python312Packages.numpy_2: 2.0.1 -> 2.1.0 (#336284)

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

···
   setuptools,
 
   # tests
-  python,
+  pytestCheckHook,
 }:
 
 buildPythonPackage rec {
···
     setuptools
   ];
 
-  # Disable static linking
-  # https://github.com/numba/llvmlite/issues/93
   postPatch = ''
-    substituteInPlace ffi/Makefile.linux --replace "-static-libstdc++" ""
-
-    substituteInPlace llvmlite/tests/test_binding.py --replace "test_linux" "nope"
+    substituteInPlace llvmlite/tests/test_binding.py \
+      --replace-fail "test_linux" "nope"
   '';
 
   # Set directory containing llvm-config binary
···
     export LLVM_CONFIG=${llvm.dev}/bin/llvm-config
   '';
 
-  checkPhase = ''
-    runHook preCheck
-    ${python.executable} runtests.py
-    runHook postCheck
+  nativeCheckInputs = [
+    pytestCheckHook
+  ];
+  # https://github.com/NixOS/nixpkgs/issues/255262
+  preCheck = ''
+    cd $out
   '';
 
   __impureHostDeps = lib.optionals stdenv.isDarwin [ "/usr/lib/libm.dylib" ];
 
   passthru.llvm = llvm;
 
-  meta = with lib; {
+  meta = {
     changelog = "https://github.com/numba/llvmlite/blob/v${version}/CHANGE_LOG";
     description = "Lightweight LLVM python binding for writing JIT compilers";
     downloadPage = "https://github.com/numba/llvmlite";
     homepage = "http://llvmlite.pydata.org/";
-    license = licenses.bsd2;
+    license = lib.licenses.bsd2;
   };
 }

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

···
   python,
   buildPythonPackage,
   setuptools,
-  numpy,
   numpy_2,
   llvmlite,
   libcxx,
···
   runCommand,
   writers,
   numba,
+  pytestCheckHook,
 
   config,
 
···
 
   # CUDA flags:
   cudaSupport ? config.cudaSupport,
+  testsWithoutSandbox ? false,
+  doFullCheck ? false,
 }:
 
 let
   cudatoolkit = cudaPackages.cuda_nvcc;
 in
 buildPythonPackage rec {
-  version = "0.60.0";
+  version = "0.61.0dev0";
   pname = "numba";
   pyproject = true;
 
···
     # that upstream relies on those strings to be valid, that's why we don't
     # use `forceFetchGit = true;`.` If in the future we'll observe the hash
     # changes too often, we can always use forceFetchGit, and inject the
-    # relevant strings ourselves, using `sed` commands, in extraPostFetch.
-    hash = "sha256-hUL281wHLA7wo8umzBNhiGJikyIF2loCzjLECuC+pO0=";
+    # relevant strings ourselves, using `substituteInPlace`, in postFetch.
+    hash = "sha256-KF9YQ6/FIfUQTJCAMgfIqnb/D8mdMbCC/tJvfYlSkgI=";
+    # TEMPORARY: The way upstream knows it's source version is explained above,
+    # and without this upstream sets the version in ${python.sitePackages} as
+    # 0.61.0dev0, which causes dependent packages fail to find a valid
+    # version of numba.
+    postFetch = ''
+      substituteInPlace $out/numba/_version.py \
+        --replace-fail \
+          'git_refnames = " (tag: ${version})"' \
+          'git_refnames = " (tag: 0.61.0, release0.61)"'
+    '';
   };
 
   postPatch = ''
···
 
   build-system = [
     setuptools
-    numpy_2
   ];
 
   nativeBuildInputs = lib.optionals cudaSupport [
···
     cudaPackages.cuda_nvcc
   ];
 
-  buildInputs = lib.optionals cudaSupport [ cudaPackages.cuda_cudart ];
+  buildInputs = [
+    # Not propagating it, because it numba can work with either numpy_2 or numpy_1
+    numpy_2
+  ] ++ lib.optionals cudaSupport [ cudaPackages.cuda_cudart ];
 
   dependencies = [
-    numpy
     llvmlite
     setuptools
   ] ++ lib.optionals (pythonOlder "3.9") [ importlib-metadata ];
···
       })
     ];
 
-  # 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 = ''
-    runHook preCheck
-
-    pushd $(mktemp -d)
-    HOME=. ${python.interpreter} -m numba.runtests -m $NIX_BUILD_CORES numba.tests.test_usecases
-    popd
+  nativeCheckInputs = [
+    pytestCheckHook
+  ];
 
-    runHook postCheck
+  preCheck = ''
+    export HOME="$(mktemp -d)"
+    # https://github.com/NixOS/nixpkgs/issues/255262
+    cd $out
   '';
 
+  pytestFlagsArray = lib.optionals (!doFullCheck) [
+    # These are the most basic tests. Running all tests is too expensive, and
+    # some of them fail (also differently on different platforms), so it will
+    # be too hard to maintain such a `disabledTests` list.
+    "${python.sitePackages}/numba/tests/test_usecases.py"
+  ];
+
+  disabledTestPaths = lib.optionals (!testsWithoutSandbox) [
+    # See NOTE near passthru.tests.withoutSandbox
+    "${python.sitePackages}/numba/cuda/tests"
+  ];
+
   pythonImportsCheck = [ "numba" ];
 
   passthru.testers.cuda-detect =
···
       '';
   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
-    '';
+    # this sandbox environment. Consider building the derivation below with
+    # --no-sandbox to get a view of how many tests succeed outside the sandbox.
+    withoutSandbox = numba.override {
+      doFullCheck = true;
+      cudaSupport = true;
+      testsWithoutSandbox = true;
+    };
+    withSandbox = numba.override {
+      cudaSupport = false;
+      doFullCheck = true;
+      testsWithoutSandbox = false;
+    };
   };
 
   meta = with lib; {

pkgs/development/python-modules/numpy/2.nix

···
 in
 buildPythonPackage rec {
   pname = "numpy";
-  version = "2.0.1";
+  version = "2.1.0";
   pyproject = true;
 
   disabled = pythonOlder "3.10";
···
   src = fetchPypi {
     inherit pname version;
     extension = "tar.gz";
-    hash = "sha256-SFuHI1eWQQw1GaaZz+H6qwl+UJ6Q67BdzQmNsq6H57M=";
+    hash = "sha256-fckNoAgffh2knsTjmO3mqOnMT16+X54GtEPtiJ7pqqI=";
   };
 
   patches = lib.optionals python.hasDistutilsCxxPatch [