Fix coverage and add lwt coverage

Author: benjeffery

.circleci/config.yml

@@ -59,18 +59,9 @@ jobs:
           name: Run gcov & upload coverage.
           command: |
             cd build-gcc
-            # TODO should be able to do this with 'find', but it's tricky and opaque.
-            gcov -pb libtskit.a.p/tskit_core.c.gcno ../c/tskit/core.c
-            gcov -pb libtskit.a.p/tskit_tables.c.gcno ../c/tskit/tables.c
-            gcov -pb libtskit.a.p/tskit_trees.c.gcno ../c/tskit/trees.c
-            gcov -pb libtskit.a.p/tskit_genotypes.c.gcno ../c/tskit/genotypes.c
-            gcov -pb libtskit.a.p/tskit_core.c.gcno ../c/tskit/core.c
-            gcov -pb libtskit.a.p/tskit_convert.c.gcno ../c/tskit/convert.c
-            gcov -pb libtskit.a.p/tskit_stats.c.gcno ../c/tskit/stats.c
-            gcov -pb libtskit.a.p/tskit_haplotype_matching.c.gcno ../c/tskit/haplotype_matching.c
-            gcov -pb libtskit.a.p/tskit_file_format.c.gcno ../c/tskit/file_format.c
+            find ../c/tskit/*.c -type f -printf "%f\n" | xargs -i gcov -pb libtskit.a.p/tskit_{}.gcno ../c/tskit/{}
             cd ..
-            bash <(curl -s https://codecov.io/bash) -X gcov -n c_tests
+            bash <(curl -s https://codecov.io/bash) -X gcov -X coveragepy -F c-tests
 
       - run:
           name: Valgrind for C tests.
@@ -110,28 +101,41 @@ jobs:
           command: |
             make -C c/examples
 
+      - run:
+          name: Build example LWT interface code and test
+          command: |
+            # We're assuming that the tskit C module has already
+            # been built, as we're testing against the local tskit version.
+            cd python/lwt_interface
+            make allchecks
+            python -m pytest
+
+      - run:
+          name: Upload LWT coverage
+          command: |
+            # Make sure the C coverage reports aren't lying around
+            rm -fR build-gcc
+            ls -R
+            cd python/lwt_interface
+            gcov -pb -o ./build/temp.linux*/*.gcno example_c_module.c
+            bash <(curl -s https://codecov.io/bash) -X gcov -F lwt-tests
+
       - run:
           name: Run Python tests
           command: |
             cd python
-            python -m pytest --cov=tskit  --cov-report=xml --cov-branch -n8 tests
+            python -m pytest --cov=tskit  --cov-report=xml --cov-branch -n16 tests
 
       - run:
           name: Upload Python coverage
           command: |
             # Make sure the C coverage reports aren't lying around
             rm -fR build-gcc
-            bash <(curl -s https://codecov.io/bash) -X gcov -n python_tests
-            # Clean up reports so we don't upload them twice.
-            rm -f coverage.xml
-
-            # Upload coverage for the Python C API.
             cd python
             gcov -pb -o ./build/temp.linux*/*.gcno _tskitmodule.c
-            cd ..
-            bash <(curl -s https://codecov.io/bash) -X gcov -n python_c_tests
-            # Clean up reports so we don't upload them twice.
-            rm -f python/*.gcov
+            bash <(curl -s https://codecov.io/bash) -f coverage.xml -F python-tests
+            rm -f coverage.xml
+            bash <(curl -s https://codecov.io/bash) -X gcov -F python-c-tests
 
       - run:
           name: Build Python package
@@ -149,12 +153,3 @@ jobs:
             python setup.py bdist_wheel
             pip install dist/*.tar.gz
             tskit --help
-
-      - run:
-          name: Build example LWT interface code and test
-          command: |
-            # We're assuming that the tskit C module has already
-            # been built, as we're testing against the local tskit version.
-            cd python/lwt_interface
-            make allchecks
-            python -m pytest

.codecov.yml

@@ -1,12 +1,18 @@
+comment:
+  layout: "diff, flags, files"
 coverage:
+  require_ci_to_pass: false
   status:
     project:
       python-tests:
         target: 95%
-        flags: python_tests
+        flags: python-tests
       python-c-tests:
         target: 85%
-        flags: python_c_tests
+        flags: python-c-tests
       c-tests:
         target: 85%
-        flags: c_tests
+        flags: c-tests
+      lwt-tests:
+        target: 85%
+        flags: lwt-tests

python/requirements/CI-complete/requirements.txt

@@ -3,7 +3,6 @@ autodocsumm==0.2.1
 biopython==1.78
 black==20.8b1
 breathe==4.23.0
-codecov==2.1.10
 coverage==5.3
 flake8==3.8.4
 h5py==3.0.0