Add CI test

Author: benjeffery

.github/workflows/tests.yml

@@ -126,23 +126,60 @@ 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
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v5.4.0
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          working-directory: python
+          fail_ci_if_error: false
+          flags: python-tests
+          name: codecov-umbrella
+          verbose: true
+
+  test-numpy1:
+    name: Numpy 1.x
+    runs-on: ubuntu-24.04
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - name: Cancel Previous Runs
+        uses: styfle/cancel-workflow-action@0.12.1
+        with:
+          access_token: ${{ github.token }}
+
+      - name: Checkout
+        uses: actions/checkout@v4.2.2
+
+      - name: Setup Python
+        uses: actions/setup-python@v5.4.0
+        with:
+          python-version: '3.12'
+
+      - name: Install dependencies
         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
+          pip install -r requirements/CI-complete/requirements.txt
+          pip install "numpy<2"
 
+      - name: Build module
+        working-directory: python
+        run: |
+          python setup.py build_ext --inplace
+
+      - name: Run tests with numpy 1.x
+        working-directory: python
+        run: |
+          python -m pytest -x --cov=tskit --cov-report=xml --cov-branch -n2 tests/test_lowlevel.py tests/test_highlevel.py
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v5.4.0
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           working-directory: python
           fail_ci_if_error: false
-          flags: python-tests
-          name: codecov-umbrella
+          flags: python-tests-numpy1
+          name: codecov-numpy1
           verbose: true
 
   msys2:

python/CHANGELOG.rst

@@ -19,6 +19,11 @@
 - Add ``TreeSequence.mutations_edge`` which returns the edge ID for each mutation's
   edge. (:user:`benjeffery`, :pr:`3226`, :issue:`3189`)
 
+- Add ``TreeSequence.sites_ancestral_state`` and ``TreeSequence.mutations_derived_state`` properties
+  to return the ancestral state of sites and derived state of mutations as NumPy arrays of
+  the new numpy 2.0 StringDType.
+  (:user:`benjeffery`, :pr:`3228`, :issue:`2632`)
+
 **Bugfixes**
 
 - Fix bug in ``TreeSequence.pair_coalescence_counts`` when ``span_normalise=True``

python/pyproject.toml

@@ -43,7 +43,7 @@ keywords = [
 requires-python = ">=3.9"
 dependencies = [
     "jsonschema>=3.0.0",
-    "numpy>2",
+    "numpy>=2",
 ]
 
 [project.urls]

python/tests/test_highlevel.py

@@ -5322,6 +5322,7 @@ def test_mixed_sample_status(self):
 
 
 class TestRaggedArrays:
+    @pytest.mark.skipif(not _tskit.HAS_NUMPY_2, reason="Requires NumPy 2.0 or higher")
     @pytest.mark.parametrize("num_rows", [0, 1, 100])
     @pytest.mark.parametrize("column", ["ancestral_state", "derived_state"])
     def test_site_ancestral_state(self, num_rows, column):
@@ -5367,6 +5368,20 @@ def test_site_ancestral_state(self, num_rows, column):
         ):
             assert state == getattr(row, column)
 
+    @pytest.mark.skipif(_tskit.HAS_NUMPY_2, reason="Test only on Numpy 1.X")
+    @pytest.mark.parametrize(
+        "column", ["sites_ancestral_state", "mutations_derived_state"]
+    )
+    def test_ragged_array_not_supported(self, column):
+        tables = tskit.TableCollection(sequence_length=100)
+        ts = tables.tree_sequence()
+
+        with pytest.raises(
+            RuntimeError,
+            match="requires numpy 2.0",
+        ):
+            getattr(ts, column)
+
 
 class TestSampleNodesByPloidy:
     @pytest.mark.parametrize(