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Merged
merged 15 commits into from
Sep 23, 2025
Merged

test: Run tutorials in tests #45

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c58bb59
simon template for examples testing
sbillinge Sep 22, 2025
7cb8a66
add psutils to tests.txt
cadenmyers13 Sep 22, 2025
86d91e8
condition that sets qdamp and qbroad if Ni fit is not ran
cadenmyers13 Sep 22, 2025
c8883e8
change mpl backend and remove old stylesheets
cadenmyers13 Sep 22, 2025
199630b
news
cadenmyers13 Sep 22, 2025
b40a87f
Remove comment from tests/conftest.py
cadenmyers13 Sep 22, 2025
c7b94c4
[pre-commit.ci] auto fixes from pre-commit hooks
pre-commit-ci[bot] Sep 22, 2025
9490394
fix typo in psutil name
cadenmyers13 Sep 22, 2025
e3d5cff
fix typo in psutil name
cadenmyers13 Sep 22, 2025
5a1091a
Add special handling to get Qdamp and Qbroad params
cadenmyers13 Sep 22, 2025
ba6825a
add bg stylesheets
cadenmyers13 Sep 22, 2025
eb8cab3
add bg stylesheets to requirments
cadenmyers13 Sep 22, 2025
b77fb30
remove mpl defaults override
cadenmyers13 Sep 22, 2025
9b7c4c2
fix so fitbulkni runs first
cadenmyers13 Sep 22, 2025
b8822b2
remove posix
cadenmyers13 Sep 23, 2025
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12 changes: 3 additions & 9 deletions docs/examples/ch03NiModelling/solutions/diffpy-cmi/fitBulkNi.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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.
Expand All @@ -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
Expand Down Expand Up @@ -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)

Expand Down
10 changes: 2 additions & 8 deletions docs/examples/ch03NiModelling/solutions/diffpy-cmi/fitNPPt.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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.
Expand Down Expand Up @@ -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)

Expand Down
10 changes: 2 additions & 8 deletions docs/examples/ch05Fit2Phase/solutions/diffpy-cmi/fit2P.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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()
Expand Down Expand Up @@ -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)

Expand Down
16 changes: 2 additions & 14 deletions docs/examples/ch06RefineCrystalStructureGen/solutions/diffpy-cmi/fitCrystalGen.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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.
Expand Down Expand Up @@ -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)

Expand Down
16 changes: 2 additions & 14 deletions docs/examples/ch07StructuralPhaseTransitions/solutions/diffpy-cmi/fitTSeries.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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.
Expand Down Expand Up @@ -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)

Expand Down
8 changes: 0 additions & 8 deletions docs/examples/ch08NPRefinement/solutions/diffpy-cmi/fitCdSeNP.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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():
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where is the group style added back in?

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@sbillinge I will have to add it to each file I think, I can do this!

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better on another PR, but can we also do this work on the examples scripts also? Not just the solutions?

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@sbillinge Yeah I can do this. Do you want me to revert back then?

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)

Expand Down
3 changes: 0 additions & 3 deletions docs/examples/ch11ClusterXYZ/solutions/diffpy-cmi/fitCdSeNP.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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)

Expand Down
23 changes: 23 additions & 0 deletions news/example-ci.rst
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Original file line number Diff line number Diff line change
@@ -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>
1 change: 1 addition & 0 deletions requirements/packs/plotting.txt
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
ipywidgets
matplotlib
ipympl
bg-mpl-stylesheets
py3dmol>=2.0.1
2 changes: 2 additions & 0 deletions requirements/tests.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -8,3 +8,5 @@ pytest-env
pytest-mock
freezegun
DeepDiff
psutil
bg-mpl-stylesheets
24 changes: 24 additions & 0 deletions tests/conftest.py
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@@ -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):
Expand Down
13 changes: 13 additions & 0 deletions tests/test_examples.py
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@@ -0,0 +1,13 @@
import runpy


def test_all_examples(tmp_examples):
"""Run all example scripts to ensure they execute without error."""
scripts = list(tmp_examples.rglob("**/solutions/diffpy-cmi/*.py"))
# sort list so that fitBulkNi.py runs first
scripts.sort(key=lambda s: 0 if s.name == "fitBulkNi.py" else 1)
for script in scripts:
script_relative_path = script.relative_to(tmp_examples).as_posix()
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what is your reason for the posix? this is likely to make it not work on windows.

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@sbillinge This is to make it compatible across operating systems when converting the path to a string. Maybe it can go either way here (use str() or posix).

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I would just delete it tbh

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Got it. Will do

print("hello", script_relative_path)
print(f"Testing {script_relative_path}")
runpy.run_path(str(script), run_name="__main__")
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