Revise pytesting, update docker, add QC notebook

[CBroz1]

See also element PR

Submission checklist

• Reviewed all Files changed prior to selecting Create Pull Request.
• Ran and passed all pytests, and ran the pipeline for features not covered by tests.
• Ran pre-commit checks, including black, flake8, etc.
• Updated the changelog and if making a new release, updated the version.py. - Will add 'release date' after review
• Updated documentation, including concepts.md, tutorials.md, and relevant docstrings.
• After merge, I will push a new tag to upstream (test* prefix if no new release).

Submission details

In this pull request, I make the following changes:

• markdown lint: standardize docs - remove trailing spaces, line length (markdownlint.yaml, pre-commit-config.yaml, readme)
• revise pytesting
  • add pyproject.toml - add default test path and configs to speed up test initialization
  • init -> conftest - following pytest documentation, startup fixtures go here. removes the need for imports in test docs
  • migrate standard funcs to element_interface (see PR #71)
  • add command-line options for verbosity and teardown
  • tests/*py remove imports per conftest change above and adjust variable names for clarity
  • conftest: add pytest fixtures
    • add fixture for element helper funcs
    • add func to loop populate command and parallel teardown func (populate_table,populate_clear)
    • add fixtures to populate motion correction, segmentation, etc post_curation
  • tests_populate - add tests for results (e.g., activity traces)
  • tests_support - add tests for element support funcs (e.g., get_root_data_dir)
• requirements.txt - remove old git+ format leftover from prior to pypi publication
• requirements_test -> requirements_dev: jupytext and pre-commit are developer dependencies. pytest/pytest-cov is also for developer testing
• sessions.csv - rename acq_software per element PR #38
• workflow structure - reorganize to avoid monkey patching
  • workflow/init: migrate db_prefix here to be available to both pipeline and reference
  • workflow/reference: migrate supplemental tables, Equipment -> Device
  • workflow/ingest: print->logger statements, Equipment -> device, parameterize print str

Coverage report

Overall, I improve coverage by ~40%

----- coverage: platform darwin, python 3.9.13-final-0 -----
Name                             Stmts   Miss  Cover   Missing
--------------------------------------------------------------------------------------------------------
element_miniscope/__init__.py        0      0   100%
element_miniscope/miniscope.py     281     57    80%   84, 87, 244, 247-267, 274, 278, 300, 497-558, 592, 604, 768-821, 843, 948, 1000, 1070, 1165, 1199
element_miniscope/version.py         1      1     0%   2
--------------------------------------------------------------------------------------------------------
TOTAL                              282     58    79%

Missing

• Single lines: primarily error statements (e.g., FileNotFound)
• 247-267 : V3 data is not in sample dataset
• 497-558 : task mode trigger is not tested - time consuming
• 768-821 : nonrigid motion correction

Docker

I'm able to install docker if I hop in to the container, but my install scripts time out during docker compose. There are perhaps workarounds, but I leave this to future PRs. Instead, I leave warnings on the topic.