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

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.
Closes changes 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 =============================================================================================================

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

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.

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.

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.

@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?

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.

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!

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 =============================================================================================================

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

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.

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.

@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 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

🚀 New features to boost your workflow:

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

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:main Apr 3, 2026
7 checks passed

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

Repository navigation

fix:hot-fix pdfgui functionality fix after skpkg - #298

fix:hot-fix pdfgui functionality fix after skpkg#298sbillinge merged 5 commits intodiffpy:maindiffpy/diffpy.pdfgui:mainfrom stevenhua0320:fix-gui-functionalitystevenhua0320/diffpy.pdfgui:fix-gui-functionalityCopy head branch name to clipboard

Conversation

stevenhua0320 commented Mar 27, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

sbillinge commented Mar 27, 2026

Uh oh!

sbillinge commented Mar 27, 2026

Uh oh!

sbillinge commented Mar 27, 2026

Uh oh!

stevenhua0320 commented Mar 29, 2026

Uh oh!

sbillinge commented Mar 29, 2026

Uh oh!

sbillinge commented Mar 29, 2026

Uh oh!

stevenhua0320 commented Mar 29, 2026

Uh oh!

stevenhua0320 commented Mar 31, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

sbillinge commented Apr 2, 2026

Uh oh!

stevenhua0320 commented Apr 2, 2026

Uh oh!

sbillinge commented Apr 3, 2026

Uh oh!

stevenhua0320 commented Apr 3, 2026

Uh oh!

codecov Bot commented Apr 3, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Codecov Report

Uh oh!

Uh oh!

Reviewers

Uh oh!

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

fix:hot-fix pdfgui functionality fix after skpkg#298
sbillinge merged 5 commits into
diffpy:mainfrom
stevenhua0320:fix-gui-functionality

stevenhua0320 commented Mar 27, 2026 •
edited
Loading

stevenhua0320 commented Mar 31, 2026 •
edited
Loading

codecov Bot commented Apr 3, 2026 •
edited
Loading