From 961b3c36f4a274dc45fa406409c6de6fae24f8ec Mon Sep 17 00:00:00 2001
From: Jerome Kelleher <jk@well.ox.ac.uk>
Date: Mon, 23 Feb 2026 10:36:00 +0000
Subject: [PATCH 1/2] Rename codecov.yml

---
 .codecov.yml => codecov.yml | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename .codecov.yml => codecov.yml (100%)

diff --git a/.codecov.yml b/codecov.yml
similarity index 100%
rename from .codecov.yml
rename to codecov.yml

From 6c4d60f2adab2ef62975783630b49dcf1807041c Mon Sep 17 00:00:00 2001
From: Jerome Kelleher <jk@well.ox.ac.uk>
Date: Mon, 23 Feb 2026 10:48:48 +0000
Subject: [PATCH 2/2] Update codecov config

---
 .github/workflows/tests.yml | 32 ++++++++++++++------------------
 codecov.yml                 | 10 ++++++++--
 2 files changed, 22 insertions(+), 20 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index ef93699be2..1c0f91ae30 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -29,6 +29,7 @@ jobs:
     name: Python-C tests
     uses: tskit-dev/.github/.github/workflows/python-c-tests.yml@main
     with:
+      tests: python/tests/test_python_c.py python/tests/test_dict_encoding.py
       pyproject-directory: python
     secrets: inherit
 
@@ -75,15 +76,7 @@ jobs:
 
       - name: Install dependencies
         working-directory: python
-        run: |
-          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 python setup.py build_ext --inplace
+        run: uv sync --locked --group test
 
       - name: Minidom test
         working-directory: python
@@ -93,9 +86,10 @@ jobs:
           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 pytest -x --cov=tskit --cov-report=xml --cov-branch -n2 tests/test_jit.py
+          NUMBA_DISABLE_JIT=1 uv run --project=python \
+            pytest --cov=tskit --cov-report=xml --cov-branch -n2 \
+            python/tests/test_jit.py
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v5.5.2
@@ -103,27 +97,29 @@ jobs:
           token: ${{ secrets.CODECOV_TOKEN }}
           working-directory: python
           fail_ci_if_error: false
-          flags: python-tests-no-jit
-          name: codecov-umbrella
+          files: coverage.xml
+          disable_search: true
           verbose: true
+          flags: python-tests-no-jit
 
       - name: Run tests
-        working-directory: python
         run: |
           if [[ "${{ matrix.os }}" == "windows-latest" ]]; then
-            uv run pytest -x --skip-slow --cov=tskit --cov-report=xml --cov-branch -n2 --durations=20 tests
+            uv run --project=python \
+              pytest --cov=tskit --skip-slow --cov-report=xml --cov-branch -n2 python/tests
           else
-            uv run pytest -x --cov=tskit --cov-report=xml --cov-branch -n2 --durations=20 tests
+            uv run --project=python \
+              pytest --cov=tskit --cov-report=xml --cov-branch -n2 python/tests
           fi
 
       - 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
-          gcov_args: --preserve-paths
+          files: coverage.xml
+          disable_search: true
           verbose: true
 
   msys2:
diff --git a/codecov.yml b/codecov.yml
index 9b33b3d056..662bcb2b7f 100644
--- a/codecov.yml
+++ b/codecov.yml
@@ -1,12 +1,17 @@
 # ignore:
 #   - "lib/tests/"
-#   - "lib/dev-tools/"
-#   - "lib/avl.c"
 #   - "lib/subprojects/**/*"
 
+codecov:
+  require_ci_to_pass: false
+
 comment:
   layout: "header, diff, flags, components"  # show component info in the PR comment
 
+# fixes:
+#   - "tskit/::python/tskit/"
+#   - "^_tskitmodule.*::python/_tskitmodule.*"
+
 component_management:
   individual_components:
     - component_id: python_code
@@ -18,6 +23,7 @@ component_management:
       name: Python C interface
       paths:
         - python/_tskitmodule.c
+        - python/lwt_interface/tskit_lwt_interface.h
 
     - component_id: c_code
       name: C library