Conditionally compile

Author: benjeffery

.github/workflows/tests.yml

@@ -126,6 +126,15 @@ jobs:
             python -m pytest -x --cov=tskit --cov-report=xml --cov-branch -n2 --durations=20 tests
           fi
 
+      - name: Build and run with numpy 1.x
+        working-directory: python
+        run: |
+          source ~/.profile
+          conda activate anaconda-client-env
+          conda install --yes "numpy<2"
+          python -m pytest -x --cov=tskit --cov-report=xml --cov-branch -n2 tests/test_lowlevel.py
+
+
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v5.4.0
         with:

python/_tskitmodule.c

@@ -23,17 +23,27 @@
  * SOFTWARE.
  */
 
-#define PY_SSIZE_T_CLEAN
-#define NPY_NO_DEPRECATED_API NPY_2_0_API_VERSION
-#define NPY_TARGET_VERSION NPY_2_0_API_VERSION
 #define TSK_BUG_ASSERT_MESSAGE                                                          \
     "Please open an issue on"                                                           \
     " GitHub, ideally with a reproducible example."                                     \
     " (https://github.com/tskit-dev/tskit/issues)"
 
+#define PY_SSIZE_T_CLEAN
 #include <Python.h>
-#include <structmember.h>
+#include <numpy/numpyconfig.h>
+
+#if defined(NPY_2_0_API_VERSION) && NPY_API_VERSION >= NPY_2_0_API_VERSION
+#define NPY_NO_DEPRECATED_API NPY_2_0_API_VERSION
+#undef NPY_FEATURE_VERSION
+#define NPY_FEATURE_VERSION NPY_2_0_API_VERSION
+#define HAVE_NUMPY_2 1
+#else
+#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
+#define HAVE_NUMPY_2 0
+#endif
 #include <numpy/arrayobject.h>
+
+#include <structmember.h>
 #include <float.h>
 
 #include "kastore.h"
@@ -10775,6 +10785,7 @@ TreeSequence_make_array(TreeSequence *self, tsk_size_t size, int dtype, void *da
     return make_owned_array((PyObject *) self, size, dtype, data);
 }
 
+#if HAVE_NUMPY_2
 PyObject *
 TreeSequence_decode_ragged_string_column(
     TreeSequence *self, tsk_size_t num_rows, const char *data, const tsk_size_t *offset)
@@ -10825,6 +10836,7 @@ TreeSequence_decode_ragged_string_column(
     Py_XDECREF(array);
     return ret;
 }
+#endif
 
 static PyObject *
 TreeSequence_get_individuals_flags(TreeSequence *self, void *closure)
@@ -11073,6 +11085,7 @@ TreeSequence_get_sites_position(TreeSequence *self, void *closure)
     return ret;
 }
 
+#if HAVE_NUMPY_2
 static PyObject *
 TreeSequence_get_sites_ancestral_state(TreeSequence *self, void *closure)
 {
@@ -11088,6 +11101,7 @@ TreeSequence_get_sites_ancestral_state(TreeSequence *self, void *closure)
 out:
     return ret;
 }
+#endif
 
 static PyObject *
 TreeSequence_get_sites_metadata(TreeSequence *self, void *closure)
@@ -11755,9 +11769,11 @@ static PyGetSetDef TreeSequence_getsetters[] = {
     { .name = "sites_position",
         .get = (getter) TreeSequence_get_sites_position,
         .doc = "The site position array" },
+#if HAVE_NUMPY_2
     { .name = "sites_ancestral_state",
         .get = (getter) TreeSequence_get_sites_ancestral_state,
         .doc = "The site ancestral state array" },
+#endif
     { .name = "sites_metadata",
         .get = (getter) TreeSequence_get_sites_metadata,
         .doc = "The site metadata array" },
@@ -14647,15 +14663,23 @@ PyInit__tskit(void)
 {
     PyObject *module;
 
+#if HAVE_NUMPY_2
     if (PyArray_ImportNumPyAPI() < 0) {
         return NULL;
     }
+#else
+    import_array();
+#endif
 
     module = PyModule_Create(&tskitmodule);
     if (module == NULL) {
         return NULL;
     }
 
+    if (PyModule_AddIntConstant(module, "HAS_NUMPY_2", HAVE_NUMPY_2)) {
+        return NULL;
+    }
+
     if (register_lwt_class(module) != 0) {
         return NULL;
     }

python/requirements/development.txt

@@ -17,7 +17,6 @@ msprime>=1.0.0
 networkx
 newick
 ninja
-numpy>=2
 packaging
 portion
 pre-commit

python/requirements/development.yml

@@ -22,7 +22,7 @@ dependencies:
   - msprime>=1.0.0
   - networkx
   - ninja
-  - numpy>2
+  - numpy
   - packaging
   - portion
   - pre-commit

python/tests/test_lowlevel.py

@@ -1193,7 +1193,6 @@ class TestTreeSequence(LowLevelTestCase, MetadataTestMixin):
         "edges_metadata",
         "edges_metadata_offset",
         "sites_position",
-        "sites_ancestral_state",
         "sites_metadata",
         "sites_metadata_offset",
         "mutations_site",
@@ -1916,29 +1915,24 @@ def test_array_read_only(self, name, ts_fixture):
             a[:] = 0
         with pytest.raises(ValueError, match="assignment destination"):
             a[0] = 0
-        if name != "sites_ancestral_state":
-            with pytest.raises(ValueError, match="cannot set WRITEABLE"):
-                a.setflags(write=True)
+        with pytest.raises(ValueError, match="cannot set WRITEABLE"):
+            a.setflags(write=True)
 
     @pytest.mark.parametrize("name", ARRAY_NAMES)
     def test_array_properties(self, name, ts_fixture):
         ts_fixture = ts_fixture.ll_tree_sequence
         a = getattr(ts_fixture, name)
-        assert a.base == ts_fixture
         assert not a.flags.writeable
         assert a.flags.aligned
         assert a.flags.c_contiguous
-        if name == "sites_ancestral_state":
-            assert a.flags.owndata
-        else:
-            assert not a.flags.owndata
+        assert not a.flags.owndata
+        assert a.base == ts_fixture
         b = getattr(ts_fixture, name)
         assert a is not b
         assert np.all(a == b)
         # This checks that the underlying pointer to memory is the same in
         # both arrays.
-        if name != "sites_ancestral_state":
-            assert a.__array_interface__ == b.__array_interface__
+        assert a.__array_interface__ == b.__array_interface__
 
     @pytest.mark.parametrize("name", ARRAY_NAMES)
     def test_array_lifetime(self, name, ts_fixture):
@@ -1980,6 +1974,7 @@ def test_individuals_nodes(self, ts_fixture):
         a2[:] = 0
         assert a3 is not a2
 
+    @pytest.mark.skipif(not _tskit.HAS_NUMPY_2, reason="Requires NumPy 2.0+")
     @pytest.mark.parametrize(
         "site_lengths",
         ["none", "all-0", "all-1", "all-2", "mixed", "very_long", "unicode"],