Merge staging-next into staging

pkgs/development/python-modules/h5py/default.nix

@@ -20,7 +20,8 @@ in buildPythonPackage rec {
   # avoid strict pinning of numpy
   postPatch = ''
     substituteInPlace setup.py \
-      --replace "numpy ==" "numpy >="
+      --replace "numpy ==" "numpy >=" \
+      --replace "mpi4py ==" "mpi4py >="
   '';
 
   HDF5_DIR = "${hdf5}";

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

@@ -1,4 +1,5 @@
-{ lib, buildPythonPackage, fetchPypi
+{ lib, buildPythonPackage, fetchFromGitHub
+, cython
 , enum34
 , glibcLocales
 , matplotlib
@@ -8,6 +9,7 @@
 , palettable
 , pandas
 , plotly
+, pybtex
 , pydispatcher
 , requests
 , ruamel-yaml
@@ -21,14 +23,20 @@
 
 buildPythonPackage rec {
   pname = "pymatgen";
-  version = "2022.1.9";
+  version = "2022.2.7";
 
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "89774c0d87a38dc2f5d4d0148091f6aa240b3633121745826de66867e8d8ecc8";
+  # sdist doesn't include c files
+  src = fetchFromGitHub {
+    owner = "materialsproject";
+    repo = "pymatgen";
+    rev= "v${version}";
+    sha256 = "sha256-92Dxmo1Z9LR2caSOftIf1I6jeZmqDe3SqhhoCofWraw=";
   };
 
-  nativeBuildInputs = [ glibcLocales ];
+  nativeBuildInputs = [
+    cython
+    glibcLocales
+  ];
 
   propagatedBuildInputs = [
     enum34
@@ -39,6 +47,7 @@ buildPythonPackage rec {
     palettable
     pandas
     plotly
+    pybtex
     pydispatcher
     requests
     ruamel-yaml

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

@@ -22,6 +22,9 @@ buildPythonPackage rec {
     sha256 = "sha256-JgAQCulv/QgjNLN441VVD++LSlKab6TDT0cTCQXHQm0=";
   };
 
+  # no longer compatible with sybil
+  # https://github.com/simplistix/testfixtures/issues/169
+  doCheck = false;
   checkInputs = [
     mock
     pytestCheckHook

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

@@ -5,12 +5,16 @@
 , pathpy
 , pytestCheckHook
 , setuptools-scm
+, pythonAtLeast
 }:
 
 buildPythonPackage rec {
   pname = "zetup";
   version = "0.2.64";
 
+  # https://github.com/zimmermanncode/zetup/issues/4
+  disabled = pythonAtLeast "3.10";
+
   src = fetchPypi {
     inherit pname version;
     sha256 = "b8a9bdcfa4b705d72b55b218658bc9403c157db7b57a14158253c98d03ab713d";