fix:hot-fix pdfgui functionality fix after skpkg by stevenhua0320 · Pull Request #298 · diffpy/diffpy.pdfgui

stevenhua0320 · 2026-03-27T02:20:44Z

We have done the skpkg for this without waiting for its dependency new version release and we merged that PR. But today when I ran it using the developer version of diffpy.pdfgui, it gives me a lot of errors other than the python version. So, I made this PR to fix all of these.

I added an __date__ variable in aboutdialog.py since it is the only place that we need the __date__. This helps us to run the pytest sucessfully.
Closeschanges when we drop python 3.11 #194, and also I updated the os.path to Path() object to comply with the group standard.
I also made an edit to the pyproject.toml, this is needed because in the skpkg it changes the actual script running the pdfgui. Therefore, I changed it back to the application and in order to comply with the name of the app in the tutorial, I also changed the name of the command from diffpy-pdfgui back to pdfgui.

After finishing up these, I ran the pytest and also running the app, it works properly now. The CI would still failing since dependecies haven't updated to 3.14 yet, but now local test would confirm that everything is right now.

(diffpy.pdfgui_env) huarundong@Stevens-MacBook-Pro-405 diffpy.pdfgui % pytest
================================================================================================================== test session starts ===================================================================================================================
platform darwin -- Python 3.13.12, pytest-9.0.2, pluggy-1.6.0
rootdir: /Users/huarundong/dbs/diffpy.pdfgui
configfile: pyproject.toml
collected 58 items tests/test_aboutdialog.py . [ 1%]
tests/test_calculation.py . [ 3%]
tests/test_constraint.py .... [ 10%]
tests/test_datasetpanels.py .... [ 17%]
tests/test_dopingseriespanel.py . [ 18%]
tests/test_extendedplotframe.py .. [ 22%]
tests/test_fitdataset.py .. [ 25%]
tests/test_fitstructure.py .......... [ 43%]
tests/test_insertrowsdialog.py . [ 44%]
tests/test_loadproject.py ...... [ 55%]
tests/test_mainframe.py .. [ 58%]
tests/test_parameter.py .. [ 62%]
tests/test_parameterspanel.py .... [ 68%]
tests/test_pdfdataset.py .. [ 72%]
tests/test_pdfguicontrol.py . [ 74%]
tests/test_pdfstructure.py ..... [ 82%]
tests/test_phaseconfigurepanel.py .. [ 86%]
tests/test_structureviewer.py ...... [ 96%]
tests/test_temperatureseriespanel.py . [ 98%]
tests/test_version.py . [100%]
==================================================================================================================== warnings summary ====================================================================================================================
tests/test_datasetpanels.py::TestDataSetPanel::test_onSampling
tests/test_loadproject.py::TestLoadProject::test___init__
tests/test_parameter.py::TestParameter::test___init__
tests/test_phaseconfigurepanel.py::TestPhaseConfigurePanel::test_onCellRightClick
/Users/huarundong/dbs/diffpy.pdfgui/src/diffpy/pdfgui/control/fitdataset.py:480: VisibleDeprecationWarning: dtype(): align should be passed as Python or NumPy boolean but got `align=0`. Did you mean to pass a tuple to create a subarray type? (Deprecated NumPy 2.4)
content = pickle.loads(z.read(subpath + "calc"), encoding="latin1")
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
============================================================================================================= 58 passed, 4 warnings in 1.22s =============================================================================================================

sbillinge · 2026-03-27T06:21:31Z

Please can you check? This seems to be failing tests. Done version compatibility on problem?

sbillinge · 2026-03-27T07:48:18Z

Please can you check? This seems to be failing tests. Done version compatibility on problem?

Ah, I read the full comment above, my apologies. I will merge this.

sbillinge · 2026-03-27T07:57:10Z

actually, let's go a bit more slowly. Let's finalize the release of pdffit2 (please see the issue over there), push out that full release and rerun the action here so it passes, then I will merge.

stevenhua0320 · 2026-03-29T21:26:03Z

As we have released the new version of both diffpy.pdffit2 and diffpy.structure, we could rerun the tests-on-pr workflow to test whether there is any errors remain.

sbillinge · 2026-03-29T21:37:59Z

@stevenhua0320 please see the message in slack. I couldn't merge diffpy.pdffit2-feedstock and it needs some help. There is a pesky circular import that only happens on windows. Pleaes could you look at that and see if we can get pdffit2 merged?

sbillinge · 2026-03-29T21:40:09Z

actually, I will have to merge it, but if you can get it passing tests I can do it. We may have to update the code in the pdffit2 itself to fix it, but hopefully it is changing how the tests are run in CF to fix it. Please make your own PR and work on that.

stevenhua0320 · 2026-03-29T21:47:28Z

actually, I will have to merge it, but if you can get it passing tests I can do it. We may have to update the code in the pdffit2 itself to fix it, but hopefully it is changing how the tests are run in CF to fix it. Please make your own PR and work on that.

I have seen your PR on the feedstock on that. Let me first inspect where the issue is!

stevenhua0320 · 2026-03-31T16:23:13Z

We still have some issues related to the python 3.14 version as indicated by the test-on-pr workflow. These issues didn't happen when we have python 3.13 version with the editable version installed on local. The local pytest on python 3.13 is shown below.

(diffpy.pdfgui_env) huarundong@Stevens-MacBook-Pro-405 diffpy.pdfgui % pytest
================================================================================================================== test session starts ===================================================================================================================
platform darwin -- Python 3.13.12, pytest-9.0.2, pluggy-1.6.0
rootdir: /Users/huarundong/dbs/diffpy.pdfgui
configfile: pyproject.toml
collected 58 items tests/test_aboutdialog.py . [ 1%]
tests/test_calculation.py . [ 3%]
tests/test_constraint.py .... [ 10%]
tests/test_datasetpanels.py .... [ 17%]
tests/test_dopingseriespanel.py . [ 18%]
tests/test_extendedplotframe.py .. [ 22%]
tests/test_fitdataset.py .. [ 25%]
tests/test_fitstructure.py .......... [ 43%]
tests/test_insertrowsdialog.py . [ 44%]
tests/test_loadproject.py ...... [ 55%]
tests/test_mainframe.py .. [ 58%]
tests/test_parameter.py .. [ 62%]
tests/test_parameterspanel.py .... [ 68%]
tests/test_pdfdataset.py .. [ 72%]
tests/test_pdfguicontrol.py . [ 74%]
tests/test_pdfstructure.py ..... [ 82%]
tests/test_phaseconfigurepanel.py .. [ 86%]
tests/test_structureviewer.py ...... [ 96%]
tests/test_temperatureseriespanel.py . [ 98%]
tests/test_version.py . [100%]
==================================================================================================================== warnings summary ====================================================================================================================
tests/test_datasetpanels.py::TestDataSetPanel::test_onSampling
tests/test_mainframe.py::TestMainFrame::test_disableMainMenuItems
tests/test_parameter.py::TestParameter::test___init__
tests/test_phaseconfigurepanel.py::TestPhaseConfigurePanel::test_onCellRightClick
/Users/huarundong/dbs/diffpy.pdfgui/src/diffpy/pdfgui/control/structureviewer.py:120: DeprecationWarning: 'diffpy.structure.outputFormats' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.structure.output_formats' instead.
return outputFormats()
tests/test_datasetpanels.py: 1 warning
tests/test_loadproject.py: 12 warnings
tests/test_parameter.py: 1 warning
tests/test_phaseconfigurepanel.py: 1 warning
/Users/huarundong/dbs/diffpy.pdfgui/src/diffpy/pdfgui/control/fitstructure.py:128: DeprecationWarning: 'diffpy.structure.PDFFitStructure.readStr' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.structure.PDFFitStructure.read_structure' instead.
p = PDFStructure.readStr(self, s, format)
tests/test_datasetpanels.py: 2 warnings
tests/test_fitstructure.py: 5 warnings
tests/test_loadproject.py: 18 warnings
tests/test_parameter.py: 2 warnings
tests/test_pdfstructure.py: 1 warning
tests/test_phaseconfigurepanel.py: 2 warnings
tests/test_structureviewer.py: 2 warnings
/opt/miniconda3/envs/diffpy.pdfgui_env/lib/python3.13/site-packages/diffpy/structure/parsers/structureparser.py:101: DeprecationWarning: 'diffpy.structure.P_pdffit.parseLines' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.structure.P_pdffit.parse_lines' instead.
stru = self.parseLines(lines)
tests/test_datasetpanels.py::TestDataSetPanel::test_onSampling
tests/test_loadproject.py::TestLoadProject::test___init__
tests/test_loadproject.py::TestLoadProject::test___init__
tests/test_loadproject.py::TestLoadProject::test___init__
tests/test_loadproject.py::TestLoadProject::test___init__
tests/test_loadproject.py::TestLoadProject::test___init__
tests/test_loadproject.py::TestLoadProject::test___init__
tests/test_parameter.py::TestParameter::test___init__
tests/test_phaseconfigurepanel.py::TestPhaseConfigurePanel::test_onCellRightClick
/Users/huarundong/dbs/diffpy.pdfgui/src/diffpy/pdfgui/control/fitstructure.py:770: DeprecationWarning: 'diffpy.structure.PDFFitStructure.readStr' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.structure.PDFFitStructure.read_structure' instead.
self.refined.readStr(refdata, "pdffit")
tests/test_datasetpanels.py::TestDataSetPanel::test_onSampling
tests/test_loadproject.py::TestLoadProject::test___init__
tests/test_parameter.py::TestParameter::test___init__
tests/test_phaseconfigurepanel.py::TestPhaseConfigurePanel::test_onCellRightClick
/Users/huarundong/dbs/diffpy.pdfgui/src/diffpy/pdfgui/control/fitdataset.py:480: VisibleDeprecationWarning: dtype(): align should be passed as Python or NumPy boolean but got `align=0`. Did you mean to pass a tuple to create a subarray type? (Deprecated NumPy 2.4)
content = pickle.loads(z.read(subpath + "calc"), encoding="latin1")
tests/test_fitstructure.py::TestFitStructure::test_applyParameters
tests/test_fitstructure.py::TestFitStructure::test_applyParameters
tests/test_pdfstructure.py::TestPDFStructure::test_setvar
/Users/huarundong/dbs/diffpy.pdfgui/src/diffpy/pdfgui/control/pdfstructure.py:105: DeprecationWarning: 'diffpy.structure.Lattice.setLatPar' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.structure.Lattice.set_latt_parms' instead.
self.lattice.setLatPar(alpha=fvalue)
tests/test_pdfstructure.py::TestPDFStructure::test_getvar
/Users/huarundong/dbs/diffpy.pdfgui/tests/test_pdfstructure.py:84: DeprecationWarning: 'diffpy.structure.Lattice.setLatPar' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.structure.Lattice.set_latt_parms' instead.
stru.lattice.setLatPar(*abcABG)
tests/test_pdfstructure.py::TestPDFStructure::test_setvar
/Users/huarundong/dbs/diffpy.pdfgui/tests/test_pdfstructure.py:47: DeprecationWarning: 'diffpy.structure.Structure.addNewAtom' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.structure.Structure.add_new_atom' instead.
stru.addNewAtom("C", [0, 0, 0], anisotropy=True)
tests/test_pdfstructure.py::TestPDFStructure::test_setvar
/Users/huarundong/dbs/diffpy.pdfgui/src/diffpy/pdfgui/control/pdfstructure.py:99: DeprecationWarning: 'diffpy.structure.Lattice.setLatPar' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.structure.Lattice.set_latt_parms' instead.
self.lattice.setLatPar(a=fvalue)
tests/test_pdfstructure.py::TestPDFStructure::test_setvar
/Users/huarundong/dbs/diffpy.pdfgui/src/diffpy/pdfgui/control/pdfstructure.py:101: DeprecationWarning: 'diffpy.structure.Lattice.setLatPar' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.structure.Lattice.set_latt_parms' instead.
self.lattice.setLatPar(b=fvalue)
tests/test_pdfstructure.py::TestPDFStructure::test_setvar
/Users/huarundong/dbs/diffpy.pdfgui/src/diffpy/pdfgui/control/pdfstructure.py:103: DeprecationWarning: 'diffpy.structure.Lattice.setLatPar' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.structure.Lattice.set_latt_parms' instead.
self.lattice.setLatPar(c=fvalue)
tests/test_pdfstructure.py::TestPDFStructure::test_setvar
/Users/huarundong/dbs/diffpy.pdfgui/src/diffpy/pdfgui/control/pdfstructure.py:107: DeprecationWarning: 'diffpy.structure.Lattice.setLatPar' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.structure.Lattice.set_latt_parms' instead.
self.lattice.setLatPar(beta=fvalue)
tests/test_pdfstructure.py::TestPDFStructure::test_setvar
/Users/huarundong/dbs/diffpy.pdfgui/src/diffpy/pdfgui/control/pdfstructure.py:109: DeprecationWarning: 'diffpy.structure.Lattice.setLatPar' is deprecated and will be removed in version 4.0.0. Please use 'diffpy.structure.Lattice.set_latt_parms' instead.
self.lattice.setLatPar(gamma=fvalue)
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
============================================================================================================ 58 passed, 74 warnings in 1.91s =============================================================================================================

sbillinge · 2026-04-02T15:49:44Z

Is this a wx issue? What do you recommend that we do?

stevenhua0320 · 2026-04-02T17:33:13Z

Is this a wx issue? What do you recommend that we do?

For this one, maybe we need to wait for wx to make the fix I'm afraid. For now this is a compatibility issue with only python 3.14.

sbillinge · 2026-04-03T12:00:55Z

Is this a wx issue? What do you recommend that we do?
For this one, maybe we need to wait for wx to make the fix I'm afraid. For now this is a compatibility issue with only python 3.14.

wx is released for python 3.14, so is this a bug in wx? In that case, we would like to post the issue on their GitHub, first searching to see if anyone else has posted about it. If they have, then add a comment that we also need this. Or post a new issue of there isn't one.

stevenhua0320 · 2026-04-03T15:17:10Z

@sbillinge I have a more careful review for the error. It seems that in the current version if we want to run wxpython on CI workflow, we should have a virtual display running. but in the original workflow we set headless to false. So, this is why we cannot pass the test.

codecov · 2026-04-03T15:17:13Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 95.10%. Comparing base (6222ee9) to head (a6c09b3).
⚠️ Report is 11 commits behind head on main.

Additional details and impacted files

@@ Coverage Diff @@## main #298 +/- ##
=======================================
Coverage 95.10% 95.10% =======================================
Files 23 23 Lines 1123 1123 =======================================
Hits 1068 1068 Misses 55 55

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fix:pdfgui functionality fix after skpkg
0763f01

stevenhua0320 mentioned this pull request Mar 30, 2026
skpkg: use scikit-package v0.1.0 to restandarlize package #278
Closed

stevenhua0320 added 3 commits March 30, 2026 15:07

fix: fix link fits with string input with error message pops
dfa6be6

chore: retrigger the workflow run after releasing pdffit2
8b8ede6

chore: revert incorrect fix
293b531

build: change headless to true to enable virtual display
a6c09b3

sbillinge merged commit 9496a69 into diffpy:mainApr 3, 2026
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