test: Run tutorials in tests

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

@@ -9,9 +9,9 @@
 # 1: Import relevant system packages that we will need...
 from pathlib import Path
 
-import matplotlib as mpl
 import matplotlib.pyplot as plt
 import numpy as np
+from bg_mpl_stylesheets.styles import all_styles
 from scipy.optimize import least_squares
 
 # ... and the relevant CMI packages
@@ -25,6 +25,7 @@
 from diffpy.srfit.structure import constrainAsSpaceGroup
 from diffpy.structure.parsers import getParser
 
+plt.style.use(all_styles["bg-style"])
 # Config
 # 2: Give a file path to where your PDF (.gr) and
 # structure (.cif) files are located.
@@ -33,7 +34,7 @@
 # First we store the absolute directory of this script,
 # then two directories above this,with the directory
 # 'data' appended
-PWD = Path(__file__).parent.absolute()
+PWD = Path(__file__).parent.resolve()
 DPATH = PWD.parent.parent / "data"
 
 # 3: Give an identifying name for the refinement, similar
@@ -264,13 +265,6 @@ def plot_results(recipe, fig_name):
     # Calculate the residual (difference) array and offset it vertically.
     diff = g - gcalc + diffzero
 
-    # Change some style details of the plot
-    mpl.rcParams.update(mpl.rcParamsDefault)
-    if (PWD.parent.parent.parent / "utils" / "billinge.mplstyle").exists():
-        plt.style.use(
-            str(PWD.parent.parent.parent / "utils" / "billinge.mplstyle")
-        )
-
     # Create a figure and an axis on which to plot
     fig, ax1 = plt.subplots(1, 1)
 

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

@@ -13,9 +13,9 @@
 # 1: Import relevant system packages that we will need...
 from pathlib import Path
 
-import matplotlib as mpl
 import matplotlib.pyplot as plt
 import numpy as np
+from bg_mpl_stylesheets.styles import all_styles
 from scipy.optimize import least_squares
 
 # ... and the relevant CMI packages
@@ -30,6 +30,7 @@
 from diffpy.srfit.structure import constrainAsSpaceGroup
 from diffpy.structure.parsers import getParser
 
+plt.style.use(all_styles["bg-style"])
 # Config ##############################
 # 2: Give a file path to where your PDF (.gr) and structure (.cif) files
 # are located.
@@ -241,13 +242,6 @@ def plot_results(recipe, fig_name):
     # Calculate the residual (difference) array and offset it vertically.
     diff = g - gcalc + diffzero
 
-    # Change some style details of the plot
-    mpl.rcParams.update(mpl.rcParamsDefault)
-    if (PWD.parent.parent.parent / "utils" / "billinge.mplstyle").exists():
-        plt.style.use(
-            str(PWD.parent.parent.parent / "utils" / "billinge.mplstyle")
-        )
-
     # Create a figure and an axis on which to plot
     fig, ax1 = plt.subplots(1, 1)
 

docs/examples/ch05Fit2Phase/solutions/diffpy-cmi/fit2P.py

@@ -10,9 +10,9 @@
 # 1: Import relevant system packages that we will need...
 from pathlib import Path
 
-import matplotlib as mpl
 import matplotlib.pyplot as plt
 import numpy as np
+from bg_mpl_stylesheets.styles import all_styles
 from scipy.optimize import least_squares
 
 # ... and the relevant CMI packages
@@ -26,6 +26,7 @@
 from diffpy.srfit.structure import constrainAsSpaceGroup
 from diffpy.structure.parsers import getParser
 
+plt.style.use(all_styles["bg-style"])
 # Config ##############################
 # 2: Give a file path to where your pdf (.gr) and (.cif) files are located.
 PWD = Path(__file__).parent.absolute()
@@ -271,13 +272,6 @@ def plot_results(recipe, fig_name):
     ni_signal = ni_scale * recipe.crystal.G_Ni.profile.ycalc
     ni_signal += min(si_signal) - np.abs(max(ni_signal))
 
-    # Change some style details of the plot
-    mpl.rcParams.update(mpl.rcParamsDefault)
-    if (PWD.parent.parent.parent / "utils" / "billinge.mplstyle").exists():
-        plt.style.use(
-            str(PWD.parent.parent.parent / "utils" / "billinge.mplstyle")
-        )
-
     # Create a figure and an axis on which to plot
     fig, ax1 = plt.subplots(1, 1)
 

docs/examples/ch06RefineCrystalStructureGen/solutions/diffpy-cmi/fitCrystalGen.py

@@ -10,9 +10,9 @@
 # 1: Import relevant system packages that we will need...
 from pathlib import Path
 
-import matplotlib as mpl
 import matplotlib.pyplot as plt
 import numpy as np
+from bg_mpl_stylesheets.styles import all_styles
 from scipy.optimize import least_squares
 
 # ... and the relevant CMI packages
@@ -27,12 +27,7 @@
 from diffpy.structure.atom import Atom
 from diffpy.structure.parsers import getParser
 
-try:
-    from bg_mpl_stylesheets.bg_mpl_stylesheet import bg_mpl_style
-
-    plt.style.use(bg_mpl_style)
-except ImportError:
-    pass
+plt.style.use(all_styles["bg-style"])
 
 # Config ##############################
 # 2: Give a file path to where your pdf (.gr) and (.cif) files are located.
@@ -246,13 +241,6 @@ def plot_results(recipe, fig_name):
     # Calculate the residual (difference) array and offset it vertically.
     diff = g - gcalc + diffzero
 
-    # Change some style details of the plot
-    mpl.rcParams.update(mpl.rcParamsDefault)
-    if (PWD.parent.parent.parent / "utils" / "billinge.mplstyle").exists():
-        plt.style.use(
-            str(PWD.parent.parent.parent / "utils" / "billinge.mplstyle")
-        )
-
     # Create a figure and an axis on which to plot
     fig, ax1 = plt.subplots(1, 1)
 

docs/examples/ch07StructuralPhaseTransitions/solutions/diffpy-cmi/fitTSeries.py

@@ -9,9 +9,9 @@
 # 1: Import relevant system packages that we will need...
 from pathlib import Path
 
-import matplotlib as mpl
 import matplotlib.pyplot as plt
 import numpy as np
+from bg_mpl_stylesheets.styles import all_styles
 from scipy.optimize import least_squares
 
 # ... and the relevant CMI packages
@@ -25,12 +25,7 @@
 from diffpy.srfit.structure import constrainAsSpaceGroup
 from diffpy.structure.parsers import getParser
 
-try:
-    from bg_mpl_stylesheets.bg_mpl_stylesheet import bg_mpl_style
-
-    plt.style.use(bg_mpl_style)
-except ImportError:
-    pass
+plt.style.use(all_styles["bg-style"])
 
 # Config ##############################
 # 2: Give a file path to where your pdf (.gr) and (.cif) files are located.
@@ -221,13 +216,6 @@ def plot_results(recipe, fig_name):
     # Calculate the residual (difference) array and offset it vertically.
     diff = g - gcalc + diffzero
 
-    # Change some style details of the plot
-    mpl.rcParams.update(mpl.rcParamsDefault)
-    if (PWD.parent.parent.parent / "utils" / "billinge.mplstyle").exists():
-        plt.style.use(
-            str(PWD.parent.parent.parent / "utils" / "billinge.mplstyle")
-        )
-
     # Create a figure and an axis on which to plot
     fig, ax1 = plt.subplots(1, 1)
 

docs/examples/ch08NPRefinement/solutions/diffpy-cmi/fitCdSeNP.py

@@ -10,7 +10,6 @@
 # 1: Import relevant system packages that we will need...
 from pathlib import Path
 
-import matplotlib as mpl
 import matplotlib.pyplot as plt
 import numpy as np
 from scipy.optimize import least_squares
@@ -445,13 +444,6 @@ def plot_results(recipe, fig_name):
     # Calculate the residual (difference) array and offset it vertically.
     diff = g - gcalc + diffzero
 
-    # Change some style details of the plot
-    mpl.rcParams.update(mpl.rcParamsDefault)
-    if (PWD.parent.parent.parent / "utils" / "billinge.mplstyle").exists():
-        plt.style.use(
-            str(PWD.parent.parent.parent / "utils" / "billinge.mplstyle")
-        )
-
     # Create a figure and an axis on which to plot
     fig, ax1 = plt.subplots(1, 1)
 

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)
 

news/example-ci.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* Add tests that run PDF example scripts
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

requirements/packs/plotting.txt

@@ -1,4 +1,5 @@
 ipywidgets
 matplotlib
 ipympl
+bg-mpl-stylesheets
 py3dmol>=2.0.1

requirements/tests.txt

@@ -8,3 +8,5 @@ pytest-env
 pytest-mock
 freezegun
 DeepDiff
+psutil
+bg-mpl-stylesheets

tests/conftest.py

@@ -1,8 +1,32 @@
 import json
+import shutil
 from pathlib import Path
 
+import matplotlib
 import pytest
 
+PROJECT_ROOT = Path(__file__).resolve().parents[1]
+EXAMPLES_ROOT = PROJECT_ROOT / "docs" / "examples"
+
+
+@pytest.fixture(scope="session")
+def tmp_examples(tmp_path_factory):
+    """Copy the entire examples/ tree into a temp directory once per
+    test session.
+
+    Returns the path to that copy.
+    """
+    tmpdir = tmp_path_factory.mktemp("examples")
+    tmp_examples = tmpdir / "examples"
+    shutil.copytree(EXAMPLES_ROOT, tmp_examples)
+    yield tmp_examples
+
+
+@pytest.fixture(scope="session", autouse=True)
+def use_headless_matplotlib():
+    """Force matplotlib to use a headless backend during tests."""
+    matplotlib.use("Agg")
+
 
 @pytest.fixture
 def user_filesystem(tmp_path):

tests/test_examples.py

@@ -0,0 +1,43 @@
+import re
+import runpy
+
+
+def get_instrument_params(res_file):
+    """Parse Qdamp and Qbroad from a .res file."""
+    qdamp = qbroad = None
+    with open(res_file, "r") as f:
+        for line in f:
+            if line.startswith("Calib_Qbroad"):
+                qbroad = float(re.split(r"\s+", line.strip())[1])
+            elif line.startswith("Calib_Qdamp"):
+                qdamp = float(re.split(r"\s+", line.strip())[1])
+    return qdamp, qbroad
+
+
+def test_all_examples(tmp_examples):
+    """Run all example scripts to ensure they execute without error."""
+    # Run Ni example first to produce .res file
+    ni_script = list(tmp_examples.rglob("**/FitBulkNi.py"))[0]
+    runpy.run_path(str(ni_script), run_name="__main__")
+    res_file = ni_script.parent / "res" / "Fit_Ni_Bulk.res"
+    assert res_file.exists(), f"Ni results file not found: {res_file}"
+
+    qdamp_i, qbroad_i = get_instrument_params(res_file)
+    pt_script = list(tmp_examples.rglob("**/fitNPPt.py"))[0]
+    refined_Ni_params = {"QDAMP_I": qdamp_i, "QBROAD_I": qbroad_i}
+    # run the NPPt script with the refined Ni params
+    runpy.run_path(
+        str(pt_script), run_name="__main__", init_globals=refined_Ni_params
+    )
+
+    # Run all other example scripts, patching the instrument values
+    all_scripts = list(tmp_examples.rglob("**/solutions/diffpy-cmi/*.py"))
+    scripts = [
+        s for s in all_scripts if s.name not in ("fitBulkNi.py", "fitNPPt.py")
+    ]
+    for script_path in scripts:
+        print(f"Testing {script_path.relative_to(tmp_examples)}")
+        mod_globals = {"QDAMP_I": qdamp_i, "QBROAD_I": qbroad_i}
+        runpy.run_path(
+            str(script_path), run_name="__main__", init_globals=mod_globals
+        )