Initial prek+ruff setup

First batch of ruff changes

Update the test suite for ruff

More python updates

Clanf-format some C examples code

Fixup some issues

Switch to uv-based docs

Finalise docs workflow

Update to use docs build

Update the docs helper makefile to use uv

Update workflows

fixup pyproject

Use standard C-test workflows

Initial standard codecov config

Udpate

Update again

Update

Update

Try

Update

Udpate

Update

add cdev group and pin gcovr, meson

Udpate

Update

Update

Switch back # Please enter the commit message for your changes. Lines starting

Update

Author: jeromekelleher

.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/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

@@ -1,3 +1,4 @@
+# DELETEME9
 name: Tests
 
 on:
@@ -10,11 +11,6 @@ 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 +19,27 @@ 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: [ 3.11, 3.14 ]
+        python: [ 3.11, 3.13 ]
         os:  [ macos-latest, ubuntu-24.04, windows-latest ]
     defaults:
       run:
@@ -97,6 +107,7 @@ jobs:
           flags: python-tests-no-jit
           name: codecov-umbrella
           verbose: true
+
       - name: Run tests
         working-directory: python
         run: |
@@ -113,7 +124,7 @@ jobs:
           working-directory: python
           fail_ci_if_error: false
           flags: python-tests
-          name: codecov-umbrella
+          gcov_args: --preserve-paths
           verbose: true
 
   msys2:

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 */

c/examples/multichrom_wright_fisher.c

@@ -212,8 +212,8 @@ 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)];
             left_is_first = rand() < 0.5;
             chunk_left = 0.0;
             for (k = 0; k < num_chroms; k++) {

c/examples/multichrom_wright_fisher_singlethreaded.c

@@ -46,8 +46,8 @@ 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)];
             left_is_first = rand() < 0.5;
             chunk_left = 0.0;
             for (k = 0; k < num_chroms; k++) {
@@ -68,18 +68,15 @@ 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;
@@ -104,7 +101,7 @@ 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[6]), atoi(argv[1]), atoi(argv[2]), atoi(argv[3]));
 
     /* Sort and index so that the result can be opened as a tree sequence */

c/examples/tree_iteration.c

@@ -26,16 +26,14 @@ main(int argc, char **argv)
 
     printf("Iterate forwards\n");
     for (ret = tsk_tree_first(&tree); ret == TSK_TREE_OK; ret = tsk_tree_next(&tree)) {
-        printf("\ttree %lld has %lld roots\n",
-            (long long) tree.index,
+        printf("\ttree %lld has %lld roots\n", (long long) tree.index,
             (long long) tsk_tree_get_num_roots(&tree));
     }
     check_tsk_error(ret);
 
     printf("Iterate backwards\n");
     for (ret = tsk_tree_last(&tree); ret == TSK_TREE_OK; ret = tsk_tree_prev(&tree)) {
-        printf("\ttree %lld has %lld roots\n",
-            (long long) tree.index,
+        printf("\ttree %lld has %lld roots\n", (long long) tree.index,
             (long long) tsk_tree_get_num_roots(&tree));
     }
     check_tsk_error(ret);

docs/Makefile

@@ -1,9 +1,3 @@
-
-# Need to set PYTHONPATH so that we pick up the local tskit
-PYPATH=$(shell pwd)/../python/
-TSK_VERSION:=$(shell PYTHONPATH=${PYPATH} \
-   python -c 'import tskit; print(tskit.__version__.split("+")[0])')
-
 BUILDDIR      = _build
 DOXYGEN_XML=doxygen/xml
 
@@ -13,13 +7,7 @@ ${DOXYGEN_XML}: ../c/tskit/*.h
 	cd doxygen && doxygen
 
 dev:
-	PYTHONPATH=${PYPATH} ./build.sh
-
-dist:
-	@echo Building distribution for tskit version ${TSK_VERSION}
-	cd doxygen && doxygen
-	sed -i -e s/__TSKIT_VERSION__/${TSK_VERSION}/g _config.yml
-	PYTHONPATH=${PYPATH} ./build.sh
+	uv --project=../python run jupyter-book build -Wn --keep-going .
 
 clean:
 	rm -fR $(BUILDDIR) $(DOXYGEN_XML)