Collect coverage of numba decorated code (#124)

* Add a test without numba enabled

* Try global disable-numba variable

* Fix matrix name

* Add numba codecov flag.

* Add test specifically for numba code coverage

* Clean test file and codecov file

* Pass codecov flags

* Use v2 of NI actions

* Only run on main

.codecov.yml

@@ -1 +1,15 @@
 comment: false
+
+
+# Add a numba flag to any files that contain code jit compiled
+# with numba. Tests are run without Numba compilation on the main
+# branch to collect code coverage, and the carryforward flags are
+# used to make sure coverage of these files does not decrease on
+# pull requests.
+flags:
+  numba:
+    paths:
+      - src/cellfinder_core/detect/filters/plane/tile_walker.py
+      - src/cellfinder_core/detect/filters/volume/ball_filter.py
+      - src/cellfinder_core/detect/filters/volume/structure_detection.py
+    carryforward: true

.github/workflows/test_and_deploy.yml

@@ -19,24 +19,26 @@ jobs:
     strategy:
       matrix:
         # Run all supported Python versions on linux
-        python-version: ["3.8", "3.9", "3.10"]
         os: [ubuntu-latest]
-        # Include one windows and macos run
+        python-version: ["3.8", "3.9", "3.10"]
+        # Include one windows, one macos run
         include:
         - os: macos-latest
           python-version: "3.9"
         - os: windows-latest
           python-version: "3.9"
+
     steps:
       - name: Cache tensorflow model
         uses: actions/cache@v3
         with:
           path: "~/.cellfinder"
           key: models-${{ hashFiles('~/.cellfinder/**') }}
-      - uses: neuroinformatics-unit/actions/test@v1.0.4
+      - uses: neuroinformatics-unit/actions/test@v2
         with:
           python-version: ${{ matrix.python-version }}
 
+
   # Run cellfinder tests to make sure cellfinder is still compatible
   # with cellfinder-core
   test_cellfinder:

.github/workflows/test_numba_off.yml

@@ -0,0 +1,27 @@
+name: Test with numba turned off
+# These tests are relatively slow (~20 minutes), but are used
+# to collect code coverage on areas of code that are otherwise
+# optimised by numba.
+
+on:
+  push:
+    branches: [ main ]
+
+
+jobs:
+  test_numba_disabled:
+    name: Run tests
+    runs-on: ubuntu-latest
+    env:
+       NUMBA_DISABLE_JIT: "1"
+
+    steps:
+      - name: Cache tensorflow model
+        uses: actions/cache@v3
+        with:
+          path: "~/.cellfinder"
+          key: models-${{ hashFiles('~/.cellfinder/**') }}
+      - uses: neuroinformatics-unit/actions/test@v2
+        with:
+          python-version: "3.10"
+          codecov-flags: "numba"

tox.ini

@@ -15,3 +15,5 @@ deps =
     pytest
     pytest-cov
     pytest-timeout
+passenv =
+    NUMBA_DISABLE_JIT