Fix GIL being re-enabled by C++ extensions (#8059)

ngoldbaum · web-flow · commit ea7afcbffb8d · 2026-02-24T16:43:16.000-08:00
Towards fixing #7464 Currently, running the scikit-image tests fails on the free-threaded build because the GIL is enabled at runtime: ``` _______________________________________________ ERROR collecting build-install/usr/lib/python3.14t/site-packages/skimage/feature/censure.py ________________________________________________ build-install/usr/lib/python3.14t/site-packages/skimage/feature/censure.py:6: in <module> from ..morphology import octagon, star build-install/usr/lib/python3.14t/site-packages/skimage/morphology/__init__.py:28: in <module> from ._skeletonize import medial_axis, skeletonize, thin build-install/usr/lib/python3.14t/site-packages/skimage/morphology/_skeletonize.py:10: in <module> from ._skeletonize_lee_cy import _compute_thin_image E RuntimeWarning: The global interpreter lock (GIL) has been enabled to load module 'skimage.morphology._skeletonize_lee_cy', which has not declared that it can run safely without the GIL. To override this behavior and keep the GIL disabled (at your own risk), run with PYTHON_GIL=0 or -Xgil=0. ``` This is happening because the `cython_args` aren't being passed to the C++ codegen function in the project's meson configuration. I changed the name of the variable to `cython_codegen_args` to make it a little clearer it has nothing to do with `cython_c_args` and `cython_cpp_args`, which are passed to e.g. clang and not Cython. I also made `cython_gen_cpp` use the same arguments as `cython_gen`. `c_undefined_ok` is unused, so I deleted it. Finally, I added a regression test for this in the project's `conftest.py`, following a similar check I added to numpy's `conftest.py` a while back. I also added a 3.14t testing job and deleted the 3.13t job and special testing logic. All of that is unnecessary now. I will follow up after this to make the 3.14t testing job use pytest-run-parallel, superseding #7678.
diff --git a/.github/workflows/test-linux.yaml b/.github/workflows/test-linux.yaml
@@ -22,7 +22,7 @@ jobs:
       # Ensure that a wheel builder finishes even if another fails
       fail-fast: false
       matrix:
-        python-version: ["3.11", "3.13", "3.14"]
+        python-version: ["3.11", "3.13", "3.14", "3.14t"]
 
         # Dependency options for setup-test-env.sh
         MINIMUM_REQUIREMENTS: [0]
@@ -131,55 +131,9 @@ jobs:
         run: |
           asv check -v -E existing
 
-  test_skimage_linux_free_threaded:
-    name: linux-cp313t-default
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Checkout scikit-image
-        uses: actions/checkout@v5
-        with:
-          persist-credentials: false
-
-      # TODO: replace with setup-python when there is support
-      - uses: deadsnakes/action@e640ac8743173a67cca4d7d77cd837e514bf98e8 # v3.2.0
-        with:
-          python-version: "3.13"
-          nogil: true
-
-      - name: Install build dependencies
-        # See special clause inside setup-build-env.sh that detects when
-        # free threaded build is used, and then installs dependencies
-        # from nightly wheels
-        env:
-          PIP_FLAGS: "--pre"
-        run: |
-          source .github/scripts/setup-build-env.sh
-
-      - name: Build and install
-        run: |
-          pip install -v --no-build-isolation .
-
-      - name: Install test dependencies
-        # See special clause inside setup-test-env.sh that detects when
-        # free threaded build is used, and then installs dependencies
-        # from nightly wheels
-        env:
-          PIP_FLAGS: "--pre"
-        run: |
-          source .github/scripts/setup-test-env.sh
-
-      - name: Run tests
-        env:
-          PYTHON_GIL: 0
-          # A lazy loader configuration parameter
-          EAGER_IMPORT: ${{ matrix.EAGER_IMPORT }}
-        run: |
-          $PYTEST --doctest-plus --showlocals --pyargs skimage ./tests
-
   report-failures:
     runs-on: ubuntu-latest
-    needs: [test_skimage_linux, test_skimage_linux_free_threaded]
+    needs: test_skimage_linux
     if: ${{ always() && github.ref == 'refs/heads/main' && contains(needs.*.result, 'failure') }}
     permissions:
       issues: write
diff --git a/src/skimage/meson.build b/src/skimage/meson.build
@@ -128,23 +128,20 @@ py3.install_sources(
 cython_cli = find_program('_build_utils/cythoner.py')
 cy = meson.get_compiler('cython')
 
-cython_args = ['@INPUT@', '@OUTPUT@']
+cython_codegen_args = ['@INPUT@', '@OUTPUT@']
+
 if cy.version().version_compare('>=3.1.0')
-  cython_args += ['-Xfreethreading_compatible=True']
+  cython_codegen_args += ['-Xfreethreading_compatible=True']
 endif
 
-cython_cpp_args = cython_args + ['--cplus']
-
 cython_gen = generator(cython_cli,
-  arguments : cython_args,
+  arguments : cython_codegen_args,
   output : '@BASENAME@.c')
 
 cython_gen_cpp = generator(cython_cli,
-  arguments : ['@INPUT@', '@OUTPUT@', '--cplus'],
+  arguments : cython_codegen_args + ['--cplus'],
   output : '@BASENAME@.cpp')
 
-c_undefined_ok = ['-Wno-maybe-uninitialized']
-
 # Suppress warning for deprecated Numpy API.
 # (Suppress warning messages emitted by #warning directives).
 # Replace with numpy_nodepr_api after Cython 3.0 is out
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -5,12 +5,17 @@
 from datetime import timedelta
 import os
 import sys
+import sysconfig
 from pytest_pretty import CustomTerminalReporter
 
 from _pytest.terminal import TerminalReporter
 from _pytest.pathlib import bestrelpath
 
 
+FREE_THREADED_BUILD = bool(sysconfig.get_config_var("Py_GIL_DISABLED"))
+GIL_ENABLED_AT_START = getattr(sys, "_is_gil_enabled", lambda: True)()
+
+
 class SKTerminalReporter(CustomTerminalReporter):
     """Custom terminal reporter to display test runtimes.
 
@@ -59,3 +64,17 @@ def pytest_configure(config: pytest.Config) -> None:
         custom_reporter._session = standard_reporter._session
     config.pluginmanager.unregister(standard_reporter)
     config.pluginmanager.register(custom_reporter, 'terminalreporter')
+
+
+def pytest_terminal_summary(terminalreporter, exitstatus, config):
+    if FREE_THREADED_BUILD and not GIL_ENABLED_AT_START and sys._is_gil_enabled():
+        tr = terminalreporter
+        tr.ensure_newline()
+        tr.section("GIL re-enabled", sep="=", red=True, bold=True)
+        tr.line("The GIL was re-enabled at runtime during the tests.")
+        tr.line("This can happen with no test failures if the RuntimeWarning")
+        tr.line("raised by Python when this happens is filtered by a test.")
+        tr.line("")
+        tr.line("Please ensure all new C and C++ extensions declare support")
+        tr.line("for running without the GIL.")
+        pytest.exit("GIL re-enabled during tests", returncode=1)
