Develop update for Oct 2025 #169
Open
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
… if requested, in the plot_density_pvals_simple() function.
Allow user to download slide-level (averaged over ROIs) heatmap data.
…irectory for manual transfer to NIDAP. This is because downloads are still not working in Streamlit in Code Workspaces, at least published.
quick little fix for ease
So they are accessible by the Neighborhood Profiles
Downloads are blocked on NIDAP, so this will suffice to add to the Output folder
Download button np
st.write update Co-authored-by: Copilot <[email protected]>
…-the-data-for-each-plot-in-the-subplots-section 166 export all button that exports the data for each plot in the subplots section
This reverts commit f98cda3.
Contributor
There was a problem hiding this comment.
Pull Request Overview
This PR updates the project for October 2025, including dependency version updates, new functionality for saving heatmap data, and improvements to the neighborhood profile visualization workflow.
- Updated parent template version and various package dependencies in the conda environment
- Added capability to save heatmap CSV data alongside visualizations
- Enhanced neighborhood profile functionality with CSV export options and improved cluster comparison handling
Reviewed Changes
Copilot reviewed 12 out of 13 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
| templateConfig.json | Updated parent template version from 0.231.0 to 0.243.0 |
| .envs/maestro/meta.yaml | Comprehensive update of conda environment dependencies with specific version pinning |
| utils.py | Added filtering to exclude CSV files from heatmaps directory listing |
| time_cell_interaction_lib.py | Added functionality to save heatmap data as CSV files and character replacement in species names |
| pages2/Tool_parameter_selection.py | Added UI control for enabling heatmap data saving |
| pages2/Run_workflow.py | Integrated new save_heatmap_data parameter into workflow execution |
| pages2/Display_average_heatmaps.py | Added UI for creating zip file of saved heatmap CSV files |
| pages2/Neighborhood_Profiles.py | Enhanced neighborhood profile with CSV export capability and removed commented code |
| basic_phenotyper_lib.py | Modified draw_neigh_profile_fig to return density dataframe and added cluster labels |
| pages2/feature_creation.py | Changed dataframe display to show sampled data with resample button |
| pages2/multiaxial_gating.py | Converted columns index to list for selectbox options |
| .publish-dashboards.py | Added support for resourcesV2 configuration |
Tip: Customize your code reviews with copilot-instructions.md. Create the file or learn how to get started.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This pull request introduces several enhancements and improvements across the environment configuration and multiple Streamlit application pages, focusing on environment reproducibility, data export functionality, and usability for cluster/heatmap analysis. The most important changes are summarized below.
Environment and Dependency Management:
.envs/maestro/meta.yamlto update, pin, and reorganize dependencies for improved reproducibility and compatibility, including explicit versioning for key packages and consolidating requirements between conda and pip.Neighborhood Profiles Export and Usability:
Enhanced the neighborhood profiles workflow in
pages2/Neighborhood_Profiles.pyandbasic_phenotyper_lib.pyto allow users to export cluster comparison results as CSV files directly to the output folder, both for individual and batch (subplot) analyses. This includes capturing the computed dataframes, managing file suffixes, and providing UI buttons for saving results. [1] [2] [3] [4] [5] [6] [7] [8] [9]Improved cluster list management to dynamically include "Average Left" and "Average Right" when cluster difference toggles are enabled, ensuring correct options are available throughout the workflow. [1] [2]
Average Heatmap Data Export:
pages2/Tool_parameter_selection.pyfor users to enable saving of slide-averaged heatmap data, and propagated this setting through the workflow. Thepages2/Display_average_heatmaps.pypage now provides a button to zip and export all relevant heatmap data CSVs, improving downstream data accessibility. [1] [2] [3] [4] [5]Miscellaneous Improvements:
resourcesV2in.publish-dashboards.py.pages2/feature_creation.py.pages2/Neighborhood_Profiles.py.These changes collectively improve the reproducibility, usability, and data export capabilities of the application, making it easier for users to manage, analyze, and extract results from their workflows.