fix: jupyter notebook tests, deprecation warnings

docs/scripts/coverage_status.py

@@ -24,7 +24,7 @@ def on_pre_build(config):
     """Generate coverage report if it is missing and create a badge."""
     if not Path("htmlcov").is_dir() or not Path(".coverage").is_file():
         log.info("Missing htmlcov or .coverage, running pytest to collect.")
-        pytest.main(["--cov", "--cov-report=html"])
+        pytest.main(["--cov=src", "--cov-report=html"])
     else:
         log.info("Using existing coverage data.")
 

pyproject.toml

@@ -70,16 +70,16 @@ testbook = "^0.4.2"
 
 [tool.poetry.group.docs.dependencies]
 mkdocs = "^1.4.2"
-mkdocstrings = {extras = ["python"], version = "^0.21.2"}
+mkdocstrings = {extras = ["python"], version = "^0.22.0"}
 mkdocs-material = "^9.1.6"
-mkdocs-gen-files = "^0.4.0"
+mkdocs-gen-files = "^0.5.0"
 mkdocs-literate-nav = "^0.6.0"
 mkdocs-section-index = "^0.3.5"
 mkdocs-macros-plugin = "^0.7.0"
 markdown-include = "^0.8.1"
 pymdown-extensions = "^10.0"
 markdown-exec = {extras = ["ansi"], version = "^1.6.0"}
-mkdocs-coverage = "^0.2.7"
+mkdocs-coverage = "^1.0.0"
 mike = "^1.1.2"
 anybadge = "^1.14.0"
 black = "^23.7.0"

tests/zz_docs/test_notebooks.py

@@ -5,7 +5,7 @@
 from testbook import testbook
 
 
-@pytest.fixture(scope="module")
+@pytest.fixture(scope="function")
 def nb_cwd():
     """Fixture to change CWD to location of notebooks."""
     old = os.getcwd()