Merge staging-next into staging

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

@@ -4,30 +4,31 @@
 , isPy27
 , ansible
 , pyyaml
-, six
-, nose
 , setuptools_scm
 , ruamel_yaml
-, pathlib2
+, rich
+, pytestCheckHook
+, pytestcov
+, pytest_xdist
+, git
 }:
 
 buildPythonPackage rec {
   pname = "ansible-lint";
-  version = "4.2.0";
+  version = "4.3.5";
   # pip is not able to import version info on raumel.yaml
   disabled = isPy27;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "eb925d8682d70563ccb80e2aca7b3edf84fb0b768cea3edc6846aac7abdc414a";
+    sha256 = "0mjn0drw3cx4pfl9qll5j7wib5r8msihs5yl8ri9fkfcbz7k1hmy";
   };
 
   format = "pyproject";
 
   nativeBuildInputs = [ setuptools_scm ];
-  propagatedBuildInputs = [ pyyaml six ansible ruamel_yaml ]
-    ++ lib.optionals isPy27 [ pathlib2 ];
-  checkInputs = [ nose ];
+  propagatedBuildInputs = [ pyyaml ansible ruamel_yaml rich ];
+  checkInputs = [ pytestCheckHook pytestcov pytest_xdist git ];
 
   postPatch = ''
     patchShebangs bin/ansible-lint
@@ -42,11 +43,11 @@ buildPythonPackage rec {
   '';
 
   checkPhase = ''
-    PATH=$out/bin:$PATH nosetests test
+    pytest -k 'not test_run_playbook_github and not test_run_single_role_path_no_trailing_slash_script'
   '';
 
   meta = with lib; {
-    homepage = "https://github.com/willthames/ansible-lint";
+    homepage = "https://github.com/ansible/ansible-lint";
     description = "Best practices checker for Ansible";
     license = licenses.mit;
     maintainers = [ maintainers.sengaya ];

pkgs/development/python-modules/aws-lambda-builders/default.nix

@@ -12,14 +12,14 @@
 
 buildPythonPackage rec {
   pname = "aws-lambda-builders";
-  version = "0.9.0";
+  version = "1.1.0";
 
   # No tests available in PyPI tarball
   src = fetchFromGitHub {
     owner = "awslabs";
     repo = "aws-lambda-builders";
     rev = "v${version}";
-    sha256 = "0cgb0hwf4xg5dmm32wwlxqy7a77jw6gpnj7v8rq5948hsy2sfrcp";
+    sha256 = "1r4939m5k1nj6l9bv972z4fkmkl0z5f5r29bq7588yk113kkqr0c";
   };
 
   # Package is not compatible with Python 3.5

pkgs/development/python-modules/aws-sam-translator/default.nix

@@ -10,11 +10,11 @@
 
 buildPythonPackage rec {
   pname = "aws-sam-translator";
-  version = "1.26.0";
+  version = "1.27.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1a3fd8e48a745967e8457b9cefdc3ad0f139ac4a25af4db9c13a9e1c19ea6910";
+    sha256 = "0m24cdiry8p74s5ysyriy6wks4ic8782sf21q4yvlwfn9hpi4n1j";
   };
 
   # Tests are not included in the PyPI package

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

@@ -4,13 +4,13 @@ let
   py = python;
 in buildPythonPackage rec {
   pname = "mysql-connector";
-  version = "8.0.21";
+  version = "8.0.22";
 
   src = fetchFromGitHub {
     owner = "mysql";
     repo = "mysql-connector-python";
     rev = version;
-    sha256 = "0ky7rn9259807gji3fhvkmdmrgyaps431l9l9y6gh66i84kw1b3l";
+    sha256 = "084q8x86ywgxgpsgdid8y9rjjys06146dqinfpmlggjswbq9kl0d";
   };
 
   propagatedBuildInputs = with py.pkgs; [ protobuf dnspython ];

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

@@ -0,0 +1,26 @@
+{ aiohttp, async-timeout, buildPythonPackage, fetchPypi, isPy3k, lib }:
+
+buildPythonPackage rec {
+  pname = "pyaftership";
+  version = "0.1.2";
+
+  disabled = !isPy3k;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "057dwzacc0lmsq00ipfbnxkq4rc2by8glmza6s8i6dzi1cc68v98";
+  };
+
+  propagatedBuildInputs = [ aiohttp async-timeout ];
+
+  # No tests
+  doCheck = false;
+  pythonImportsCheck = [ "pyaftership.tracker" ];
+
+  meta = with lib; {
+    description = "Python wrapper package for the AfterShip API";
+    homepage = "https://github.com/ludeeus/pyaftership";
+    license = licenses.mit;
+    maintainers = with maintainers; [ jamiemagee ];
+  };
+}

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

@@ -18,12 +18,11 @@
 
 buildPythonPackage rec {
   pname = "pyatv";
-  version = "v0.7.4";
-
+  version = "0.7.4";
   src = fetchFromGitHub {
     owner = "postlund";
     repo = pname;
-    rev = version;
+    rev = "v${version}";
     sha256 = "17gsamn4aibsx4w50r9dwr5kr9anc7dd0f0dvmdl717rkgh13zyi";
   };
 
@@ -37,7 +36,6 @@ buildPythonPackage rec {
     cryptography
     netifaces
     zeroconf
-    pytestCheckHook
   ];
 
   checkInputs = [
@@ -45,6 +43,7 @@ buildPythonPackage rec {
     pytest
     pytest-aiohttp
     pytest-asyncio
+    pytestCheckHook
   ];
 
   meta = with stdenv.lib; {

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

@@ -6,6 +6,7 @@
 , curl
 , cython
 , htslib
+, libdeflate
 , lzma
 , pytest
 , samtools
@@ -27,22 +28,72 @@ buildPythonPackage rec {
   };
 
   nativeBuildInputs = [ samtools ];
-  buildInputs = [ bzip2 curl cython lzma zlib ];
+  buildInputs = [
+    bzip2
+    curl
+    cython
+    libdeflate
+    lzma
+    zlib
+  ];
 
-  checkInputs = [ pytest bcftools htslib ];
-  checkPhase = "py.test";
+  # Use nixpkgs' htslib instead of the bundled one
+  # See https://pysam.readthedocs.io/en/latest/installation.html#external
+  # NOTE that htslib should be version compatible with pysam
+  preBuild = ''
+    export HTSLIB_MODE=shared
+    export HTSLIB_LIBRARY_DIR=${htslib}/lib
+    export HTSLIB_INCLUDE_DIR=${htslib}/include
+  '';
 
-  # tests require samtools<=1.9
-  doCheck = false;
-  preCheck = ''
+  checkInputs = [
+    pytest
+    bcftools
+    htslib
+  ];
+
+  # See https://github.com/NixOS/nixpkgs/pull/100823 for why we aren't using
+  # disabledTests and pytestFlagsArray through pytestCheckHook
+  checkPhase = ''
+    # Needed to avoid /homeless-shelter error
     export HOME=$(mktemp -d)
+
+    # To avoid API incompatibilities, these should ideally show the same version
+    echo "> samtools --version"
+    samtools --version
+    echo "> htsfile --version"
+    htsfile --version
+    echo "> bcftools --version"
+    bcftools --version
+
+    # Create auxiliary test data
     make -C tests/pysam_data
     make -C tests/cbcf_data
+
+    # Delete pysam folder in current directory to avoid importing it during testing
+    rm -rf pysam
+
+    # Deselect tests that are known to fail due to upstream issues
+    # See https://github.com/pysam-developers/pysam/issues/961
+    py.test \
+      --deselect tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works \
+      --deselect tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected \
+      --deselect tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works \
+      --deselect tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected \
+      --deselect tests/AlignmentFile_test.py::TestIO::testBAM2SAM \
+      --deselect tests/AlignmentFile_test.py::TestIO::testSAM2BAM \
+      --deselect tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile \
+      --deselect tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile \
+      --deselect tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader \
+      --deselect tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader \
+      --deselect tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing \
+      tests/
   '';
 
   pythonImportsCheck = [
     "pysam"
     "pysam.bcftools"
+    "pysam.libchtslib"
     "pysam.libcutils"
     "pysam.libcvcf"
   ];

pkgs/development/python-modules/python-markdown-math/default.nix

@@ -2,11 +2,13 @@
 , buildPythonPackage
 , fetchPypi
 , markdown
+, isPy27
 }:
 
 buildPythonPackage rec {
   pname = "python-markdown-math";
   version = "0.7";
+  disabled = isPy27;
 
   src = fetchPypi {
     inherit pname version;