PR: Avoid future deprecations and decrease general technical debt

[CAM-Gerlach]

Fixes a number of minor problems in the codebase, including:

• Replace the deprecated tmpdir pytest fixture which uses legacy py.path objects with tmp_path, which uses standard pathlib.Paths (and rename helper function arg to avoid confusion)
• Use explicit encoding on open(), to avoid platform/environment-dependent bugs, deprecation warning on Py3.10 and eventual removal
• Fix other correctness issues, including:
  • Bad indent levels in some lines/blocks
  • Missing raise from on re-raised exceptions to re-raise correctly
  • Bare except that will trap KeyboardInterrupt, termination and other unwanted errors
  • Misplaced strings intended as docstrings but not the first line in their module/callable

[dalthviz]

Hi @CAM-Gerlach thanks for checking into this! However, just to understand better some of the changes here, the deprecations (pytest fixture, open with enconding kwarg) are related with Python 3.10?

[CAM-Gerlach]

@dalthviz Sure:

• The Pytest tmpdir fixture has been targeted for removal in Pytest for some time as it relies on the long-deprecated py package and legacy py.path objects; there's no connection to Python version. See Please remove the dependency on 'py' pytest-dev/pytest#7259
• The lack of an explicit encoding kwarg on open will become an optional warning in Python 3.10, with the plan to be a DeprecationWarning in future Python versions, and possibly eventually an error. However, the problem it fixes is present in all past and present Python versions, namely that the current default encoding is platform, environment and user-dependent (e.g. on Windows, some Linux and other platforms it is not UTF-8, as many developers assume, and can be anything, potentially not even ASCII-compatible) and is unsafe to rely upon, as attempting to open files in an arbitrary encoding is liable to cause an error or undesired behavior. See PEP 597 for more details (N.B., I helped some with the PEP and docs, and a bit with the implementation).
• The other changes are all relatively smaller but non-trivial correctness issues that have actual runtime impact and don't directly involve a deprecation, they've been problems ab initio

[dalthviz]

Thanks @CAM-Gerlach ! LGTM 👍

[CAM-Gerlach]

Thanks @dalthviz ; revised the PR title again to fix some introduced grammar and clarity issues