Refactor testing

- Migrate to pytest testing
- Move tests out of main folder
- Add coverage reporting to github
- Add testing for pyyaml
- Refactor how ruamel vs pyyaml is implemented

.github/workflows/test_castep_outputs.yml

@@ -6,7 +6,7 @@ name: Python application
 on:
   push:
     branches: [ "main" ]
-  pull_request: 
+  pull_request:
     types:
       - opened
       - synchronize
@@ -17,9 +17,9 @@ permissions:
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
-
+    permissions:
+      pull-requests: write
     strategy:
       matrix:
         python-version: ["3.8", "3.9", "3.10"]
@@ -33,8 +33,12 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install ruamel.yaml coverage
+        pip install ".[test,ruamel,yaml]"
     - name: Run tests
       run: |
-        PYTHONPATH=. coverage run -m unittest discover castep_outputs/test/
-        coverage report
+        pytest --doctest-modules --cov=castep_outputs --cov-report xml:coverage.xml
+    - name: Get Coverage
+      uses: orgoro/[email protected]
+      with:
+        coverageFile: coverage.xml
+        token: ${{ secrets.GITHUB_TOKEN }}

castep_outputs/utilities/dumpers.py

@@ -3,17 +3,18 @@
 
 import json
 import pprint
+from contextlib import suppress
 from typing import Any, Callable, TextIO
 
-try:
-    from ruamel import yaml
+_YAML_TYPE = None
+
+with suppress(ImportError):
+    import yaml
+    _YAML_TYPE = "pyyaml"
+
+with suppress(ImportError):
+    from ruamel import yaml as ruamel
     _YAML_TYPE = "ruamel"
-except ImportError:
-    try:
-        import yaml
-        _YAML_TYPE = "yaml"
-    except ImportError:
-        _YAML_TYPE = None
 
 
 #: Dumping function protocol.
@@ -45,11 +46,11 @@ def ruamel_dumper(data: Any, file: TextIO):
     file
         File to dump to.
     """
-    yaml_eng = yaml.YAML(typ="unsafe")
+    yaml_eng = ruamel.YAML(typ="unsafe")
     yaml_eng.dump(data, file)
 
 
-def yaml_dumper(data: Any, file: TextIO):
+def pyyaml_dumper(data: Any, file: TextIO):
     """
     YAML (pyyaml) format dumper.
 
@@ -117,21 +118,21 @@ def get_dumpers(dump_fmt: str) -> Dumper:
     SUPPORTED_FORMATS
         Acceptable values for `dump_fmt`.
     """
-    if dump_fmt not in SUPPORTED_FORMATS:
-        raise ValueError(f"Cannot output in {dump_fmt} format. "
-                         f"Valid keys are: {', '.join(SUPPORTED_FORMATS.keys())}")
-
     if dump_fmt == "yaml":
         if _YAML_TYPE is None:
             raise ImportError("Couldn't find valid yaml dumper (ruamel.yaml / yaml)"
                               "please install and try again.")
         dump_fmt = _YAML_TYPE
 
+    if dump_fmt not in SUPPORTED_FORMATS:
+        raise ValueError(f"Cannot output in {dump_fmt} format. "
+                         f"Valid keys are: {', '.join(SUPPORTED_FORMATS.keys())}")
+
     return SUPPORTED_FORMATS[dump_fmt]
 
 #: Currently supported dumpers.
 SUPPORTED_FORMATS: dict[str, Dumper] = {"json": json_dumper,
                                         "ruamel": ruamel_dumper,
-                                        "yaml": yaml_dumper,
+                                        "pyyaml": pyyaml_dumper,
                                         "pprint": pprint_dumper,
                                         "print": print_dumper}

pyproject.toml

@@ -32,6 +32,7 @@ ruamel = ["ruamel.yaml>=0.17.22"]
 yaml = ["pyYAML>=3.13"]
 docs = ["jupyter-book>=0.13.1", "sphinx-book-theme>=0.3.3", "sphinx-argparse>=0.4.0", "sphinx-autodoc-typehints"]
 lint = ["ruff==0.8.0"]
+test = ["pytest==8.3.4", "pytest-cov==5.0.0"]
 
 [project.scripts]
 castep_outputs = "castep_outputs.cli.castep_outputs_main:main"