Level 5

[TingwenZhang]

No description provided.

[sbillinge]

This PR seems to be mixing auto-fixes and hand-edited fixes. This makes it very hard to review (I have to go line by line through 76 files). Please could you put all the autofixes on one or ore separate PRs (preferrably one for each auto-fix). LIkely either pre-commit or CI will be failing, but this is ok. It is more important to me to know that all the fixes were done by black/docformatter etc., which are not 100% safe but nearly 100% safe. We can merge these changes and you can build new branches and your hand edits will be on only a few files.

[TingwenZhang]

Thank you for clarifying, Simon.

I have two questions:

1. Should line length be 79 or 105? In the previous commit I saw line length is 105, but in scikit-package line length is 79.

2. When I did package create public, scikit-package automatically deleted many files:

 deleted:    devutils/sgtbx_extra_groups.py
        deleted:    doc/manual/Makefile
        deleted:    doc/manual/requirements.txt
        deleted:    doc/source/api/diffpy.structure.apps.rst
        deleted:    doc/source/api/diffpy.structure.expansion.rst
        deleted:    doc/source/api/diffpy.structure.parsers.rst
        modified:   doc/source/api/diffpy.structure.rst
        modified:   doc/source/conf.py
        deleted:    doc/source/diffpy.structure.apps.rst
        deleted:    doc/source/diffpy.structure.expansion.rst
        deleted:    doc/source/diffpy.structure.parsers.rst
        modified:   doc/source/index.rst
        modified:   doc/source/license.rst
        deleted:    doc/source/mod-atom.rst
        deleted:    doc/source/mod-lattice.rst
        deleted:    doc/source/mod-spacegroup.rst
        deleted:    environment.yml
        deleted:    news/codecov.rst
...

I wonder why did scikit-package do this.

[sbillinge]

These are great questions. For the line length, 79 is the skpkg standard, but we can deviate from that for legacy code. Pavol did all his coding with a line-length limit of 115 (not 105 but whatever). At this point we can decide to keep 115 or move to the 79 standard. The first would be more work (it has to be done manually) but would remove technical debt for the future. I am not sure the best decision here. I tend to like to remove technical debt as I revisit these packages again and again, and get the same pain each time, but we should conserve our energies too and not do it now if that makes more sense. If you simply run flake8 with a line length of 79 we will see how much fixing we are looking at.....

For the deleted files, it should be explained in the docs, but if you moved the .git file over correctly, these are files that are in the git database but have not been moved over. They haven't been deleted.

Sometimes a quick zoom can make these things a bit clearer. I would be happy to do that if you like.

[TingwenZhang]

Yes, I would like a Zoom meeting. I am free anytime today from 3 pm to the end of the day.

[sbillinge]

sorry @TingwenZhang It got a little late today. I had zooms all day. Can you do it at 12pm tomorrow? I will send a calendar invite. If that isn't convenient, we can find another time.

[TingwenZhang]

Yes, that time works. I just accepted the invite.