Update ci uv+py311

.codecov.yml

@@ -1,34 +1,61 @@
-codecov:
-  require_ci_to_pass: false
+# ignore:
+#   - "lib/tests/"
+#   - "lib/dev-tools/"
+#   - "lib/avl.c"
+#   - "lib/subprojects/**/*"
+
 comment:
-  layout: "diff, flags, files"
-fixes:
-  - "tskit/::python/tskit/"
-flag_management:
-  individual_flags:
-    - name: python-tests
+  layout: "header, diff, flags, components"  # show component info in the PR comment
+
+component_management:
+  individual_components:
+    - component_id: python_code
+      name: Python API
       paths:
         - python/tskit/*.py
-      statuses:
-        - type: project
-          target: 95%
-    - name: python-c-tests
+
+    - component_id: python_c_code
+      name: Python C interface
       paths:
         - python/_tskitmodule.c
-      statuses:
-        - type: project
-          target: 85%
-    - name: c-tests
+
+    - component_id: c_code
+      name: C library
       paths:
-        - c/tskit/*.c
-        - c/tskit/*.h
-      statuses:
-        - type: project
-          target: 85%
-    - name: lwt-tests
-      paths:
-        - python/lwt_interface/*.c
-        - python/lwt_interface/*.h
-      statuses:
-        - type: project
-          target: 80%
+        - c
+
+#
+# codecov:
+#   require_ci_to_pass: false
+# comment:
+#   layout: "diff, flags, files"
+# fixes:
+#   - "tskit/::python/tskit/"
+# flag_management:
+#   individual_flags:
+#     - name: python-tests
+#       paths:
+#         - python/tskit/*.py
+#       statuses:
+#         - type: project
+#           target: 95%
+#     - name: python-c-tests
+#       paths:
+#         - python/_tskitmodule.c
+#       statuses:
+#         - type: project
+#           target: 85%
+#     - name: c-tests
+#       paths:
+#         - c/tskit/*.c
+#         - c/tskit/*.h
+#       statuses:
+#         - type: project
+#           target: 85%
+#     - name: lwt-tests
+#       paths:
+#         - python/lwt_interface/*.c
+#         - python/lwt_interface/*.h
+#       statuses:
+#         - type: project
+#           target: 80%

.github/workflows/docker/shared.env

@@ -3,5 +3,4 @@ PYTHON_VERSIONS=(
     cp313-cp313
     cp312-cp312
     cp311-cp311
-    cp310-cp310
 )

.github/workflows/docs.yml

@@ -12,7 +12,7 @@ env:
 
 jobs:
   Docs:
-    uses: tskit-dev/.github/.github/workflows/docs-build-template.yml@v1
+    uses: tskit-dev/.github/.github/workflows/docs.yml@main
     with:
-      additional-setup: sudo apt-get install -y doxygen
-      make-command: make -C python
+      pyproject-directory: python
+      doxygen-directory: docs/doxygen

.github/workflows/lint.yml

@@ -0,0 +1,10 @@
+name: Lint
+
+on:
+  pull_request:
+
+jobs:
+  Lint:
+    uses: tskit-dev/.github/.github/workflows/lint.yml@main
+    with:
+      pyproject-directory: python

.github/workflows/tests.yml

@@ -10,11 +10,6 @@ env:
   FORCE_COLOR: 1
 
 jobs:
-  pre-commit:
-    name: Lint
-    uses: tskit-dev/.github/.github/workflows/lint.yml@v5
-    with:
-      clang-format-version: 21.1.8
 
   packaging:
     name: Python packaging
@@ -23,13 +18,27 @@ jobs:
       working-directory: python
       cli-test-cmd: tskit --help
 
+  test-c:
+    name: C tests
+    uses: tskit-dev/.github/.github/workflows/c-tests.yml@main
+    with:
+      library-directory: c
+    secrets: inherit
+
+  test-python-c:
+    name: Python-C tests
+    uses: tskit-dev/.github/.github/workflows/python-c-tests.yml@main
+    with:
+      pyproject-directory: python
+    secrets: inherit
+
   test:
     name: Python
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        python: [ "3.10", 3.14 ]
+        python: [ 3.11, 3.13 ]
         os:  [ macos-latest, ubuntu-24.04, windows-latest ]
     defaults:
       run:
@@ -67,27 +76,26 @@ jobs:
       - name: Install dependencies
         working-directory: python
         run: |
-          uv venv
-          uv pip install -r pyproject.toml --extra test
+          uv sync --locked --group test
           # Remove tskit installed as a dep of msprime
           uv pip uninstall tskit
 
       - name: Build module
         working-directory: python
         run: |
-          uv run --no-sync python setup.py build_ext --inplace
+          uv run python setup.py build_ext --inplace
 
       - name: Minidom test
         working-directory: python
         # Importing either IPython or pytest causes import of xml.dom.minidom
         # So to actually test that tskit imports it, we need a minimal test
         run: |
-          uv run --no-sync python -c "import tskit;tskit.Tree.generate_star(5).tree_sequence.draw_svg(path='test.svg')"
+          uv run python -c "import tskit;tskit.Tree.generate_star(5).tree_sequence.draw_svg(path='test.svg')"
 
       - name: Run JIT code coverage
         working-directory: python
         run: |
-          NUMBA_DISABLE_JIT=1 uv run --no-sync python -m pytest -x --cov=tskit --cov-report=xml --cov-branch -n2 tests/test_jit.py
+          NUMBA_DISABLE_JIT=1 uv run pytest -x --cov=tskit --cov-report=xml --cov-branch -n2 tests/test_jit.py
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v5.5.2
@@ -98,13 +106,14 @@ jobs:
           flags: python-tests-no-jit
           name: codecov-umbrella
           verbose: true
+
       - name: Run tests
         working-directory: python
         run: |
           if [[ "${{ matrix.os }}" == "windows-latest" ]]; then
-            uv run --no-sync python -m pytest -x --skip-slow --cov=tskit --cov-report=xml --cov-branch -n2 --durations=20 tests
+            uv run pytest -x --skip-slow --cov=tskit --cov-report=xml --cov-branch -n2 --durations=20 tests
           else
-            uv run --no-sync python -m pytest -x --cov=tskit --cov-report=xml --cov-branch -n2 --durations=20 tests
+            uv run pytest -x --cov=tskit --cov-report=xml --cov-branch -n2 --durations=20 tests
           fi
 
       - name: Upload coverage to Codecov
@@ -114,61 +123,7 @@ jobs:
           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@0.13.0
-        with:
-          access_token: ${{ github.token }}
-
-      - name: Checkout
-        uses: actions/checkout@v6.0.2
-
-      - name: Setup Python
-        uses: actions/setup-python@v6.1.0
-        with:
-          python-version: '3.12'
-
-      - name: Install uv
-        uses: astral-sh/setup-uv@v7
-        with:
-          version: "0.8.15"
-
-      - name: Install dependencies
-        working-directory: python
-        run: |
-          uv venv
-          uv pip install -r pyproject.toml --extra test
-          uv pip uninstall tskit
-          uv pip install "numpy<2"
-
-      - name: Build module
-        working-directory: python
-        run: |
-          uv run --no-sync python setup.py build_ext --inplace
-
-      - name: Run tests with numpy 1.x
-        working-directory: python
-        run: |
-          uv run --no-sync 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@v5.5.2
-        with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-          working-directory: python
-          fail_ci_if_error: false
-          flags: python-tests-numpy1
-          name: codecov-numpy1
+          gcov_args: --preserve-paths
           verbose: true
 
   msys2:

.github/workflows/wheels.yml

@@ -20,7 +20,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python: ["3.10", 3.11, 3.12, 3.13, 3.14]
+        python: [3.11, 3.12, 3.13, 3.14]
     steps:
       - name: Checkout
         uses: actions/checkout@v6.0.2
@@ -51,7 +51,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python: ["3.10", 3.11, 3.12, 3.13, 3.14]
+        python: [3.11, 3.12, 3.13, 3.14]
         wordsize: [64]
     steps:
       - name: Checkout
@@ -91,10 +91,10 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v6.0.2
 
-      - name: Set up Python 3.10
+      - name: Set up Python 3.11
         uses: actions/setup-python@v6.1.0
         with:
-          python-version: "3.10"
+          python-version: 3.11
 
       - name: Build sdist
         shell: bash
@@ -125,7 +125,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python: ["3.10", 3.11, 3.12, 3.13, 3.14]
+        python: [3.11, 3.12, 3.13, 3.14]
         runner: [macos-15, macos-15-intel]
         include:
           - runner: macos-15
@@ -163,7 +163,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python: ["3.10", 3.11, 3.12, 3.13, 3.14]
+        python: [3.11, 3.12, 3.13, 3.14]
         wordsize: [64]
     steps:
       - name: Download wheels
@@ -188,10 +188,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python: ["3.10", 3.11, 3.12, 3.13, 3.14]
+        python: [3.11, 3.12, 3.13, 3.14]
         include:
-          - python: "3.10"
-            wheel: cp310
           - python: 3.11
             wheel: cp311
           - python: 3.12

c/examples/error_handling.c

@@ -21,8 +21,7 @@ main(int argc, char **argv)
     }
     printf("Loaded tree sequence with %lld nodes and %lld edges from %s\n",
         (long long) tsk_treeseq_get_num_nodes(&ts),
-        (long long) tsk_treeseq_get_num_edges(&ts),
-        argv[1]);
+        (long long) tsk_treeseq_get_num_edges(&ts), argv[1]);
     tsk_treeseq_free(&ts);
 
     return EXIT_SUCCESS;

c/examples/haploid_wright_fisher.c

@@ -11,8 +11,7 @@
     }
 
 void
-simulate(
-    tsk_table_collection_t *tables, int N, int T, int simplify_interval)
+simulate(tsk_table_collection_t *tables, int N, int T, int simplify_interval)
 {
     tsk_id_t *buffer, *parents, *children, child, left_parent, right_parent;
     double breakpoint;
@@ -44,10 +43,10 @@ simulate(
              * research code and proper random number generator
              * libraries should be preferred.
              */
-            left_parent = parents[(size_t)((rand()/(1.+RAND_MAX))*N)];
-            right_parent = parents[(size_t)((rand()/(1.+RAND_MAX))*N)];
+            left_parent = parents[(size_t) ((rand() / (1. + RAND_MAX)) * N)];
+            right_parent = parents[(size_t) ((rand() / (1. + RAND_MAX)) * N)];
             do {
-                breakpoint = rand()/(1.+RAND_MAX);
+                breakpoint = rand() / (1. + RAND_MAX);
             } while (breakpoint == 0); /* tiny proba of breakpoint being 0 */
             ret = tsk_edge_table_add_row(
                 &tables->edges, 0, breakpoint, left_parent, child, NULL, 0);
@@ -58,18 +57,15 @@ simulate(
             children[j] = child;
         }
         if (t % simplify_interval == 0) {
-            printf("Simplify at generation %lld: (%lld nodes %lld edges)",
-                (long long) t,
-                (long long) tables->nodes.num_rows,
-                (long long) tables->edges.num_rows);
+            printf("Simplify at generation %lld: (%lld nodes %lld edges)", (long long) t,
+                (long long) tables->nodes.num_rows, (long long) tables->edges.num_rows);
             /* Note: Edges must be sorted for simplify to work, and we use a brute force
              * approach of sorting each time here for simplicity. This is inefficient. */
             ret = tsk_table_collection_sort(tables, NULL, 0);
             check_tsk_error(ret);
             ret = tsk_table_collection_simplify(tables, children, N, 0, NULL);
             check_tsk_error(ret);
-            printf(" -> (%lld nodes %lld edges)\n",
-                (long long) tables->nodes.num_rows,
+            printf(" -> (%lld nodes %lld edges)\n", (long long) tables->nodes.num_rows,
                 (long long) tables->edges.num_rows);
             for (j = 0; j < N; j++) {
                 children[j] = j;
@@ -90,7 +86,7 @@ main(int argc, char **argv)
     }
     ret = tsk_table_collection_init(&tables, 0);
     check_tsk_error(ret);
-    srand((unsigned)atoi(argv[5]));
+    srand((unsigned) atoi(argv[5]));
     simulate(&tables, atoi(argv[1]), atoi(argv[2]), atoi(argv[3]));
 
     /* Sort and index so that the result can be opened as a tree sequence */