test: Run tutorials in tests #45

cadenmyers13 · 2025-09-22T15:49:50Z

closes #8

cadenmyers13 · 2025-09-22T15:53:13Z

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

-
+    print("Setting Q_damp and Q_broad to the refined values\n")
+    QDAMP_I = 0.045298
+    QBROAD_I = 0.016809


If user doesn't run the bulkNi script, the Qdamp and Qbroad values will be defined here. This is also needed to run tests (for now).

let's see if we can fix this properly and not this ugly workaround.

@sbillinge To handle this, I had to add special handling for this script. I've pushed said special handling. Let me know if that looks okay.

codecov · 2025-09-22T16:23:20Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 81.75%. Comparing base (6167dd9) to head (b8822b2).
⚠️ Report is 16 commits behind head on main.

Additional details and impacted files

@@             Coverage Diff             @@
##             main      #45       +/-   ##
===========================================
+ Coverage   50.00%   81.75%   +31.75%     
===========================================
  Files           2       11        +9     
  Lines          18     1211     +1193     
===========================================
+ Hits            9      990      +981     
- Misses          9      221      +212

Files with missing lines	Coverage Δ
.../ch03NiModelling/solutions/diffpy-cmi/fitBulkNi.py	`97.54% <100.00%> (ø)`
...es/ch03NiModelling/solutions/diffpy-cmi/fitNPPt.py	`86.86% <100.00%> (ø)`
...amples/ch05Fit2Phase/solutions/diffpy-cmi/fit2P.py	`90.14% <100.00%> (ø)`
...StructureGen/solutions/diffpy-cmi/fitCrystalGen.py	`89.28% <100.00%> (ø)`
...haseTransitions/solutions/diffpy-cmi/fitTSeries.py	`89.85% <100.00%> (ø)`
...ch08NPRefinement/solutions/diffpy-cmi/fitCdSeNP.py	`89.07% <ø> (ø)`
...s/ch11ClusterXYZ/solutions/diffpy-cmi/fitCdSeNP.py	`90.24% <ø> (ø)`
tests/conftest.py	`66.66% <100.00%> (+30.95%)`	⬆️
tests/test_examples.py	`100.00% <100.00%> (ø)`

... and 1 file with indirect coverage changes

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❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

cadenmyers13 · 2025-09-22T16:31:15Z

@sbillinge ready for review.

Thanks for your help on this. I think this is nice and clean and it looks like the temp dir gets removed. Currently looking into ways of initializing the refinements with the refined values so this test runs quicker.

sbillinge

pls see comments

sbillinge · 2025-09-22T18:20:07Z

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


    # Change some style details of the plot
    mpl.rcParams.update(mpl.rcParamsDefault)
-    if (PWD.parent.parent.parent / "utils" / "billinge.mplstyle").exists():


where is the group style added back in?

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

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

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

sbillinge · 2025-09-22T18:20:27Z

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

-
+    print("Setting Q_damp and Q_broad to the refined values\n")
+    QDAMP_I = 0.045298
+    QBROAD_I = 0.016809


let's see if we can fix this properly and not this ugly workaround.

sbillinge

pls see comments

sbillinge · 2025-09-22T19:19:41Z

tests/test_examples.py

-    scripts = list(tmp_examples.rglob("**/solutions/diffpy-cmi/*.py"))
+    """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]


This seems to have turned something beautiful into something very ugly though. I think the figbulkNI runs first anyway so we probably don't need any of this. Do you want to have another crack at it, or should I try and see what I can come up with?

Also why are you recursively globbing a single file? I can see we need to work a bit on your coding skills......

@sbillinge Let me give this another shot. Im just trying to figure out how to pull the results file from the temp dir.

sbillinge

nice progress. Please see my comment. Looking much more in the right direction though..... I will wait for your next iteration.

sbillinge · 2025-09-22T20:18:54Z

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


    # Change some style details of the plot
    mpl.rcParams.update(mpl.rcParamsDefault)
-    if (PWD.parent.parent.parent / "utils" / "billinge.mplstyle").exists():


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

cadenmyers13 · 2025-09-22T20:31:39Z

@sbillinge I figured out whats going on. rglob wasn't sorting the files in the right way so it was running PtNP example first so there was no file to grab the params from 🤦‍♂️ . I was racking my brain trying to figure out what was happening 😂 I'll make a push in a bit that should fix this.

cadenmyers13 · 2025-09-22T21:20:34Z

@sbillinge ready for review

sbillinge

one last thing.

sbillinge · 2025-09-22T23:42:02Z

tests/test_examples.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()


what is your reason for the posix? this is likely to make it not work on windows.

@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).

I would just delete it tbh

Got it. Will do

cadenmyers13 · 2025-09-23T00:09:51Z

@sbillinge responded to your comment

sbillinge

respond to comment

sbillinge · 2025-09-23T00:17:34Z

tests/test_examples.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()


I would just delete it tbh

cadenmyers13 · 2025-09-23T00:24:34Z

@sbillinge Made the change. This test should pass in ~20 min.

sbillinge and others added 4 commits September 22, 2025 09:20

simon template for examples testing

c58bb59

add psutils to tests.txt

7cb8a66

condition that sets qdamp and qbroad if Ni fit is not ran

86d91e8

change mpl backend and remove old stylesheets

c8883e8

cadenmyers13 mentioned this pull request Sep 22, 2025

CI: test that runs pdf pack examples in CI #40

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cadenmyers13 commented Sep 22, 2025

View reviewed changes

cadenmyers13 and others added 4 commits September 22, 2025 11:54

Remove comment from tests/conftest.py

b40a87f

[pre-commit.ci] auto fixes from pre-commit hooks

c7b94c4

fix typo in psutil name

9490394

fix typo in psutil name

e3d5cff

sbillinge reviewed Sep 22, 2025

View reviewed changes

cadenmyers13 added 4 commits September 22, 2025 14:50

Add special handling to get Qdamp and Qbroad params

5a1091a

add bg stylesheets

ba6825a

add bg stylesheets to requirments

eb8cab3

remove mpl defaults override

b77fb30

sbillinge reviewed Sep 22, 2025

View reviewed changes

fix so fitbulkni runs first

9b7c4c2

sbillinge reviewed Sep 22, 2025

View reviewed changes

sbillinge reviewed Sep 23, 2025

View reviewed changes

remove posix

b8822b2

sbillinge merged commit 656e3f3 into diffpy:main Sep 23, 2025
3 checks passed

cadenmyers13 deleted the example-ci branch September 23, 2025 15:32

test: Run tutorials in tests #45

test: Run tutorials in tests #45

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