Table redesign, Tutorial docs

[CBroz1]

See also workflow 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: see wf PR 32.
• Ran pre-commit checks, including black, flake8, etc.
• Updated the changelog and if making a new release, updated the version.py.
• 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 linting - ensure standardization across markdown files via linting. Remove trailing spaces, standardize bullets, etc.
  • Conduct, Contributing, concepts, index
  • cspell.json - spell checker config - spelling revisions applied to various pages
  • readme/index.md - remove hardwrap that split links
• isort - organize python imports for miniscope.py
• Migrate recording info attributes to relevant tables in element-session (Move recording_directory to Recording part table #20 , Insert recording_datetime into RecordingInfo table #22 )
• Revise variable names to align with changes to element-calcium-imaging #26
  • Revise table structure to reflect Element Calcium imaging
  • acquisition_software -> acq_software
  • recording_directory: remove in favor of session.SessionDirectory
  • Segmentation.Mask.mask_id -> mask to reflect calcium-imaging
  • Move MaskType to after ProcessingParamSet to match ordering
  • extraction_method varchar(200) -> varchar(32)
  • Preserving differences:
    • AnatomicalLocation differs, but this is workflow-calcium-imaging bug (see Add Inscopix metadata ingestion & update table definitions + make functions #57)
    • RecordingInfo.File has a file_id that calcium-imaging does not. Paths should be secondary attributes in case they change
    • Many tables in calcium imaging permit z-depth information. Miniscope is 2D
• Add notebook rendering as mkdocs tutorial pages #34
  • gitignore: add docs items
  • docs/docker/pip_requirements - add mkdocs-jupyter extension
  • docs/docker-compose - migrate workflow download from make_pages to docker compose
  • mkdocs.yaml - add notebook pages
• Null defaults in Mask table #24
• mask key caused issues with example data. Changed to also accept mask_id