Merge All High Schoolers' PRs #61

zhan4329 · 2025-10-31T21:34:15Z

This pull request merges all six open PRs and introduces some other necessary changes. Here are the details.

New Features from Previous PRs

Introduced font size sliders to all plotting tabs, including
- From PR Add font size sliders to plotting tabs #57: Annotations, Anno. Vs Anno., Boxplot, Features, Nearest Neighbors, Scatterplot, Spatial, UMAP
- From PR Feat vs Anno Tab Labels Readability Fix (Cleaner Files) #51: Feat. Vs Anno.
Introduced a y-axis rotator and an abbreviate toggle to Feat. Vs Anno. tab (from PR Feat vs Anno Tab Labels Readability Fix (Cleaner Files) #51)
Introduced a heatmap mode in scatter plot (from PR Integration of Datashader Library into Automatically Scaling Scatter Plot Heatmaps #53)

Code Refactoring

Refactored some codes to make the ui more user-friendly
Refactored some codes for better logic

Dependency Management

Added two new packages (colorcet and datashader) to requirements.txt to support the newly introduced heatmap mode in scatter plot
Updated environment.yml:
- Updated packages and versions to keep it consistent with requirement.txt
- Added a quick guide to create conda environment and a special reminder for MacArm64 devices (extracted from PR Creating a quickstart file for how to run SPAC Shiny on MacArm64 #54).

Development and Deployment Infrastructure

Updated Dockerfile:
- Updated Python image from 3.9.19 to 3.10 to support the new package 'datashader' used by the heatmap mode in scatter plot
- Added a layer to disable the proxy cache in Dockerfile to fix 'Hash Sum Mismatch' bug on mac devices mentioned here: Bmc paper updates #59 (comment) and Bmc paper updates #59 (comment)
Updated .gitignore to exclude an unnecessary Jupyter-related file format

Documentation

Updated README.md to include names of this year's Data Mine Team contributors and TA
Added a CONTRIBUTING.md with links to the copilot-based instructions as well as SPAC Package project's contributing guide

Remarks About the Six Open PRs

The six open PRs are No.51, 53, 54, 55, 56, and 57.
Both PR Feat vs Anno Tab Labels Readability Fix (Cleaner Files) #51 and PR Add font size sliders to plotting tabs #57 have been fully merged into this branch.
PR Integration of Datashader Library into Automatically Scaling Scatter Plot Heatmaps #53 is fully merged. However, we think the logic of the heatmap mode for the scatter plot needs further investigation. We plan to look into it later.
Changes from PR Display supported file types on Data Input tab #55 already exist on the current "main" branch.
We did not formally merge PR WSL Quickstart Tutorial #56 into our branch. We do formally merge PR Creating a quickstart file for how to run SPAC Shiny on MacArm64 #54. However, we think both are redundant since the standard way now is to use docker. That's why we put the quickstart guide for conda only inside environment.yml.
We are still working on a guide for docker. It is not in this PR.

Remarks About Other Changes

We are not fully confident of the changes we made to Dockerfile, especially the Python version. We haven't found any new issues though.

…ronment config

…ize_rk

Small fixes: - Update environment.yml to make it consistent with requirement.txt Comments: - Update .gitignore to include Jupyter section - Write clearer comments in Dockerfile; remove redundant comments Files clean up: - Remove redundant quickstart guide

Small fixes: - Update environment.yml to make it consistent with requirement.txt - Update README.md to include TA's name Comments: - Update .gitignore to include Jupyter section - Write clearer comments in Dockerfile; remove redundant comments Files clean up: - Remove redundant quickstart guide

small fixes - Update environment.yml to make it consistent with requirement.txt - Update README.md to include TA's name docs clean-up - Update .gitignore to include Jupyter section - Write clearer comments in Dockerfile; remove redundant comments - Remove redundant quickstart guide server files clean-up: anno_vs_anno_server.py, feat_vs_anno_server.py, nearest_neighbor_server.py, scatterplot_server.py ui files clean-up: anno_vs_anno_ui.py, annotations_ui.py, feat_vs_anno_ui.py, features_ui.py, scatterplot_ui.py

zhan4329 · 2025-11-01T16:17:31Z

@georgezakinih Hi George, could you review this Pull Request for high schoolers' PRs as well as some other necessary changes done by us? Thank you!

- Update SPAC package - Add comments to the two new packages

small fixes - Update environment.yml to make it consistent with requirement.txt - Update README.md to include TA's name docs clean-up - Update .gitignore to include Jupyter section - Write clearer comments in Dockerfile; remove redundant comments - Remove redundant quickstart guide server files clean-up: anno_vs_anno_server.py, feat_vs_anno_server.py, nearest_neighbor_server.py, scatterplot_server.py ui files clean-up: anno_vs_anno_ui.py, annotations_ui.py, feat_vs_anno_ui.py, features_ui.py, scatterplot_ui.py

…AP#61 small fixes - Update environment.yml to make it consistent with requirement.txt - Update README.md to include TA's name docs clean-up - Update .gitignore to include Jupyter section - Write clearer comments in Dockerfile; remove redundant comments

small fixes - Update environment.yml to make it consistent with requirement.txt - Update README.md to include TA's name docs clean-up - Update .gitignore to include Jupyter section - Write clearer comments in Dockerfile; remove redundant comments - Remove redundant quickstart guide server files clean-up: anno_vs_anno_server.py, feat_vs_anno_server.py, nearest_neighbor_server.py, scatterplot_server.py ui files clean-up: anno_vs_anno_ui.py, annotations_ui.py, feat_vs_anno_ui.py, features_ui.py, scatterplot_ui.py

root and others added 30 commits July 6, 2025 10:40

Add README with Windows and Ubuntu installation guide

1b37039

Update README with additional setup details

5901c97

Update README with more additional setup details

106804a

Update README with more additional setup details

8ea7a23

Update README with additional setup details

f59a8b5

✨ Abbreviation toggle, font styling, and heatmap controls implemented

adc6775

🔧 Updated issues relating to overlapping labels

d574b0a

Merge remote-tracking branch 'upstream/main' into Sudeep

3748c49

Update feat_vs_anno_server.py with better readibality

59c26d5

Update feat_vs_anno_server.py with better readability for the labels

c7ea3ea

Integrated datashader library into heatmaps for scatterplots and envi…

75731ec

…ronment config

Full integration: Datashader updates, utils, and heatmap UI

90c4513

Update to python version to 3.9.13

33aba4b

Moving colorcet library under pip for better organization

d387d64

Update Quickstart_MacArm64.md with improved setup instructions

5a1be36

Fix typo in Quickstart_MacArm64.md

ec7b22c

feat: Add list of supported file types under the file upload button

8834bb4

Removed mac quickstart file

47aefca

Merge remote-tracking branch 'origin/Feat_vs_Anno_Labels' into font_s…

a8706ed

…ize_rk

feat: Add font size sliders to plot tabs

b061f42

add boqiang as a contributer

bc03645

sungmin

88e2891

Testing

93acb1f

Noah Lee

28b5c41

add boqiang

c7b4d23

add Heaven

83ac232

add gitignore, rm __pycache__

ef8377f

update gitignore to include .ipynb_checkpoints/

f989aa4

update README

57f3da7

fix(docs): replace the spac channel to solve import error

885e06a

zhan4329 force-pushed the merge/high-school-prs-issue-7 branch 4 times, most recently from fa81212 to 3dc2a08 Compare November 1, 2025 01:01

zhan4329 force-pushed the merge/high-school-prs-issue-7 branch from 3dc2a08 to 53e8c5f Compare November 1, 2025 03:00

zhan4329 added 2 commits October 31, 2025 23:14

docs: add a link to the SPAC contributing guide

b2798ff

docs(contri): add link to the copilot-instructions file

5111a99

zhan4329 mentioned this pull request Nov 1, 2025

Verify and Merge High School PRs Saran-Nag/SPAC_Shiny-Purdue-2025#7

Open

6 tasks

zhan4329 marked this pull request as ready for review November 1, 2025 16:14

zhan4329 added 3 commits November 3, 2025 12:58

Merge branch 'FNLCR-DMAP:main' into main

43a02b4

Merge branch 'main' into merge/high-school-prs-issue-7

730d0a1

- Update SPAC package - Add comments to the two new packages

chore(env): update environment.yml accordingly

95d41db

zhan4329 force-pushed the merge/high-school-prs-issue-7 branch from c0c4621 to 95d41db Compare November 3, 2025 18:10

zhan4329 closed this Nov 4, 2025

zhan4329 added a commit to Saran-Nag/SPAC_Shiny-Purdue-2025 that referenced this pull request Nov 7, 2025

chore(ui/serv): files clean-up for Pull Request FNLCR-DMAP#61

a354712

zhan4329 added a commit to Saran-Nag/SPAC_Shiny-Purdue-2025 that referenced this pull request Nov 11, 2025

chore(ui/serv): files clean-up for Pull Request FNLCR-DMAP#61

79e8d25

zhan4329 added a commit to Saran-Nag/SPAC_Shiny-Purdue-2025 that referenced this pull request Nov 12, 2025

chore(ui/serv): files clean-up for Pull Request FNLCR-DMAP#61

6aff7e1

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Merge All High Schoolers' PRs #61

Merge All High Schoolers' PRs #61

Uh oh!

zhan4329 commented Oct 31, 2025 •

edited

Loading

Uh oh!

zhan4329 commented Nov 1, 2025

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

7 participants

Merge All High Schoolers' PRs #61

Merge All High Schoolers' PRs #61

Uh oh!

Conversation

zhan4329 commented Oct 31, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

zhan4329 commented Nov 1, 2025

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

7 participants

zhan4329 commented Oct 31, 2025 •

edited

Loading