[x] Reviewed all Files changed prior to selecting Create Pull Request.
[x] Ran and passed all pytests, and ran the pipeline for features not covered by tests.
[X] Ran pre-commit checks, including black, flake8, etc.
[X] Updated the changelog and if making a new release, updated the version.py.
[x] Updated documentation, including concepts.md, tutorials.md, and relevant docstrings.
[x] After merge, I will push a new tag to upstream (test* prefix if no new release).
Submission details
In this pull request, I make changes to parallel my ephys QC dashboard for the corresponding U24 milestone:
changelog - add mention of QC additions
miniscope.py - add add report schema activation to central schema activation
miniscope_report.py - add simple table for collecting each of the QC metrics on populate command
element_miniscope/plotting/qc.py add class. Much of this is the exact same as the ephys component with a few exceptions:
no cutoffs
units -> components: these are attributes of the CaImAn estimates class
_default_bins: gives a set of bins for histogram plots
Added mkdocstring rendering for new qc script and mkdocs pages for new workflow notebook PR
Note: I encountered a bug where the mkdocstring-python handler could not render a subfolder script in my local deployment. I did a deep dive on the inner workings of this process, but could not find any differences between this and other repos. As a workaround, I added a line to the docker compose to generate a soft link on build. This renders correctly in my local deployment.
Submission checklist
Files changed
prior to selectingCreate Pull Request
.Submission details
In this pull request, I make changes to parallel my ephys QC dashboard for the corresponding U24 milestone:
changelog
- add mention of QC additionsminiscope.py
- add add report schema activation to central schema activationminiscope_report.py
- add simple table for collecting each of the QC metrics on populate commandelement_miniscope/plotting/qc.py
add class. Much of this is the exact same as the ephys component with a few exceptions: