Merge branch 'staging-next' into staging

The transmission conflict was non-trivial:
- libbrotli added to apparmor rules <https://github.com/NixOS/nixpkgs/commit/1bdda029cd85b5f4358697afd2c8f6a1996c6ccf>
- apparmor rules rewritten <https://github.com/NixOS/nixpkgs/commit/b280e64078d69c59cf4fccfcaa9d56a59d789dc9>

Chosen the rewrite and verified that brotli is part of the rule set generated by `apparmorRulesFromClosure`.

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

@@ -42,6 +42,11 @@ buildPythonPackage rec {
     pytest-httpx
   ];
 
+  disabledTests = [
+    # fails with pytest-httpx>=0.12.0
+    "test__query_rmv_api_fail"
+  ];
+
   meta = with lib; {
     homepage = "https://github.com/cgtobi/PyRMVtransport";
     description = "Get transport information from opendata.rmv.de";

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

@@ -10,18 +10,18 @@
 
 buildPythonPackage rec {
   pname = "aiobotocore";
-  version = "1.2.2";
+  version = "1.3.0";
   disabled = pythonOlder "3.7";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "37c23166603a3bd134e5f6fc22dbbf8c274d4d24c71418fba292ed2cd7a0bf43";
+    sha256 = "17pcdi69bwdfw2wv3a0fhira5gimw88sp2wf47yqz50z1ckhv2c1";
   };
 
   # relax version constraints: aiobotocore works with newer botocore versions
   # the pinning used to match some `extras_require` we're not using.
-  preConfigure = ''
-    substituteInPlace setup.py --replace 'botocore>=1.17.44,<1.17.45' 'botocore'
+  postPatch = ''
+    substituteInPlace setup.py --replace 'botocore>=1.20.49,<1.20.50' 'botocore'
   '';
 
   propagatedBuildInputs = [ wrapt aiohttp aioitertools botocore ];
@@ -31,7 +31,7 @@ buildPythonPackage rec {
   pythonImportsCheck = [ "aiobotocore" ];
 
   meta = with lib; {
-    description = "Async client for amazon services using botocore and aiohttp/asyncio.";
+    description = "Python client for amazon services";
     license = licenses.asl20;
     homepage = "https://github.com/aio-libs/aiobotocore";
     maintainers = with maintainers; [ teh ];

pkgs/development/python-modules/aniso8601/default.nix

@@ -1,22 +1,35 @@
-{ lib, buildPythonPackage, fetchPypi
-, dateutil, mock, isPy3k }:
+{ lib
+, buildPythonPackage
+, dateutil
+, fetchPypi
+, isPy3k
+, mock
+, pytestCheckHook
+}:
 
 buildPythonPackage rec {
   pname = "aniso8601";
   version = "9.0.1";
 
-  meta = with lib; {
-    description = "Parses ISO 8601 strings.";
-    homepage    = "https://bitbucket.org/nielsenb/aniso8601";
-    license     = licenses.bsd3;
-  };
-
-  propagatedBuildInputs = [ dateutil ];
-
-  checkInputs = lib.optional (!isPy3k) mock;
-
   src = fetchPypi {
     inherit pname version;
-    sha256 = "72e3117667eedf66951bb2d93f4296a56b94b078a8a95905a052611fb3f1b973";
+    sha256 = "sha256-cuMRdmfu32aVG7LZP0KWpWuUsHioqVkFoFJhH7PxuXM=";
+  };
+
+  propagatedBuildInputs = [
+    dateutil
+  ];
+
+  checkInputs = [
+    pytestCheckHook
+  ] ++ lib.optional (!isPy3k) mock;
+
+  pythonImportsCheck = [ "aniso8601" ];
+
+  meta = with lib; {
+    description = "Python Parser for ISO 8601 strings";
+    homepage = "https://bitbucket.org/nielsenb/aniso8601";
+    license = with licenses; [ bsd3 ];
+    maintainers = with maintainers; [ fab ];
   };
 }

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

@@ -3,25 +3,42 @@
 , fetchPypi
 , numpy
 , astropy
-, astropy-helpers
+, astropy-extension-helpers
+, setuptools-scm
+, pytestCheckHook
+, pytest-doctestplus
+, hypothesis
 }:
 
 buildPythonPackage rec {
   pname = "astropy-healpix";
   version = "0.6";
 
-  doCheck = false; # tests require pytest-astropy
-
   src = fetchPypi {
-    inherit pname version;
+    inherit version;
+    pname = lib.replaceStrings ["-"] ["_"] pname;
     sha256 = "409a6621c383641456c074f0f0350a24a4a58e910eaeef14e9bbce3e00ad6690";
   };
 
-  propagatedBuildInputs = [ numpy astropy astropy-helpers ];
+  nativeBuildInputs = [
+    astropy-extension-helpers
+    setuptools-scm
+  ];
 
-  # Disable automatic update of the astropy-helper module
-  postPatch = ''
-    substituteInPlace setup.cfg --replace "auto_use = True" "auto_use = False"
+  propagatedBuildInputs = [
+    numpy
+    astropy
+  ];
+
+  checkInputs = [
+    pytestCheckHook
+    pytest-doctestplus
+    hypothesis
+  ];
+
+  # tests must be run in the build directory
+  preCheck = ''
+    cd build/lib*
   '';
 
   meta = with lib; {

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

@@ -12,11 +12,11 @@
 
 buildPythonPackage rec {
   pname = "breezy";
-  version = "3.1.0";
+  version = "3.2.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1eff207403f48898fa3b3ffa7a4275197c6c58fec105ef267caf1f5fd5a6c7be";
+    sha256 = "sha256-lwKPk+UxKAhfIgUb1xPLJ/za53VdHenmBrr85RTpEps=";
   };
 
   propagatedBuildInputs = [ configobj patiencediff six fastimport dulwich launchpadlib ];

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

@@ -17,13 +17,13 @@
 
 buildPythonPackage rec {
   pname = "debugpy";
-  version = "1.2.1";
+  version = "1.3.0";
 
   src = fetchFromGitHub {
     owner = "Microsoft";
     repo = pname;
     rev = "v${version}";
-    sha256 = "1dgjbbhy228w2zbfq5pf0hkai7742zw8mmybnzjdc9l6pw7360rq";
+    hash = "sha256-YGzc9mMIzPTmUgIXuZROLdYKjUm69x9SR+JtYRVpn24=";
   };
 
   patches = [
@@ -33,6 +33,7 @@ buildPythonPackage rec {
       inherit gdb;
     })
 
+    # Use nixpkgs version instead of versioneer
     (substituteAll {
       src = ./hardcode-version.patch;
       inherit version;
@@ -87,6 +88,8 @@ buildPythonPackage rec {
     "gevent"
   ];
 
+  pythonImportsCheck = [ "debugpy" ];
+
   meta = with lib; {
     description = "An implementation of the Debug Adapter Protocol for Python";
     homepage = "https://github.com/microsoft/debugpy";

pkgs/development/python-modules/debugpy/fix-test-pythonpath.patch

@@ -1,8 +1,8 @@
 diff --git a/tests/debug/session.py b/tests/debug/session.py
-index 2b39106..6d45a10 100644
+index 101492f..4ee7cfb 100644
 --- a/tests/debug/session.py
 +++ b/tests/debug/session.py
-@@ -625,6 +625,7 @@ class Session(object):
+@@ -630,6 +630,7 @@ class Session(object):
          if "PYTHONPATH" in self.config.env:
              # If specified, launcher will use it in lieu of PYTHONPATH it inherited
              # from the adapter when spawning debuggee, so we need to adjust again.

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

@@ -5,25 +5,23 @@
 , libopus
 , pynacl
 , pythonOlder
-, websockets
 , withVoice ? true
 }:
 
 buildPythonPackage rec {
   pname = "discord.py";
-  version = "1.7.1";
+  version = "1.7.2";
   disabled = pythonOlder "3.8";
 
   src = fetchFromGitHub {
     owner = "Rapptz";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-dpASIqe6rJEyiWJyPbQhq9M54lX1ilfp4UuGnbJcFLo=";
+    sha256 = "sha256-NY1/RKp8w9gAqGYXnCNhNZqR/inGMvUvxjJ1MMs62B8=";
   };
 
   propagatedBuildInputs = [
     aiohttp
-    websockets
   ] ++ lib.optionalString withVoice [
     libopus
     pynacl

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

@@ -4,12 +4,15 @@
 , httpx
 , poetry-core
 , pythonOlder
+, pytest-asyncio
+, pytest-httpx
+, pytestCheckHook
 , yarl
 }:
 
 buildPythonPackage rec {
   pname = "elmax";
-  version = "0.1.1";
+  version = "0.1.2";
   format = "pyproject";
   disabled = pythonOlder "3.7";
 
@@ -17,7 +20,7 @@ buildPythonPackage rec {
     owner = "home-assistant-ecosystem";
     repo = "python-elmax";
     rev = version;
-    sha256 = "sha256-vDISJ/CVOjpM+GPF2TCm3/AMFTWTM0b/+ZPCpAEvNvY=";
+    sha256 = "sha256-Aq/OHxOmtUUmBNlFPu892C8AkTX+Ee0oca7D79InPXQ=";
   };
 
   nativeBuildInputs = [ poetry-core ];
@@ -27,8 +30,12 @@ buildPythonPackage rec {
     yarl
   ];
 
-  # Project has no tests
-  doCheck = false;
+  checkInputs = [
+    pytest-asyncio
+    pytest-httpx
+    pytestCheckHook
+  ];
+
   pythonImportsCheck = [ "elmax" ];
 
   meta = with lib; {

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

@@ -2,10 +2,10 @@
 , buildPythonPackage
 , fetchFromGitHub
 , numpy
-, python
 , scikitimage
 , openjpeg
 , procps
+, pytestCheckHook
 , contextlib2
 , mock
 , importlib-resources
@@ -14,13 +14,13 @@
 
 buildPythonPackage rec {
   pname = "glymur";
-  version = "0.8.18";
+  version = "0.9.3";
 
   src = fetchFromGitHub {
     owner = "quintusdias";
     repo = pname;
     rev = "v${version}";
-    sha256 = "1zbghzw1q4fljb019lsrhka9xrnn4425qnxrjbmbv7dssgkkywd7";
+    sha256 = "1xlpax56qg5qqh0s19xidgvv2483sc684zj7rh6zw1m1z9m37drr";
   };
 
   propagatedBuildInputs = [
@@ -30,16 +30,21 @@ buildPythonPackage rec {
   checkInputs = [
     scikitimage
     procps
+    pytestCheckHook
   ];
 
   postConfigure = ''
     substituteInPlace glymur/config.py \
-    --replace "path = read_config_file(libname)" "path = '${openjpeg}/lib' + libname + ${if stdenv.isDarwin then "'.dylib'" else "'.so'"}"
+    --replace "path = read_config_file(libname)" "path = '${openjpeg}/lib/lib' + libname + ${if stdenv.isDarwin then "'.dylib'" else "'.so'"}"
   '';
 
-  checkPhase = ''
-    ${python.interpreter} -m unittest discover
-  '';
+  disabledTestPaths = [
+    # this test involves glymur's different ways of finding the openjpeg path on
+    # fsh systems by reading an .rc file and such, and is obviated by the patch
+    # in postConfigure
+    "tests/test_config.py"
+  ];
+
 
   meta = with lib; {
     description = "Tools for accessing JPEG2000 files";

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

@@ -5,24 +5,25 @@
 , h11
 , h2
 , pproxy
+, pytest-asyncio
+, pytest-trio
 , pytestCheckHook
 , pytestcov
 , sniffio
-, uvicorn
 , trustme
-, trio
+, uvicorn
 }:
 
 buildPythonPackage rec {
   pname = "httpcore";
-  version = "0.12.3";
+  version = "0.13.0";
   disabled = pythonOlder "3.6";
 
   src = fetchFromGitHub {
     owner = "encode";
     repo = pname;
     rev = version;
-    sha256 = "09hbjc5wzhrnri5y3idxcq329d7jiaxljc7y6npwv9gh9saln109";
+    sha256 = "sha256-KvqBVQUaF3p2oJz0tt3Bkn2JiKEHqrZ3b6I9f0JK5h8=";
   };
 
   propagatedBuildInputs = [
@@ -33,18 +34,19 @@ buildPythonPackage rec {
 
   checkInputs = [
     pproxy
+    pytest-asyncio
+    pytest-trio
     pytestCheckHook
     pytestcov
-    uvicorn
     trustme
-    trio
+    uvicorn
   ];
 
-  pytestFlagsArray = [
+  disabledTestPaths = [
     # these tests fail during dns lookups: httpcore.ConnectError: [Errno -2] Name or service not known
-    "--ignore=tests/test_threadsafety.py"
-    "--ignore=tests/sync_tests/test_interfaces.py"
-    "--ignore=tests/sync_tests/test_retries.py"
+    "tests/test_threadsafety.py"
+    "tests/sync_tests/test_interfaces.py"
+    "tests/sync_tests/test_retries.py"
   ];
 
   pythonImportsCheck = [ "httpcore" ];

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

@@ -18,14 +18,14 @@
 
 buildPythonPackage rec {
   pname = "httpx";
-  version = "0.17.1";
+  version = "0.18.0";
   disabled = pythonOlder "3.6";
 
   src = fetchFromGitHub {
     owner = "encode";
     repo = pname;
     rev = version;
-    sha256 = "sha256-P4Uki+vlAgVECBUz9UGvv1ip49jmf0kYbyU2/mkWE3U=";
+    sha256 = "sha256-6EYBTRXaVHBgW/JzZvWLz55AqgocOyym2FVtu2Nkp/U=";
   };
 
   propagatedBuildInputs = [

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

@@ -7,11 +7,11 @@
 
 buildPythonPackage rec {
   pname = "pykmtronic";
-  version = "0.2.0";
+  version = "0.3.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "9d0301882f06a0c4865c89bb6c2a381c4a1ba6fe2a7a07d56351bdf5f96c9fa5";
+    sha256 = "sha256-8qLyBJp7C93x0PWbgDAtNEDJ5VLNfwZ3DRZfudRCBgo=";
   };
 
   propagatedBuildInputs = [ aiohttp lxml ];

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

@@ -4,7 +4,9 @@
 , isPy27
 , six
 , pytest
+, pytestCheckHook
 , numpy
+, setuptools_scm
 }:
 
 buildPythonPackage rec {
@@ -17,7 +19,12 @@ buildPythonPackage rec {
     sha256 = "6fe747418461d7b202824a3486ba8f4fa17a9bd0b1eddc743ba1d6d87f03391a";
   };
 
-  buildInputs = [ pytest ];
+  nativeBuildInputs = [
+    setuptools_scm
+  ];
+  buildInputs = [
+    pytest
+  ];
 
   propagatedBuildInputs = [
     six
@@ -25,14 +32,9 @@ buildPythonPackage rec {
   ];
 
   checkInputs = [
-    pytest
+    pytestCheckHook
   ];
 
-  # check_distribution incorrectly pulls pytest version
-  checkPhase = ''
-    pytest -k 'not check_distribution'
-  '';
-
   meta = with lib; {
     description = "Pytest plugin with advanced doctest features";
     homepage = "https://astropy.org";

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

@@ -9,13 +9,13 @@
 
 buildPythonPackage rec {
   pname = "pytest-httpx";
-  version = "0.11.0";
+  version = "0.12.0";
 
   src = fetchFromGitHub {
     owner = "Colin-b";
     repo = "pytest_httpx";
     rev = "v${version}";
-    sha256 = "08idd3y6khxjqkn46diqvkjvsl4w4pxhl6z1hspbkrj0pqwf9isi";
+    sha256 = "sha256-Awhsm8jmoCZTBnfrrauLxAEKtpxTzjPMXmx7HR0f/g4=";
   };
 
   buildInputs = [ pytest ];

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

@@ -2,9 +2,8 @@
 , fetchPypi
 , buildPythonPackage
 , astropy
-, pytest
-, pytest-astropy
-, astropy-helpers
+, pytestCheckHook
+, pytest-doctestplus
 , scipy
 }:
 
@@ -13,25 +12,18 @@ buildPythonPackage rec {
   version = "0.3.3";
 
   src = fetchPypi {
-    inherit pname version;
+    inherit version;
+    pname = "radio-beam";
     sha256 = "e34902d91713ccab9f450b9d3e82317e292cf46a30bd42f9ad3c9a0519fcddcd";
   };
 
   propagatedBuildInputs = [ astropy ];
 
-  nativeBuildInputs = [ astropy-helpers ];
-
-  # Disable automatic update of the astropy-helper module
-  postPatch = ''
-    substituteInPlace setup.cfg --replace "auto_use = True" "auto_use = False"
-  '';
-
-  checkInputs = [ pytest pytest-astropy scipy ];
+  checkInputs = [ pytestCheckHook pytest-doctestplus scipy ];
 
   # Tests must be run in the build directory
-  checkPhase = ''
+  preCheck = ''
     cd build/lib
-    pytest
   '';
 
   meta = {

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

@@ -11,13 +11,13 @@
 
 buildPythonPackage rec {
   pname = "respx";
-  version = "0.16.3";
+  version = "0.17.0";
 
   src = fetchFromGitHub {
     owner = "lundberg";
     repo = pname;
     rev = version;
-    sha256 = "0if9sg83rznl37hsjw6pfk78jpxi421g9p21wd92jcd6073g4nbd";
+    sha256 = "sha256-unGAIsslGXOUHXr0FKzC9bX6+Q3mNGZ9Z/dtjz0gkj4=";
   };
 
   # Coverage is under 100 % due to the excluded tests

pkgs/development/python-modules/sanic-testing/default.nix

@@ -20,6 +20,12 @@ buildPythonPackage rec {
     hash = "sha256-hBAq+/BKs0a01M89Nb8HaClqxB+W5PTfjVzef/m9SWs=";
   };
 
+  postPatch = ''
+    substituteInPlace setup.py \
+      --replace 'httpx>=0.16, <0.18' 'httpx' \
+      --replace 'httpcore==0.12.*' 'httpcore'
+  '';
+
   propagatedBuildInputs = [ httpx sanic websockets httpcore ];
 
   # `sanic` is explicitly set to null when building `sanic` itself

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

@@ -1,11 +1,12 @@
 { lib
 , fetchPypi
+, fetchpatch
 , buildPythonPackage
 , aplpy
 , joblib
 , astropy
 , radio_beam
-, pytest
+, pytestCheckHook
 , pytest-astropy
 , astropy-helpers
 }:
@@ -20,13 +21,18 @@ buildPythonPackage rec {
     sha256 = "17zisr26syfb8kn89xj17lrdycm0hsmy5yp5zrn236wgd8rjriki";
   };
 
+  patches = [
+    # Fix compatibility with radio_beam >= 0.3.3. Will be included
+    # in the next release of spectral cube > 0.5.0
+    (fetchpatch {
+      url = "https://github.com/radio-astro-tools/spectral-cube/commit/bbe4295ebef7dfa6fe4474275a29acd6cb0cb544.patch";
+    sha256 = "1qddfm3364kc34yf6wd9nd6rxh4qc2v5pqilvz9adwb4a50z28bf";
+    })
+  ];
+
   nativeBuildInputs = [ astropy-helpers ];
   propagatedBuildInputs = [ astropy radio_beam joblib ];
-  checkInputs = [ aplpy pytest pytest-astropy ];
-
-  checkPhase = ''
-    pytest spectral_cube
-  '';
+  checkInputs = [ pytestCheckHook aplpy pytest-astropy ];
 
   meta = {
     description = "Library for reading and analyzing astrophysical spectral data cubes";

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

@@ -11,6 +11,7 @@
 , beautifulsoup4
 , drms
 , glymur
+, h5netcdf
 , hypothesis
 , matplotlib
 , numpy
@@ -50,6 +51,7 @@ buildPythonPackage rec {
     pandas
     astropy
     astropy-helpers
+    h5netcdf
     parfive
     sqlalchemy
     scikitimage