Add test coverage

Configure future PRs to require an equal or greater level of test
coverage than previous

.github/workflows/test.yml

@@ -76,9 +76,18 @@ jobs:
           HYPOTHESIS_PROFILE: pr
         run: >-
           poetry run pytest -n auto --splits 5 --group ${{ matrix.split }}
+          --cov=snakebids --cov-report=xml
           --doctest-modules --ignore=docs
           --ignore=snakebids/project_template --benchmark-disable
 
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          verbose: true
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+
   deployment_on_base:
     runs-on: ubuntu-latest
     if: ${{ contains(github.event_name, 'pull_request') }}

codecov.yml

@@ -0,0 +1,6 @@
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 0%

pyproject.toml

@@ -86,6 +86,7 @@ pytest-xdist = "^3.3.1"
 pytest-split = "^0.8.1"
 tomli = "^2.0.1"
 requests-mock = "^1.11.0"
+pytest-cov = "^4.1.0"
 
 [tool.poetry.scripts]
 snakebids = "snakebids.admin:main"
@@ -123,6 +124,18 @@ markers = [
     "docker: marks tests as requiring docker (deselect with '-m \"not docker\"')",
 ]
 
+[tool.coverage.run]
+omit = [
+    "snakebids/project_template/**",
+    "snakebids/tests/**",
+]
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: not covered",
+    "@overload",
+]
+
 [tool.isort]
 profile = "black"
 multi_line_output = 3