Merge staging-next into staging

13 files changed, 129 insertions, 38 deletions

diff --git a/pkgs/development/python-modules/apache-beam/default.nix b/pkgs/development/python-modules/apache-beam/default.nix
index 44748f2fdb05..f3e47bfc9010 100644
--- a/pkgs/development/python-modules/apache-beam/default.nix
+++ b/pkgs/development/python-modules/apache-beam/default.nix
@@ -57,6 +57,12 @@ buildPythonPackage rec {
     ./fix-cython.patch
   ];
 
+  # See https://github.com/NixOS/nixpkgs/issues/156957.
+  postPatch = ''
+    substituteInPlace setup.py \
+      --replace "typing-extensions>=3.7.0,<4" "typing-extensions"
+  '';
+
   sourceRoot = "source/sdks/python";
 
   nativeBuildInputs = [
diff --git a/pkgs/development/python-modules/cfn-flip/default.nix b/pkgs/development/python-modules/cfn-flip/default.nix
index bf3eab19d4fa..105775a4547e 100644
--- a/pkgs/development/python-modules/cfn-flip/default.nix
+++ b/pkgs/development/python-modules/cfn-flip/default.nix
@@ -1,25 +1,25 @@
-{ buildPythonPackage
-, fetchFromGitHub
-, lib
-
-# pythonPackages
+{ lib
+, buildPythonPackage
 , click
-, pytest
-, pytest-cov
-, pytest-runner
+, fetchFromGitHub
+, pytestCheckHook
+, pythonOlder
 , pyyaml
 , six
 }:
 
 buildPythonPackage rec {
   pname = "cfn-flip";
-  version = "1.2.2";
+  version = "1.3.0";
+  format = "setuptools";
+
+  disabled = pythonOlder "3.7";
 
   src = fetchFromGitHub {
     owner = "awslabs";
     repo = "aws-cfn-template-flip";
     rev = version;
-    sha256 = "05fk725a1i3zl3idik2hxl3w6k1ln0j33j3jdq1gvy1sfyc79ifm";
+    hash = "sha256-1cV0mHc6+P0CbnLIMSSwNEzDB+1QzNjioH/EoIo40xU=";
   };
 
   propagatedBuildInputs = [
@@ -29,27 +29,27 @@ buildPythonPackage rec {
   ];
 
   checkInputs = [
-    pytest
-    pytest-cov
-    pytest-runner
+    pytestCheckHook
   ];
 
-  checkPhase = ''
-    py.test \
-      --cov=cfn_clean \
-      --cov=cfn_flip \
-      --cov=cfn_tools \
-      --cov-report term-missing \
-      --cov-report html
+  postPatch = ''
+    sed -i "/--cov/d" tox.ini
   '';
 
+  disabledTests = [
+    # TypeError: load() missing 1 required positional argument: 'Loader'
+    "test_flip_to_yaml_with_longhand_functions"
+    "test_yaml_no_ordered_dict"
+  ];
+
+  pythonImportsCheck = [
+    "cfn_flip"
+  ];
+
   meta = with lib; {
     description = "Tool for converting AWS CloudFormation templates between JSON and YAML formats";
     homepage = "https://github.com/awslabs/aws-cfn-template-flip";
     license = licenses.asl20;
-    maintainers = with maintainers; [
-      kamadorueda
-      psyanticy
-    ];
+    maintainers = with maintainers; [ kamadorueda psyanticy ];
   };
 }
diff --git a/pkgs/development/python-modules/dm-haiku/default.nix b/pkgs/development/python-modules/dm-haiku/default.nix
index 5468776c72d1..14ceebf0a19b 100644
--- a/pkgs/development/python-modules/dm-haiku/default.nix
+++ b/pkgs/development/python-modules/dm-haiku/default.nix
@@ -4,6 +4,7 @@
 , dill
 , dm-tree
 , fetchFromGitHub
+, jaxlib
 , jmp
 , lib
 , pytestCheckHook
@@ -31,6 +32,7 @@ buildPythonPackage rec {
     chex
     cloudpickle
     dm-tree
+    jaxlib
     pytestCheckHook
     tensorflow
   ];
diff --git a/pkgs/development/python-modules/elegy/default.nix b/pkgs/development/python-modules/elegy/default.nix
index ec968dce8ec3..5b0cb293c0a3 100644
--- a/pkgs/development/python-modules/elegy/default.nix
+++ b/pkgs/development/python-modules/elegy/default.nix
@@ -4,6 +4,7 @@
 , deepmerge
 , dm-haiku
 , fetchFromGitHub
+, jaxlib
 , lib
 , poetry
 , pytestCheckHook
@@ -35,6 +36,8 @@ buildPythonPackage rec {
     poetry
   ];
 
+  buildInputs = [ jaxlib ];
+
   propagatedBuildInputs = [
     cloudpickle
     deepdish
diff --git a/pkgs/development/python-modules/flax/default.nix b/pkgs/development/python-modules/flax/default.nix
index b8479c0f73ca..b5a22858b57a 100644
--- a/pkgs/development/python-modules/flax/default.nix
+++ b/pkgs/development/python-modules/flax/default.nix
@@ -1,5 +1,6 @@
 { buildPythonPackage
 , fetchFromGitHub
+, jaxlib
 , keras
 , lib
 , matplotlib
@@ -21,6 +22,8 @@ buildPythonPackage rec {
     sha256 = "0zvq0vl88hiwmss49bnm7gdmndr1dfza2bcs1fj88a9r7w9dmlsr";
   };
 
+  buildInputs = [ jaxlib ];
+
   propagatedBuildInputs = [
     matplotlib
     msgpack
diff --git a/pkgs/development/python-modules/jmp/default.nix b/pkgs/development/python-modules/jmp/default.nix
index dc096b93ae46..09c41a7ededd 100644
--- a/pkgs/development/python-modules/jmp/default.nix
+++ b/pkgs/development/python-modules/jmp/default.nix
@@ -19,10 +19,9 @@ buildPythonPackage rec {
     sha256 = "0hh4cmp93wjyidj48gh07vhx2kjvpwd23xvy79bsjn5qaaf6q4cm";
   };
 
-  # Wheel requires only `numpy`, but the import needs both `jax` and `jaxlib`.
+  # Wheel requires only `numpy`, but the import needs `jax`.
   propagatedBuildInputs = [
     jax
-    jaxlib
   ];
 
   pythonImportsCheck = [
@@ -30,6 +29,7 @@ buildPythonPackage rec {
   ];
 
   checkInputs = [
+    jaxlib
     pytestCheckHook
   ];
 
diff --git a/pkgs/development/python-modules/optax/default.nix b/pkgs/development/python-modules/optax/default.nix
index bf0383fa1530..6a3b6a9d3e67 100644
--- a/pkgs/development/python-modules/optax/default.nix
+++ b/pkgs/development/python-modules/optax/default.nix
@@ -22,10 +22,11 @@ buildPythonPackage rec {
     sha256 = "1q8cxc42a5xais2ll1l238cnn3l7w28savhgiz0lg01ilz2ysbli";
   };
 
+  buildInputs = [ jaxlib ];
+
   propagatedBuildInputs = [
     absl-py
     chex
-    jaxlib
     numpy
   ];
 
diff --git a/pkgs/development/python-modules/pycfmodel/default.nix b/pkgs/development/python-modules/pycfmodel/default.nix
new file mode 100644
index 000000000000..320e6d51c7ac
--- /dev/null
+++ b/pkgs/development/python-modules/pycfmodel/default.nix
@@ -0,0 +1,48 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, httpx
+, pydantic
+, pytestCheckHook
+, pythonOlder
+}:
+
+buildPythonPackage rec {
+  pname = "pycfmodel";
+  version = "0.13.0";
+  format = "setuptools";
+
+  disabled = pythonOlder "3.7";
+
+  src = fetchFromGitHub {
+    owner = "Skyscanner";
+    repo = pname;
+    rev = version;
+    hash = "sha256-BlnLf0C/wxPXhoAH0SRB22eGWbbZ05L20rNy6qfOI+A=";
+  };
+
+  propagatedBuildInputs = [
+    pydantic
+  ];
+
+  checkInputs = [
+    httpx
+    pytestCheckHook
+  ];
+
+  disabledTests = [
+    # Test require network access
+    "test_cloudformation_actions"
+  ];
+
+  pythonImportsCheck = [
+    "pycfmodel"
+  ];
+
+  meta = with lib; {
+    description = "Model for Cloud Formation scripts";
+    homepage = "https://github.com/Skyscanner/pycfmodel";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ fab ];
+  };
+}
diff --git a/pkgs/development/python-modules/pydash/default.nix b/pkgs/development/python-modules/pydash/default.nix
index 7d75896397f3..5b0ffade5885 100644
--- a/pkgs/development/python-modules/pydash/default.nix
+++ b/pkgs/development/python-modules/pydash/default.nix
@@ -1,23 +1,46 @@
-{ lib, buildPythonPackage, fetchFromGitHub, mock, pytestCheckHook, invoke }:
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, invoke
+, mock
+, pytestCheckHook
+, pythonOlder
+, sphinx_rtd_theme
+}:
 
 buildPythonPackage rec {
   pname = "pydash";
-  version = "4.9.3";
+  version = "5.1.0";
+  format = "setuptools";
+
+  disabled = pythonOlder "3.6";
 
   src = fetchFromGitHub {
     owner = "dgilland";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-BAyiSnILvujUOFOAkiXSgyozs2Q809pYihHwa+6BHcQ=";
+    hash = "sha256-BAyiSnILvujUOFOAkiXSgyozs2Q809pYihHwa+6BHcQ=";
   };
 
-  patches = [ ./0001-Only-build-unit-tests.patch ];
+  checkInputs = [
+    invoke
+    mock
+    sphinx_rtd_theme
+    pytestCheckHook
+  ];
+
+  postPatch = ''
+    sed -i "/--cov/d" setup.cfg
+    sed -i "/--no-cov/d" setup.cfg
+  '';
 
-  checkInputs = [ mock pytestCheckHook invoke ];
+  pythonImportsCheck = [
+    "pydash"
+  ];
 
   meta = with lib; {
-    homepage = "https://github.com/dgilland/pydash";
-    description = "The kitchen sink of Python utility libraries for doing \"stuff\" in a functional way. Based on the Lo-Dash Javascript library.";
+    description = "Python utility libraries for doing stuff in a functional way";
+    homepage = "https://pydash.readthedocs.io";
     license = licenses.mit;
     maintainers = with maintainers; [ ma27 ];
   };
diff --git a/pkgs/development/python-modules/pytest-httpserver/default.nix b/pkgs/development/python-modules/pytest-httpserver/default.nix
index cd07a104038c..eb04881455d7 100644
--- a/pkgs/development/python-modules/pytest-httpserver/default.nix
+++ b/pkgs/development/python-modules/pytest-httpserver/default.nix
@@ -9,12 +9,12 @@
 
 buildPythonPackage rec {
   pname = "pytest-httpserver";
-  version = "1.0.3";
+  version = "1.0.4";
 
   src = fetchPypi {
     pname = "pytest_httpserver";
     inherit version;
-    sha256 = "87561c4fa6a7bc306d76d1979a3eb9d54eb26bfb2f3f51f1643bf3c090ce629d";
+    sha256 = "6de464ba5f74628d6182ebbdcb56783edf2c9b0caf598dc35c11f014f24a3f0d";
   };
 
   propagatedBuildInputs = [ werkzeug ];
diff --git a/pkgs/development/python-modules/sentry-sdk/default.nix b/pkgs/development/python-modules/sentry-sdk/default.nix
index a59ec10be037..26ccb1aacc51 100644
--- a/pkgs/development/python-modules/sentry-sdk/default.nix
+++ b/pkgs/development/python-modules/sentry-sdk/default.nix
@@ -109,6 +109,8 @@ buildPythonPackage rec {
     "test_circular_references"
     # Failing wsgi test
     "test_session_mode_defaults_to_request_mode_in_wsgi_handler"
+    # Network requests to public web
+    "test_crumb_capture"
   ];
 
   disabledTestPaths = [
diff --git a/pkgs/development/python-modules/treeo/default.nix b/pkgs/development/python-modules/treeo/default.nix
index d0293d3e2c06..c8329f99a60e 100644
--- a/pkgs/development/python-modules/treeo/default.nix
+++ b/pkgs/development/python-modules/treeo/default.nix
@@ -22,12 +22,12 @@ buildPythonPackage rec {
     poetry-core
   ];
 
-  # These deps are not needed for the wheel, but required during the import.
+  # jax is not declared in the dependencies, but is necessary.
   propagatedBuildInputs = [
     jax
-    jaxlib
   ];
 
+  checkInputs = [ jaxlib ];
   pythonImportsCheck = [
     "treeo"
   ];
diff --git a/pkgs/development/python-modules/treex/default.nix b/pkgs/development/python-modules/treex/default.nix
index 1f4a55416d56..0b5ad0c89839 100644
--- a/pkgs/development/python-modules/treex/default.nix
+++ b/pkgs/development/python-modules/treex/default.nix
@@ -5,6 +5,7 @@
 , fetchFromGitHub
 , flax
 , hypothesis
+, jaxlib
 , keras
 , lib
 , poetry-core
@@ -38,6 +39,8 @@ buildPythonPackage rec {
     poetry-core
   ];
 
+  buildInputs = [ jaxlib ];
+
   propagatedBuildInputs = [
     einops
     flax