Refactor code structure for improved readability and maintainability

.github/workflows/CI-CD.yml

@@ -34,7 +34,7 @@ jobs:
 
       - name: Install linting tools
         run: |
-          python -m pip install shyaml flake8 black black-nb flake8-nb ruff
+          python -m pip install ruff
 
       - name: Check Ruff formatting
         id: ruff-format
@@ -47,10 +47,6 @@ jobs:
         run: |
           echo "::warning::Ruff formatting issues detected. Run 'ruff format .' locally to apply formatting fixes."
 
-      - name: Run black formatter
-        run: |
-          black -l 99 . --exclude '\.ipynb$'
-
       - name: Install pytest and run tests
         run: |
           pip install pytest pytest-cov

MANIFEST.in

@@ -1,6 +1,5 @@
 include LICENSE
 include MANIFEST.in
-include versioneer.py
 
 graft openmmdl
 global-exclude *.py[cod] __pycache__ *.so

environment.yml

@@ -7,7 +7,6 @@ channels:
 dependencies:
   - pip
   - setuptools>=61.0
-  - versioningit~=2.0
   - sqlite>=3.40
   - pytest>=6.1.2
   - pytest-runner

openmmdl/cli/cli.py

@@ -77,30 +77,17 @@ def _normalize_help_tokens(argv: List[str]) -> List[str]:
 
 def _run_target(target: str, forwarded: List[str], prog: str) -> int:
     """
-    Import target and call either:
-      - module:function     (callable)
-      - module              (expects main())
-    Forward argv via sys.argv.
+    Import 'module:function' target, call it, and forward argv via sys.argv.
     """
     old_argv = sys.argv
     sys.argv = [prog, *forwarded]
     try:
-        if ":" in target:
-            mod_name, func_name = target.split(":", 1)
-            mod = importlib.import_module(mod_name)
-            fn = getattr(mod, func_name, None)
-            if fn is None or not callable(fn):
-                raise RuntimeError(f"Module '{mod_name}' does not expose callable '{func_name}'.")
-            rc = fn()
-            return 0 if rc is None else int(rc)
-
-        mod = importlib.import_module(target)
-        if not hasattr(mod, "main"):
-            raise RuntimeError(
-                f"Module '{target}' does not expose a main() function. "
-                "Add def main(argv=None) and call it from __main__."
-            )
-        rc = mod.main()  # type: ignore[attr-defined]
+        mod_name, func_name = target.split(":", 1)
+        mod = importlib.import_module(mod_name)
+        fn = getattr(mod, func_name, None)
+        if fn is None or not callable(fn):
+            raise RuntimeError(f"Module '{mod_name}' does not expose callable '{func_name}'.")
+        rc = fn()
         return 0 if rc is None else int(rc)
     finally:
         sys.argv = old_argv

openmmdl/utils/logging_utils.py

@@ -94,10 +94,6 @@ def setup_logging(
     logging.getLogger("matplotlib").setLevel(logging.WARNING)
 
 
-def get_logger(name: str) -> logging.Logger:
-    return logging.getLogger(name)
-
-
 def _clear_handlers(logger: logging.Logger) -> None:
     for handler in list(logger.handlers):
         try:

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools>=61.0", "versioningit"]
+requires = ["setuptools>=61.0"]
 build-backend = "setuptools.build_meta"
 
 # Self-descriptive entries which should always be present

setup.cfg

@@ -1,22 +1,7 @@
-[flake8]
-max-line-length = 100
-ignore = E122,E123,E126,E127,E128,E731,E722
-exclude =
-    build,
-    openmmdl/_version.py,
-    tests,
-    conda.recipe,
-    .git,
-    versioneer.py,
-    benchmarks,
-    .asv
-
 [tool:pytest]
 norecursedirs = .* *.egg* build dist conda.recipe
 addopts =
     --junitxml=junit.xml
-    --ignore setup.py
-    --ignore run_test.py
     --tb native
     --strict-markers
     --durations=20