ENH: enable CPython free-threading support (#468)

- Test the package using `pytest-run-parallel`, which allows pytest suites to be run
  concurrently (per test). This analysis didn't throw any major concurrency-related
  issues, the only tests that were marked as thread-unsafe were related to memory
  usage checking and concurrent file overwriting.
- Add a CI to run tests in parallel, as well to build and release free-threaded wheels
- Mark each C module as free-threaded compatible

Author: andfoy

.github/workflows/ci.yml

@@ -7,7 +7,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.13t"]
         architecture: [x86, x64]
         os:
           [
@@ -34,6 +34,12 @@ jobs:
           python-version: ${{ matrix.python-version }}
           architecture: ${{ matrix.architecture }}
 
+
+      - if: ${{ endsWith(matrix.python-version, 't') }}
+        run: |
+          pip install pytest-run-parallel
+          echo "PYTEST_ADDOPTS=--parallel-threads=4" >> "$GITHUB_ENV"
+
       - name: Install
         run: |
           pip install . -v
@@ -69,7 +75,8 @@ jobs:
       - name: Build wheels
         uses: pypa/[email protected]
         env:
-          CIBW_SKIP: pp*
+          CIBW_SKIP: "pp* *t-manylinux_i686 *t-musllinux_i686"
+          CIBW_ENABLE: cpython-freethreading
 
       - name: Store wheel artifacts
         uses: actions/upload-artifact@v4

bottleneck/conftest.py

@@ -0,0 +1,32 @@
+
+import pytest
+
+try:
+    import pytest_run_parallel  # noqa:F401
+
+    PARALLEL_RUN_AVAILABLE = True
+except Exception:
+    PARALLEL_RUN_AVAILABLE = False
+
+
+def pytest_configure(config):
+    if not PARALLEL_RUN_AVAILABLE:
+        config.addinivalue_line(
+            'markers',
+            'parallel_threads(n): run the given test function in parallel '
+            'using `n` threads.',
+        )
+        config.addinivalue_line(
+            "markers",
+            "thread_unsafe: mark the test function as single-threaded",
+        )
+        config.addinivalue_line(
+            "markers",
+            "iterations(n): run the given test function `n` times in each thread",
+        )
+
+
+if not PARALLEL_RUN_AVAILABLE:
+    @pytest.fixture
+    def num_parallel_threads():
+        return 1

bottleneck/src/move_template.c

@@ -1519,6 +1519,11 @@ PyInit_move(void)
 {
     PyObject *m = PyModule_Create(&move_def);
     if (m == NULL) return NULL;
+
+    #ifdef Py_GIL_DISABLED
+        PyUnstable_Module_SetGIL(m, Py_MOD_GIL_NOT_USED);
+    #endif
+
     import_array();
     if (!intern_strings()) {
         return NULL;

bottleneck/src/nonreduce_axis_template.c

@@ -1027,6 +1027,11 @@ PyInit_nonreduce_axis(void)
 {
     PyObject *m = PyModule_Create(&nra_def);
     if (m == NULL) return NULL;
+
+    #ifdef Py_GIL_DISABLED
+        PyUnstable_Module_SetGIL(m, Py_MOD_GIL_NOT_USED);
+    #endif
+
     import_array();
     if (!intern_strings()) {
         return NULL;

bottleneck/src/nonreduce_template.c

@@ -345,6 +345,11 @@ PyInit_nonreduce(void)
 {
     PyObject *m = PyModule_Create(&nonreduce_def);
     if (m == NULL) return NULL;
+
+    #ifdef Py_GIL_DISABLED
+        PyUnstable_Module_SetGIL(m, Py_MOD_GIL_NOT_USED);
+    #endif
+
     import_array();
     if (!intern_strings()) {
         return NULL;

bottleneck/src/reduce_template.c

@@ -1966,6 +1966,11 @@ PyInit_reduce(void)
 {
     PyObject *m = PyModule_Create(&reduce_def);
     if (m == NULL) return NULL;
+
+    #ifdef Py_GIL_DISABLED
+        PyUnstable_Module_SetGIL(m, Py_MOD_GIL_NOT_USED);
+    #endif
+
     import_array();
     if (!intern_strings()) {
         return NULL;

bottleneck/tests/memory_test.py

@@ -4,6 +4,7 @@
 import pytest
 
 
+@pytest.mark.thread_unsafe
 @pytest.mark.skipif(
     sys.platform.startswith("win"), reason="resource module not available on windows"
 )

bottleneck/tests/test_template.py

@@ -1,9 +1,11 @@
 import os
 import posixpath as path
+import pytest
 
 from ..src.bn_template import make_c_files
 
 
+@pytest.mark.thread_unsafe
 def test_make_c_files() -> None:
     dirpath = os.path.join(os.path.dirname(__file__), "data/template_test/")
     modules = ["test"]