Add test infrastructure

- Add pytest configuration with verbose output
- Add mypy configuration with strict type checking
- Add coverage configuration and reporting
- Add development dependencies in requirements.txt
- Update CI workflow to run tests, type checks and coverage
- Update gitignore for test artifacts

Co-Authored-By: K. Yanagisawa <[email protected]>

.coveragerc

@@ -0,0 +1,14 @@
+[run]
+source = script
+omit = 
+    script/test_*.py
+    script/**/test_*.py
+
+[report]
+exclude_lines =
+    pragma: no cover
+    def __repr__
+    raise NotImplementedError
+    if __name__ == .__main__.:
+    pass
+    raise ImportError

.github/workflows/unittest.yml

@@ -22,4 +22,8 @@ jobs:
           options: -v ${{ github.workspace }}:/work
           run: |
             cd /work
-            python -m pytest .
+            pip install mypy coverage
+            python -m pytest .
+            python -m mypy script/
+            coverage run -m pytest
+            coverage report -m

.gitignore

@@ -137,7 +137,10 @@ dmypy.json
 **~
 \#**
 
-**test**
+**/test_data/**
+**/test_output/**
+.coverage
+htmlcov/
 **rmsd.dat
 **.out
-**.err
+**.err

mypy.ini

@@ -0,0 +1,36 @@
+[mypy]
+python_version = 3.12
+warn_return_any = True
+warn_unused_configs = True
+disallow_untyped_defs = True
+disallow_incomplete_defs = True
+check_untyped_defs = True
+disallow_untyped_decorators = True
+no_implicit_optional = True
+warn_redundant_casts = True
+warn_unused_ignores = True
+warn_no_return = True
+warn_unreachable = True
+strict_optional = True
+ignore_missing_imports = True
+
+[mypy.plugins.numpy.*]
+ignore_missing_imports = True
+
+[mypy-gridData.*]
+ignore_missing_imports = True
+
+[mypy-Bio.*]
+ignore_missing_imports = True
+
+[mypy-scipy.*]
+ignore_missing_imports = True
+
+[mypy-jinja2.*]
+ignore_missing_imports = True
+
+[mypy-tqdm.*]
+ignore_missing_imports = True
+
+[mypy-yaml.*]
+ignore_missing_imports = True

pytest.ini

@@ -0,0 +1,5 @@
+[pytest]
+python_files = test_*.py
+python_functions = test_*
+addopts = --maxfail=1 --disable-warnings -v
+testpaths = script

requirements.txt

@@ -0,0 +1,10 @@
+pytest>=7.0.0
+coverage>=7.0.0
+mypy>=1.0.0
+numpy>=1.24.0
+gridData>=1.0.0
+scipy>=1.10.0
+Bio>=1.0.0
+jinja2>=3.0.0
+tqdm>=4.65.0
+pyyaml>=6.0.0