Update to kastore C_2.1.2

c/subprojects/kastore/VERSION.txt

@@ -1 +1 @@
-2.1.1
+2.1.2

c/subprojects/kastore/kastore.h

@@ -157,7 +157,7 @@ to the API or ABI are introduced, i.e., the addition of a new function.
 The library patch version. Incremented when any changes not relevant to the
 to the API or ABI are introduced, i.e., internal refactors of bugfixes.
 */
-#define KAS_VERSION_PATCH   1
+#define KAS_VERSION_PATCH   2
 /** @} */
 
 #define KAS_HEADER_SIZE             64

c/subprojects/kastore/meson.build

@@ -26,25 +26,29 @@ if not meson.is_subproject()
     shared_library('kastore', 'kastore.c', install: true)
     executable('example', ['example.c'], link_with: kastore)
 
-    # Note: we don't declare these as meson tests because they depend on 
-    # being run from the current working directory because of the paths
-    # to example files.
     cunit_dep = dependency('cunit')
-    executable('tests', ['tests.c', 'kastore.c'], dependencies: cunit_dep,
+    src_root = meson.project_source_root()
+
+    tests_exe = executable('tests', ['tests.c', 'kastore.c'], dependencies: cunit_dep,
       c_args: ['-DMESON_VERSION="@0@"'.format(meson.project_version())])
+    test('tests', tests_exe,
+      env: ['KAS_TEST_DATA_PREFIX=' + src_root + '/test-data/'])
 
-    executable('cpp_tests', ['cpp_tests.cpp'], link_with: kastore)
+    cpp_tests_exe = executable('cpp_tests', ['cpp_tests.cpp'], link_with: kastore)
+    test('cpp_tests', cpp_tests_exe)
 
-    executable('malloc_tests', ['malloc_tests.c', 'kastore.c'], 
-        dependencies: cunit_dep, 
+    malloc_tests_exe = executable('malloc_tests', ['malloc_tests.c', 'kastore.c'],
+        dependencies: cunit_dep,
         link_args:['-Wl,--wrap=malloc', '-Wl,--wrap=realloc', '-Wl,--wrap=calloc'])
+    test('malloc_tests', malloc_tests_exe, workdir: src_root)
 
-    executable('io_tests', ['io_tests.c', 'kastore.c'], 
-        dependencies: cunit_dep, 
+    io_tests_exe = executable('io_tests', ['io_tests.c', 'kastore.c'],
+        dependencies: cunit_dep,
         link_args:[
-            '-Wl,--wrap=fwrite', 
-            '-Wl,--wrap=fread', 
+            '-Wl,--wrap=fwrite',
+            '-Wl,--wrap=fread',
             '-Wl,--wrap=fclose',
             '-Wl,--wrap=ftell',
             '-Wl,--wrap=fseek'])
+    test('io_tests', io_tests_exe, workdir: src_root)
 endif

python/Makefile

@@ -1,17 +1,11 @@
-PYTHON := $(shell command -v python 2> /dev/null)
-ifndef PYTHON
-$(error "python is not available via the `python` executable. If you have python only via `python3` you may need to `apt install python-is-python3`")
-endif
-
 all: ext3
 
 allchecks: _tskitmodule.c
 	CFLAGS="-std=c99 --coverage -Wall -Wextra -Werror -Wno-unused-parameter -Wno-cast-function-type" \
-	python setup.py build_ext --inplace
+	uv run python setup.py build_ext --inplace
 
 ext3: _tskitmodule.c
-
-	python setup.py build_ext --inplace
+	uv run python setup.py build_ext --inplace
 
 ctags:
 	ctags lib/*.c lib/*.h tskit/*.py

python/tests/test_python_c.py

@@ -5073,7 +5073,7 @@ class TestModuleFunctions:
 
     def test_kastore_version(self):
         version = _tskit.get_kastore_version()
-        assert version == (2, 1, 1)
+        assert version == (2, 1, 2)
 
     def test_tskit_version(self):
         version = _tskit.get_tskit_version()
@@ -5365,15 +5365,6 @@ def test_cpy_bad_node_bin_map(self):
         with pytest.raises(TypeError, match="cast array data"):
             self.pair_coalescence_quantiles(ts, node_bin_map=np.zeros(num_nodes))
 
-    def test_cpy_bad_quantiles(self):
-        ts = self.example_ts()
-        quantiles = np.zeros(0)
-        with pytest.raises(ValueError, match="at least one quantile"):
-            self.pair_coalescence_quantiles(ts, quantiles=quantiles)
-        quantiles = np.zeros((3, 3))
-        with pytest.raises(ValueError, match="object too deep"):
-            self.pair_coalescence_quantiles(ts, quantiles=quantiles)
-
     def test_cpy_bad_inputs(self):
         ts = self.example_ts()
         with pytest.raises(TypeError, match="at most 6 keyword"):
@@ -5387,6 +5378,15 @@ def test_cpy_bad_inputs(self):
                 foo="bar",
             )
 
+    def test_cpy_bad_quantiles(self):
+        ts = self.example_ts()
+        quantiles = np.zeros(0)
+        with pytest.raises(ValueError, match="at least one quantile"):
+            self.pair_coalescence_quantiles(ts, quantiles=quantiles)
+        quantiles = np.zeros((3, 3))
+        with pytest.raises(ValueError, match="object too deep"):
+            self.pair_coalescence_quantiles(ts, quantiles=quantiles)
+
 
 class TestPairCoalescenceRatesErrors:
     def example_ts(self, sample_size=10):