Fix code coverage (#432)

* Add codecov logging and function check

* revert codecov config changes

* add text report

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* try removing source

* specify source using CLI

* run coverage directly

* remove misleading __init__.py

* remove hatch config, oops

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.github/workflows/test.yml

@@ -52,7 +52,13 @@ jobs:
                   MPLBACKEND: agg
                   PLATFORM: ${{ matrix.os }}
                   DISPLAY: :42
-              run: pytest -v --cov --color=yes
+              run: coverage run -m pytest -v --color=yes
+
+            - name: Show coverage report
+              run: coverage report -m
 
             - name: Upload coverage
               uses: codecov/codecov-action@v3
+              with:
+                  fail_ci_if_error: true
+                  verbose: true

codecov.yml

@@ -1,13 +1,16 @@
-comment: false
+codecov:
+    require_ci_to_pass: no
+
 coverage:
     status:
         project:
             default:
-                target: auto
-        patch:
-            default:
-                enabled: no
-    ignore:
-        - "test/"
-github_checks:
-    annotations: false
+                # Require 1% coverage, i.e., succeed as long as coverage collection works
+                target: 1
+        patch: false
+        changes: false
+
+comment:
+    layout: diff, flags, files
+    behavior: once
+    require_base: no

pyproject.toml

@@ -100,20 +100,20 @@ doc = [
 ]
 test = [
     "pytest",
-    "pytest-cov",
+    "coverage",
 ]
 
 [tool.hatch.version]
 source = "vcs"
 
 [tool.coverage.run]
-source = ["pertpy"]
+source_pkgs = ["pertpy"]
 omit = [
     "**/test_*.py",
 ]
 
 [tool.pytest.ini_options]
-testpaths = "pertpy/tests"
+testpaths = "tests"
 xfail_strict = true
 addopts = [
     "--import-mode=importlib",  # allow using test files with same name