Merge pull request #188085 from tjni/fix-atomman

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

@@ -4,6 +4,7 @@
 , cython
 , datamodeldict
 , fetchFromGitHub
+, fetchpatch
 , matplotlib
 , numericalunits
 , numpy
@@ -12,6 +13,7 @@
 , potentials
 , pymatgen
 , pytest
+, pytestCheckHook
 , pythonOlder
 , pythonAtLeast
 , requests
@@ -21,19 +23,44 @@
 }:
 
 buildPythonPackage rec {
-  version = "1.4.4";
+  version = "1.4.5";
   pname = "atomman";
   format = "setuptools";
 
-  disabled = pythonOlder "3.6" || pythonAtLeast "3.10";
+  disabled = pythonOlder "3.6";
 
   src = fetchFromGitHub {
     owner = "usnistgov";
     repo = "atomman";
     rev = "v${version}";
-    hash = "sha256-iLAB0KMtrTCyGpx+81QfHDPVDhq8OA6CDL/ipVRpyo0=";
+    hash = "sha256-wXz/uHjXKHVKJu/HoFF2mADSBLp6UGF9ivOp2ZOz/Ys=";
   };
 
+  patches = [
+    # Fix several tests that are failing on master.
+    # https://github.com/usnistgov/atomman/pull/9
+    (fetchpatch {
+      name = "fix-tests-1.patch";
+      url = "https://github.com/usnistgov/atomman/commit/d255977a5e0ce4584e2c886f6c55ccb9f5932731.patch";
+      hash = "sha256-lBFOgcozY85JfQVsVjd51Jf9mrokwQuYdxa8l7VzkqU=";
+    })
+    (fetchpatch {
+      name = "fix-tests-2.patch";
+      url = "https://github.com/usnistgov/atomman/commit/de4177f28ad7c48d482cb606f323128e2fcb86aa.patch";
+      hash = "sha256-+YpwdKCT/OTue3b2GOk9Jagg26r1PTTV2Zg+GGBd8sM=";
+    })
+    (fetchpatch {
+      name = "fix-tests-3.patch";
+      url = "https://github.com/usnistgov/atomman/commit/10b168493ee883348699f1e42680423cec84bed5.patch";
+      hash = "sha256-b4f3POjiceq3xApfjnKAs9dEf1trCiTIyu7hMPL0ZTw=";
+    })
+    (fetchpatch {
+      name = "fix-tests-4.patch";
+      url = "https://github.com/usnistgov/atomman/commit/057d24c70427bab3c7c530251ceb5f4e27eb5c56.patch";
+      hash = "sha256-FTg/GNRZ5xigGW8SpUTIw2/GEzOxwb1rsv2wGebmZOk=";
+    })
+  ];
+
   propagatedBuildInputs = [
     cython
     datamodeldict
@@ -48,22 +75,25 @@ buildPythonPackage rec {
     xmltodict
   ];
 
+  preCheck = ''
+    # By default, pytestCheckHook imports atomman from the current directory
+    # instead of from where `pip` installs it and fails due to missing Cython
+    # modules. Fix this by removing atomman from the current directory.
+    #
+    rm -r atomman
+  '';
+
   checkInputs = [
     ase
     phonopy
     pymatgen
     pytest
+    pytestCheckHook
   ];
 
-  checkPhase = ''
-    # pytestCheckHook doesn't work
-    pytest tests -k "not test_rootdir and not test_version \
-      and not test_atomic_mass and not imageflags \
-      and not test_build_unit and not test_set_and_get_in_units \
-      and not test_set_literal and not test_scalar_model " \
-      --ignore tests/plot/test_interpolate.py \
-      --ignore tests/tools/test_vect_angle.py
-  '';
+  disabledTests = [
+    "test_unique_shifts_prototype" # needs network access to download database files
+  ];
 
   pythonImportsCheck = [
     "atomman"