Integrate workflow-calcium-imaging's tutorial environment, notebooks, and tests

[kabilar]

Description

• The workflow-calcium-imaging repository provides a tutorial environment and notebooks (and pytests) for running element-calcium-imaging.
• In the proposed changes, we integrate the contents of workflow-calcium-imaging into element-calcium-imaging, and will subsequently archive workflow-calcium-imaging.

Changes

• Use git merge to merge the workflow-calcium-imaging git history into element-calcium-imaging
• Subsequently made the following updates
  • Update version and changelog
  • Update setup.py
    • Add extras_require feature
    • Move installation of sbxreader and scanreader to the Dockerfile so that element-calcium-imaging can be published to PyPI.
  • Update Dev Container
    • Update Dockerfile to install all extras_require for element-calcium-imaging
    • Rename docker-compose.yaml to docker-compose-db.yaml
  • Update GitHub Actions
    • Replace previous workflows with reusable workflows in the datajoint/.github repository for GitHub, PyPI, and MkDocs releases
    • Add workflow to build and publish Dev Container Docker image
    • Add tests to ensure black formatter compliance
  • Update imaging* and scan schemas with backwards incompatible change to simplify user experience
    • Add get_image_files function and replace get_nd2_files, get_prairieview_files, get_scan_box_files, get_scan_image_files.
  • Update docs
    • workflow -> pipeline
  • Update notebooks
    • Add tutorial_pipeline script to import and activate schemas
    • reference.Equipment -> lab.Device
    • Remove demo_prepare.ipynb, which can be replaced by tutorial.ipynb
    • Rename demo_run.ipynb to demo.ipynb
  • element_calcium_imaging/__init__.py now uses environment variables (if available) in place of dj.config['custom'] values
  • Update tests
    • Remove most of the previous tests since they are dependent on private data. Will update tests in a future pull request for public data.
    • Fix Remove order requirements for test_pipeline_generation.py #139