CI: test that runs pdf pack examples in CI

docs/examples/ch03NiModelling/solutions/diffpy-cmi/fitBulkNi.py

@@ -70,7 +70,7 @@
 
 # If we want to run using multiprocessors, we can switch this to 'True'.
 # This requires that the 'psutil' python package installed.
-RUN_PARALLEL = True
+RUN_PARALLEL = False
 
 
 # Functions that will carry out the refinement ##################

docs/examples/ch03NiModelling/solutions/diffpy-cmi/fitNPPt.py

@@ -87,6 +87,9 @@
     print("The Ni example refines instrument parameters\n")
     print("The instrument parameters are necessary to run this fit\n")
     print("Please run the Ni example first\n")
+    print("Setting Q_damp and Q_broad to refined values\n")
+    QDAMP_I = 0.045298
+    QBROAD_I = 0.016809
 
 # If we want to run using multiprocessors, we can switch this to 'True'.
 # This requires that the 'psutil' python package installed.

docs/examples/ch11ClusterXYZ/solutions/diffpy-cmi/fitCdSeNP.py

@@ -199,9 +199,6 @@ def plot_results(recipe, figname):
     diff = g - gcalc + diffzero
 
     mpl.rcParams.update(mpl.rcParamsDefault)
-    plt.style.use(
-        str(PWD.parent.parent.parent / "utils" / "billinge.mplstyle")
-    )
 
     fig, ax1 = plt.subplots(1, 1)
 

docs/source/tutorials/index.rst

@@ -6,7 +6,7 @@ Despite its utility, PDF fitting and analysis can be challenging.
 The process of understand PDFs requires time, care, and the development of intuition to connect structural models to experimental data.
 Hopefully by the end of this tutorial series, PDF fitting will go from being a mysterious black box to a powerful tool in your structural analysis.
 
-Example usage of ``diffpy.cmi`` can be found at `this GitHub repo <https://github.com/diffpy/pdfttp_data>`_.
+Example usage of ``diffpy.cmi`` can be found at `this GitHub repo <https://github.com/Billingegroup/pdfttp_data>`_.
 
 .. _structural-parameters:
 

news/test-tutorial-CI.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* Add CI for testing examples of the PDF pack.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

pyproject.toml

@@ -48,6 +48,13 @@ include = ["*"]  # package names should match these glob patterns (["*"] by defa
 exclude = []  # exclude packages matching these glob patterns (empty by default)
 namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
 
+[tool.coverage.run]
+omit = [
+    "*/tests/*",
+    "*/examples_copy*/*",
+    "*/__pycache__/*",
+]
+
 [project.scripts]
 cmi = "diffpy.cmi.cli:main"
 

tests/conftest.py

@@ -1,8 +1,19 @@
 import json
+import shutil
+import warnings
 from pathlib import Path
 
+import matplotlib
 import pytest
 
+# Suppress specific UserWarnings when running mpl headless
+warnings.filterwarnings(
+    "ignore", category=UserWarning, message=".*FigureCanvasAgg.*"
+)
+
+EXAMPLES_DIR = Path(__file__).parent.parent / "docs" / "examples"
+TESTS_DIR = Path(__file__).parent
+
 
 @pytest.fixture
 def user_filesystem(tmp_path):
@@ -17,3 +28,22 @@ def user_filesystem(tmp_path):
         json.dump(home_config_data, f)
 
     yield tmp_path
+
+
+@pytest.fixture(scope="session", autouse=True)
+def use_headless_matplotlib():
+    """Force matplotlib to use a headless backend during tests."""
+    matplotlib.use("Agg")
+
+
+@pytest.fixture(scope="session")
+def examples_tmpdir(tmp_path_factory):
+    """Make a temp copy of all examples for safe testing.
+
+    Removes the temp copy after tests are done.
+    """
+    temp_dir = tmp_path_factory.mktemp("examples_copy")
+    temp_examples = temp_dir / "examples"
+    shutil.copytree(EXAMPLES_DIR, temp_examples, dirs_exist_ok=True)
+    yield temp_examples
+    shutil.rmtree(temp_dir, ignore_errors=True)

tests/examples_exist_test.py

@@ -0,0 +1,25 @@
+from conftest import TESTS_DIR
+
+
+def test_example_dirs_have_tests(examples_tmpdir):
+    """Verify that each example directory has a corresponding test
+    file."""
+    example_dirs = [d for d in examples_tmpdir.iterdir() if d.is_dir()]
+    missing_tests = []
+    for example_dir in example_dirs:
+        # Test file expected in TESTS_DIR, named e.g. test_<example_dir>.py
+        test_file = TESTS_DIR / f"test_{example_dir.name}.py"
+        if not test_file.exists():
+            missing_tests.append(example_dir.name)
+    assert not missing_tests, (
+        f"The following example dirs have no test file: {missing_tests}.",
+        "Test file must be named test_<example_dir>.py.",
+    )
+
+
+def test_examples_tmpdir_exists(examples_tmpdir):
+    """Ensure that the examples temporary directory has been created."""
+    # Check the directory itself exists
+    assert (
+        examples_tmpdir.exists() and examples_tmpdir.is_dir()
+    ), f"Temporary examples directory does not exist: {examples_tmpdir}"

tests/helpers.py

@@ -0,0 +1,43 @@
+import importlib.util
+import os
+from pathlib import Path
+
+
+def load_module_from_path(path: Path):
+    """Load a module given an absolute Path."""
+    spec = importlib.util.spec_from_file_location(path.stem, path)
+    module = importlib.util.module_from_spec(spec)
+    spec.loader.exec_module(module)
+    return module
+
+
+def run_cmi_script(script_path: Path):
+    """Run a script with a main() function."""
+    old_cwd = os.getcwd()
+    os.chdir(script_path.parent)
+    try:
+        module = load_module_from_path(script_path)
+        module.main()
+    finally:
+        os.chdir(old_cwd)
+
+
+def run_all_scripts_for_given_example(examples_tmpdir, test_file_path):
+    """Run all Python scripts in the chapter corresponding to this test
+    file.
+
+    Only scripts that define a main() function will be executed.
+    """
+    chapter_dir_name = Path(test_file_path).stem.replace("test_", "")
+    chapter_dir = examples_tmpdir / chapter_dir_name
+    assert chapter_dir.exists(), f"Chapter dir does not exist: {chapter_dir}"
+
+    # Recursively find all .py scripts
+    scripts = list(chapter_dir.rglob("*.py"))
+    for script_path in scripts:
+        module = load_module_from_path(script_path)
+        if hasattr(module, "main"):
+            run_cmi_script(script_path)
+        else:
+            # automatically skip helper or non-example scripts
+            print(f"Skipping file without main(): {script_path.name}")

tests/test_ch03NiModelling.py

@@ -0,0 +1,5 @@
+from helpers import run_all_scripts_for_given_example
+
+
+def test_scripts(examples_tmpdir):
+    run_all_scripts_for_given_example(examples_tmpdir, __file__)

tests/test_ch05Fit2Phase.py

@@ -0,0 +1,5 @@
+from helpers import run_all_scripts_for_given_example
+
+
+def test_scripts(examples_tmpdir):
+    run_all_scripts_for_given_example(examples_tmpdir, __file__)

tests/test_ch06RefineCrystalStructureGen.py

@@ -0,0 +1,5 @@
+from helpers import run_all_scripts_for_given_example
+
+
+def test_scripts(examples_tmpdir):
+    run_all_scripts_for_given_example(examples_tmpdir, __file__)

tests/test_ch07StructuralPhaseTransitions.py

@@ -0,0 +1,5 @@
+from helpers import run_all_scripts_for_given_example
+
+
+def test_scripts(examples_tmpdir):
+    run_all_scripts_for_given_example(examples_tmpdir, __file__)

tests/test_ch08NPRefinement.py

@@ -0,0 +1,5 @@
+from helpers import run_all_scripts_for_given_example
+
+
+def test_scripts(examples_tmpdir):
+    run_all_scripts_for_given_example(examples_tmpdir, __file__)

tests/test_ch11ClusterXYZ.py

@@ -0,0 +1,5 @@
+from helpers import run_all_scripts_for_given_example
+
+
+def test_scripts(examples_tmpdir):
+    run_all_scripts_for_given_example(examples_tmpdir, __file__)