2903ada
+  patches = [ ./disable-env-test.patch ];
+
+  meta = with lib; {
     description = "Dump the Python traceback";
-    license = stdenv.lib.licenses.bsd2;
-    maintainers = with stdenv.lib.maintainers; [ sauyon ];
-    homepage = https://faulthandler.readthedocs.io/;
+    license = licenses.bsd2;
+    maintainers = with maintainers; [ sauyon ];
+    homepage = "https://faulthandler.readthedocs.io/";
   };
 }

pkgs/development/python-modules/faulthandler/disable-env-test.patch

@@ -0,0 +1,13 @@
+diff --git a/tests.py b/tests.py
+index e5a2811..16e7a0f 100644
+--- a/tests.py
++++ b/tests.py
+@@ -394,7 +394,7 @@ class FaultHandlerTests(unittest.TestCase):
+             print(faulthandler.is_enabled())
+             """,
+             env=dict(os.environ, PYTHONFAULTHANDLER='x'))
+-        self.assertEqual(output, ["True"])
++        #self.assertEqual(output, ["True"])
+         self.assertEqual(exitcode, 0)
+ 
+         output, exitcode = self.get_output("""

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

@@ -14,6 +14,8 @@
 , gmsh
 , python
 , stdenv
+, openssh
+, fetchurl
 }:
 
 let
@@ -21,12 +23,11 @@ let
 in
   buildPythonPackage rec {
     pname = "fipy";
-    version = "3.3";
+    version = "3.4.1";
 
-    src = fetchPypi {
-      pname = "FiPy";
-      inherit version;
-      sha256 = "11agpg3d6yrns8igkpml1mxy3mkqkjq2yrw1mw12y07dkk12ii19";
+    src = fetchurl {
+      url = "https://github.com/usnistgov/fipy/releases/download/${version}/FiPy-${version}.tar.gz";
+      sha256 = "0078yg96fknqhywn1v26ryc5z47c0j0c1qwz6p8wsjn0wmzggaqk";
     };
 
     propagatedBuildInputs = [
@@ -38,11 +39,13 @@ in
       mpi4py
       future
       scikit-fmm
+      openssh
     ] ++ lib.optionals isPy27 [ pysparse ] ++ not_darwin_inputs;
 
     checkInputs = not_darwin_inputs;
 
     checkPhase = ''
+      export OMPI_MCA_plm_rsh_agent=${openssh}/bin/ssh
       ${python.interpreter} setup.py test --modules
     '';
 

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

@@ -1,30 +1,27 @@
-{ lib, fetchFromGitHub, buildPythonPackage, fetchpatch, flake8, six }:
+{ lib, isPy27, fetchFromGitHub, buildPythonPackage, fetchpatch, flake8, six }:
 
 buildPythonPackage rec {
   pname = "flake8-future-import";
-  version = "0.4.5";
+  version = "0.4.6";
 
   # PyPI tarball doesn't include the test suite
   src = fetchFromGitHub {
     owner = "xZise";
     repo = "flake8-future-import";
     rev = version;
-    sha256 = "00fpxa6g8cabybnciwnpsbg60zhgydc966jgwyyggw1pcg0frdqr";
+    sha256 = "00q8n15xdnvqj454arn7xxksyrzh0dw996kjyy7g9rdk0rf8x82z";
   };
 
-  patches = [
-    # Add Python 3.7 support. Remove with the next release
-    (fetchpatch {
-      url = https://github.com/xZise/flake8-future-import/commit/cace194a44d3b95c9c1ed96640bae49183acca04.patch;
-      sha256 = "17pkqnh035j5s5c53afs8bk49bq7lnmdwqp5k7izx7sw80z73p9r";
-    })
-  ];
-
   propagatedBuildInputs = [ flake8 six ];
 
-  meta = {
-    homepage = https://github.com/xZise/flake8-future-import;
+  # Upstream disables this test case naturally on python 3, but it also fails
+  # inside NixPkgs for python 2. Since it's going to be deleted, we just skip it
+  # on py2 as well.
+  patches = lib.optionals isPy27 [ ./skip-test.patch ];
+
+  meta = with lib; {
     description = "A flake8 extension to check for the imported __future__ modules to make it easier to have a consistent code base";
-    license = lib.licenses.mit;
+    homepage = "https://github.com/xZise/flake8-future-import";
+    license = licenses.mit;
   };
 }

pkgs/development/python-modules/flake8-future-import/skip-test.patch

@@ -0,0 +1,13 @@
+diff --git a/test_flake8_future_import.py b/test_flake8_future_import.py
+index 84fde59..345f23f 100644
+--- a/test_flake8_future_import.py
++++ b/test_flake8_future_import.py
+@@ -230,7 +230,7 @@ class TestBadSyntax(TestCaseBase):
+     """Test using various bad syntax examples from Python's library."""
+ 
+ 
+-@unittest.skipIf(sys.version_info[:2] >= (3, 7), 'flake8 supports up to 3.6')
++@unittest.skip("Has issue with installed path for flake8 in python2")
+ class Flake8TestCase(TestCaseBase):
+ 
+     """

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

@@ -10,7 +10,7 @@
 buildPythonPackage rec {
   pname = "ftfy";
 
-  version = "5.6";
+  version = "5.7";
   # ftfy v5 only supports python3. Since at the moment the only
   # packages that use ftfy are spacy and textacy which both support
   # python 2 and 3, they have pinned ftfy to the v4 branch.
@@ -20,7 +20,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1k4vr5rfa62yafwpmb4827n50pwb79if0vhg1y4yqbb0bv20jxbd";
+    sha256 = "1j143kfpnskksfzs0pnr37kwph6m7c71p8gdldv26x2b7arwiyb7";
   };
 
   propagatedBuildInputs = [

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

@@ -13,10 +13,11 @@ buildPythonPackage rec {
 
   checkPhase = ''
     touch Makefile
-    # Disable tests that require network access or access /home
+    # Disable tests that require network access or access /home or assume execution before year 2020
     py.test test \
       -k "not test_public_servers and not test_real_ftp \
-          and not test_set_parser and not test_repr"
+          and not test_set_parser and not test_repr \
+          and not test_conditional_upload and not test_conditional_download_with_older_target"
   '';
 
   meta = with lib; {

pkgs/development/python-modules/gunicorn/19.nix

@@ -0,0 +1,39 @@
+{ stdenv, buildPythonPackage, fetchPypi
+, coverage
+, mock
+, pytest
+, pytestcov
+, setuptools
+}:
+
+buildPythonPackage rec {
+  pname = "gunicorn";
+  version = "19.10.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1080jk1ly8j0rc6lv8i33sj94rxjaskd1732cdq5chdqb3ij9ppr";
+  };
+
+  propagatedBuildInputs = [ setuptools ];
+
+  checkInputs = [ pytest mock pytestcov coverage ];
+
+  prePatch = ''
+    substituteInPlace requirements_test.txt --replace "==" ">=" \
+      --replace "coverage>=4.0,<4.4" "coverage"
+  '';
+
+  # better than no tests
+  checkPhase = ''
+    $out/bin/gunicorn --help > /dev/null
+  '';
+
+  pythonImportsCheck = [ "gunicorn" ];
+
+  meta = with stdenv.lib; {
+    homepage = "https://github.com/benoitc/gunicorn";
+    description = "WSGI HTTP Server for UNIX";
+    license = licenses.mit;
+  };
+}

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

@@ -5,11 +5,11 @@
 
 buildPythonPackage rec {
   pname = "gym";
-  version = "0.15.4";
+  version = "0.16.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "3b930cbe1c76bbd30455b5e82ba723dea94159a5f988e927f443324bf7cc7ddd";
+    sha256 = "06h5b639nmzhmy4m1j3vigm86iv5pv7k8jy6xpldyd4jdlf37nn5";
   };
 
   postPatch = ''
@@ -26,7 +26,7 @@ buildPythonPackage rec {
 
   meta = with lib; {
     description = "A toolkit by OpenAI for developing and comparing your reinforcement learning agents";
-    homepage = https://gym.openai.com/;
+    homepage = "https://gym.openai.com/";
     license = licenses.mit;
     maintainers = with maintainers; [ hyphon81 ];
   };

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

@@ -37,6 +37,7 @@ buildPythonPackage rec {
     "tests.functional.test_httplib2.test_callback_response"
     "tests.functional.test_requests.test_streaming_responses"
     "tests.functional.test_httplib2.test_callback_response"
+    "tests.functional.test_requests.test_httpretty_should_allow_adding_and_overwritting_by_kwargs_u2"
   ];
 
   meta = with stdenv.lib; {

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

@@ -16,7 +16,6 @@
 buildPythonPackage rec {
   pname = "ipykernel";
   version = "5.1.4";
-  disabled = pythonOlder "3.4";
 
   src = fetchPypi {
     inherit pname version;
@@ -38,12 +37,23 @@ buildPythonPackage rec {
   preCheck = ''
     export HOME=$(mktemp -d)
   '';
-  disabledTests = lib.optionals stdenv.isDarwin [
+  disabledTests = lib.optionals stdenv.isDarwin ([
     # see https://github.com/NixOS/nixpkgs/issues/76197
     "test_subprocess_print"
     "test_subprocess_error"
     "test_ipython_start_kernel_no_userns"
-  ];
+  ] ++ lib.optionals (pythonOlder "3.8") [
+    # flaky test https://github.com/ipython/ipykernel/issues/485
+    "test_shutdown"
+
+    # test regression https://github.com/ipython/ipykernel/issues/486
+    "test_sys_path_profile_dir"
+    "test_save_history"
+    "test_help_output"
+    "test_write_kernel_spec"
+    "test_ipython_start_kernel_userns"
+    "ZMQDisplayPublisherTests"
+  ]);
 
   # Some of the tests use localhost networking.
   __darwinAllowLocalNetworking = true;

pkgs/development/python-modules/jinja2/default.nix

@@ -1,5 +1,9 @@
-{ stdenv, buildPythonPackage, fetchPypi
-, pytest, markupsafe }:
+{ stdenv
+, buildPythonPackage
+, isPy3k
+, fetchPypi
+, pytest
+, markupsafe }:
 
 buildPythonPackage rec {
   pname = "Jinja2";
@@ -13,6 +17,10 @@ buildPythonPackage rec {
   checkInputs = [ pytest ];
   propagatedBuildInputs = [ markupsafe ];
 
+  # Multiple tests run out of stack space on 32bit systems with python2.
+  # See https://github.com/pallets/jinja/issues/1158
+  doCheck = !stdenv.is32bit || isPy3k;
+
   checkPhase = ''
     pytest -v tests
   '';

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

@@ -2,9 +2,11 @@
 , buildPythonPackage
 , fetchPypi
 , twisted
+, passlib
 , pycrypto
 , pyopenssl
 , pyparsing
+, service-identity
 , zope_interface
 , isPy3k
 }:
@@ -19,7 +21,7 @@ buildPythonPackage rec {
   };
 
   propagatedBuildInputs = [
-    twisted pycrypto pyopenssl pyparsing zope_interface
+    twisted passlib pycrypto pyopenssl pyparsing service-identity zope_interface
   ];
 
   disabled = isPy3k;
@@ -32,4 +34,4 @@ buildPythonPackage rec {
     homepage = https://github.com/twisted/ldaptor;
     license = lib.licenses.mit;
   };
-}
+}

pkgs/development/python-modules/libvirt/5.9.0.nix

@@ -0,0 +1,27 @@
+{ stdenv, buildPythonPackage, fetchgit, pkgconfig, lxml, libvirt, nose }:
+
+buildPythonPackage rec {
+  pname = "libvirt";
+  version = "5.9.0";
+
+  src = fetchgit {
+    url = git://libvirt.org/libvirt-python.git;
+    rev = "v${version}";
+    sha256 = "0qvr0s7yasswy1s5cvkm91iifk33pb8s7nbb38zznc46706b358r";
+  };
+
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libvirt lxml ];
+
+  checkInputs = [ nose ];
+  checkPhase = ''
+    nosetests
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = http://www.libvirt.org/;
+    description = "libvirt Python bindings";
+    license = licenses.lgpl2;
+    maintainers = [ maintainers.fpletz ];
+  };
+}

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

@@ -2,12 +2,12 @@
 
 buildPythonPackage rec {
   pname = "libvirt";
-  version = "5.4.0";
+  version = "6.1.0";
 
   src = assert version == libvirt.version; fetchgit {
     url = git://libvirt.org/libvirt-python.git;
     rev = "v${version}";
-    sha256 = "0ja35z90i3m7vsjfpzfm7awkmja3h0150376i5pzmf2q8vp61fi5";
+    sha256 = "0h3w1p5y4kg2hdbhxmg4lphcnmr7979iwi0m750f8vzbfccsrp7k";
   };
 
   nativeBuildInputs = [ pkgconfig ];

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

@@ -4,11 +4,11 @@
 
 buildPythonPackage rec {
   pname = "mautrix";
-  version = "0.4.1";
+  version = "0.4.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0mfxfc1y317h90h1jx7amsk09jwzxbvfc75qxzl9nf8ah432yfpr";
+    sha256 = "0f8pzi7ip82p7hn6d9xrgp5wsl4s3w6gmjsgb8gjy2606f7czqyg";
   };
 
   propagatedBuildInputs = [

pkgs/development/python-modules/mkl-service/default.nix

@@ -2,13 +2,13 @@
 
 buildPythonPackage rec {
   pname = "mkl-service";
-  version = "2.1.0";
+  version = "2.3.0";
 
   src = fetchFromGitHub {
     owner = "IntelPython";
     repo = "mkl-service";
     rev = "v${version}";
-    sha256 = "1bnpgx629rxqf0yhn0jn68ypj3dqv6njc3981j1g8j8rsm5lycrn";
+    sha256 = "1b4dkkl439rfaa86ywzc2zf9ifawhvdlaiqcg0il83cn5bzs7g5z";
   };
 
   MKLROOT = mkl;

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

@@ -1,12 +1,12 @@
 { stdenv, buildPythonPackage, fetchPypi, isPy3k, funcsigs, pytest, numpy }:
 
 buildPythonPackage rec {
-  version = "1.2.0";
+  version = "1.2.1";
   pname = "mockito";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "2a1cbae9d0aef4ae7586b03f2a463e8c5ba96aa937c0535ced4a5621f851feeb";
+    sha256 = "1ilj73bdk81v4l7ir6hbfvmslzbsxkgvz1asngbyf7w5gl2y5nyf";
   };
 
   propagatedBuildInputs = stdenv.lib.optionals (!isPy3k) [ funcsigs ];
@@ -20,7 +20,7 @@ buildPythonPackage rec {
 
   meta = with stdenv.lib; {
     description = "Spying framework";
-    homepage = https://github.com/kaste/mockito-python;
+    homepage = "https://github.com/kaste/mockito-python";
     license = licenses.mit;
     maintainers = [ maintainers.marsam ];
   };

pkgs/development/python-modules/mysql-connector/default.nix

@@ -1,9 +1,7 @@
-{ lib, buildPythonPackage, fetchFromGitHub
-, python3, protobuf3_6
-}:
+{ lib, buildPythonPackage, fetchFromGitHub, python, protobuf3_6 }:
 
 let
-  python = python3.override {
+  py = python.override {
     packageOverrides = self: super: {
       protobuf = super.protobuf.override {
         protobuf = protobuf3_6;
@@ -21,7 +19,7 @@ in buildPythonPackage rec {
     sha256 = "1jscmc5s7mwx43gvxjlqc30ylp5jjpmkqx7s3b9nllbh926p3ixg";
   };
 
-  propagatedBuildInputs = with python.pkgs; [ protobuf dnspython ];
+  propagatedBuildInputs = with py.pkgs; [ protobuf dnspython ];
 
   # Tests are failing (TODO: unknown reason)
   # TypeError: __init__() missing 1 required positional argument: 'string'

pkgs/development/python-modules/ntlm-auth/default.nix

@@ -3,22 +3,23 @@
 , fetchFromGitHub
 , mock
 , pytest
+, requests
 , unittest2
 , six
 }:
 
 buildPythonPackage rec {
   pname = "ntlm-auth";
-  version = "1.0.3";
+  version = "1.4.0";
 
   src = fetchFromGitHub {
     owner = "jborean93";
     repo = "ntlm-auth";
     rev = "v${version}";
-    sha256 = "09f2g4ivfi9lh1kr30hlg0q4n2imnvmd79w83gza11q9nmhhiwpz";
+    sha256 = "168k3ygwbvnfcwn7q1nv3vvy6b9jc4cnpix0xgg5j8av7v1x0grn";
   };
 
-  checkInputs = [ mock pytest unittest2 ];
+  checkInputs = [ mock pytest requests unittest2 ];
   propagatedBuildInputs = [ six ];
 
   # Functional tests require networking
@@ -28,8 +29,8 @@ buildPythonPackage rec {
 
   meta = with lib; {
     description = "Calculates NTLM Authentication codes";
-    homepage = https://github.com/jborean93/ntlm-auth;
-    license = licenses.lgpl3;
+    homepage = "https://github.com/jborean93/ntlm-auth";
+    license = licenses.mit;
     maintainers = with maintainers; [ elasticdog ];
     platforms = platforms.all;
   };

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

@@ -1,4 +1,5 @@
 { stdenv
+, pythonOlder
 , fetchPypi
 , python
 , buildPythonPackage
@@ -15,6 +16,8 @@
 buildPythonPackage rec {
   version = "0.48.0";
   pname = "numba";
+  # uses f-strings
+  disabled = pythonOlder "3.6";
 
   src = fetchPypi {
     inherit pname version;

pkgs/development/python-modules/openapi-spec-validator/default.nix

@@ -1,6 +1,6 @@
 { lib, buildPythonPackage, isPy27, fetchPypi
 , jsonschema, pyyaml, six, pathlib
-, mock, pytest, pytestcov, pytest-flake8, tox }:
+, mock, pytest, pytestcov, pytest-flake8, tox, setuptools }:
 
 buildPythonPackage rec {
   pname = "openapi-spec-validator";
@@ -11,7 +11,7 @@ buildPythonPackage rec {
     sha256 = "1kav0jlgdpgwx4am09ja7cr8s1g8h8a7j8mcfy1cfjr8fficg2g4";
   };
 
-  propagatedBuildInputs = [ jsonschema pyyaml six ]
+  propagatedBuildInputs = [ jsonschema pyyaml six setuptools ]
     ++ (lib.optionals (isPy27) [ pathlib ]);
 
   checkInputs = [ mock pytest pytestcov pytest-flake8 tox ];

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

@@ -1,5 +1,5 @@
 { lib, buildPythonPackage, fetchPypi, callPackage
-, isPy27, isPy34
+, isPy27, isPy34, pythonOlder
 , cleo
 , requests
 , cachy
@@ -7,7 +7,6 @@
 , pyrsistent
 , pyparsing
 , cachecontrol
-, lockfile
 , pkginfo
 , html5lib
 , shellingham
@@ -17,42 +16,43 @@
 , pathlib2
 , virtualenv
 , functools32
+, clikit
+, keyring
+, pexpect
+, importlib-metadata
 , pytest
 , jsonschema
+, intreehooks
+, lockfile
 }:
 
 let
-  cleo6 = cleo.overridePythonAttrs (oldAttrs: rec {
-    version = "0.6.8";
-    src = fetchPypi {
-      inherit (oldAttrs) pname;
-      inherit version;
-      sha256 = "06zp695hq835rkaq6irr1ds1dp2qfzyf32v60vxpd8rcnxv319l5";
-    };
-  });
   glob2 = callPackage ./glob2.nix { };
 
 in buildPythonPackage rec {
   pname = "poetry";
-  version = "0.12.17";
+  version = "1.0.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0gxwcd65qjmzqzppf53x51sic1rbcd9py6cdzx3aprppipimslvf";
+    sha256 = "0fx1ilgkrsqjjnpgv5zljsp0wpcsywdqvvi8im9z396qq6qpk830";
   };
 
   postPatch = ''
-    substituteInPlace setup.py --replace \
-      "requests-toolbelt>=0.8.0,<0.9.0" \
-      "requests-toolbelt>=0.8.0,<0.10.0" \
-      --replace 'pyrsistent>=0.14.2,<0.15.0' 'pyrsistent>=0.14.2,<0.16.0'
+    substituteInPlace pyproject.toml \
+     --replace "pyrsistent = \"^0.14.2\"" "pyrsistent = \"^0.15.0\"" \
+     --replace "requests-toolbelt = \"^0.8.0\"" "requests-toolbelt = \"^0.9.0\"" \
+     --replace "importlib-metadata = {version = \"~1.1.3\", python = \"<3.8\"}" \
+       "importlib-metadata = {version = \"~1.3.0\", python = \"<3.8\"}"
   '';
 
   format = "pyproject";
 
+  nativeBuildInputs = [ intreehooks ];
+
   propagatedBuildInputs = [
-    cachy
-    cleo6
+    cleo
+    clikit
     requests
     cachy
     requests-toolbelt
@@ -60,13 +60,16 @@ in buildPythonPackage rec {
     pyrsistent
     pyparsing
     cachecontrol
-    lockfile
     pkginfo
     html5lib
     shellingham
     tomlkit
+    pexpect
+    keyring
+    lockfile
   ] ++ lib.optionals (isPy27 || isPy34) [ typing pathlib2 glob2 ]
-    ++ lib.optionals isPy27 [ virtualenv functools32 subprocess32 ];
+    ++ lib.optionals isPy27 [ virtualenv functools32 subprocess32 ]
+    ++ lib.optionals (pythonOlder "3.8") [ importlib-metadata ];
 
   postInstall = ''
     mkdir -p "$out/share/bash-completion/completions"
@@ -85,7 +88,7 @@ in buildPythonPackage rec {
   '';
 
   meta = with lib; {
-    homepage = https://github.com/sdispater/poetry;
+    homepage = "https://python-poetry.org/";
     description = "Python dependency management and packaging made easy";
     license = licenses.mit;
     maintainers = with maintainers; [ jakewaksbaum ];

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

@@ -3,15 +3,16 @@
 , fetchPypi
 , libGLU, libGL
 , xorg
+, numpy
 }:
 
 buildPythonPackage rec {
   pname = "pybullet";
-  version = "2.6.1";
+  version = "2.6.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "c6da064687ae481c73b744b9f3a62d8231349a6bf368d7a2e564f71ef73e9403";
+    sha256 = "1lsvjqij1vb9w8j6lvnq7lppflc7svz4cj37n74q67mb46gq3dxr";
   };
 
   buildInputs = [
@@ -19,6 +20,8 @@ buildPythonPackage rec {
     xorg.libX11
   ];
 
+  propagatedBuildInputs =  [ numpy ];
+
   patches = [
     # make sure X11 and OpenGL can be found at runtime
     ./static-libs.patch

pkgs/development/python-modules/pybullet/static-libs.patch

@@ -1,13 +1,13 @@
 diff --git a/setup.py b/setup.py
-index 98efabdbf..e69e79084 100644
+index 6f7bd7589..321fc6ab0 100644
 --- a/setup.py
 +++ b/setup.py
-@@ -563,6 +563,8 @@ print("-----")
+@@ -465,6 +465,8 @@ print("-----")
  
  extensions = []
  
 +libraries += [ "X11", "GL" ] # statically link x11 and opengl
 +
- pybullet_ext = Extension("pybullet",
-         sources =  sources,
-         libraries = libraries,
+ pybullet_ext = Extension(
+     "pybullet",
+     sources=sources,

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

@@ -1,14 +1,14 @@
 { stdenv
 , buildPythonPackage
 , fetchPypi
-, isPy3k
 , isPyPy
+, six
 }:
 
 buildPythonPackage rec {
   version = "0.12.0";
   pname = "pyfribidi";
-  disabled = isPy3k || isPyPy;
+  disabled = isPyPy;
 
   src = fetchPypi {
     inherit pname version;
@@ -16,6 +16,10 @@ buildPythonPackage rec {
     sha256 = "64726a4a56783acdc79c6b9b3a15f16e6071077c897a0b999f3b43f744bc621c";
   };
 
+  patches = stdenv.lib.optional stdenv.cc.isClang ./pyfribidi-clang.patch;
+
+  propagatedBuildInputs = [ six ];
+
   meta = with stdenv.lib; {
     description = "A simple wrapper around fribidi";
     homepage = https://github.com/pediapress/pyfribidi;

pkgs/development/python-modules/pyfribidi/pyfribidi-clang.patch

@@ -0,0 +1,17 @@
+diff --git a/pyfribidi.c b/pyfribidi.c
+index 9a0120d..238134a 100644
+--- a/pyfribidi.c
++++ b/pyfribidi.c
+@@ -148,10 +148,11 @@ init_pyfribidi (void)
+ {
+ #if PY_MAJOR_VERSION >= 3
+         PyObject *module = PyModule_Create (&pyfribidi_moduledef);
++        if (module == NULL) return NULL;
+ #else
+         PyObject *module = Py_InitModule ("_pyfribidi", PyfribidiMethods);
++        if (module == NULL) return;
+ #endif
+-	if (module == NULL) return NULL;
+ 
+ 	PyModule_AddIntConstant (module, "RTL", (long) FRIBIDI_TYPE_RTL);
+ 	PyModule_AddIntConstant (module, "LTR", (long) FRIBIDI_TYPE_LTR);

pkgs/development/python-modules/pyproj/001.proj.patch

@@ -1,47 +1,62 @@
-diff a/pyproj/datadir.py b/pyproj/datadir.py
---- a/pyproj/datadir.py
-+++ b/pyproj/datadir.py
-@@ -52,6 +52,7 @@ def get_data_dir():
-     str: The valid data directory.
-
-     """
-+    return "@proj@/share/proj"
-     # to avoid re-validating
-     global _VALIDATED_PROJ_DATA
+diff -Nur a/pyproj/datadir.py b/pyproj/datadir.py
+--- a/pyproj/datadir.py	2020-03-24 12:53:39.417440608 +0100
++++ b/pyproj/datadir.py	2020-03-24 12:56:19.870089479 +0100
+@@ -66,9 +66,7 @@
      if _VALIDATED_PROJ_DATA is not None:
-diff a/setup.py b/setup.py
---- a/setup.py
-+++ b/setup.py
-@@ -16,7 +16,7 @@ INTERNAL_PROJ_DIR = os.path.join(CURRENT_FILE_PATH, "pyproj", BASE_INTERNAL_PROJ
-
+         return _VALIDATED_PROJ_DATA
+     global _USER_PROJ_DATA
+-    internal_datadir = os.path.join(
+-        os.path.dirname(os.path.abspath(__file__)), "proj_dir", "share", "proj"
+-    )
++    internal_datadir = "@proj@/share/proj"
+     proj_lib_dirs = os.environ.get("PROJ_LIB", "")
+     prefix_datadir = os.path.join(sys.prefix, "share", "proj")
+ 
+diff -Nur a/setup.py b/setup.py
+--- a/setup.py	2020-03-24 12:53:39.415440624 +0100
++++ b/setup.py	2020-03-24 12:52:05.311232522 +0100
+@@ -11,7 +11,7 @@
+ PROJ_MIN_VERSION = parse_version("6.2.0")
+ CURRENT_FILE_PATH = os.path.dirname(os.path.abspath(__file__))
+ BASE_INTERNAL_PROJ_DIR = "proj_dir"
+-INTERNAL_PROJ_DIR = os.path.join(CURRENT_FILE_PATH, "pyproj", BASE_INTERNAL_PROJ_DIR)
++INTERNAL_PROJ_DIR = "@proj@"
+ 
+ 
  def check_proj_version(proj_dir):
-     """checks that the PROJ library meets the minimum version"""
--    proj = os.path.join(proj_dir, "bin", "proj")
-+    proj = "@proj@/bin/proj"
-     proj_ver_bytes = subprocess.check_output(proj, stderr=subprocess.STDOUT)
-     proj_ver_bytes = (proj_ver_bytes.decode("ascii").split()[1]).strip(",")
-     proj_version = parse_version(proj_ver_bytes)
-@@ -33,6 +33,7 @@ def get_proj_dir():
-     """
-     This function finds the base PROJ directory.
-     """
-+    return "@proj@"
-     proj_dir = os.environ.get("PROJ_DIR")
-     if proj_dir is None and os.path.exists(INTERNAL_PROJ_DIR):
-         proj_dir = INTERNAL_PROJ_DIR
-@@ -56,6 +57,7 @@ def get_proj_libdirs(proj_dir):
-     """
-     This function finds the library directories
-     """
-+    return ["@proj@/lib"]
-     proj_libdir = os.environ.get("PROJ_LIBDIR")
-     libdirs = []
-     if proj_libdir is None:
-@@ -77,6 +79,7 @@ def get_proj_incdirs(proj_dir):
-     """
-     This function finds the include directories
-     """
-+    return ["@proj@/include"]
-     proj_incdir = os.environ.get("PROJ_INCDIR")
-     incdirs = []
-     if proj_incdir is None:
+@@ -146,7 +146,7 @@
+     # By default we'll try to get options PROJ_DIR or the local version of proj
+     proj_dir = get_proj_dir()
+     library_dirs = get_proj_libdirs(proj_dir)
+-    include_dirs = get_proj_incdirs(proj_dir)
++    include_dirs = get_proj_incdirs("@projdev@")
+ 
+     # setup extension options
+     ext_options = {
+diff -Nur a/test/conftest.py b/test/conftest.py
+--- a/test/conftest.py	2020-03-24 12:53:39.417440608 +0100
++++ b/test/conftest.py	2020-03-24 23:16:47.373972786 +0100
+@@ -1,6 +1,7 @@
+ import os
+ import shutil
+ import tempfile
++import stat
+ 
+ import pytest
+ 
+@@ -17,6 +18,15 @@
+     with tempfile.TemporaryDirectory() as tmpdir:
+         tmp_data_dir = os.path.join(tmpdir, "proj")
+         shutil.copytree(data_dir, tmp_data_dir)
++
++        # Data copied from the nix store is readonly (causes cleanup problem).
++        # Make it writable.
++        for r, d, files in os.walk(tmp_data_dir):
++            os.chmod(r, os.stat(r).st_mode | stat.S_IWUSR)
++            for f in files:
++                fpath = os.path.join(r, f)
++                os.chmod(fpath, os.stat(fpath).st_mode | stat.S_IWUSR)
++
+         try:
+             os.remove(os.path.join(str(tmp_data_dir), "ntv2_0.gsb"))
+         except OSError:

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

@@ -1,20 +1,22 @@
-{ lib, buildPythonPackage, fetchFromGitHub, python, pkgs, pythonOlder, substituteAll
+{ lib, buildPythonPackage, fetchFromGitHub, python, pkgs, pythonOlder, isPy27, substituteAll
 , aenum
 , cython
 , pytest
 , mock
 , numpy
+, shapely
 }:
 
 buildPythonPackage rec {
   pname = "pyproj";
-  version = "2.2.2";
+  version = "2.6.0";
+  disabled = isPy27;
 
   src = fetchFromGitHub {
     owner = "pyproj4";
     repo = "pyproj";
     rev = "v${version}rel";
-    sha256 = "0mb0jczgqh3sma69k7237i38h09gxgmvmddls9hpw4f3131f5ax7";
+    sha256 = "0fyggkbr3kp8mlq4c0r8sl5ah58bdg2mj4kzql9p3qyrkcdlgixh";
   };
 
   # force pyproj to use ${pkgs.proj}
@@ -22,13 +24,14 @@ buildPythonPackage rec {
     (substituteAll {
       src = ./001.proj.patch;
       proj = pkgs.proj;
+      projdev = pkgs.proj.dev;
     })
   ];
 
   buildInputs = [ cython pkgs.proj ];
 
   propagatedBuildInputs = [
-    numpy
+    numpy shapely
   ] ++ lib.optional (pythonOlder "3.6") aenum;
 
   checkInputs = [ pytest mock ];
@@ -38,6 +41,9 @@ buildPythonPackage rec {
   checkPhase = ''
     pytest . -k 'not alternative_grid_name \
                  and not transform_wgs84_to_alaska \
+                 and not transformer_group__unavailable \
+                 and not transform_group__missing_best \
+                 and not datum \
                  and not repr' \
             --ignore=test/test_doctest_wrapper.py \
             --ignore=test/test_datadir.py

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

@@ -14,7 +14,7 @@
 
 buildPythonPackage rec {
   pname   = "pysam";
-  version = "0.15.3";
+  version = "0.15.4";
 
   # Fetching from GitHub instead of PyPi cause the 0.13 src release on PyPi is
   # missing some files which cause test failures.
@@ -23,26 +23,35 @@ buildPythonPackage rec {
     owner = "pysam-developers";
     repo = "pysam";
     rev = "v${version}";
-    sha256 = "0g6md20gsr24pdr9b8nj403w31ixfjv8bjhdvg3x476kjiq1kvyb";
+    sha256 = "04w6h6mv6lsr74hj9gy4r2laifcbhgl2bjcr4r1l9r73xdd45mdy";
   };
 
+  nativeBuildInputs = [ samtools ];
   buildInputs = [ bzip2 curl cython lzma zlib ];
 
-  checkInputs = [ pytest bcftools htslib samtools ];
-
+  checkInputs = [ pytest bcftools htslib ];
   checkPhase = "py.test";
 
-  preInstall = ''
+  # tests require samtools<=1.9
+  doCheck = false;
+  preCheck = ''
     export HOME=$(mktemp -d)
     make -C tests/pysam_data
     make -C tests/cbcf_data
   '';
 
-  meta = {
-    homepage = https://pysam.readthedocs.io/;
+  pythonImportsCheck = [
+    "pysam"
+    "pysam.bcftools"
+    "pysam.libcutils"
+    "pysam.libcvcf"
+  ];
+
+  meta = with lib; {
     description = "A python module for reading, manipulating and writing genome data sets";
-    maintainers = with lib.maintainers; [ unode ];
-    license = lib.licenses.mit;
+    homepage = "https://pysam.readthedocs.io/";
+    maintainers = with maintainers; [ unode ];
+    license = licenses.mit;
     platforms = [ "i686-linux" "x86_64-linux" ];
   };
 }

pkgs/development/python-modules/pysaml2/default.nix

@@ -2,6 +2,7 @@
 , buildPythonPackage
 , isPy3k
 , fetchFromGitHub
+, fetchpatch
 , substituteAll
 , xmlsec
 , cryptography, defusedxml, future, pyopenssl, dateutil, pytz, requests, six
@@ -27,8 +28,19 @@ buildPythonPackage rec {
       src = ./hardcode-xmlsec1-path.patch;
       inherit xmlsec;
     })
+    # remove on next release
+    (fetchpatch {
+      name = "fix-test-dates.patch";
+      url = "https://github.com/IdentityPython/pysaml2/commit/1d97d2d26f63e42611558fdd0e439bb8a7496a27.patch";
+      sha256 = "0r6d6hkk6z9yw7aqnsnylii516ysmdsc8dghwmgnwvw6cm7l388p";
+    })
   ];
 
+  postPatch = ''
+    # fix failing tests on systems with 32bit time_t
+    sed -i 's/2999\(-.*T\)/2029\1/g' tests/*.xml
+  '';
+
   propagatedBuildInputs = [ cryptography defusedxml future pyopenssl dateutil pytz requests six ];
 
   checkInputs = [ mock pyasn1 pymongo pytest responses ];

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

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "pytesseract";
-  version = "0.3.2";
+  version = "0.3.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1b6hmz9dqfn8il1g5vyz6izsxqjrbvrr2gs8gwwadyz8fx4vghx8";
+    sha256 = "0lml55jrvdzy9fm31zpw64fqc4d6p5djg1ax2kgnimzfscxghh8h";
   };
 
   patches = [

pkgs/development/python-modules/pytest-faulthandler/default.nix

@@ -1,34 +0,0 @@
-{ lib
-, buildPythonPackage
-, fetchPypi
-, setuptools_scm
-, pytest
-, pytest-mock
-, pythonOlder
-, faulthandler
-}:
-
-buildPythonPackage rec {
-  pname = "pytest-faulthandler";
-  version = "2.0.1";
-
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "ed72bbce87ac344da81eb7d882196a457d4a1026a3da4a57154dacd85cd71ae5";
-  };
-
-  nativeBuildInputs = [ setuptools_scm pytest ];
-  checkInputs = [ pytest-mock ];
-  propagatedBuildInputs = lib.optional (pythonOlder "3.0") faulthandler;
-
-  checkPhase = ''
-    py.test
-  '';
-
-  meta = {
-    description = "Py.test plugin that activates the fault handler module for tests";
-    homepage = https://github.com/pytest-dev/pytest-faulthandler;
-    license = lib.licenses.mit;
-    maintainers = with lib.maintainers; [ costrouc ];
-  };
-}

pkgs/development/python-modules/pytest-timeout/default.nix

@@ -21,7 +21,10 @@ buildPythonPackage rec {
   };
 
   checkInputs = [ pytest pexpect ];
-  checkPhase = ''pytest -ra'';
+  checkPhase = ''
+    # test_suppresses_timeout_when_pdb_is_entered fails under heavy load
+    pytest -ra -k 'not test_suppresses_timeout_when_pdb_is_entered'
+  '';
 
   meta = with lib;{
     description = "py.test plugin to abort hanging tests";

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

@@ -34,7 +34,7 @@ buildPythonPackage rec {
     description = "Python bindings for the remote Jenkins API";
     homepage = https://pypi.python.org/pypi/python-jenkins;
     license = licenses.bsd3;
-    maintainers = with maintainers; [ ma27 ];
+    maintainers = with maintainers; [ ];
   };
 
 }

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

@@ -1,6 +1,8 @@
 { lib
 , buildPythonPackage
 , fetchPypi
+, isPy38
+, kerberos
 , mock
 , pytest
 , requests
@@ -12,6 +14,7 @@
 buildPythonPackage rec {
   pname = "pywinrm";
   version = "0.4.1";
+  disabled = isPy38;
 
   src = fetchPypi {
     inherit pname version;
@@ -19,13 +22,16 @@ buildPythonPackage rec {
   };
 
   checkInputs = [ mock pytest ];
-  propagatedBuildInputs = [ requests requests_ntlm six xmltodict ];
+  propagatedBuildInputs = [ requests requests_ntlm six kerberos xmltodict ];
 
   meta = with lib; {
     description = "Python library for Windows Remote Management";
-    homepage = https://github.com/diyan/pywinrm/;
+    homepage = "https://github.com/diyan/pywinrm";
     license = licenses.mit;
-    maintainers = with maintainers; [ elasticdog ];
+    maintainers = with maintainers; [
+      elasticdog
+      kamadorueda
+    ];
     platforms = platforms.all;
   };
 }

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

@@ -1,6 +1,7 @@
 { lib
 , buildPythonPackage
 , fetchPypi
+, fetchpatch
 , numpy
 , astropy
 , astropy-healpix
@@ -24,6 +25,12 @@ buildPythonPackage rec {
 
   nativeBuildInputs = [ astropy-helpers cython ];
 
+  # Fix tests
+  patches = [ (fetchpatch {
+    url = "https://github.com/astropy/reproject/pull/218/commits/4661e075137424813ed77f1ebcbc251fee1b8467.patch";
+    sha256 = "13g3h824pqn2lgypzg1b87vkd44y7m302lhw3kh4rfww1dkzhm9v";
+  }) ];
+
   # Disable automatic update of the astropy-helper module
   postPatch = ''
     substituteInPlace setup.cfg --replace "auto_use = True" "auto_use = False"

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

@@ -1,9 +1,11 @@
-{ stdenv, buildPythonPackage, fetchPypi, nose }:
+{ stdenv, buildPythonPackage, fetchPypi, pythonAtLeast, nose }:
 
 buildPythonPackage rec {
   pname = "rope";
   version = "0.14.0";
 
+  disabled = pythonAtLeast "3.8";  # 0.17 should support Python 3.8
+
   src = fetchPypi {
     inherit pname version;
     sha256 = "1bwayj0hh459s3yh0sdrxksr9wfilgi3a49izfaj06kvgyladif5";

pkgs/development/python-modules/scikit-build/default.nix

@@ -1,7 +1,28 @@
-{ lib, buildPythonPackage, fetchPypi, wheel, setuptools, packaging
-, cmake, ninja, cython, codecov, coverage, six, virtualenv, pathpy
-, pytest, pytestcov, pytest-virtualenv, pytest-mock, pytestrunner
-, requests, flake8 }:
+{ lib
+, buildPythonPackage
+, fetchPypi
+, fetchpatch
+, distro
+, packaging
+, setuptools
+, wheel
+# Test Inputs
+, cmake
+, codecov
+, coverage
+, cython
+, flake8
+, ninja
+, pathpy
+, pytest
+, pytestcov
+, pytest-mock
+, pytestrunner
+, pytest-virtualenv
+, requests
+, six
+, virtualenv
+}:
 
 buildPythonPackage rec {
   pname = "scikit-build";
@@ -12,15 +33,41 @@ buildPythonPackage rec {
     sha256 = "7342017cc82dd6178e3b19377389b8a8d1f8b429d9cdb315cfb1094e34a0f526";
   };
 
-  propagatedBuildInputs = [ wheel setuptools packaging ];
-  checkInputs = [ 
-    cmake ninja cython codecov coverage six pathpy
-    pytest pytestcov pytest-mock pytest-virtualenv pytestrunner
-    requests flake8
+  propagatedBuildInputs = [
+    distro
+    packaging
+    setuptools
+    wheel
+  ];
+  checkInputs = [
+    cmake
+    codecov
+    coverage
+    cython
+    flake8
+    ninja
+    pathpy
+    pytest
+    pytestcov
+    pytest-mock
+    pytestrunner
+    pytest-virtualenv
+    requests
+    six
+    virtualenv
   ];
 
   dontUseCmakeConfigure = true;
 
+  # scikit-build PR #458. Remove in version > 0.10.0
+  patches = [
+    (fetchpatch {
+      name = "python38-platform_linux_distribution-fix-458";
+      url = "https://github.com/scikit-build/scikit-build/commit/faa7284e5bc4c72bc8744987acdf3297b5d2e7e4.patch";
+      sha256 = "1hgl3cnkf266zaw534b64c88waxfz9721wha0m6j3hsnxk76ayjv";
+    })
+  ];
+
   disabledTests = lib.concatMapStringsSep " and " (s: "not " + s) ([
     "test_hello_develop" # tries setuptools develop install
     "test_source_distribution" # pip has no way to install missing dependencies
@@ -35,9 +82,9 @@ buildPythonPackage rec {
   '';
 
   meta = with lib; {
-    homepage = http://scikit-build.org/;
     description = "Improved build system generator for CPython C/C++/Fortran/Cython extensions";
+    homepage = "http://scikit-build.org/";
     license = with licenses; [ mit bsd2 ]; # BSD due to reuses of PyNE code
-    maintainers = [ maintainers.FlorianFranzen ];
+    maintainers = with maintainers; [ FlorianFranzen ];
   };
 }

pkgs/development/python-modules/seaborn/0.9.1.nix

@@ -0,0 +1,33 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, nose
+, pandas
+, matplotlib
+}:
+
+buildPythonPackage rec {
+  pname = "seaborn";
+  version = "0.9.1";
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "da33aa8c20a9a342ce73831d02831a10413f54a05471c7f31edf34f225d456ae";
+  };
+
+  checkInputs = [ nose ];
+  propagatedBuildInputs = [ pandas matplotlib ];
+
+  checkPhase = ''
+    nosetests -v
+  '';
+
+  # Computationally very demanding tests
+  doCheck = false;
+
+  meta = {
+    description = "Statisitical data visualization";
+    homepage = "http://stanford.edu/~mwaskom/software/seaborn/";
+    license = with lib.licenses; [ bsd3 ];
+    maintainers = [ ];
+  };
+}

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

@@ -13,11 +13,11 @@
 
 buildPythonPackage rec {
   name = "sfepy_${version}";
-  version = "2019.2";
+  version = "2019.4";
 
   src = fetchurl {
     url="https://github.com/sfepy/sfepy/archive/release_${version}.tar.gz";
-    sha256 = "17dj0wbchcfa6x27yx4d4jix4z4nk6r2640xkqcsw0mf62x5l1pj";
+    sha256 = "1l9vgcw09l6bwhgfzlbn68fzpvns25r6nkd1pcp7hz5165hs6zzn";
   };
 
   propagatedBuildInputs = [
@@ -33,6 +33,7 @@ buildPythonPackage rec {
   postPatch = ''
     # broken test
     rm tests/test_homogenization_perfusion.py
+    rm tests/test_splinebox.py
 
     # slow tests
     rm tests/test_input_*.py

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

@@ -4,19 +4,20 @@
 , canonicaljson
 , unpaddedbase64
 , pynacl
+, typing-extensions
 }:
 
 buildPythonPackage rec {
   pname = "signedjson";
-  version = "1.0.0";
+  version = "1.1.0";
 
   src = fetchgit {
     url = "https://github.com/matrix-org/python-signedjson.git";
     rev = "refs/tags/v${version}";
-    sha256 = "0b8xxhc3npd4567kqapfp4gs7m0h057xam3an7424az262ind82n";
+    sha256 = "18s388hm3babnvakbbgfqk0jzq25nnznvhygywd3azp9b4yzmd5c";
   };
 
-  propagatedBuildInputs = [ canonicaljson unpaddedbase64 pynacl ];
+  propagatedBuildInputs = [ canonicaljson unpaddedbase64 pynacl typing-extensions ];
 
   meta = with stdenv.lib; {
     homepage = https://pypi.org/project/signedjson/;

pkgs/development/python-modules/spyder-kernels/0.x.nix

@@ -0,0 +1,72 @@
+{ 
+  lib
+  , buildPythonPackage
+  , fetchFromGitHub
+  , cloudpickle
+  , ipykernel
+  , wurlitzer
+  , jupyter_client
+  , pyzmq 
+  , numpy
+  , pandas
+  , scipy
+  , matplotlib
+  , xarray
+  , pytest
+  , flaky
+  , isPy3k
+}:
+
+buildPythonPackage rec {
+  pname = "spyder-kernels";
+  version = "0.5.2";
+
+  src = fetchFromGitHub {
+    owner = "spyder-ide";
+    repo = "spyder-kernels";
+    rev = "v0.5.2";
+    sha256 = "1yan589g0470y61bcyjy3wj13i94ndyffckqdyrg97vw2qhfrisb";
+  };
+
+  # requirement xarray not available on Py2k
+  disabled = !isPy3k;
+
+  propagatedBuildInputs = [
+    cloudpickle
+    ipykernel
+    wurlitzer
+    jupyter_client
+    pyzmq
+  ];
+
+  checkInputs = [
+    numpy
+    pandas
+    scipy
+    matplotlib
+    xarray
+    pytest
+    flaky
+  ];
+
+  # skipped tests:
+  # turtle requires graphics
+  # cython test fails, I don't think this can ever access cython?
+  # umr pathlist test assumes standard directories, not compatible with nix
+  checkPhase = ''
+    export JUPYTER_RUNTIME_DIR=$(mktemp -d)
+    pytest -x -vv -k '\
+      not test_turtle_launch \
+      and not test_umr_skip_cython \
+      and not test_umr_pathlist' \
+      -W 'ignore::DeprecationWarning' \
+      spyder_kernels
+  '';
+
+  meta = with lib; {
+    description = "Jupyter kernels for Spyder's console";
+    homepage = "https://github.com/spyder-ide/spyder-kernels";
+    license = licenses.mit;
+    maintainers = with maintainers; [ gebner marcus7070 ];
+  };
+}

pkgs/development/python-modules/spyder/3.nix

@@ -0,0 +1,70 @@
+{ stdenv, buildPythonPackage, fetchPypi, makeDesktopItem, jedi, pycodestyle,
+  psutil, pyflakes, rope, numpy, scipy, matplotlib, pylint, keyring, numpydoc,
+  qtconsole, qtawesome, nbconvert, mccabe, pyopengl, cloudpickle, pygments,
+  spyder-kernels_0_5, qtpy, pyzmq, chardet
+, pyqtwebengine
+}:
+
+buildPythonPackage rec {
+  pname = "spyder";
+  version = "3.3.6";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1z7qw1h3rhca12ycv8xrzw6z2gf81v0j6lfq9kpwh472w4vk75v1";
+  };
+
+  nativeBuildInputs = [ pyqtwebengine.wrapQtAppsHook ];
+
+  propagatedBuildInputs = [
+    jedi pycodestyle psutil pyflakes rope numpy scipy matplotlib pylint keyring
+    numpydoc qtconsole qtawesome nbconvert mccabe pyopengl cloudpickle spyder-kernels_0_5
+    pygments qtpy pyzmq chardet pyqtwebengine
+  ];
+
+  # There is no test for spyder
+  doCheck = false;
+
+  desktopItem = makeDesktopItem {
+    name = "Spyder";
+    exec = "spyder";
+    icon = "spyder";
+    comment = "Scientific Python Development Environment";
+    desktopName = "Spyder";
+    genericName = "Python IDE";
+    categories = "Application;Development;Editor;IDE;";
+  };
+
+  postPatch = ''
+    # remove dependency on pyqtwebengine
+    # this is still part of the pyqt 5.11 version we have in nixpkgs
+    sed -i /pyqtwebengine/d setup.py
+    substituteInPlace setup.py --replace "pyqt5<5.13" "pyqt5"
+  '';
+
+  # Create desktop item
+  postInstall = ''
+    mkdir -p $out/share/icons
+    cp spyder/images/spyder.svg $out/share/icons
+    cp -r $desktopItem/share/applications/ $out/share
+  '';
+
+  dontWrapQtApps = true;
+
+  preFixup = ''
+    makeWrapperArgs+=("''${qtWrapperArgs[@]}")
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Scientific python development environment";
+    longDescription = ''
+      Spyder (previously known as Pydee) is a powerful interactive development
+      environment for the Python language with advanced editing, interactive
+      testing, debugging and introspection features.
+    '';
+    homepage = "https://github.com/spyder-ide/spyder/";
+    license = licenses.mit;
+    platforms = platforms.linux;
+    maintainers = with maintainers; [ gebner ];
+  };
+}

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

@@ -1,7 +1,7 @@
 { lib
 , stdenv
 , buildPythonPackage
-, fetchPypi
+, fetchFromGitHub
 , aiofiles
 , graphene
 , itsdangerous
@@ -20,12 +20,20 @@
 
 buildPythonPackage rec {
   pname = "starlette";
-  version = "0.13.0";
+
+  # This is not the latest version of Starlette, however, later
+  # versions of Starlette break FastAPI due to
+  # https://github.com/tiangolo/fastapi/issues/683. Please update when
+  # possible. FastAPI is currently Starlette's only dependent.
+
+  version = "0.12.9";
   disabled = isPy27;
 
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "6bd414152d40d000ccbf6aa40ed89718b40868366a0f69fb83034f416303acef";
+  src = fetchFromGitHub {
+    owner = "encode";
+    repo = pname;
+    rev = version;
+    sha256 = "0w44s8ynzy8w8dgm755c8jina9i4dd87vqkcv7jc1kwkg384w9i5";
   };
 
   propagatedBuildInputs = [

pkgs/development/python-modules/swagger-spec-validator/default.nix

@@ -2,13 +2,13 @@
 
 buildPythonPackage rec {
   pname = "swagger-spec-validator";
-  version = "2.4.3";
+  version = "2.5.0";
 
   src = fetchFromGitHub {
     owner = "Yelp";
     repo = "swagger_spec_validator";
     rev = "v" + version;
-    sha256 = "02f8amc6iq2clxxmrz8hirbb57sizaxijp0higqy16shk63ibalw";
+    sha256 = "0qlkiyncdh7cdyjvnwjpv9i7y75ghwnpyqkkpfaa8hg698na13pw";
   };
 
   checkInputs = [

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

@@ -16,12 +16,12 @@
 }:
 buildPythonPackage rec {
   pname = "Twisted";
-  version = "19.10.0";
+  version = "20.3.0";
 
   src = fetchPypi {
     inherit pname version;
     extension = "tar.bz2";
-    sha256 = "7394ba7f272ae722a74f3d969dcf599bc4ef093bc392038748a490f1724a515d";
+    sha256 = "040yzha6cyshnn6ljgk2birgh6mh2cnra48xp5ina5vfsnsmab6p";
   };
 
   propagatedBuildInputs = [ zope_interface incremental automat constantly hyperlink pyhamcrest attrs setuptools ];

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

@@ -1,5 +1,17 @@
-{ stdenv, lib, buildPythonPackage, fetchPypi, python, zlib, clang
-, ncurses, pytest, docutils, pygments, numpy, scipy, scikitlearn }:
+{ stdenv
+, lib
+, fetchPypi
+, buildPythonPackage
+, cmake
+, python
+, zlib
+, ncurses
+, pytest
+, docutils
+, pygments
+, numpy
+, scipy
+, scikitlearn }:
 
 buildPythonPackage rec {
   pname = "vowpalwabbit";
@@ -10,21 +22,27 @@ buildPythonPackage rec {
     sha256 = "bd4c7e49a6ddaa1afedf97b22b822c7322328d686d45151b47a5127fc409c2af";
   };
 
-  # Should be fixed in next Python release after 8.5.0:
-  # https://github.com/JohnLangford/vowpal_wabbit/pull/1533
-  patches = [
-    ./vowpal-wabbit-find-boost.diff
+  nativeBuildInputs = [
+    cmake
   ];
 
-  # vw tries to write some explicit things to home
-  # python installed: The directory '/homeless-shelter/.cache/pip/http'
-  preInstall = ''
-    export HOME=$PWD
-  '';
+  buildInputs = [
+    docutils
+    ncurses
+    pygments
+    python.pkgs.boost
+    zlib.dev
+  ];
 
-  nativeBuildInputs = [ clang ];
-  buildInputs = [ python.pkgs.boost zlib.dev ncurses pytest docutils pygments ];
-  propagatedBuildInputs = [ numpy scipy scikitlearn ];
+  propagatedBuildInputs = [
+    numpy
+    scikitlearn
+    scipy
+  ];
+
+  # Python build script uses CMake, but we don't want CMake to do the
+  # configuration.
+  dontUseCmakeConfigure = true;
 
   # Python ctypes.find_library uses DYLD_LIBRARY_PATH.
   preConfigure = lib.optionalString stdenv.isDarwin ''
@@ -34,12 +52,12 @@ buildPythonPackage rec {
   checkPhase = ''
     # check-manifest requires a git clone, not a tarball
     # check-manifest --ignore "Makefile,PACKAGE.rst,*.cc,tox.ini,tests*,examples*,src*"
-    ${python.interpreter} setup.py check -mrs
+    ${python.interpreter} setup.py check -ms
   '';
 
   meta = with lib; {
     description = "Vowpal Wabbit is a fast machine learning library for online learning, and this is the python wrapper for the project.";
-    homepage    = https://github.com/JohnLangford/vowpal_wabbit;
+    homepage    = "https://github.com/JohnLangford/vowpal_wabbit";
     license     = licenses.bsd3;
     broken      = stdenv.isAarch64;
     maintainers = with maintainers; [ teh ];

pkgs/development/python-modules/vowpalwabbit/vowpal-wabbit-find-boost.diff

@@ -1,34 +0,0 @@
---- vowpalwabbit-8.5.0.orig/setup.py	2018-09-03 20:32:39.000000000 +0200
-+++ vowpalwabbit-8.5.0/setup.py	2018-09-03 20:34:09.000000000 +0200
-@@ -23,18 +23,11 @@
- 
- def find_boost():
-     """Find correct boost-python library information """
--    if system == 'Linux':
-+    if system == 'Linux' or system == 'Darwin':
-         # use version suffix if present
--        boost_lib = 'boost_python-py{v[0]}{v[1]}'.format(v=sys.version_info)
--        if sys.version_info.major == 3:
--            for candidate in ['-py36', '-py35', '-py34', '3']:
--                boost_lib = 'boost_python{}'.format(candidate)
--                if find_library(boost_lib):
--                    exit
-+        boost_lib = 'boost_python{v[0]}{v[1]}'.format(v=sys.version_info)
-         if not find_library(boost_lib):
-             boost_lib = "boost_python"
--    elif system == 'Darwin':
--        boost_lib = 'boost_python-mt' if sys.version_info[0] == 2 else 'boost_python3-mt'
-     elif system == 'Cygwin':
-         boost_lib = 'boost_python-mt' if sys.version_info[0] == 2 else 'boost_python3-mt'
-     else:
---- vowpalwabbit-8.5.0.orig/src/Makefile	2018-09-03 20:32:40.000000000 +0200
-+++ vowpalwabbit-8.5.0/src/Makefile	2018-09-03 21:42:30.000000000 +0200
-@@ -37,7 +37,7 @@
-   NPROCS:=$(shell grep -c ^processor /proc/cpuinfo)
- endif
- ifeq ($(UNAME), Darwin)
--  LIBS = -lboost_program_options-mt -lboost_serialization-mt -l pthread -l z
-+  LIBS = -lboost_program_options -lboost_serialization -l pthread -l z
-   # On Macs, the location isn't always clear
-   #	brew uses /usr/local
-   #	but /opt/local seems to be preferred by some users

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

@@ -1,4 +1,4 @@
-{ stdenv, buildPythonPackage, fetchPypi
+{ lib, buildPythonPackage, fetchPypi
 , setuptools_scm, pathpy, nbconvert
 , pytest }:
 
@@ -11,11 +11,10 @@ buildPythonPackage rec {
     sha256 = "b8a9bdcfa4b705d72b55b218658bc9403c157db7b57a14158253c98d03ab713d";
   };
 
-  # Python 3.7 compatibility
-  # See https://github.com/zimmermanncode/zetup/pull/1
+  # Python 3.8 compatibility
   postPatch = ''
     substituteInPlace zetup/zetup_config.py \
-      --replace "'3.6']" "'3.6', '3.7']"
+      --replace "'3.7']" "'3.7', '3.8']"
   '';
 
   checkPhase = ''
@@ -25,11 +24,9 @@ buildPythonPackage rec {
   checkInputs = [ pytest pathpy nbconvert ];
   propagatedBuildInputs = [ setuptools_scm ];
 
-  meta = with stdenv.lib; {
-    description = ''
-      Zimmermann's Extensible Tools for Unified Project setups
-    '';
-    homepage = https://github.com/zimmermanncode/zetup;
+  meta = with lib; {
+    description = "Zimmermann's Extensible Tools for Unified Project setups";
+    homepage = "https://github.com/zimmermanncode/zetup";
     license = licenses.gpl3Plus;
     platforms = platforms.unix;
   };