-
Notifications
You must be signed in to change notification settings - Fork 4
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Initial Release for element-moseq
#2
Conversation
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
@MilagrosMarin great work!
The design and implementation are well structured and cleanly executed.
I left a few comments.
For next steps, we will want to do some further cleanup, no major changes in the logic
- rethink the naming
kpms_pca
->moseq_train
kpms_model
->moseq_inference
- activate - we don't need to activate the 2 modules twice, as they go hand in hand (users can't use one without the other). We can use the same implementation as in
element-calcium-imaging
forscan
andimaging
modules
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Looks great overall, @MilagrosMarin. Just a few changes in the docs section. I haven't looked through the tutorial yet but can do so after we've finalized all the table names and the logic in the make functions in these rounds of review.
|
||
| Table | Description | | ||
| --- | --- | | ||
| Device | Scanner metadata | |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Does this Element use the Device table? Or are we too far downstream to need this here?
Merging this first PR - new revisions will be in separate PRs |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
@MilagrosMarin I've add further review comments on this PR - please incorporate the changes to the new PR as well
This PR introduces the initial release for
element-moseq
version 0.1.0 to the DataJoint repository, adhering to the standardized practices across DataJoint Elements. Here's a summary of the changes:Changelog and version:
CHANGELOG
andversion
to document the changes made for this first release.DevContainer Configuration:
example_data
from a deeplabcut project in the S3 bucket and validated in Codespaces.setup.py
withextras_require
andtests
functionalities.GitHub Actions:
.github
directoryDocumentation:
docs
regardingelement-moseq
andKeypoint-MoSeq
.README
to align with DataJoint Elements standards.Pipeline Development:
kpms_reader
readers.element_moseq pipeline
architecture containingkpms_pca
andkpms_model
modules.Images:
images
directoryNotebooks:
tutorial.ipynb
notebook consistent with other DataJoint Elements.tutorial_pipeline.py
to facilitate schema importation and activation.Other files:
Code formatting:
This PR marks a significant milestone in the advancement of
element-moseq
, laying the groundwork for future enhancements and contributions.