macOS Python 3.9-3.12 installation problem due to older version of wxpython on conda-forge

[bobleesj]

Following the instruction: https://www.diffpy.org/products/pdfgui.html

conda create --name=pdfgui2 python=3.9
conda activate pdfgui2 # Install 3.0.5
conda install -c conda-forge diffpy.pdfgui

I get the following error message:

(pdfgui2) macbook@Macbook-Air-327 ~ % pdfgui
Traceback (most recent call last):
  File "/Users/macbook/miniconda3/envs/pdfgui2/bin/pdfgui", line 11, in <module>
    sys.exit(main())
  File "/Users/macbook/miniconda3/envs/pdfgui2/lib/python3.9/site-packages/diffpy/pdfgui/applications/pdfgui.py", line 117, in main
    import diffpy.pdfgui.gui.main as guimain
  File "/Users/macbook/miniconda3/envs/pdfgui2/lib/python3.9/site-packages/diffpy/pdfgui/gui/main.py", line 19, in <module>
    import wx
  File "/Users/macbook/miniconda3/envs/pdfgui2/lib/python3.9/site-packages/wx/__init__.py", line 17, in <module>
    from wx.core import *
  File "/Users/macbook/miniconda3/envs/pdfgui2/lib/python3.9/site-packages/wx/core.py", line 12, in <module>
    from ._core import *
ImportError: dlopen(/Users/macbook/miniconda3/envs/pdfgui2/lib/python3.9/site-packages/wx/_core.cpython-39-darwin.so, 0x0002): Library not loaded: @rpath/libwx_osx_cocoau_core-3.2.0.2.3.dylib
  Referenced from: <DFCA0D82-07A5-319D-A434-ECCDA751BA46> /Users/macbook/miniconda3/envs/pdfgui2/lib/python3.9/site-packages/wx/_core.cpython-39-darwin.so
  Reason: tried: '/Users/macbook/miniconda3/envs/pdfgui2/lib/python3.9/site-packages/wx/../../../libwx_osx_cocoau_core-3.2.0.2.3.dylib' (no such file), '/Users/macbook/miniconda3/envs/pdfgui2/lib/python3.9/site-packages/wx/../../../libwx_osx_cocoau_core-3.2.0.2.3.dylib' (no such file), '/Users/macbook/miniconda3/envs/pdfgui2/bin/../lib/libwx_osx_cocoau_core-3.2.0.2.3.dylib' (no such file), '/Users/macbook/miniconda3/envs/pdfgui2/bin/../lib/libwx_osx_cocoau_core-3.2.0.2.3.dylib' (no such file), '/usr/local/lib/libwx_osx_cocoau_core-3.2.0.2.3.dylib' (no such file), '/usr/lib/libwx_osx_cocoau_core-3.2.0.2.3.dylib' (no such file, not in dyld cache)

This error message is also reproduced for Python 3.12 when I follow the standard:

conda create -n pdfgui_env python=3.12
conda activate pdfgui_env
conda install --file requirements/run.txt --file requirements/test.txt
pip install --no-deps .
pytest

One way to fix the problem is moving wxpython from run.txt to pip.txt and do the following:

conda create -n pdfgui_env python=3.12
conda activate pdfgui_env
conda install --file requirements/run.txt --file requirements/test.txt
pip install -r requirements/pip.txt
pip install --no-deps .
pytest

We need to understand why the error occurs in the first place.

[Tieqiong]

@bobleesj pdfgui don't have arm build on conda-forge, so doesn't pdffit2. So when testing with arm Mac make sure you get the latest pdffit2 via pypi.

The wxpython error is from its latest conda-forge release: wxpython=4.2.1=py312h10d1a2f_6. If you instead install a previous release (for example conda install wxpython=4.2.1=py312h4fd8812_5) the error goes away. Same idea apply to pip install wxpython.

One thing to notice is that we include the entire run.txt as dependencies in pyproject.toml. This could be problematic because pypi don't have matplotlib-base (it only exists for conda-forge). So potentially when people install pdfgui from pypi there might be dependency installing issues.

[bobleesj]

Thanks Tieqiong. Very helpful.

Just to note the error also occurs for non arm64 macOS as well. This seems to be a very high priority task.

The problem is resolved with the latest 4.2.2 wxpython on pypi but it is not available on conda forge yet.

I will suggest a solution regarding matplotlib-base and the rest.

[bobleesj]

Note to myself: the following works using build 5, 4.2.1. wxpython (macOS Intel)

conda create -n pdfgui_env python=3.12
conda install --file requirements/run.txt. # do not include wxpython
conda install wxpython=4.2.1=py312h4fd8812_5   # the last few numbers depend on OS
pip install pytest
pytest

Installed dependencies:

  diffpy.pdffit2     conda-forge/osx-64::diffpy.pdffit2-1.4.3-py312he44c6bd_8 
  diffpy.structure   conda-forge/noarch::diffpy.structure-3.2.2rc0-pyhd8ed1ab_0 
  diffpy.utils       conda-forge/noarch::diffpy.utils-3.4.2-pyhd8ed1ab_1 
  numpy              conda-forge/osx-64::numpy-2.1.1-py312he4d506f_0 
  wxpython           conda-forge/osx-64::wxpython-4.2.1-py312hba984fc_5 

```=========== 58 passed, 3 warnings in 29.79s ===========```

[bobleesj]

@sbillinge Could you please add this to 3.1.0 milestone as well?

[bobleesj]

Closing - today 4.2.2 is released via conda-forge as of now, conda install wxpython automatically installs 4.2.2 (the latest version released a few weeks ago). Tested.