Fix #466 projex generates pyproject.toml

[robnagler]

• pksetup: removed tox, readthedocs support Fix Make readthedocs conform to current build process #429 added readthedocs.yml
  Fix 20240131 Update readthedocs generation #386 projex generates proper sphinx and readthedocs.yml Fix Extract readthedocs content from pksetup to a pkcli #393 added pkcli.sphinx.prepare for readthedocs
• Added sphinx test which also tests projex
• Fixed various RST errors in modules Fix node.js github actions are deprecated #449 use GitHub workflow actions/checkout@v4 (also projex)

[rorour]

g tox still shows some instances that I think can be removed.

[rorour]

I'm getting this error. Is projex broken?

[rorour]

Actually not exactly that error, but it seems related.

[py3;@v wxyz]$ pykern projex init_rs_tree "my wxyz project"
Traceback (most recent call last):
  File "/home/vagrant/.pyenv/versions/py3/bin/pykern", line 8, in <module>
    sys.exit(main())
  File "/home/vagrant/src/radiasoft/pykern/pykern/pykern_console.py", line 17, in main
    return pkcli.main("pykern")
  File "/home/vagrant/src/radiasoft/pykern/pykern/pkcli/__init__.py", line 166, in main
    res = argh.dispatch(parser, argv=argv)
  File "/home/vagrant/.pyenv/versions/3.9.15/envs/py3/lib/python3.9/site-packages/argh/dispatching.py", line 183, in dispatch
    for line in lines:
  File "/home/vagrant/.pyenv/versions/3.9.15/envs/py3/lib/python3.9/site-packages/argh/dispatching.py", line 294, in _execute_command
    for line in result:
  File "/home/vagrant/.pyenv/versions/3.9.15/envs/py3/lib/python3.9/site-packages/argh/dispatching.py", line 277, in _call
    result = function(*positional, **keywords)
  File "/home/vagrant/src/radiasoft/pykern/pykern/pkcli/projex.py", line 76, in init_rs_tree
    init_tree(
  File "/home/vagrant/src/radiasoft/pykern/pykern/pkcli/projex.py", line 108, in init_tree
    base = pkresource.filename("projex")
  File "/home/vagrant/src/radiasoft/pykern/pykern/pkresource.py", line 47, in filename
    for f, p in _files(relative_filename, caller_context, packages):
  File "/home/vagrant/src/radiasoft/pykern/pykern/pkresource.py", line 90, in _files
    pkg_resources.resource_filename(
  File "/home/vagrant/.pyenv/versions/3.9.15/envs/py3/lib/python3.9/site-packages/pkg_resources/__init__.py", line 1181, in resource_filename
    return get_provider(package_or_requirement).get_resource_filename(
  File "/home/vagrant/.pyenv/versions/3.9.15/envs/py3/lib/python3.9/site-packages/pkg_resources/__init__.py", line 391, in get_provider
    return _find_adapter(_provider_factories, loader)(module)
  File "/home/vagrant/.pyenv/versions/3.9.15/envs/py3/lib/python3.9/site-packages/pkg_resources/__init__.py", line 1460, in __init__
    self.module_path = os.path.dirname(getattr(module, '__file__', ''))
  File "/home/vagrant/.pyenv/versions/3.9.15/lib/python3.9/posixpath.py", line 152, in dirname
    p = os.fspath(p)
TypeError: expected str, bytes or os.PathLike object, not NoneType

[robnagler]

@rorour I can't reproduce the projex failure above:

$ mkdir wxyz; cd wxyz; git init .; pykern projex init_rs_tree "my wxyz project"
Initialized empty Git repository in /home/vagrant/src/radiasoft/wxyz/.git/
$

[robnagler]

g tox still shows some instances that I think can be removed.

11e648a

[rorour]

It works in my vm_devbox but not my local vm. I tried radia_run sirepo-dev and uninstalled/reinstalled pykern. I don't have any idea what's causing the failure.

[robnagler]

It's probably an old python package on your local vm.

[rorour]

Do you know how I can find out which package and/or how to fix it?

[moellep]

You could run "pip list --outdated" to see old packages and update them using a command found here:
https://stackoverflow.com/questions/2720014/how-to-upgrade-all-python-packages-with-pip

Probably need to run "pip install -e ." in the sirepo and pykern directory afterward to downgrade anything.

Maybe @robnagler has a better way to do this.

[robnagler]

Try this first:

cd ~/src/radiasoft/pykern
pip install --upgrade --upgrade-strategy only-if-needed .

If projex still fails, we have something that needs bumping in pyproject.toml. Then we would want to know which packages need updating and that's trickier to debug, because you have to upgrade packages one at a time.

[rorour]

cd ~/src/radiasoft/pykern
pip install --upgrade --upgrade-strategy only-if-needed .

This fixed it. Thanks