Merge master into staging-next

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

@@ -27,10 +27,13 @@ buildPythonPackage rec {
     async-timeout
   ];
 
+  doCheck = false; # requires siosocks, not packaged yet
   checkPhase = ''
     pytest
   '';
 
+  pythonImportsCheck = [ "aioftp" ];
+
   meta = with lib; {
     description = "Ftp client/server for asyncio";
     homepage = "https://github.com/aio-libs/aioftp";

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

@@ -62,6 +62,7 @@ buildPythonPackage rec {
     "test_read_incomplete_chunk"
     "test_request_tracing_exception"
   ] ++ lib.optionals stdenv.isDarwin [
+    "test_addresses"  # https://github.com/aio-libs/aiohttp/issues/3572
     "test_close"
   ];
 

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

@@ -35,7 +35,7 @@ buildPythonPackage rec {
 
   # Skip a test which makes requests to httpbin.org
   checkPhase = ''
-    pytest -k "not test_address_as_instance_of_url_combined_with_pass_through"
+    pytest -k "not (test_address_as_instance_of_url_combined_with_pass_through or test_pass_through_with_origin_params)"
   '';
 
   meta = {

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

@@ -18,13 +18,13 @@
 
 buildPythonPackage rec {
   pname = "ansible";
-  version = "2.9.9";
+  version = "2.9.10";
 
   src = fetchFromGitHub {
     owner = "ansible";
     repo = "ansible";
     rev = "v${version}";
-    sha256 = "06a9iq7w2cm0hsxaw5irsja8w44gffiw09ly27jxklpa8gv57rml";
+    sha256 = "1979522k57gafvq9vx3lbc3zah7jq3kiy98ji9x5bmxyddmgr9ch";
   };
 
   prePatch = ''

pkgs/development/python-modules/catalogue/1.nix

@@ -1,24 +0,0 @@
-{ stdenv
-, buildPythonPackage
-, fetchPypi
-, importlib-metadata
-}:
-
-buildPythonPackage rec {
-  pname = "catalogue";
-  version = "1.0.0";
-
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "d74d1d856c6b36a37bf14aa6dbbc27d0582667b7ab979a6108e61a575e8723f5";
-  };
-
-  propagatedBuildInputs = [ importlib-metadata ];
-
-  meta = with stdenv.lib; {
-    description = "Tiny library for adding function or object registries";
-    homepage = "https://github.com/explosion/catalogue";
-    license = licenses.mit;
-    maintainers = with maintainers; [ danieldk ];
-    };
-}

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

@@ -1,6 +1,7 @@
 { stdenv
 , buildPythonPackage
 , fetchPypi
+, pythonOlder
 , importlib-metadata
 }:
 
@@ -8,6 +9,8 @@ buildPythonPackage rec {
   pname = "catalogue";
   version = "2.0.0";
 
+  disabled = pythonOlder "3.6";
+
   src = fetchPypi {
     inherit pname version;
     sha256 = "34f8416ec5e7ed08e55c10414416e67c3f4d66edf83bc67320c3290775293816";

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

@@ -1,18 +1,18 @@
 { lib, buildPythonPackage, fetchPypi
 , isPy27
-, pylev, pastel, typing, enum34 }:
+, pylev, pastel, typing, enum34, crashtest }:
 
 buildPythonPackage rec {
   pname = "clikit";
-  version = "0.6.1";
+  version = "0.6.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0603e3c19fa106f5df5f224826c92e57221f48ec969e42744173e0458d359354";
+    sha256 = "0ngdkmb73gkp5y00q7r9k1cdlfn0wyzws2wrqlshc4hlkbdyabj4";
   };
 
   propagatedBuildInputs = [
-    pylev pastel
+    crashtest pylev pastel
   ] ++ lib.optionals isPy27 [ typing enum34 ];
 
   # The Pypi tarball doesn't include tests, and the GitHub source isn't

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

@@ -0,0 +1,25 @@
+{ lib, buildPythonPackage, fetchFromGitHub, fetchPypi, isPy27, pytest }:
+
+buildPythonPackage rec {
+  pname = "crashtest";
+  version = "0.3.0";
+  disabled = isPy27;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "056zzbznl3xfnbblfci8lvcam3h7k7va68vi6asrm4q0ck4nrh79";
+  };
+
+  # has tests, but only on GitHub, however the pyproject build fails for me
+  pythonImportsCheck = [
+    "crashtest.frame"
+    "crashtest.inspector"
+  ];
+
+  meta = with lib; {
+    homepage = "https://github.com/sdispater/crashtest";
+    description = "Manage Python errors with ease";
+    license = licenses.mit;
+    maintainers = with maintainers; [ ];
+  };
+}

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

@@ -18,11 +18,11 @@ in
 
 buildPythonPackage rec {
   pname = "entrance";
-  version = "1.1.12";
+  version = "1.1.13";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "ef7cdf76226344f7cb92c8f81b6c03bbe944a095434f86275f178809c84108ca";
+    sha256 = "1vmyfhlpcz9fip89z7bl9va3bybz4p3clifn6x3329v1ms9bm1gc";
   };
 
   # The versions of `sanic` and `websockets` in nixpkgs only support 3.6 or later

pkgs/development/python-modules/extension-helpers/default.nix

@@ -0,0 +1,41 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, isPy27
+, pytestCheckHook
+, setuptools_scm
+}:
+
+buildPythonPackage rec {
+  pname = "extension-helpers";
+  version = "0.1";
+  disabled = isPy27;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "10iqjzmya2h4sk765dlm1pbqypwlqyh8rw59a5m9i63d3klnz2mc";
+  };
+
+  nativeBuildInputs = [
+    setuptools_scm
+  ];
+
+  propagatedBuildInputs = [
+    pytestCheckHook
+  ];
+
+  # avoid importing local module
+  preCheck = ''
+    cd extension_helpers
+  '';
+
+  # assumes setup.py is in pwd
+  disabledTests = [ "compiler_module" ];
+
+  meta = with lib; {
+    description = "Helpers to assist with building packages with compiled C/Cython extensions";
+    homepage = "https://github.com/astropy/extension-helpers";
+    license = licenses.bsd3;
+    maintainers = [ ];
+  };
+}

pkgs/development/python-modules/flask-caching/default.nix

@@ -1,8 +1,9 @@
-{ lib, buildPythonPackage, fetchPypi, flask, pytest, pytestcov, pytest-xprocess, pytestcache }:
+{ lib, buildPythonPackage, fetchPypi, isPy27, flask, pytest, pytestcov, pytest-xprocess, pytestcache }:
 
 buildPythonPackage rec {
   pname = "Flask-Caching";
   version = "1.9.0";
+  disabled = isPy27; # invalid python2 syntax
 
   src = fetchPypi {
     inherit pname version;

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

@@ -5,6 +5,8 @@
 , dateutil
 , pytz
 , six
+, msgpack
+, fetchpatch
 }:
 
 buildPythonPackage rec {
@@ -16,9 +18,16 @@ buildPythonPackage rec {
     sha256 = "9bcaafd57ac152b9824ab12ed19f204206ef5df8af68404770554c5b55b475f6";
   };
 
+  patches = [
+    (fetchpatch {
+      url = "https://github.com/influxdata/influxdb-python/commit/cc41e290f690c4eb67f75c98fa9f027bdb6eb16b.patch";
+      sha256 = "1fb9qrq1kp24pixjwvzhdy67z3h0wnj92aj0jw0a25fd0rdxdvg4";
+    })
+  ];
+
   # ImportError: No module named tests
   doCheck = false;
-  propagatedBuildInputs = [ requests dateutil pytz six ];
+  propagatedBuildInputs = [ requests dateutil pytz six msgpack ];
 
   meta = with stdenv.lib; {
     description = "Python client for InfluxDB";

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

@@ -1,9 +1,9 @@
 { lib, buildPythonPackage, fetchFromGitHub, xdg_utils
 , requests, filetype, pyparsing, configparser, arxiv2bib
 , pyyaml, chardet, beautifulsoup4, colorama, bibtexparser
-, pylibgen, click, python-slugify, habanero, isbnlib
+, click, python-slugify, habanero, isbnlib, typing-extensions
 , prompt_toolkit, pygments, stevedore, tqdm, lxml
-, python-doi, isPy3k, pythonOlder
+, python-doi, isPy3k, pythonOlder, pytestcov
 #, optional, dependencies
 , whoosh, pytest
 , stdenv
@@ -11,7 +11,7 @@
 
 buildPythonPackage rec {
   pname = "papis";
-  version = "0.9";
+  version = "0.10";
   disabled = !isPy3k;
 
   # Missing tests on Pypi
@@ -19,14 +19,14 @@ buildPythonPackage rec {
     owner = "papis";
     repo = pname;
     rev = "v${version}";
-    sha256 = "15i79q6nr7gcpcafdz5797axmp6r3081sys07k1k2vi5b2g3qc4k";
+    sha256 = "0fmrvxs6ixfwjlp96b69db7fpvyqfy2n3c23kdz8yr0vhnp82l93";
   };
 
   propagatedBuildInputs = [
     requests filetype pyparsing configparser arxiv2bib
     pyyaml chardet beautifulsoup4 colorama bibtexparser
-    pylibgen click python-slugify habanero isbnlib
-    prompt_toolkit pygments
+    click python-slugify habanero isbnlib
+    prompt_toolkit pygments typing-extensions
     stevedore tqdm lxml
     python-doi
     # optional dependencies
@@ -36,6 +36,7 @@ buildPythonPackage rec {
   postPatch = ''
     substituteInPlace setup.py \
       --replace "lxml<=4.3.5" "lxml~=4.3" \
+      --replace "isbnlib>=3.9.1,<3.10" "isbnlib~=3.9" \
       --replace "python-slugify>=1.2.6,<4" "python-slugify"
   '';
 
@@ -43,7 +44,7 @@ buildPythonPackage rec {
   doCheck = !stdenv.isDarwin && pythonOlder "3.8";
 
   checkInputs = ([
-    pytest
+    pytest pytestcov
   ]) ++ [
     xdg_utils
   ];
@@ -54,7 +55,7 @@ buildPythonPackage rec {
   checkPhase = ''
     HOME=$(mktemp -d) pytest papis tests --ignore tests/downloaders \
       -k "not test_get_data and not test_doi_to_data and not test_general and not get_document_url \
-      and not test_validate_arxivid and not test_downloader_getter"
+      and not test_validate_arxivid and not test_downloader_getter and not match"
   '';
 
   meta = {

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

@@ -10,14 +10,14 @@
 buildPythonPackage rec {
 
   pname = "peewee";
-  version = "3.11.2";
+  version = "3.13.3";
 
   # pypi release does not provide tests
   src = fetchFromGitHub {
     owner = "coleifer";
     repo = pname;
     rev = version;
-    sha256 = "097cafqgk46bf0innwm7xnmsfs6z37hv3alyvrfz6d0iy4scshm5";
+    sha256 = "1r67hxb9m6v0xbnbqfnsw6dahmdr94pf81b4x51jfw6x9sa4izi4";
   };
 
 
@@ -38,6 +38,8 @@ buildPythonPackage rec {
   ] ++ (lib.optional withPostgres psycopg2)
     ++ (lib.optional withMysql mysql-connector);
 
+  doCheck = withPostgres;
+
   meta = with stdenv.lib;{
     description = "a small, expressive orm";
     homepage    = "http://peewee-orm.com";

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

@@ -1,74 +1,74 @@
-{ lib, buildPythonPackage, fetchPypi, callPackage
-, isPy27
-, pythonOlder
-, cleo
-, requests
-, cachy
-, requests-toolbelt
-, pyrsistent
-, pyparsing
+{ lib, buildPythonPackage, fetchFromGitHub, isPy27, pythonOlder
 , cachecontrol
-, pkginfo
-, html5lib
-, shellingham
-, subprocess32
-, tomlkit
-, typing
-, pathlib2
-, virtualenv
-, functools32
+, cachy
+, cleo
 , clikit
-, keyring
-, pexpect
+, html5lib
+, httpretty
 , importlib-metadata
-, pytest
-, jsonschema
 , intreehooks
+, jsonschema
+, keyring
 , lockfile
+, pexpect
+, pkginfo
+, pygments
+, pyparsing
+, pyrsistent
+, pytestCheckHook
+, pytestcov
+, pytest-mock
+, requests
+, requests-toolbelt
+, shellingham
+, tomlkit
 }:
 
-let
-  glob2 = callPackage ./glob2.nix { };
-
-in buildPythonPackage rec {
+buildPythonPackage rec {
   pname = "poetry";
-  version = "1.0.5";
+  version = "1.0.9";
   format = "pyproject";
+  disabled = isPy27;
 
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "02h387k0xssvv78yy82pcpknpq4w5ym2in1zl8cg9r5wljl5w6cf";
+  src = fetchFromGitHub {
+    owner = "python-poetry";
+    repo = pname;
+    rev = version;
+    sha256 = "0gi1li55rim60hf1gdpgpx84zlkaj0wv12wbv7dib9malhfj3pnz";
   };
 
   postPatch = ''
     substituteInPlace pyproject.toml \
-     --replace "pyrsistent = \"^0.14.2\"" "pyrsistent = \"^0.15.0\"" \
-     --replace "requests-toolbelt = \"^0.8.0\"" "requests-toolbelt = \"^0.9.0\"" \
+     --replace "pyrsistent = \"^0.14.2\"" "pyrsistent = \"^0.16.0\"" \
+     --replace "requests-toolbelt = \"^0.8.0\"" "requests-toolbelt = \"^0.9.1\"" \
      --replace 'importlib-metadata = {version = "~1.1.3", python = "<3.8"}' \
-       'importlib-metadata = {version = ">=1.3,<2", python = "<3.8"}'
+       'importlib-metadata = {version = ">=1.3,<2", python = "<3.8"}' \
+     --replace "tomlkit = \"^0.5.11\"" "tomlkit = \"^0.6.0\"" \
+     --replace "cleo = \"^0.7.6\"" "cleo = \"^0.8.0\"" \
+     --replace "version = \"^20.0.1\", python = \"^3.5\"" "version = \"^21.0.0\", python = \"^3.5\"" \
+     --replace "clikit = \"^0.4.2\"" "clikit = \"^0.6.2\""
   '';
 
   nativeBuildInputs = [ intreehooks ];
 
   propagatedBuildInputs = [
+    cachecontrol
+    cachy
     cleo
     clikit
-    requests
-    cachy
-    requests-toolbelt
-    jsonschema
-    pyrsistent
-    pyparsing
-    cachecontrol
-    pkginfo
     html5lib
-    shellingham
-    tomlkit
-    pexpect
+    jsonschema
     keyring
     lockfile
-  ] ++ lib.optionals isPy27 [ typing pathlib2 glob2 virtualenv functools32 subprocess32 ]
-    ++ lib.optionals (pythonOlder "3.8") [ importlib-metadata ];
+    pexpect
+    pkginfo
+    pyparsing
+    pyrsistent
+    requests
+    requests-toolbelt
+    shellingham
+    tomlkit
+  ] ++ lib.optionals (pythonOlder "3.8") [ importlib-metadata ];
 
   postInstall = ''
     mkdir -p "$out/share/bash-completion/completions"
@@ -79,12 +79,18 @@ in buildPythonPackage rec {
     "$out/bin/poetry" completions fish > "$out/share/fish/vendor_completions.d/poetry.fish"
   '';
 
-  # No tests in Pypi tarball
-  doCheck = false;
-  checkInputs = [ pytest ];
-  checkPhase = ''
-    pytest tests
-  '';
+  checkInputs = [ pytestCheckHook httpretty pytest-mock pygments pytestcov ];
+  preCheck = "export HOME=$TMPDIR";
+  disabledTests = [
+    # touches network
+    "git"
+    "solver"
+    "load"
+    "vcs"
+    "prereleases_if_they_are_compatible"
+    # requires git history to work correctly
+    "default_with_excluded_data"
+  ];
 
   meta = with lib; {
     homepage = "https://python-poetry.org/";

pkgs/development/python-modules/poetry/glob2.nix

@@ -1,11 +0,0 @@
-{ buildPythonPackage, fetchPypi }:
-
-buildPythonPackage rec {
-  pname = "glob2";
-  version = "0.6";
-
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "1miyz0pjyji4gqrzl04xsxcylk3h2v9fvi7hsg221y11zy3adc7m";
-  };
-}

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

@@ -16,7 +16,7 @@ buildPythonPackage rec {
 
   # arch doesn't report frequency is the same way
   # tests segfaults on darwin https://github.com/giampaolo/psutil/issues/1715
-  doCheck = stdenv.isDarwin || stdenv.isx86_64;
+  doCheck = !stdenv.isDarwin && stdenv.isx86_64;
   checkInputs = [ pytest ]
     ++ lib.optionals isPy27 [ mock ipaddress ];
   # out must be referenced as test import paths are relative

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

@@ -1,7 +1,9 @@
 { lib
 , buildPythonPackage
 , fetchPypi
+, oauthlib
 , requests
+, requests_oauthlib
 }:
 
 buildPythonPackage rec {
@@ -13,7 +15,7 @@ buildPythonPackage rec {
     sha256 = "9949338833a27b6c3251b52bf70b73aa99c43c56153541338cb63001afafdd1e";
   };
 
-  propagatedBuildInputs = [ requests ];
+  propagatedBuildInputs = [ oauthlib requests requests_oauthlib ];
 
   # Upstream provides no unit tests.
   doCheck = false;

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

@@ -38,9 +38,10 @@ buildPythonPackage rec {
 
   postPatch = ''
     sed -i \
-      -e 's!click>=6.0,<7.0!click!' \
-      -e 's!keyring>=8.0,<9.0!keyring!' \
-      -e 's!keyrings.alt>=1.0,<2.0!keyrings.alt!' \
+      -e 's!click>=.*!click!' \
+      -e 's!keyring>=.*!keyring!' \
+      -e 's!keyrings.alt>=.*!keyrings.alt!' \
+      -e 's!tzlocal==.*!tzlocal!' \
       requirements.txt
   '';
 

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

@@ -1,33 +0,0 @@
-{ lib, buildPythonPackage, fetchFromGitHub
-, pythonOlder
-, requests
-, pytest
-, pre-commit
-}:
-
-buildPythonPackage rec {
-  pname = "pylibgen";
-  version = "2.0.2";
-  disabled = pythonOlder "3.6";
-
-  src = fetchFromGitHub {
-    owner = "joshuarli";
-    repo = pname;
-    rev = "v${version}";
-    sha256 = "1a9vhkgnkiwkicr2s287254mrkpnw9jq5r63q820dp3h74ba4kl1";
-  };
-
-  propagatedBuildInputs = [ requests ];
-
-  checkInputs = [ pytest pre-commit ];
-
-  # literally every tests does a network call
-  doCheck = false;
-
-  meta = with lib; {
-    description = "Python interface to Library Genesis";
-    homepage = "https://pypi.org/project/pylibgen/";
-    license = licenses.mit;
-    maintainers = [ maintainers.nico202 ];
-  };
-}

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

@@ -9,13 +9,13 @@
 
 buildPythonPackage rec {
   pname = "PyMetno";
-  version = "0.5.0";
+  version = "0.5.1";
 
   src = fetchFromGitHub {
     repo = pname;
     owner = "Danielhiversen";
     rev = version;
-    sha256 = "00v2r3nn48svni9rbmbf0a4ylgfcf93gk2wg7qnm1fv1qrkgscvg";
+    sha256 = "1ihq1lzgzcxbg916izakx9jp0kp1vdrcdwcwwwsws838wc08ax6m";
   };
 
   propagatedBuildInputs = [ aiohttp async-timeout pytz xmltodict ];

pkgs/development/python-modules/pytest-astropy-header/default.nix

@@ -0,0 +1,37 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, pytest
+, pytestcov
+, pytestCheckHook
+, numpy
+, astropy
+}:
+
+buildPythonPackage rec {
+  pname = "pytest-astropy-header";
+  version = "0.1.2";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1y87agr324p6x5gvhziymxjlw54pyn4gqnd49papbl941djpkp5g";
+  };
+
+  propagatedBuildInputs = [
+    pytest
+  ];
+
+  checkInputs = [
+    pytestCheckHook
+    pytestcov
+    numpy
+    astropy
+  ];
+
+  meta = with lib; {
+    description = "Plugin to add diagnostic information to the header of the test output";
+    homepage = "https://astropy.org";
+    license = licenses.bsd3;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

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

@@ -1,11 +1,15 @@
 { lib
 , buildPythonPackage
 , fetchPypi
+, hypothesis
 , pytest
+, pytest-astropy-header
 , pytest-doctestplus
+, pytest-filter-subpackage
 , pytest-remotedata
 , pytest-openfiles
 , pytest-arraydiff
+, setuptools_scm
 }:
 
 buildPythonPackage rec {
@@ -17,16 +21,23 @@ buildPythonPackage rec {
     sha256 = "619800eb2cbf64548fbea25268efe7c6f6ae206cb4825f34abd36f27bcf946a2";
   };
 
+  nativeBuildInputs = [
+    setuptools_scm
+  ];
+
   propagatedBuildInputs = [
+    hypothesis
     pytest
+    pytest-astropy-header
     pytest-doctestplus
+    pytest-filter-subpackage
     pytest-remotedata
     pytest-openfiles
     pytest-arraydiff
   ];
 
   # pytest-astropy is a meta package and has no tests
-  doCheck = false;
+  checkPhase = ":";
 
   meta = with lib; {
     description = "Meta-package containing dependencies for testing";

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

@@ -1,6 +1,7 @@
 { lib
 , buildPythonPackage
 , fetchPypi
+, isPy27
 , six
 , pytest
 , numpy
@@ -9,6 +10,7 @@
 buildPythonPackage rec {
   pname = "pytest-doctestplus";
   version = "0.7.0";
+  disabled = isPy27; # abandoned upstream
 
   src = fetchPypi {
     inherit pname version;

pkgs/development/python-modules/pytest-filter-subpackage/default.nix

@@ -0,0 +1,39 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, pytest
+, pytestcov
+, pytest-doctestplus
+, pytestCheckHook
+, setuptools_scm
+}:
+
+buildPythonPackage rec {
+  pname = "pytest-filter-subpackage";
+  version = "0.1.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1s4s2kd31yc65rfvl4xhy8xx806xhy59kc7668h6b6wq88xgrn5p";
+  };
+
+  nativeBuildInputs = [
+    setuptools_scm
+  ];
+
+  propagatedBuildInputs = [
+    pytest
+    pytest-doctestplus
+    pytestcov
+    pytestCheckHook
+  ];
+
+  # missing some files
+  disabledTests = [ "with_rst" ];
+
+  meta = with lib; {
+    description = "Meta-package containing dependencies for testing";
+    homepage = "https://astropy.org";
+    license = licenses.bsd3;
+  };
+}

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

@@ -6,30 +6,26 @@
 , astropy
 , astropy-healpix
 , astropy-helpers
+, extension-helpers
 , scipy
 , pytest
 , pytest-astropy
+, setuptools_scm
 , cython
 }:
 
 buildPythonPackage rec {
   pname = "reproject";
-  version = "0.6";
+  version = "0.7.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "484fde86d70d972d703038f138d7c2966ddf51171a6e79bd84e82ea270e27af3";
+    sha256 = "1jsc3ad518vyys5987fr1achq8qvnz8rm80zp5an9qxlwr4zmh4m";
   };
 
   propagatedBuildInputs = [ numpy astropy astropy-healpix astropy-helpers scipy ];
 
-  nativeBuildInputs = [ astropy-helpers cython ];
-
-  # Fix tests
-  patches = [ (fetchpatch {
-    url = "https://github.com/astropy/reproject/pull/218/commits/4661e075137424813ed77f1ebcbc251fee1b8467.patch";
-    sha256 = "13g3h824pqn2lgypzg1b87vkd44y7m302lhw3kh4rfww1dkzhm9v";
-  }) ];
+  nativeBuildInputs = [ astropy-helpers cython extension-helpers setuptools_scm ];
 
   # Disable automatic update of the astropy-helper module
   postPatch = ''

pkgs/development/python-modules/requests-file/default.nix

@@ -1,4 +1,4 @@
-{ lib, fetchPypi, buildPythonPackage, requests, six }:
+{ lib, fetchPypi, buildPythonPackage, pytestCheckHook, requests, six }:
 
 buildPythonPackage rec {
   pname   = "requests-file";
@@ -11,6 +11,8 @@ buildPythonPackage rec {
 
   propagatedBuildInputs = [ requests six ];
 
+  checkInputs = [ pytestCheckHook ];
+
   meta = {
     homepage = "https://github.com/dashea/requests-file";
     description = "Transport adapter for fetching file:// URLs with the requests python library";

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

@@ -54,9 +54,15 @@ buildPythonPackage rec {
   # '';
 
   postPatch = ''
-    substituteInPlace setup.cfg --replace "thinc==7.4.1" "thinc>=7.4.1,<8"
+    substituteInPlace setup.cfg \
+      --replace "catalogue>=0.0.7,<1.1.0" "catalogue>=0.0.7,<3.0" \
+      --replace "plac>=0.9.6,<1.2.0" "plac>=0.9.6,<2.0" \
+      --replace "srsly>=1.0.2,<1.1.0" "srsly>=1.0.2,<3.0" \
+      --replace "thinc==7.4.1" "thinc>=7.4.1,<8"
   '';
 
+  pythonImportsCheck = [ "spacy" ];
+
   meta = with lib; {
     description = "Industrial-strength Natural Language Processing (NLP) with Python and Cython";
     homepage = "https://github.com/explosion/spaCy";

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

@@ -1,6 +1,7 @@
 { lib
 , fetchFromGitHub
 , buildPythonPackage
+, aplpy
 , astropy
 , radio_beam
 , pytest
@@ -24,7 +25,7 @@ buildPythonPackage rec {
 
   nativeBuildInputs = [ astropy-helpers ];
 
-  checkInputs = [ pytest pytest-astropy ];
+  checkInputs = [ aplpy pytest pytest-astropy ];
 
   # Disable automatic update of the astropy-helper module
   postPatch = ''

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

@@ -15,6 +15,8 @@ buildPythonPackage rec {
   pname = "srsly";
   version = "2.0.1";
 
+  disabled = pythonOlder "3.6";
+
   src = fetchPypi {
     inherit pname version;
     sha256 = "fa3c7375be8fe75f23c27feafbfb5f738d55ffdbf02964c6896fb7684f519a52";
@@ -22,8 +24,6 @@ buildPythonPackage rec {
 
   nativeBuildInputs = [ cython ];
 
-  propagatedBuildInputs = lib.optional (pythonOlder "3.4") pathlib;
-
   checkInputs = [
     mock
     numpy
@@ -35,6 +35,8 @@ buildPythonPackage rec {
   # Possibly because of sandbox restrictions.
   doCheck = false;
 
+  pythonImportsCheck = [ "srsly" ];
+
   meta = with stdenv.lib; {
     description = "Modern high-performance serialization utilities for Python";
     homepage = "https://github.com/explosion/srsly";

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

@@ -2,6 +2,7 @@
 , buildPythonPackage
 , fetchPypi
 , pytest
+, pytest-asyncio
 , python-rapidjson
 , pretend
 , freezegun
@@ -20,7 +21,7 @@ buildPythonPackage rec {
     sha256 = "7a48375db6274ed1d0ae6123c486472aa1d0890b08d314d2b016f3aa7f35990b";
   };
 
-  checkInputs = [ pytest pretend freezegun simplejson twisted ]
+  checkInputs = [ pytest pytest-asyncio pretend freezegun simplejson twisted ]
     ++ lib.optionals (pythonAtLeast "3.6") [ python-rapidjson ];
   propagatedBuildInputs = [ six ];
 

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

@@ -58,10 +58,19 @@ buildPythonPackage rec {
   # Cannot find cython modules.
   doCheck = false;
 
+  postPatch = ''
+    substituteInPlace setup.py \
+      --replace "catalogue>=0.0.7,<1.1.0" "catalogue>=0.0.7,<3.0" \
+      --replace "plac>=0.9.6,<1.2.0" "plac>=0.9.6,<2.0" \
+      --replace "srsly>=0.0.6,<1.1.0" "srsly>=0.0.6,<3.0"
+  '';
+
   checkPhase = ''
     pytest thinc/tests
   '';
 
+  pythonImportsCheck = [ "thinc" ];
+
   meta = with stdenv.lib; {
     description = "Practical Machine Learning for NLP in Python";
     homepage = "https://github.com/explosion/thinc";

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

@@ -55,6 +55,9 @@ buildPythonPackage rec {
     export TEST_DIR=$(mktemp -d)
     cp -r tests $TEST_DIR
     pushd $TEST_DIR
+  '' + lib.optionalString stdenv.isDarwin ''
+    # Some tests fail on Darwin
+    rm tests/test_[stu]*.py
   '';
   postCheck = ''
     popd

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

@@ -5,6 +5,7 @@
 , flake8-import-order
 , pyflakes
 , mock
+, setuptools
 }:
 
 buildPythonPackage rec {
@@ -23,12 +24,19 @@ buildPythonPackage rec {
   propagatedBuildInputs = [
     pyflakes
     flake8-import-order
+    setuptools
   ];
 
   checkInputs = [
     mock
   ];
 
+  checkPhase = ''
+    runHook preInstallCheck
+    PYTHONPATH= $out/bin/zimports --help >/dev/null
+    runHook postInstallCheck
+  '';
+
   meta = with lib; {
     description = "Python import rewriter";
     homepage = "https://github.com/sqlalchemyorg/zimports";