Tox integration & use in GitHub actions

[jared321]

The work associated with Issue #106 appears to be finished. The following are the steps I will carry out as part of a self-review of this PR

• Full review of all changes made to the code
• Run all tox tasks locally and check products
• Add bad style to file and see tox and CI action fail as expected
• Break code and see nocoverage/coverage fail in tox and in all CI actions as expected
• Breaks docs so that a warning is issued. Confirm warning treated as error with tox and CI actions as expected.
• Breaks docs so that an error is issued. Confirm error with tox and CI actions as expected.
• Alter code so that coverage changes. Check for changes in local tox report and Coveralls.
• Download HTML and PDF docs and sanity check contents. Review tox section carefully.
• Download coverage reports and sanity check
• Read through all action logs for correctness

I injected many different errors into the sphinx documentation including using tx.rst instead of tox.rst when including the latter and writing :mah: instead of :math:. In such cases, sphinx-build reports these as errors in its output but returns a zero exit code, which indicates success. I saw this when running sphinx-build from the command line and tox reports success. When I use the flag --fail-on-warning with sphinx-build, the output states that these are warnings that are being treated as errors and a nonzero exit code is emitted. It appears that sphinx-build does not have errors or handle these in normal ways. Therefore, I would never use sphinx-build in automated processes without that flag.

Note that this work has also instituted the necessary changes so that Python 3.8 is no longer a supported version. See Issue #112. All tests are passing with 3.12 for Windows, Ubuntu, and macOS. I updated all actions that use a single Python version to use 3.12 except for building sphinx document, which reported an error associated with loading sphinxcontrib.bibtex.

I have changed the RTD setup so that build warnings are treated as errors. We need to check that manually once this branch is in main.

@mosesyhc I have finished my review and have added you as a reviewer. Some potentially useful information for you:

• When I run the test suite locally, I get three warnings about transposing f. However, some CI testing actions report (e.g. macOS 3.11) the following as well

tests/test_emu_cal/test_cal_mh.py::test_cal_MLcal[input13-input23-expectation3]
  /home/runner/work/surmise/surmise/surmise/utilitiesmethods/metropolis_hastings.py:80: RuntimeWarning: overflow encountered in exp
    p_accept = min(1, np.exp(logpost - lposterior[i-1]))

• Also, the Windows testing actions logs do not suggest that the test suite was actually run. In particular, there is no standard output logging from your testing script.

[jared321]

@mosesyhc The repo currently specifies dependencies in pyproject.toml and requirements.txt. Can we get rid of the latter?

[mosesyhc]

@mosesyhc The repo currently specifies dependencies in pyproject.toml and requirements.txt. Can we get rid of the latter?

Yes, we can.

[mosesyhc]

@jared321 : I removed the dependencies mentions in README.

The building of docs is inherited from the first version of surmise. Since we have effectively included the capability in tox, we can simply point to the tox info.

[mosesyhc]

I reviewed by performing these tasks:

• I have installed tox locally following tox instruction.
• I ran the tox commands and verified the usages.
  • tox -e check is scanning every directory under surmise, including local builds and IDE-generated venvs. I am including these into .flake8 ignores.

All look fine to me otherwise.