Merge master into haskell-updates

31 files changed, 354 insertions, 114 deletions

diff --git a/pkgs/development/python-modules/Cython/default.nix b/pkgs/development/python-modules/Cython/default.nix
index c09f1586fd6..dcede9506e3 100644
--- a/pkgs/development/python-modules/Cython/default.nix
+++ b/pkgs/development/python-modules/Cython/default.nix
@@ -37,9 +37,9 @@ in buildPythonPackage rec {
     pkg-config
   ];
   checkInputs = [
-    numpy ncurses
+    gdb numpy ncurses
   ];
-  buildInputs = [ glibcLocales gdb ];
+  buildInputs = [ glibcLocales ];
   LC_ALL = "en_US.UTF-8";
 
   patches = [
diff --git a/pkgs/development/python-modules/agate-sql/default.nix b/pkgs/development/python-modules/agate-sql/default.nix
index 890f44b4ad3..68f166b3c7c 100644
--- a/pkgs/development/python-modules/agate-sql/default.nix
+++ b/pkgs/development/python-modules/agate-sql/default.nix
@@ -22,6 +22,10 @@ buildPythonPackage rec {
 
   propagatedBuildInputs = [ agate sqlalchemy ];
 
+  # crate is broken in nixpkgs, with SQLAlchemy > 1.3
+  # Skip tests for now as they rely on it.
+  doCheck = false;
+
   checkInputs = [ crate nose geojson ];
 
   checkPhase = ''
diff --git a/pkgs/development/python-modules/ansible/base.nix b/pkgs/development/python-modules/ansible/base.nix
index 0a5cc01d929..0c88c378516 100644
--- a/pkgs/development/python-modules/ansible/base.nix
+++ b/pkgs/development/python-modules/ansible/base.nix
@@ -28,11 +28,11 @@ let
 in
 buildPythonPackage rec {
   pname = "ansible-base";
-  version = "2.10.11";
+  version = "2.10.12";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0jr3cxqiami9k07g2kmvfp54iafbcnd1d66l8fdnaqka5bc19wdw";
+    sha256 = "sha256-qWVW4tI5+Sg+FWVNQMGqhmgqTntD9Qtf8CK8jkK2mHg=";
   };
 
   # ansible_connection is already wrapped, so don't pass it through
diff --git a/pkgs/development/python-modules/ansible/core.nix b/pkgs/development/python-modules/ansible/core.nix
index 4dd606c9adb..8584ba7166a 100644
--- a/pkgs/development/python-modules/ansible/core.nix
+++ b/pkgs/development/python-modules/ansible/core.nix
@@ -23,17 +23,17 @@
 
 let
   ansible-collections = callPackage ./collections.nix {
-    version = "4.1.0";
-    sha256 = "0rrivq1g0vizah8zmf012lzig2xxfk5x1371k16s3nn4zfkwqqgm";
+    version = "4.2.0";
+    sha256 = "1l30j97q24klylchvbskdmp1xllswn9xskjvg4l0ra6pzfgq2zbk";
   };
 in
 buildPythonPackage rec {
   pname = "ansible-core";
-  version = "2.11.2";
+  version = "2.11.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1syadgzn5ww5bhq9s2py4h1hkh11h7aac5b37zi8rw2xfvdc7r2s";
+    sha256 = "sha256-DO0bT2cZftsntQk0yV1MtkTG1jXXLH+CbEQl3+RTdnQ=";
   };
 
   # ansible_connection is already wrapped, so don't pass it through
diff --git a/pkgs/development/python-modules/ansible/legacy.nix b/pkgs/development/python-modules/ansible/legacy.nix
index 12eed6bdb29..95b127a0db3 100644
--- a/pkgs/development/python-modules/ansible/legacy.nix
+++ b/pkgs/development/python-modules/ansible/legacy.nix
@@ -1,5 +1,5 @@
 { lib
-, fetchFromGitHub
+, fetchPypi
 , buildPythonPackage
 , pycrypto
 , paramiko
@@ -18,13 +18,11 @@
 
 buildPythonPackage rec {
   pname = "ansible";
-  version = "2.9.23";
+  version = "2.9.24";
 
-  src = fetchFromGitHub {
-    owner = "ansible";
-    repo = "ansible";
-    rev = "v${version}";
-    sha256 = "0mikykpzyqpmaiczz53f71mcyc4qvahi9ckn7wgfx7sw7s2z3skk";
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "sha256-DC9Tt75z3cNCPZZY/NGQeYl9Wx/FM8StVQ21ixea64o=";
   };
 
   prePatch = ''
diff --git a/pkgs/development/python-modules/btrees/default.nix b/pkgs/development/python-modules/btrees/default.nix
index cebe542de26..49acee691cf 100644
--- a/pkgs/development/python-modules/btrees/default.nix
+++ b/pkgs/development/python-modules/btrees/default.nix
@@ -5,24 +5,45 @@
 , zope_interface
 , transaction
 , zope_testrunner
+, python
 }:
 
 buildPythonPackage rec {
   pname = "BTrees";
   version = "4.9.2";
 
-  buildInputs = [ transaction ];
-  propagatedBuildInputs = [ persistent zope_interface ];
-  checkInputs = [ zope_testrunner ];
-
   src = fetchPypi {
     inherit pname version;
     sha256 = "d33323655924192c4ac998d9ee3002e787915d19c1e17a6baf47c9a63d9556e3";
   };
 
+  propagatedBuildInputs = [
+    persistent
+    zope_interface
+  ];
+
+  checkInputs = [
+    transaction
+    zope_testrunner
+  ];
+
+  checkPhase = ''
+    runHook preCheck
+    ${python.interpreter} -m zope.testrunner --test-path=src --auto-color --auto-progress
+    runHook postCheck
+  '';
+
+  pythonImportsCheck = [
+    "BTrees.OOBTree"
+    "BTrees.IOBTree"
+    "BTrees.IIBTree"
+    "BTrees.IFBTree"
+  ];
+
   meta = with lib; {
     description = "Scalable persistent components";
     homepage = "http://packages.python.org/BTrees";
     license = licenses.zpl21;
+    maintainers = with maintainers; [ ];
   };
 }
diff --git a/pkgs/development/python-modules/crate/default.nix b/pkgs/development/python-modules/crate/default.nix
index 07b9652e775..c4a698c5250 100644
--- a/pkgs/development/python-modules/crate/default.nix
+++ b/pkgs/development/python-modules/crate/default.nix
@@ -39,5 +39,11 @@ buildPythonPackage rec {
     description = "A Python client library for CrateDB";
     license = licenses.asl20;
     maintainers = with maintainers; [ doronbehar ];
+    # 2021-07-12 (@layus): Please unbreak when an update fixes compatibility
+    # with the version of SQLAlchemy in nixpkgs
+    # And also re-enable tests in pythonPackages.agate-sql.
+    # The version string below is intentionally split, so nixpkgs-update does
+    # not change it. That would make this warning pretty useless.
+    broken = assert version == "0.2"+"6.0"; true;
   };
 }
diff --git a/pkgs/development/python-modules/faker/default.nix b/pkgs/development/python-modules/faker/default.nix
index 196c7e47b39..ae47989141e 100644
--- a/pkgs/development/python-modules/faker/default.nix
+++ b/pkgs/development/python-modules/faker/default.nix
@@ -6,16 +6,18 @@
 , freezegun
 , pytestCheckHook
 , ukpostcodeparser
+, pillow
 , validators
 }:
 
 buildPythonPackage rec {
-  pname = "Faker";
-  version = "6.6.3";
+  pname = "faker";
+  version = "8.8.2";
 
   src = fetchPypi {
-    inherit pname version;
-    sha256 = "c2852cadc99a4ebdbf06934e4c15e30f2307d414ead21d15605759602645f152";
+    pname = "Faker";
+    inherit version;
+    sha256 = "sha256-IlNMOqbS7584QDojTcm3G1y4ePt2XHKZS+Xce06vCGU=";
   };
 
   propagatedBuildInputs = [
@@ -25,6 +27,7 @@ buildPythonPackage rec {
 
   checkInputs = [
     freezegun
+    pillow
     pytestCheckHook
     ukpostcodeparser
     validators
diff --git a/pkgs/development/python-modules/flake8-future-import/default.nix b/pkgs/development/python-modules/flake8-future-import/default.nix
index 661b7c71c33..41e9680937d 100644
--- a/pkgs/development/python-modules/flake8-future-import/default.nix
+++ b/pkgs/development/python-modules/flake8-future-import/default.nix
@@ -1,4 +1,12 @@
-{ lib, isPy27, isPy38, fetchFromGitHub, buildPythonPackage, pythonOlder, fetchpatch, flake8, importlib-metadata, six }:
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, pythonAtLeast
+, isPy27
+, flake8
+, six
+, python
+}:
 
 buildPythonPackage rec {
   pname = "flake8-future-import";
@@ -12,16 +20,22 @@ buildPythonPackage rec {
     sha256 = "00q8n15xdnvqj454arn7xxksyrzh0dw996kjyy7g9rdk0rf8x82z";
   };
 
-  propagatedBuildInputs = [ flake8 six ]
-    ++ lib.optionals (pythonOlder "3.8") [
-      importlib-metadata
-    ];
+  patches = lib.optionals (pythonAtLeast "3.8") [
+    ./fix-annotations-version.patch
+  ] ++ lib.optionals isPy27 [
+    # 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.
+    ./skip-test.patch
+  ];
 
-  # 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 isPy38 [ ./fix-annotations-version.patch ]
-    ++ lib.optionals isPy27 [ ./skip-test.patch ];
+  propagatedBuildInputs = [ flake8 ];
+
+  checkInputs = [ six ];
+
+  checkPhase = ''
+    ${python.interpreter} -m test_flake8_future_import
+  '';
 
   meta = with lib; {
     description = "A flake8 extension to check for the imported __future__ modules to make it easier to have a consistent code base";
diff --git a/pkgs/development/python-modules/fontmath/default.nix b/pkgs/development/python-modules/fontmath/default.nix
index 7a23abdd037..a6982037c1e 100644
--- a/pkgs/development/python-modules/fontmath/default.nix
+++ b/pkgs/development/python-modules/fontmath/default.nix
@@ -1,18 +1,21 @@
-{ lib, buildPythonPackage, fetchPypi
-, fonttools
+{ lib, buildPythonPackage, fetchPypi, isPy27
+, fonttools, setuptools-scm
 , pytest, pytestrunner
 }:
 
 buildPythonPackage rec {
   pname = "fontMath";
-  version = "0.6.0";
+  version = "0.8.1";
+  disabled = isPy27;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "09xdqdjyjlx5k9ymi36d7hkgvn55zzjzd65l2yqidkfazlmh14ss";
+    sha256 = "0m2z2wwbxwljfcrg8hx4xq538adzcjpc352yqbfw0czbgs5ixmrr";
     extension = "zip";
   };
 
+  nativeBuildInputs = [ setuptools-scm ];
+
   propagatedBuildInputs = [ fonttools ];
   checkInputs = [ pytest pytestrunner ];
 
diff --git a/pkgs/development/python-modules/google-i18n-address/default.nix b/pkgs/development/python-modules/google-i18n-address/default.nix
index 53ce654e41b..e2724ac123c 100644
--- a/pkgs/development/python-modules/google-i18n-address/default.nix
+++ b/pkgs/development/python-modules/google-i18n-address/default.nix
@@ -1,18 +1,26 @@
-{ buildPythonPackage, fetchPypi, pythonAtLeast, lib, requests, pytestCheckHook, mock }:
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, requests
+, pytestCheckHook
+}:
 
 buildPythonPackage rec {
   pname = "google-i18n-address";
-  version = "2.4.0";
-  disabled = pythonAtLeast "3.9";
+  version = "2.5.0";
 
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "8454a58f254a29988b8d1ca9ab663fd28a1f392a3d29b844d8824807db6333d7";
+  src = fetchFromGitHub {
+    owner = "mirumee";
+    repo = "google-i18n-address";
+    rev = version;
+    sha256 = "0fn5sph6fq68zrjssgvnnvrkavs8arshjwgxng5dr5fsn6qii3mq";
   };
 
   propagatedBuildInputs = [ requests ];
 
-  checkInputs = [ pytestCheckHook mock ];
+  checkInputs = [ pytestCheckHook ];
+
+  pythonImportsCheck = [ "i18naddress" ];
 
   meta = with lib; {
     description = "Google's i18n address data packaged for Python";
diff --git a/pkgs/development/python-modules/gprof2dot/default.nix b/pkgs/development/python-modules/gprof2dot/default.nix
index 28609919098..3170d199cf5 100644
--- a/pkgs/development/python-modules/gprof2dot/default.nix
+++ b/pkgs/development/python-modules/gprof2dot/default.nix
@@ -1,12 +1,13 @@
 { lib, fetchFromGitHub, buildPythonApplication, python, graphviz }:
 
-buildPythonApplication {
-  name = "gprof2dot-2019-11-30";
+buildPythonApplication rec {
+  pname = "gprof2dot";
+  version = "2019.11.30";
 
   src = fetchFromGitHub {
     owner = "jrfonseca";
     repo = "gprof2dot";
-    rev = "2019.11.30";
+    rev = version;
     sha256 = "1nw4cfwimd0djarw4wc756q095xir78js8flmycg6g7sl3l6p27s";
   };
 
diff --git a/pkgs/development/python-modules/graphene/default.nix b/pkgs/development/python-modules/graphene/default.nix
index c2776e20e2b..30947c14303 100644
--- a/pkgs/development/python-modules/graphene/default.nix
+++ b/pkgs/development/python-modules/graphene/default.nix
@@ -50,7 +50,8 @@ buildPythonPackage rec {
   pytestFlagsArray = [ "--benchmark-disable" ];
 
   disabledTests = [
-    # TypeError: Failed: DID NOT RAISE <class...
+    # Expects different Exeception classes, but receives none of them
+    # https://github.com/graphql-python/graphene/issues/1346
     "test_unexpected_error"
   ];
 
diff --git a/pkgs/development/python-modules/greenlet/default.nix b/pkgs/development/python-modules/greenlet/default.nix
index 8762d62e59b..4d829f3d647 100644
--- a/pkgs/development/python-modules/greenlet/default.nix
+++ b/pkgs/development/python-modules/greenlet/default.nix
@@ -3,6 +3,7 @@
 , fetchPypi
 , six
 , isPyPy
+, python
 }:
 
 
@@ -16,11 +17,18 @@ buildPythonPackage rec {
     sha256 = "c87df8ae3f01ffb4483c796fe1b15232ce2b219f0b18126948616224d3f658ee";
   };
 
-  propagatedBuildInputs = [ six ];
+  checkPhase = ''
+    runHook preCheck
+    ${python.interpreter} -m unittest discover -v greenlet.tests
+    runHook postCheck
+  '';
 
-  meta = {
-    homepage = "https://pypi.python.org/pypi/greenlet";
+  meta = with lib; {
+    homepage = "https://github.com/python-greenlet/greenlet";
     description = "Module for lightweight in-process concurrent programming";
-    license = lib.licenses.lgpl2;
+    license = with licenses; [
+      psfl  # src/greenlet/slp_platformselect.h & files in src/greenlet/platform/ directory
+      mit
+    ];
   };
 }
diff --git a/pkgs/development/python-modules/httplib2/default.nix b/pkgs/development/python-modules/httplib2/default.nix
index 40bfe4d3e88..756d3e4ddcc 100644
--- a/pkgs/development/python-modules/httplib2/default.nix
+++ b/pkgs/development/python-modules/httplib2/default.nix
@@ -2,6 +2,7 @@
 , stdenv
 , buildPythonPackage
 , fetchFromGitHub
+, fetchpatch
 , isPy27
 , mock
 , pyparsing
@@ -24,6 +25,14 @@ buildPythonPackage rec {
     sha256 = "sha256-e0Mq9AVJEWQ9GEtYFXk2fMIs7GtAUsyJN6XheqAnD3I=";
   };
 
+  patches = [
+    # fix test_inject_space
+    (fetchpatch {
+      url = "https://github.com/httplib2/httplib2/commit/08d6993b69256fbc6c0b1c615c24910803c4d610.patch";
+      sha256 = "0kbd1skn58m20kfkh4qzd66g9bvj31xlkbhsg435dkk4qz6l3yn3";
+    })
+  ];
+
   postPatch = ''
     sed -i "/--cov/d" setup.cfg
   '';
diff --git a/pkgs/development/python-modules/loguru/default.nix b/pkgs/development/python-modules/loguru/default.nix
index 8146f8b183e..3134d956af7 100644
--- a/pkgs/development/python-modules/loguru/default.nix
+++ b/pkgs/development/python-modules/loguru/default.nix
@@ -6,15 +6,14 @@
 , isPy27
 , colorama
 , pytestCheckHook
-, pythonAtLeast
 }:
 
 buildPythonPackage rec {
   pname = "loguru";
   version = "0.5.3";
 
-  # python3.9 compatibility should be in the next release after 0.5.3
-  disabled = isPy27 || pythonAtLeast "3.9";
+  disabled = isPy27;
+
   src = fetchPypi {
     inherit pname version;
     sha256 = "b28e72ac7a98be3d28ad28570299a393dfcd32e5e3f6a353dec94675767b6319";
@@ -26,6 +25,11 @@ buildPythonPackage rec {
       url = "https://github.com/Delgan/loguru/commit/31cf758ee9d22dbfa125f38153782fe20ac9dce5.patch";
       sha256 = "1lzbs8akg1s7s6xjl3samf4c4bpssqvwg5fn3mwlm4ysr7jd5y67";
     })
+    # fix tests with Python 3.9
+    (fetchpatch {
+      url = "https://github.com/Delgan/loguru/commit/19f518c5f1f355703ffc4ee62f0e1e397605863e.patch";
+      sha256 = "0yn6smik58wdffr4svqsy2n212fwdlcfcwpgqhl9hq2zlivmsdc6";
+    })
   ];
 
   checkInputs = [ pytestCheckHook colorama ];
diff --git a/pkgs/development/python-modules/markupsafe/default.nix b/pkgs/development/python-modules/markupsafe/default.nix
index d48359af0fc..12845da7e37 100644
--- a/pkgs/development/python-modules/markupsafe/default.nix
+++ b/pkgs/development/python-modules/markupsafe/default.nix
@@ -6,12 +6,13 @@
 }:
 
 buildPythonPackage rec {
-  pname = "MarkupSafe";
+  pname = "markupsafe";
   version = "2.0.1";
   disabled = pythonOlder "3.6";
 
   src = fetchPypi {
-    inherit pname version;
+    pname = "MarkupSafe";
+    inherit version;
     sha256 = "02k2ynmqvvd0z0gakkf8s4idyb606r7zgga41jrkhqmigy06fk2r";
   };
 
@@ -19,11 +20,12 @@ buildPythonPackage rec {
     pytestCheckHook
   ];
 
+  pythonImportsCheck = [ "markupsafe" ];
+
   meta = with lib; {
     description = "Implements a XML/HTML/XHTML Markup safe string";
-    homepage = "http://dev.pocoo.org";
+    homepage = "https://palletsprojects.com/p/markupsafe/";
     license = licenses.bsd3;
     maintainers = with maintainers; [ domenkozar ];
   };
-
 }
diff --git a/pkgs/development/python-modules/numba/default.nix b/pkgs/development/python-modules/numba/default.nix
index e4af2ddadb5..74f7d4003dc 100644
--- a/pkgs/development/python-modules/numba/default.nix
+++ b/pkgs/development/python-modules/numba/default.nix
@@ -14,8 +14,7 @@
 buildPythonPackage rec {
   version = "0.53.1";
   pname = "numba";
-  # uses f-strings, python 3.9 is not yet supported
-  disabled = pythonOlder "3.6" || pythonAtLeast "3.9";
+  disabled = pythonOlder "3.6" || pythonAtLeast "3.10";
 
   src = fetchPypi {
     inherit pname version;
diff --git a/pkgs/development/python-modules/parameterizedtestcase/default.nix b/pkgs/development/python-modules/parameterizedtestcase/default.nix
new file mode 100644
index 00000000000..20e662cd66d
--- /dev/null
+++ b/pkgs/development/python-modules/parameterizedtestcase/default.nix
@@ -0,0 +1,31 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, python
+, isPy27
+}:
+
+buildPythonPackage rec {
+  pname = "parameterizedtestcase";
+  version = "0.1.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "4ccc1d15d7e7ef153619a6a9cd45b170268cf82c67fdd336794c75139aae127e";
+  };
+
+  checkPhase = ''
+    runHook preCheck
+    ${python.interpreter} -m parameterizedtestcase.tests
+    runHook postCheck
+  '';
+
+  doCheck = isPy27;
+
+  meta = with lib; {
+    description = "Parameterized tests for Python's unittest module";
+    homepage = "https://github.com/msabramo/python_unittest_parameterized_test_case";
+    license = licenses.mit;
+    maintainers = with maintainers; [ dotlambda ];
+  };
+}
diff --git a/pkgs/development/python-modules/phonopy/default.nix b/pkgs/development/python-modules/phonopy/default.nix
index 2ca29ffd8e3..af728d414c1 100644
--- a/pkgs/development/python-modules/phonopy/default.nix
+++ b/pkgs/development/python-modules/phonopy/default.nix
@@ -5,6 +5,7 @@
 , pyyaml
 , matplotlib
 , h5py
+, scipy
 , spglib
 , pytestCheckHook
 }:
@@ -18,9 +19,18 @@ buildPythonPackage rec {
     sha256 = "58485042ab7d88fc8b83744d18b2aefd677adb071c8a717ac3710458192743d7";
   };
 
-  propagatedBuildInputs = [ numpy pyyaml matplotlib h5py spglib ];
+  propagatedBuildInputs = [
+    h5py
+    matplotlib
+    numpy
+    pyyaml
+    scipy
+    spglib
+  ];
 
-  checkInputs = [ pytestCheckHook ];
+  checkInputs = [
+    pytestCheckHook
+  ];
 
   # prevent pytest from importing local directory
   preCheck = ''
diff --git a/pkgs/development/python-modules/pillow/default.nix b/pkgs/development/python-modules/pillow/default.nix
index 0f747a8d73e..af6c3d80dea 100644
--- a/pkgs/development/python-modules/pillow/default.nix
+++ b/pkgs/development/python-modules/pillow/default.nix
@@ -1,17 +1,17 @@
 { lib, stdenv, buildPythonPackage, fetchPypi, isPyPy, isPy3k
-, olefile, freetype, libjpeg, zlib, libtiff, libwebp, tcl, lcms2, tk, libX11
+, defusedxml, olefile, freetype, libjpeg, zlib, libtiff, libwebp, tcl, lcms2, tk, libX11
 , libxcb, openjpeg, libimagequant, pyroma, numpy, pytestCheckHook
 }@args:
 
 import ./generic.nix (rec {
   pname = "Pillow";
-  version = "8.2.0";
+  version = "8.3.1";
 
   disabled = !isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1qf3bz1sfz58ff6hclg8phgqyy210x3aqdk5yzjr8m5vsw8ap1x7";
+    sha256 = "2cac53839bfc5cece8fdbe7f084d5e3ee61e1303cccc86511d351adcb9e2c792";
   };
 
   meta = with lib; {
diff --git a/pkgs/development/python-modules/pillow/generic.nix b/pkgs/development/python-modules/pillow/generic.nix
index 64ae9189559..3e33f1a8aa0 100644
--- a/pkgs/development/python-modules/pillow/generic.nix
+++ b/pkgs/development/python-modules/pillow/generic.nix
@@ -31,7 +31,8 @@ buildPythonPackage rec {
     "test_custom_metadata"
   ];
 
-  propagatedBuildInputs = [ olefile ];
+  propagatedBuildInputs = [ olefile ]
+    ++ lib.optionals (lib.versionAtLeast version "8.2.0") [ defusedxml ];
 
   checkInputs = [ pytestCheckHook pyroma numpy ];
 
diff --git a/pkgs/development/python-modules/pylsp-mypy/default.nix b/pkgs/development/python-modules/pylsp-mypy/default.nix
new file mode 100644
index 00000000000..a7d13bb32a2
--- /dev/null
+++ b/pkgs/development/python-modules/pylsp-mypy/default.nix
@@ -0,0 +1,33 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, mock
+, mypy
+, pytestCheckHook
+, python-lsp-server
+, pythonOlder
+}:
+
+buildPythonPackage rec {
+  pname = "pylsp-mypy";
+  version = "0.5.1";
+  disabled = pythonOlder "3.6";
+
+  src = fetchFromGitHub {
+    owner = "Richardk2n";
+    repo = "pylsp-mypy";
+    rev = version;
+    sha256 = "1d119csj1k5m9j0f7wdvpvnd02h548css6ybxqah92nk2v0rjscr";
+  };
+
+  checkInputs = [ pytestCheckHook mock ];
+
+  propagatedBuildInputs = [ mypy python-lsp-server ];
+
+  meta = with lib; {
+    homepage = "https://github.com/Richardk2n/pylsp-mypy";
+    description = "Mypy plugin for the Python LSP Server";
+    license = licenses.mit;
+    maintainers = with maintainers; [ cpcloud ];
+  };
+}
diff --git a/pkgs/development/python-modules/pyqtgraph/default.nix b/pkgs/development/python-modules/pyqtgraph/default.nix
index fd2b9d46185..54a136d5dcd 100644
--- a/pkgs/development/python-modules/pyqtgraph/default.nix
+++ b/pkgs/development/python-modules/pyqtgraph/default.nix
@@ -1,26 +1,57 @@
 { lib
 , buildPythonPackage
-, fetchPypi
+, fetchFromGitHub
+, scipy
 , numpy
-, pyopengl
 , pyqt5
-, scipy
+, pyopengl
+, qt5
+, python
+, pytestCheckHook
+, freefont_ttf
+, makeFontsConf
+, fetchpatch
 }:
 
+let
+  fontsConf = makeFontsConf {
+    fontDirectories = [ freefont_ttf ];
+  };
+in
 buildPythonPackage rec {
   pname = "pyqtgraph";
-  version = "0.12.1";
+  version = "0.12.2";
 
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "d2ef3b5289184fb48dfe5f44ccb58d9d64ffb5452fc524a2bd7a640a36b3874d";
+  src = fetchFromGitHub {
+    owner = "pyqtgraph";
+    repo = "pyqtgraph";
+    rev = "pyqtgraph-${version}";
+    sha256 = "093kkxwj75nb508vz7px4x7lxrwpaff10pl15m4h74hjwyvbsg3d";
   };
 
-  propagatedBuildInputs = [ numpy pyopengl pyqt5 scipy ];
+  # TODO: remove when updating to 0.12.3
+  patches = [
+    (fetchpatch {
+      url = "https://github.com/pyqtgraph/pyqtgraph/commit/2de5cd78da92b48e48255be2f41ae332cf8bb675.patch";
+      sha256 = "1hy86psqyl6ipvbg23zvackkd6f7ajs6qll0mbs0x2zmrj92hk00";
+    })
+  ];
+
+  propagatedBuildInputs = [
+    numpy
+    pyqt5
+    scipy
+    pyopengl
+  ];
 
-  doCheck = false;  # tries to create windows (QApps) on collection, which fails (probably due to no display)
+  checkInputs = [ pytestCheckHook ];
 
-  pythonImportsCheck = [ "pyqtgraph" ];
+  preCheck = ''
+    export QT_PLUGIN_PATH="${qt5.qtbase.bin}/${qt5.qtbase.qtPluginPrefix}"
+    export QT_QPA_PLATFORM=offscreen
+    export DYLD_FRAMEWORK_PATH=/System/Library/Frameworks
+    export FONTCONFIG_FILE=${fontsConf}
+  '';
 
   meta = with lib; {
     description = "Scientific Graphics and GUI Library for Python";
diff --git a/pkgs/development/python-modules/pyyaml/default.nix b/pkgs/development/python-modules/pyyaml/default.nix
index 93cfad78d50..10073176aeb 100644
--- a/pkgs/development/python-modules/pyyaml/default.nix
+++ b/pkgs/development/python-modules/pyyaml/default.nix
@@ -1,18 +1,37 @@
-{ lib, buildPythonPackage, fetchPypi, cython, libyaml, buildPackages }:
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, cython
+, libyaml
+, isPy27
+, python
+}:
 
 buildPythonPackage rec {
   pname = "PyYAML";
-  version = "5.4.1";
+  version = "5.4.1.1";
 
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "607774cbba28732bfa802b54baa7484215f530991055bb562efbed5b2f20a45e";
+  src = fetchFromGitHub {
+    owner = "yaml";
+    repo = "pyyaml";
+    rev = version;
+    sha256 = "1v386gzdvsjg0mgix6v03rd0cgs9dl81qvn3m547849jm8r41dx8";
   };
 
-  nativeBuildInputs = [ cython buildPackages.stdenv.cc ];
+  nativeBuildInputs = [ cython ];
 
   buildInputs = [ libyaml ];
 
+  checkPhase = let
+    testdir = if isPy27 then "tests/lib" else "tests/lib3";
+  in ''
+    runHook preCheck
+    PYTHONPATH="${testdir}:$PYTHONPATH" ${python.interpreter} -m test_all
+    runHook postCheck
+  '';
+
+  pythonImportsCheck = [ "yaml" ];
+
   meta = with lib; {
     description = "The next generation YAML parser and emitter for Python";
     homepage = "https://github.com/yaml/pyyaml";
diff --git a/pkgs/development/python-modules/smart-open/default.nix b/pkgs/development/python-modules/smart-open/default.nix
index 051d6c97397..d4ad901fb9b 100644
--- a/pkgs/development/python-modules/smart-open/default.nix
+++ b/pkgs/development/python-modules/smart-open/default.nix
@@ -1,39 +1,75 @@
 { lib
 , buildPythonPackage
-, fetchPypi
 , pythonOlder
-, boto
+, fetchFromGitHub
+, azure-common
+, azure-core
+, azure-storage-blob
 , boto3
-, bz2file
-, mock
-, moto
+, google-cloud-storage
 , requests
-, responses
+, moto
+, parameterizedtestcase
+, pytestCheckHook
 }:
 
 buildPythonPackage rec {
   pname = "smart-open";
-  version = "4.2.0";
+  version = "5.1.0";
+
   disabled = pythonOlder "3.5";
 
-  src = fetchPypi {
-    pname = "smart_open";
-    inherit version;
-    sha256 = "d9f5a0f173ccb9bbae528db5a3804f57145815774f77ef755b9b0f3b4b2a9dcb";
+  src = fetchFromGitHub {
+    owner = "RaRe-Technologies";
+    repo = "smart_open";
+    rev = "v${version}";
+    sha256 = "0gv3vxpglnhh6d80wsqigxi7psn6s7ylz20kx5ahblcx5rqyhjmi";
   };
 
-  # moto>=1.0.0 is backwards-incompatible and some tests fail with it,
-  # so disable tests for now
-  doCheck = false;
+  propagatedBuildInputs = [
+    azure-common
+    azure-core
+    azure-storage-blob
+    boto3
+    google-cloud-storage
+    requests
+  ];
+
+  checkInputs = [
+    moto
+    parameterizedtestcase
+    pytestCheckHook
+  ];
+
+  pytestFlagsArray = [ "smart_open" ];
+
+  disabledTestPaths = [
+    "smart_open/tests/test_http.py"
+    "smart_open/tests/test_s3.py"
+    "smart_open/tests/test_s3_version.py"
+    "smart_open/tests/test_sanity.py"
+  ];
 
-  checkInputs = [ mock moto responses ];
+  disabledTests = [
+    "test_compression_invalid"
+    "test_gs_uri_contains_question_mark"
+    "test_gzip_compress_sanity"
+    "test_http"
+    "test_ignore_ext"
+    "test_initialize_write"
+    "test_read_explicit"
+    "test_s3_handles_querystring"
+    "test_s3_uri_contains_question_mark"
+    "test_webhdfs"
+    "test_write"
+  ];
 
-  # upstream code requires both boto and boto3
-  propagatedBuildInputs = [ boto boto3 bz2file requests ];
+  pythonImportsCheck = [ "smart_open" ];
 
-  meta = {
-    license = lib.licenses.mit;
+  meta = with lib; {
     description = "Library for efficient streaming of very large file";
-    maintainers = with lib.maintainers; [ jyp ];
+    homepage = "https://github.com/RaRe-Technologies/smart_open";
+    license = licenses.mit;
+    maintainers = with maintainers; [ jyp ];
   };
 }
diff --git a/pkgs/development/python-modules/sqlalchemy/default.nix b/pkgs/development/python-modules/sqlalchemy/default.nix
index 605334adf0c..6c576f0b85e 100644
--- a/pkgs/development/python-modules/sqlalchemy/default.nix
+++ b/pkgs/development/python-modules/sqlalchemy/default.nix
@@ -14,11 +14,11 @@
 
 buildPythonPackage rec {
   pname = "SQLAlchemy";
-  version = "1.4.18";
+  version = "1.4.20";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0k3yfarfa0hcc0bza6nccy685gnmq6gikynqayrvddx6y7si0lnj";
+    sha256 = "1l5miq1nzvg51yqw3pnaq17dgibhgx2m0il2ha79gwpyd8k3mviq";
   };
 
   propagatedBuildInputs = [
@@ -36,8 +36,6 @@ buildPythonPackage rec {
     sed -e 's:--max-worker-restart=5::g' -i setup.cfg
   '';
 
-  dontUseSetuptoolsCheck = true;
-
   # disable mem-usage tests on mac, has trouble serializing pickle files
   disabledTests = lib.optionals stdenv.isDarwin [
     "MemUsageWBackendTest"
diff --git a/pkgs/development/python-modules/urllib3/default.nix b/pkgs/development/python-modules/urllib3/default.nix
index 6d73357e3bc..1c25612a16d 100644
--- a/pkgs/development/python-modules/urllib3/default.nix
+++ b/pkgs/development/python-modules/urllib3/default.nix
@@ -19,11 +19,11 @@
 
 buildPythonPackage rec {
   pname = "urllib3";
-  version = "1.26.5";
+  version = "1.26.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "sha256-p6zQl3ElMl9Ra9qXNfpxQrkJqNAeiy5MgQjQmE5uAJg=";
+    sha256 = "sha256-9XtMFsYvonYLfj2Xw1slVRL7a1miWXMPNroyzp+ONC8=";
   };
 
   propagatedBuildInputs = [
diff --git a/pkgs/development/python-modules/warrant/default.nix b/pkgs/development/python-modules/warrant/default.nix
index a4bbee43d01..8da1cf55b54 100644
--- a/pkgs/development/python-modules/warrant/default.nix
+++ b/pkgs/development/python-modules/warrant/default.nix
@@ -17,7 +17,7 @@ buildPythonPackage {
   patches = [
     (fetchpatch {
       name = "fix-pip10-compat.patch";
-      url = " https://github.com/capless/warrant/commit/ae17d17d9888b9218a8facf6f6ad0bf4adae9a12.patch";
+      url = "https://github.com/capless/warrant/commit/ae17d17d9888b9218a8facf6f6ad0bf4adae9a12.patch";
       sha256 = "1lvqi2qfa3kxdz05ab2lc7xnd3piyvvnz9kla2jl4pchi876z17c";
     })
   ];
diff --git a/pkgs/development/python-modules/watchdog/default.nix b/pkgs/development/python-modules/watchdog/default.nix
index e5d742bef28..921ed5af4aa 100644
--- a/pkgs/development/python-modules/watchdog/default.nix
+++ b/pkgs/development/python-modules/watchdog/default.nix
@@ -13,11 +13,11 @@
 
 buildPythonPackage rec {
   pname = "watchdog";
-  version = "2.1.2";
+  version = "2.1.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "sha256-AjfbTZAkhZvqJ9DvtZ/nXu8pCDP9mIuOrXqHmwMIwts=";
+    sha256 = "sha256-5SNqjoYCq220uHNmTC01bDZas8rJb73sSXCtYWQV3UU=";
   };
 
   buildInputs = lib.optionals stdenv.isDarwin [ CoreServices ];
diff --git a/pkgs/development/python-modules/xdis/default.nix b/pkgs/development/python-modules/xdis/default.nix
index 59cad86606f..aec8b13a122 100644
--- a/pkgs/development/python-modules/xdis/default.nix
+++ b/pkgs/development/python-modules/xdis/default.nix
@@ -6,14 +6,14 @@
 
 buildPythonPackage rec {
   pname = "xdis";
-  version = "5.0.9";
+  version = "5.0.10";
   disabled = isPy27;
 
   src = fetchFromGitHub {
     owner = "rocky";
     repo = "python-xdis";
     rev = version;
-    sha256 = "sha256-joKPTEq0UabXMyld0DHrhC1D/Om2B5st0qa2F9r0muA=";
+    sha256 = "sha256-/3qyMgliua7W4Va1HdRbHyiR/eBQzHK+GrZVAMvMhLA=";
   };
 
   checkInputs = [ pytest ];