python3Packages.numba: 0.56.2 -> 0.56.4, fix tests and CUDA

pkgs/development/python-modules/numba/cuda_path.patch

@@ -1,5 +1,5 @@
 diff --git a/numba/cuda/cuda_paths.py b/numba/cuda/cuda_paths.py
-index b9988bc..a642680 100644
+index 0da435d33..7b1fde087 100644
 --- a/numba/cuda/cuda_paths.py
 +++ b/numba/cuda/cuda_paths.py
 @@ -24,10 +24,7 @@ def _find_valid_path(options):
@@ -14,15 +14,12 @@ index b9988bc..a642680 100644
      ]
      by, libdir = _find_valid_path(options)
      return by, libdir
-@@ -35,18 +32,16 @@ def _get_libdevice_path_decision():
+@@ -35,16 +32,14 @@ def _get_libdevice_path_decision():
  
  def _nvvm_lib_dir():
      if IS_WIN32:
 -        return 'nvvm', 'bin'
 +        return 'bin',
-     elif IS_OSX:
--        return 'nvvm', 'lib'
-+        return 'lib',
      else:
 -        return 'nvvm', 'lib64'
 +        return 'lib64',
@@ -33,13 +30,13 @@ index b9988bc..a642680 100644
 -        ('Conda environment', get_conda_ctk()),
 -        ('CUDA_HOME', get_cuda_home(*_nvvm_lib_dir())),
 -        ('System', get_system_ctk(*_nvvm_lib_dir())),
-+        ('Nix store', get_nix_ctk(*_nvvm_lib_dir())),        
++        ('Nix store', get_nix_ctk(*_nvvm_lib_dir())),
      ]
      by, path = _find_valid_path(options)
      return by, path
-@@ -74,14 +69,12 @@ def _cudalib_path():
-     elif IS_OSX:
-         return 'lib'
+@@ -64,14 +59,12 @@ def _cudalib_path():
+     if IS_WIN32:
+         return 'bin'
      else:
 -        return 'lib64'
 +        return 'lib'
@@ -54,7 +51,7 @@ index b9988bc..a642680 100644
      ]
      by, libdir = _find_valid_path(options)
      return by, libdir
-@@ -92,6 +85,22 @@ def _get_cudalib_dir():
+@@ -82,6 +75,22 @@ def _get_cudalib_dir():
      return _env_path_tuple(by, libdir)
  
  

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

@@ -11,6 +11,8 @@
 , libcxx
 , importlib-metadata
 , substituteAll
+, runCommand
+, fetchpatch
 
 # CUDA-only dependencies:
 , addOpenGLRunpath ? null
@@ -23,14 +25,14 @@
 let
   inherit (cudaPackages) cudatoolkit;
 in buildPythonPackage rec {
-  version = "0.56.2";
+  version = "0.56.4";
   pname = "numba";
   format = "setuptools";
   disabled = pythonOlder "3.6" || pythonAtLeast "3.11";
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-NJLwpdCeJX/FIfU3emxrkH7sGSDRRznwskWLnSmUalo=";
+    hash = "sha256-Mtn+9BLIFIPX7+DOts9NMxD96LYkqc7MoA95BXOslu4=";
   };
 
   postPatch = ''
@@ -55,7 +57,15 @@ in buildPythonPackage rec {
     cudatoolkit.lib
   ];
 
-  patches = lib.optionals cudaSupport [
+  patches = [
+    # fix failure in test_cache_invalidate (numba.tests.test_caching.TestCache)
+    # remove when upgrading past version 0.56
+    (fetchpatch {
+      name = "fix-test-cache-invalidate-readonly.patch";
+      url = "https://github.com/numba/numba/commit/993e8c424055a7677b2755b184fc9e07549713b9.patch";
+      hash = "sha256-IhIqRLmP8gazx+KWIyCxZrNLMT4jZT8CWD3KcH4KjOo=";
+    })
+  ] ++ lib.optionals cudaSupport [
     (substituteAll {
       src = ./cuda_path.patch;
       cuda_toolkit_path = cudatoolkit;
@@ -70,18 +80,40 @@ in buildPythonPackage rec {
     done
   '';
 
-  # Copy test script into $out and run the test suite.
+  # run a smoke test in a temporary directory so that
+  # a) Python picks up the installed library in $out instead of the build files
+  # b) we have somewhere to put $HOME so some caching tests work
+  # c) it doesn't take 6 CPU hours for the full suite
   checkPhase = ''
-    ${python.interpreter} -m numba.runtests
-  '';
+    runHook preCheck
 
-  # ImportError: cannot import name '_typeconv'
-  doCheck = false;
+    pushd $(mktemp -d)
+    HOME=. ${python.interpreter} -m numba.runtests -m $NIX_BUILD_CORES numba.tests.test_usecases
+    popd
+
+    runHook postCheck
+  '';
 
   pythonImportsCheck = [
     "numba"
   ];
 
+  passthru.tests = {
+    # CONTRIBUTOR NOTE: numba also contains CUDA tests, though these cannot be run in
+    # this sandbox environment. Consider running similar commands to those below outside the
+    # sandbox manually if you have the appropriate hardware; support will be detected
+    # and the corresponding tests enabled automatically.
+    # Also, the full suite currently does not complete on anything but x86_64-linux.
+    fullSuite = runCommand "${pname}-test" {} ''
+      pushd $(mktemp -d)
+      # pip and python in $PATH is needed for the test suite to pass fully
+      PATH=${python.withPackages (p: [ p.numba p.pip ])}/bin:$PATH
+      HOME=$PWD python -m numba.runtests -m $NIX_BUILD_CORES
+      popd
+      touch $out # stop Nix from complaining no output was generated and failing the build
+    '';
+  };
+
   meta =  with lib; {
     description = "Compiling Python code using LLVM";
     homepage = "https://numba.pydata.org/";