Add codecov token (#403)

* add codecov token

* generate xml coverage report

* add timeout to testing jobs

.github/workflows/test_and_deploy.yml

@@ -65,11 +65,13 @@ jobs:
       - uses: neuroinformatics-unit/actions/test@v2
         with:
           python-version: ${{ matrix.python-version }}
+          secret-codecov-token: ${{ secrets.CODECOV_TOKEN }}
           use-xvfb: true
 
   test_numba_disabled:
     needs: [linting, manifest]
     name: Run tests with numba disabled
+    timeout-minutes: 60
     runs-on: ubuntu-latest
     env:
        NUMBA_DISABLE_JIT: "1"
@@ -89,13 +91,15 @@ jobs:
       - uses: neuroinformatics-unit/actions/test@v2
         with:
           python-version: "3.10"
+          secret-codecov-token: ${{ secrets.CODECOV_TOKEN }}
           codecov-flags: "numba"
 
   # Run brainglobe-workflows brainmapper-CLI tests to check for
   # breakages
   test_brainmapper_cli:
     needs: [linting, manifest]
     name: Run brainmapper tests to check for breakages
+    timeout-minutes: 60
     runs-on: ubuntu-latest
     steps:
       - name: Cache tensorflow model

pyproject.toml

@@ -120,7 +120,7 @@ python =
     3.10: py310
 
 [testenv]
-commands = python -m pytest -v --color=yes
+commands = python -m pytest -v --color=yes --cov=cellfinder --cov-report=xml
 deps =
     pytest
     pytest-cov