Merge remote-tracking branch 'origin/master' into staging-next

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

@@ -17,14 +17,19 @@ buildPythonPackage rec {
     sha256 = "1qg7dgl81yq0sp50pkhgvmf8az1svx20zmpkfa68ka9d0ssh1wjw";
   };
 
-  # Skip date-dependent test. See
-  # https://github.com/adobe-type-tools/afdko/pull/1232
-  # https://github.com/NixOS/nixpkgs/pull/98158#issuecomment-704321117
   patches = [
+    # Skip date-dependent test. See
+    # https://github.com/adobe-type-tools/afdko/pull/1232
+    # https://github.com/NixOS/nixpkgs/pull/98158#issuecomment-704321117
     (fetchpatch {
       url = "https://github.com/adobe-type-tools/afdko/commit/2c36ad10f9d964759f643e8ed7b0972a27aa26bd.patch";
       sha256 = "0p6a485mmzrbfldfbhgfghsypfiad3cabcw7qlw2rh993ivpnibf";
     })
+    # fix tests for fonttools 4.21.1
+    (fetchpatch {
+      url = "https://github.com/adobe-type-tools/afdko/commit/0919e7454a0a05a1b141c23bf8134c67e6b688fc.patch";
+      sha256 = "0glly85swyl1kcc0mi8i0w4bm148bb001jz1winz5drfrw3a63jp";
+    })
   ];
 
   nativeBuildInputs = [ setuptools_scm ];

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

@@ -7,14 +7,14 @@
 
 buildPythonPackage rec {
   pname = "ailment";
-  version = "9.0.5739";
+  version = "9.0.5903";
   disabled = pythonOlder "3.6";
 
   src = fetchFromGitHub {
     owner = "angr";
     repo = pname;
     rev = "v${version}";
-    sha256 = "1fjwksia6h7w7m5zhys65yr4zxvyfgp9hr1k5dn802p9kvz34bpc";
+    sha256 = "sha256-75Ul9JfMFYv3AfBlgmer6IDyfgOAS4AdXexznoxi35Y=";
   };
 
   propagatedBuildInputs = [ pyvex ];

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

@@ -7,13 +7,13 @@
 
 buildPythonPackage rec {
   pname = "archinfo";
-  version = "9.0.5739";
+  version = "9.0.5903";
 
   src = fetchFromGitHub {
     owner = "angr";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-6qjX0r2vLYgJdrKBVKedplfa1yhWv9tBvTu5BsViXBc=";
+    sha256 = "sha256-4e+ZGIt/ouZj5rsmaVxUrz8gAq4Yq2+Qx4jdOojB4Sw=";
   };
 
   checkInputs = [

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

@@ -7,14 +7,14 @@
 
 buildPythonPackage rec {
   pname = "asteval";
-  version = "0.9.22";
+  version = "0.9.23";
   disabled = pythonOlder "3.6";
 
   src = fetchFromGitHub {
     owner = "newville";
     repo = pname;
     rev = version;
-    sha256 = "sha256-93IBv6beYE/VTKJCWUbA1QTRdmQdn2kg35KBw6kmDis=";
+    sha256 = "sha256-9Zxb2EzB6nxDQHdlryFiwyNW+76VvysLUB78bXKzfv0=";
   };
 
   checkInputs = [ pytestCheckHook ];

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

@@ -5,11 +5,11 @@
 
 buildPythonPackage rec {
   pname = "asysocks";
-  version = "0.1.0";
+  version = "0.1.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "sha256-NH53FaOJx79q5IIYeiz976H9Q8Vnw13qFw4zgRc2TTw=";
+    sha256 = "sha256-7EzSALAJcx8BNHX44FeeiSPRcTe9UFHXQ4IoSKxMU8w=";
   };
 
   # Upstream hasn't release the tests yet

pkgs/development/python-modules/boto3/default.nix

@@ -13,11 +13,11 @@
 
 buildPythonPackage rec {
   pname = "boto3";
-  version = "1.17.12"; # N.B: if you change this, change botocore too
+  version = "1.17.17"; # N.B: if you change this, change botocore and awscli to a matching version
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "sha256-YvBs0eenjYqqTlJ8MnZT6abBr0FbWYNgSKkMKKJ+Xwk=";
+    sha256 = "sha256-RSPqs3/wBdUXQIO1k4LP1ia3iQwI1WzhYqS9kq99RN8=";
   };
 
   propagatedBuildInputs = [ botocore jmespath s3transfer ] ++ lib.optionals (!isPy3k) [ futures ];

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

@@ -12,11 +12,11 @@
 
 buildPythonPackage rec {
   pname = "botocore";
-  version = "1.20.12"; # N.B: if you change this, change boto3 and awscli to a matching version
+  version = "1.20.17"; # N.B: if you change this, change boto3 and awscli to a matching version
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "sha256-OakjFaF6b4vBkU27Ag9S6SnxjluZpPocXYeF+RNCftg=";
+    sha256 = "sha256-F4zjFdGf4O8z6M5nVKSC0Ano0TLFrcxFf1zx2ZqYdTs=";
   };
 
   propagatedBuildInputs = [

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

@@ -13,14 +13,14 @@
 
 buildPythonPackage rec {
   pname = "claripy";
-  version = "9.0.5739";
+  version = "9.0.5903";
   disabled = pythonOlder "3.6";
 
   src = fetchFromGitHub {
     owner = "angr";
     repo = pname;
     rev = "v${version}";
-    sha256 = "1aym01f99zwb9w8qwy8gz631ka7g6akzdld0m4ykc5ip0rq70mki";
+    sha256 = "sha256-NIKWUx1VT5TjnuqppuT6VzwNRwcBLc0xI5k3F2Nmj8A=";
   };
 
   # Use upstream z3 implementation

pkgs/development/python-modules/databricks-connect/default.nix

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "databricks-connect";
-  version = "7.3.8";
+  version = "7.3.9";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0c0f036cf30e00fdc47c983875c72d16a3073ae9be9bcf39371514280f00a82d";
+    sha256 = "f789515f3be1bd1f88043110d62859b01a9661e384a81f1768fca4e4bb49a358";
   };
 
   sourceRoot = ".";

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

@@ -0,0 +1,36 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, pytestCheckHook
+, cython
+}:
+
+buildPythonPackage rec {
+  pname = "editdistance";
+  version = "0.5.3";
+
+
+  src = fetchFromGitHub {
+    owner = "roy-ht";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "0vk8vz41p2cs7s7zbaw3cnw2jnvy5rhy525xral68dh14digpgsd";
+  };
+
+  nativeBuildInputs = [ cython ];
+
+  preBuild = ''
+    cythonize --inplace editdistance/bycython.pyx
+  '';
+
+  checkInputs = [ pytestCheckHook ];
+
+  pythonImportsCheck = [ "editdistance" ];
+
+  meta = with lib; {
+    description = "Python implementation of the edit distance (Levenshtein distance)";
+    homepage = "https://github.com/roy-ht/editdistance";
+    license = with licenses; [ mit ];
+    maintainers = with maintainers; [ fab ];
+  };
+}

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

@@ -0,0 +1,40 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, httpx
+, poetry-core
+, pythonOlder
+, yarl
+}:
+
+buildPythonPackage rec {
+  pname = "elmax";
+  version = "0.1.1";
+  format = "pyproject";
+  disabled = pythonOlder "3.7";
+
+  src = fetchFromGitHub {
+    owner = "home-assistant-ecosystem";
+    repo = "python-elmax";
+    rev = version;
+    sha256 = "sha256-vDISJ/CVOjpM+GPF2TCm3/AMFTWTM0b/+ZPCpAEvNvY=";
+  };
+
+  nativeBuildInputs = [ poetry-core ];
+
+  propagatedBuildInputs = [
+    httpx
+    yarl
+  ];
+
+  # Project has no tests
+  doCheck = false;
+  pythonImportsCheck = [ "elmax" ];
+
+  meta = with lib; {
+    description = "Python API client for the Elmax Cloud services";
+    homepage = "https://github.com/home-assistant-ecosystem/python-elmax";
+    license = with licenses; [ asl20 ];
+    maintainers = with maintainers; [ fab ];
+  };
+}

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

@@ -20,14 +20,14 @@
 
 buildPythonPackage rec {
   pname = "fonttools";
-  version = "4.20.0";
+  version = "4.21.1";
   disabled = pythonOlder "3.6";
 
   src = fetchFromGitHub {
     owner  = pname;
     repo   = pname;
     rev    = version;
-    sha256 = "0yj83vsjh23g7gkmq6svbgc898x3qgygkhvpcbpycvmpwxxqxh1v";
+    sha256 = "1x9qrg6ppqhm5214ymwvn0r34qdz8pqvyxd0sj7rkp06wa757z2i";
   };
 
   # all dependencies are optional, but
@@ -67,9 +67,10 @@ buildPythonPackage rec {
       -k 'not ttcompile_timestamp_calcs and not recalc_timestamp'
   '';
 
-  meta = {
+  meta = with lib; {
     homepage = "https://github.com/fonttools/fonttools";
     description = "A library to manipulate font files from Python";
-    license = lib.licenses.mit;
+    license = licenses.mit;
+    maintainers = [ maintainers.sternenseemann ];
   };
 }

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

@@ -18,14 +18,14 @@
 
 buildPythonPackage rec {
   pname = "httpx";
-  version = "0.16.1";
+  version = "0.17.0";
   disabled = pythonOlder "3.6";
 
   src = fetchFromGitHub {
     owner = "encode";
     repo = pname;
     rev = version;
-    sha256 = "00gmq45fckcqkj910bvd7pyqz1mvgsdvz4s0k7dzbnc5czzq1f4a";
+    sha256 = "sha256-pRdhPAxKZOVbRhOm4881Dn+IRtpX5T3oFuYdtWp3cgY=";
   };
 
   propagatedBuildInputs = [

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

@@ -1,22 +1,33 @@
-{ lib, buildPythonPackage, fetchPypi }:
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, pytestCheckHook
+, editdistance
+}:
 
 buildPythonPackage rec {
   pname = "identify";
   version = "1.6.1";
 
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "7b435803dc79a0f0ce887887a62ad360f3a9e8162ac0db9ee649d5d24085bf30";
+
+  src = fetchFromGitHub {
+    owner = "pre-commit";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "1sqhqqjp53dwm8yq4nrgggxbvzs3szbg49z5sj2ss9xzlgmimclm";
   };
 
-  pythonImportsCheck = [ "identify" ];
+  checkInputs = [
+    editdistance
+    pytestCheckHook
+  ];
 
-  # Tests not included in PyPI tarball
-  doCheck = false;
+  pythonImportsCheck = [ "identify" ];
 
   meta = with lib; {
     description = "File identification library for Python";
     homepage = "https://github.com/chriskuehl/identify";
     license = licenses.mit;
+    maintainers = with maintainers; [ fab ];
   };
 }

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

@@ -13,14 +13,14 @@
 
 buildPythonPackage rec {
   pname = "ircrobots";
-  version = "0.3.6";
+  version = "0.3.7";
   disabled = pythonOlder "3.6";
 
   src = fetchFromGitHub {
     owner = "jesopo";
     repo = pname;
     rev = "v${version}";
-    sha256 = "1c8h8b78gmnfipppr9dxp7sl6wd9lx4l3pdwykaib1f49dqwavys";
+    sha256 = "0cm4hcmprca24d979ydbzwn9mfxw16jki6ld7yykxryf0983nqc7";
   };
 
   postPatch = ''

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

@@ -8,25 +8,23 @@
 , service-identity
 , zope_interface
 , isPy3k
-, pythonAtLeast
 , python
 }:
 
 buildPythonPackage rec {
   pname = "ldaptor";
-  version = "20.1.1";
+  version = "21.2.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "778f45d68a0b5d63a892c804c05e57b464413a41d8ae52f92ae569321473ab67";
+    sha256 = "sha256-jEnrGTddSqs+W4NYYGFODLF+VrtaIOGHSAj6W+xno1g=";
   };
 
   propagatedBuildInputs = [
     twisted passlib pyopenssl pyparsing service-identity zope_interface
   ];
 
-  # https://github.com/twisted/ldaptor/pull/210
-  disabled = !isPy3k || pythonAtLeast "3.9";
+  disabled = !isPy3k;
 
   checkPhase = ''
     ${python.interpreter} -m twisted.trial ldaptor

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

@@ -34,6 +34,8 @@ buildPythonPackage rec {
     inherit pname version;
     sha256 = "14ed84b463e9b84c8ff9308a79b04bf591ae3122a376ee0f62c68a1bd917a773";
   };
+  # See https://github.com/scipy/scipy/issues/13585 and https://github.com/pandas-dev/pandas/pull/40020
+  patches = [ ./fix-tests.patch ];
 
   nativeBuildInputs = [ cython ];
   buildInputs = lib.optional stdenv.isDarwin libcxx;
@@ -59,16 +61,6 @@ buildPythonPackage rec {
   # https://github.com/NixOS/nixpkgs/issues/39687
   hardeningDisable = lib.optional stdenv.cc.isClang "strictoverflow";
 
-  # For OSX, we need to add a dependency on libcxx, which provides
-  # `complex.h` and other libraries that pandas depends on to build.
-  postPatch = lib.optionalString stdenv.isDarwin ''
-    cpp_sdk="${libcxx}/include/c++/v1";
-    echo "Adding $cpp_sdk to the setup.py common_include variable"
-    substituteInPlace setup.py \
-      --replace "['pandas/src/klib', 'pandas/src']" \
-                "['pandas/src/klib', 'pandas/src', '$cpp_sdk']"
-  '';
-
   # Parallel Cythonization is broken in Python 3.8 on Darwin. Fixed in the next
   # release. https://github.com/pandas-dev/pandas/pull/30862
   setupPyBuildFlags = lib.optionals (!(isPy38 && stdenv.isDarwin)) [

pkgs/development/python-modules/pandas/fix-tests.patch

@@ -0,0 +1,12 @@
+diff --color -ur a/pandas/tests/arrays/sparse/test_array.py b/pandas/tests/arrays/sparse/test_array.py
+--- a/pandas/tests/arrays/sparse/test_array.py	2020-12-07 12:42:08.000000000 +0100
++++ b/pandas/tests/arrays/sparse/test_array.py	2021-02-27 21:48:16.483903149 +0100
+@@ -1188,7 +1188,7 @@
+         row = [0, 3, 1, 0]
+         col = [0, 3, 1, 2]
+         data = [4, 5, 7, 9]
+-        sp_array = scipy.sparse.coo_matrix((data, (row, col)))
++        sp_array = scipy.sparse.coo_matrix((data, (row, col)), dtype="int")
+         result = pd.Series.sparse.from_coo(sp_array)
+ 
+         index = pd.MultiIndex.from_arrays([[0, 0, 1, 3], [0, 2, 1, 3]])

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

@@ -1,44 +1,45 @@
 { lib
 , buildPythonPackage
-, fetchFromGitHub
-, ujson
 , email_validator
-, typing-extensions
-, python
-, isPy3k
-, pytest
-, pytestcov
+, fetchFromGitHub
 , pytest-mock
+, pytestCheckHook
+, python-dotenv
+, pythonOlder
+, typing-extensions
+, ujson
 }:
 
 buildPythonPackage rec {
   pname = "pydantic";
-  version = "1.7.3";
-  disabled = !isPy3k;
+  version = "1.8";
+  disabled = pythonOlder "3.7";
 
   src = fetchFromGitHub {
     owner = "samuelcolvin";
     repo = pname;
     rev = "v${version}";
-    sha256 = "xihEDmly0vprmA+VdeCoGXg9PjWRPmBWAwk/9f2DLts=";
+    sha256 = "sha256-+HfnM/IrFlUyQJdiOYyaJUNenh8dLtd8CUJWSbn6hwQ=";
   };
 
   propagatedBuildInputs = [
-    ujson
     email_validator
+    python-dotenv
     typing-extensions
+    ujson
   ];
 
   checkInputs = [
-    pytest
-    pytestcov
     pytest-mock
+    pytestCheckHook
   ];
 
-  checkPhase = ''
-    pytest
+  preCheck = ''
+    export HOME=$(mktemp -d)
   '';
 
+  pythonImportsCheck = [ "pydantic" ];
+
   meta = with lib; {
     homepage = "https://github.com/samuelcolvin/pydantic";
     description = "Data validation and settings management using Python type hinting";

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

@@ -1,20 +1,33 @@
-{ lib, buildPythonPackage, fetchPypi, httpx, pytest }:
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, httpx
+, pytest
+, pytest-asyncio
+, pytestCheckHook
+}:
 
 buildPythonPackage rec {
   pname = "pytest-httpx";
-  version = "0.10.1";
+  version = "0.11.0";
 
-  src = fetchPypi {
-    inherit version;
-    pname = "pytest_httpx";
-    extension = "tar.gz";
-    sha256 = "13ld6nnsc3f7i4zl4qm1jh358z0awr6xfk05azwgngmjb7jmcz0a";
+  src = fetchFromGitHub {
+    owner = "Colin-b";
+    repo = "pytest_httpx";
+    rev = "v${version}";
+    sha256 = "08idd3y6khxjqkn46diqvkjvsl4w4pxhl6z1hspbkrj0pqwf9isi";
   };
 
-  propagatedBuildInputs = [ httpx pytest ];
+  propagatedBuildInputs = [
+    httpx
+    pytest
+  ];
+
+  checkInputs = [
+    pytest-asyncio
+    pytestCheckHook
+  ];
 
-  # not in pypi tarball
-  doCheck = false;
   pythonImportsCheck = [ "pytest_httpx" ];
 
   meta = with lib; {

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

@@ -1,29 +1,38 @@
-{ lib, buildPythonPackage, fetchPypi, isPy27
+{ lib
+, buildPythonPackage
 , click
+, fetchPypi
 , ipython
-, pytest
-, sh
-, typing
 , mock
+, pytestCheckHook
+, pythonOlder
+, sh
 }:
 
 buildPythonPackage rec {
   pname = "python-dotenv";
   version = "0.15.0";
+  disabled = pythonOlder "3.5";
 
   src = fetchPypi {
     inherit pname version;
     sha256 = "587825ed60b1711daea4832cf37524dfd404325b7db5e25ebe88c495c9f807a0";
   };
 
-  propagatedBuildInputs = [ click ] ++ lib.optionals isPy27 [ typing ];
+  propagatedBuildInputs = [ click ];
 
-  checkInputs = [ ipython mock pytest sh ];
+  checkInputs = [
+    ipython
+    mock
+    pytestCheckHook
+    sh
+  ];
 
-  # cli tests are impure
-  checkPhase = ''
-    pytest tests/ -k 'not cli'
-  '';
+  disabledTests = [
+    "cli"
+  ];
+
+  pythonImportsCheck = [ "dotenv" ];
 
   meta = with lib; {
     description = "Add .env support to your django/flask apps in development and deployments";

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

@@ -1,28 +1,32 @@
 { lib
 , buildPythonPackage
-, isPyPy
-, pkgs
+, fetchFromGitHub
+, libuv
 }:
 
 buildPythonPackage rec {
   pname = "pyuv";
-  version = "1.2.0";
-  disabled = isPyPy;  # see https://github.com/saghul/pyuv/issues/49
+  version = "1.4.0";
 
-  src = pkgs.fetchurl {
-    url = "https://github.com/saghul/pyuv/archive/${pname}-${version}.tar.gz";
-    sha256 = "19yl1l5l6dq1xr8xcv6dhx1avm350nr4v2358iggcx4ma631rycx";
+  src = fetchFromGitHub {
+    owner = "saghul";
+    repo = "pyuv";
+    rev = "pyuv-${version}";
+    sha256 = "1wiwwdylz66lfsjh6p4iv7pfhzvnhwjk332625njizfhz3gq9fwr";
   };
 
-  patches = [ ./pyuv-external-libuv.patch ];
+  setupPyBuildFlags = [ "--use-system-libuv" ];
 
-  buildInputs = [ pkgs.libuv ];
+  buildInputs = [ libuv ];
+
+  doCheck = false; # doesn't work in sandbox
+
+  pythonImportsCheck = [ "pyuv" ];
 
   meta = with lib; {
     description = "Python interface for libuv";
     homepage = "https://github.com/saghul/pyuv";
-    repositories.git = "git://github.com/saghul/pyuv.git";
     license = licenses.mit;
+    maintainers = with maintainers; [ dotlambda ];
   };
-
 }

pkgs/development/python-modules/pyuv/pyuv-external-libuv.patch

@@ -1,25 +0,0 @@
-diff --git a/setup.py b/setup.py
-index 5071c3b..4b4a176 100644
---- a/setup.py
-+++ b/setup.py
-@@ -7,7 +7,6 @@ try:
-     from setuptools import setup, Extension
- except ImportError:
-     from distutils.core import setup, Extension
--from setup_libuv import libuv_build_ext, libuv_sdist
-
-
- def get_version():
-@@ -35,11 +34,10 @@ setup(name             = "pyuv",
-           "Programming Language :: Python :: 3.3",
-           "Programming Language :: Python :: 3.4"
-       ],
--      cmdclass     = {'build_ext': libuv_build_ext,
--                      'sdist'    : libuv_sdist},
-       packages     = ['pyuv'],
-       ext_modules  = [Extension('pyuv._cpyuv',
-                                 sources = ['src/pyuv.c'],
-+                                libraries = ['uv']
-                      )]
-      )
-

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

@@ -1,4 +1,5 @@
 { lib
+, stdenv
 , archinfo
 , bitstring
 , fetchPypi
@@ -14,7 +15,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "aa12e546599be3cce18d7daef70e93555bf681bd04f6449aa5a6e2bfebb8276b";
+    sha256 = "sha256-qhLlRlmb48zhjX2u9w6TVVv2gb0E9kSapabiv+u4J2s=";
   };
 
   propagatedBuildInputs = [
@@ -35,5 +36,7 @@ buildPythonPackage rec {
     homepage = "https://github.com/angr/pyvex";
     license = with licenses; [ bsd2 gpl3Plus lgpl3Plus ];
     maintainers = with maintainers; [ fab ];
+    # ERROR: pyvex-X-py3-none-manylinux1_aarch64.whl is not a supported wheel on this platform.
+    broken = stdenv.isAarch64;
   };
 }

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

@@ -34,7 +34,7 @@ buildPythonPackage rec {
     pytestCheckHook
   ];
 
-  # environment variable used in shapely/_buildcfg.py
+  # Environment variable used in shapely/_buildcfg.py
   GEOS_LIBRARY_PATH = "${geos}/lib/libgeos_c${stdenv.hostPlatform.extensions.sharedLibrary}";
 
   patches = [
@@ -48,18 +48,12 @@ buildPythonPackage rec {
         ".travis.yml"
       ];
     })
-
     # Patch to search form GOES .so/.dylib files in a Nix-aware way
     (substituteAll {
       src = ./library-paths.patch;
       libgeos_c = GEOS_LIBRARY_PATH;
       libc = lib.optionalString (!stdenv.isDarwin) "${stdenv.cc.libc}/lib/libc${stdenv.hostPlatform.extensions.sharedLibrary}.6";
     })
-   # included in next release.
-   (fetchpatch {
-     url = "https://github.com/Toblerity/Shapely/commit/ea5b05a0c87235d3d8f09930ad47c396a76c8b0c.patch";
-     sha256 = "sha256-egdydlV+tpXosSQwQFHaXaeBhXEHAs+mn7vLUDpvybA=";
-   })
  ];
 
   preCheck = ''
@@ -70,9 +64,12 @@ buildPythonPackage rec {
     "test_collection"
   ];
 
+  pythonImportsCheck = [ "shapely" ];
+
   meta = with lib; {
     description = "Geometric objects, predicates, and operations";
-    maintainers = with maintainers; [ knedlsepp ];
     homepage = "https://pypi.python.org/pypi/Shapely/";
+    license = with licenses; [ bsd3 ];
+    maintainers = with maintainers; [ knedlsepp ];
   };
 }

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

@@ -1,6 +1,6 @@
 { lib
 , buildPythonPackage
-, fetchPypi
+, fetchFromGitHub
 , boto3
 , diskcache
 , enum34
@@ -10,7 +10,7 @@
 , requests
 , scikitimage
 , six
-, pytest
+, pytestCheckHook
 , isPy27
 , tifffile
 }:
@@ -19,9 +19,11 @@ buildPythonPackage rec {
   pname = "slicedimage";
   version = "4.1.1";
 
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "7369f1d7fa09f6c9969625c4b76a8a63d2507a94c6fc257183da1c10261703e9";
+  src = fetchFromGitHub {
+    owner = "spacetx";
+    repo = pname;
+    rev = version;
+    sha256 = "1vpg8varvfx0nj6xscdfm7m118hzsfz7qfzn28r9rsfvrhr0dlcw";
   };
 
   propagatedBuildInputs = [
@@ -36,13 +38,13 @@ buildPythonPackage rec {
   ] ++ lib.optionals isPy27 [ pathlib enum34 ];
 
   checkInputs = [
-    pytest
+    pytestCheckHook
   ];
 
-  # ignore tests which require setup
-  checkPhase = ''
-    pytest --ignore tests/io_
-  '';
+  # Ignore tests which require setup, check again if disabledTestFiles can be used
+  pytestFlagsArray = [ "--ignore tests/io_" ];
+
+  pythonImportsCheck = [ "slicedimage" ];
 
   meta = with lib; {
     description = "Library to access sliced imaging data";

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

@@ -1,12 +1,15 @@
 { buildPythonPackage
-, coveralls
 , fetchFromGitHub
-, flake8
+, fetchpatch
 , graphviz
+, ifaddr
+, isPy27
 , lib
 , mock
+, nix-update-script
 , pytestCheckHook
 , requests
+, requests-mock
 , sphinx
 , sphinx_rtd_theme
 , toml
@@ -15,7 +18,8 @@
 
 buildPythonPackage rec {
   pname = "soco";
-  version = "0.20";
+  version = "0.21.2";
+  disabled = isPy27;
 
   # N.B. We fetch from GitHub because the PyPI tarball doesn't contain the
   # required files to run the tests.
@@ -23,34 +27,46 @@ buildPythonPackage rec {
     owner = "SoCo";
     repo = "SoCo";
     rev = "v${version}";
-    sha256 = "0p87aw7wxgdjz0m0nqqcfvbn24hlbq1hh1zxdq2c0k2jcbmaj8zc";
+    sha256 = "sha256-CCgkzUkt9YqTJt9tPBLmYXW6ZuRoMDd7xahYmNXgfM0=";
   };
 
+  patches = [(fetchpatch {
+    url = "https://patch-diff.githubusercontent.com/raw/SoCo/SoCo/pull/811.patch";
+    sha256 = "sha256-GBd74c8zc25ROO411SZ9TTa+bi8yXJaaOQqY9FM1qj4=";
+  })];
+
   # N.B. These exist because:
   # 1. Upstream's pinning isn't well maintained, leaving dependency versions no
   #    longer in nixpkgs.
   # 2. There is no benefit for us to be running linting and coverage tests.
   postPatch = ''
     sed -i "/black/d" ./requirements-dev.txt
+    sed -i "/coveralls/d" ./requirements-dev.txt
+    sed -i "/flake8/d" ./requirements-dev.txt
     sed -i "/pylint/d" ./requirements-dev.txt
     sed -i "/pytest-cov/d" ./requirements-dev.txt
   '';
 
   propagatedBuildInputs = [
+    ifaddr
     requests
     toml
     xmltodict
   ];
+
   checkInputs = [
     pytestCheckHook
-    coveralls
-    flake8
     graphviz
     mock
+    requests-mock
     sphinx
     sphinx_rtd_theme
   ];
 
+  passthru.updateScript = nix-update-script {
+    attrPath = "python3Packages.${pname}";
+  };
+
   meta = with lib; {
     homepage = "http://python-soco.com/";
     description = "A CLI and library to control Sonos speakers";

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

@@ -51,6 +51,9 @@ buildPythonPackage rec {
   '';
 
   meta = with lib; {
+    # scikit-learn in pythonPackages is too new for textacy
+    # remove as soon as textacy support scikit-learn >= 0.24
+    broken = true;
     description = "Higher-level text processing, built on spaCy";
     homepage = "https://textacy.readthedocs.io/";
     license = licenses.asl20;

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

@@ -1,6 +1,7 @@
 { lib, stdenv
 , buildPythonPackage
 , fetchPypi
+, fetchpatch
 , argh
 , pathtools
 , pyyaml
@@ -11,13 +12,21 @@
 
 buildPythonPackage rec {
   pname = "watchdog";
-  version = "2.0.1";
+  version = "2.0.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0d1c763652c255e2af00d76cf7d05c7b4867e960092b2696db031f69661c0785";
+    sha256 = "sha256-Uy/t2ZPnVVRnH6o2zQTFgM7T+uCEJUp3mvu9iq8AVms=";
   };
 
+  patches = [
+    (fetchpatch {
+      # Fix test flakiness on Apple Silicon, remove after upgrade to 2.0.6.
+      url = "https://github.com/gorakhargosh/watchdog/commit/331fd7c2c819663be39bc146e78ce67553f265fa.patch";
+      sha256 = "sha256-pLkZmbPN3qRNHs53OP0HIyDxqYCPPo6yOcBLD3aO2YE=";
+    })
+  ];
+
   buildInputs = lib.optionals stdenv.isDarwin
     [ pkgs.darwin.apple_sdk.frameworks.CoreServices ];