MAINT: Bugs and updates

[aburrell]

Description

Addresses several issues - #128, #126, and #109 - and also:

• Finishes transition to pyproject.toml,
• Updates GitHub Actions yamls,
• Added a RTD yaml,
• Addresses numpy DeprecationWarnings,
• Addresses updates to pysat,
• Reduces duplication in the unit tests, and
• Improves docstrings in the unit tests.

Type of change

Please delete options that are not relevant.

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• This change requires a documentation update

How Has This Been Tested?

Ran unit tests locally.

Test Configuration

• Operating system: OS X Big Sur
• Version number: Python 3.9
• Any details about your local setup that are relevant: pysat 3.2.0

Checklist:

• [x] Make sure you are merging into the develop (not main) branch
• [x] My commits are formatted appropriately (following the SciPy/NumPy style)
• [x] My code follows the style guidelines of this project
• [x] I have performed a self-review of my own code
• [x] I have commented my code, particularly in hard-to-understand areas
• [x] I have made corresponding changes to the documentation
• [x] My changes generate no new warnings
• [x] I have added tests that prove my fix is effective or that my feature works
• [x] New and existing unit tests pass locally with my changes
• [x] Any dependent changes have been merged and published in downstream modules
• [x] Add a note to Changelog.rst, summarising the changes
• [x] Add yourself to AUTHORS.rst and .zenodo.json

[jklenzing]

For the coveralls bug, the individual jobs show up as "successful", but in the coveralls section I found this:

Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.7.17/x64/bin/coveralls", line 5, in <module>
    from coveralls.cli import main
  File "/opt/hostedtoolcache/Python/3.7.[17](https://github.com/aburrell/ocbpy/actions/runs/8481925380/job/23240181317#step:10:18)/x64/lib/python3.7/site-packages/coveralls/__init__.py", line 2, in <module>
    from .api import Coveralls
  File "/opt/hostedtoolcache/Python/3.7.17/x64/lib/python3.7/site-packages/coveralls/api.py", line 13, in <module>
    from .reporter import CoverallReporter
  File "/opt/hostedtoolcache/Python/3.7.17/x64/lib/python3.7/site-packages/coveralls/reporter.py", line 10, in <module>
    from coverage.report import Reporter
ImportError: cannot import name 'Reporter' from 'coverage.report' (/opt/hostedtoolcache/Python/3.7.17/x64/lib/python3.7/site-packages/coverage/report.py)

It looks like the jobs are not being uploaded for some reason.

[coveralls]

coverage: 99.574% (+0.5%) from 99.089% when pulling 294ddd6d1bbdba0dc76b561cc31543bf3875616e on bug_and_updates into 1046849b460fbabf1dabfbedf7f543d90c2cae85 on develop.

[aburrell]

The GitHub Actions coveralls app was not useful because:

• it didn't work on MacOS
• it counted docstrings as uncovered lines
• it counted else lines (that were accessed) as uncovered lines

[aburrell]

coveralls coverage report still differs from local coverage report by 11% due to:

• some docstrings
• some second lines in logic statements
• some “else” lines from if/else commands where both outcomes are covered.