Skip to content
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.

Sign up for GitHub

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

Jump to bottom

Clean jump notebook #21

Merged
merged 10 commits into from
Nov 10, 2023
Merged

Clean jump notebook #21

merged 10 commits into from
Nov 10, 2023

Conversation

safiyecelik
Copy link
Collaborator

What?

  • I am simplifying the jump notebook as it was originally built for the cytodata workshop and has things that do not necessarily need to be here in this repo. I am also adding the efaar pipeline functions to efaar.py script for modularity.

Why?

  • because we want an easier life for users who want to run the notebook.

@safiyecelik safiyecelik requested a review from a team as a code owner November 9, 2023 19:39
@review-notebook-app Review Notebook App
Copy link

Check out this pull request on  ReviewNB

See visual diffs & provide feedback on Jupyter Notebooks.

Powered by ReviewNB

@safiyecelik safiyecelik removed the request for review from QuantumPlatypus November 9, 2023 19:39
ctilling
ctilling reviewed Nov 10, 2023
View reviewed changes
Copy link
Contributor

@ctilling ctilling left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Some quick thoughts on a first glance

efaar_benchmarking/data_loading.py Outdated Show resolved Hide resolved
efaar_benchmarking/data_loading.py Outdated Show resolved Hide resolved
safiyecelik and others added 5 commits November 9, 2023 21:37
@safiyecelik
separate filtering from data loading
3f4426c
@safiyecelik
fix median syntax
967d6ba
@safiyecelik @dependabot
Bump pyarrow from 13.0.0 to 14.0.1 in /requirements (#22) (#23)
48c0593 
Bumps [pyarrow](https://github.com/apache/arrow) from 13.0.0 to 14.0.1.
- [Commits](apache/arrow@go/v13.0.0...apache-arrow-14.0.1)

---
updated-dependencies:
- dependency-name: pyarrow
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@safiyecelik
add no scaling option to align_on_controls
e26dbd3
@safiyecelik
update docstring and delete the jump metadata files
70f3bb8
ctilling
ctilling previously approved these changes Nov 10, 2023
View reviewed changes
Copy link
Contributor

@ctilling ctilling left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Looks good to me, thanks for cleaning up the notebook!

@safiyecelik safiyecelik merged commit b190fa3 into trunk Nov 10, 2023
10 checks passed
@safiyecelik safiyecelik deleted the clean_jump_notebook branch November 10, 2023 22:55
safiyecelik added a commit that referenced this pull request Nov 14, 2023
@safiyecelik @dependabot
Merge trunk (#25)
7170154 
* Bump pyarrow from 13.0.0 to 14.0.1 in /requirements (#22)

Bumps [pyarrow](https://github.com/apache/arrow) from 13.0.0 to 14.0.1.
- [Commits](apache/arrow@go/v13.0.0...apache-arrow-14.0.1)

---
updated-dependencies:
- dependency-name: pyarrow
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Clean jump notebook (#21)

* convert string to Path in reading benchmark data

* simple jump notebook

* fix perturbation column

* separate filtering from data loading

* fix median syntax

* Bump pyarrow from 13.0.0 to 14.0.1 in /requirements (#22) (#23)

Bumps [pyarrow](https://github.com/apache/arrow) from 13.0.0 to 14.0.1.
- [Commits](apache/arrow@go/v13.0.0...apache-arrow-14.0.1)

---
updated-dependencies:
- dependency-name: pyarrow
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* add no scaling option to align_on_controls

* update docstring and delete the jump metadata files

* convert read_parquet function to lambda function

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@ctilling ctilling ctilling left review comments

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@safiyecelik @ctilling