Post-BTEP Presentation Updates

[djsmith17]

Tracking new updates to MAWA following the BTEP presentation

[Copilot]

Pull Request Overview

This PR contains updates following the BTEP presentation that adjust plotting performance and appearance in several modules, update package installation preferences, and remove obsolete configuration files.

• Updated plotting functions to use Scattergl and refined aesthetic parameters in Pheno Cluster plots.
• Introduced new normalization toggles and adjusted marker sizes in UMAP and scatter plots.
• Modified package installer preference and updated channel checks; removed the legacy pages.toml configuration.

Reviewed Changes

Copilot reviewed 10 out of 13 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
pages2/robust_scatter_plotter.py	Switched to Scattergl for improved performance in scatter plotting.
pages2/Pheno_Cluster_b.py	Updated plotting layout, normalization options, and marker sizes.
pages2/Pheno_Cluster_a.py	Adjusted plotly layout settings to ensure consistent aspect ratios.
install_missing_packages.py	Removed 'conda' from the list of installers to use.
app_top_of_page.py & Multiplex_Analysis_Web_Apps.py	Updated channel checking logic.
.streamlit/pages.toml	Removed configuration file likely reflecting a reorganization.
.envs/maestro/meta.yaml	Added metadata and package dependency definitions.

Files not reviewed (3)

• .hooks/startup.sh: Language not supported
• environment.yml: Language not supported
• templateConfig.json: Language not supported

Comments suppressed due to low confidence (4)

.streamlit/pages.toml:1

• [nitpick] The removal of the pages.toml file suggests a change in navigation configuration; please confirm that this removal aligns with the updated app navigation design.

Removed file content

pages2/Pheno_Cluster_b.py:127

• [nitpick] The new figure size setting is significantly smaller than before; please confirm that this change improves visualization and does not adversely affect readability.

plotnine.options.figure_size = (5, 4)

pages2/Pheno_Cluster_b.py:156

• [nitpick] The marker size has been reduced from 8 to 3 in the scatterplot; please verify that the smaller markers maintain adequate visibility across different displays.

palette='viridis', ax=ax, s=3)

install_missing_packages.py:71

• Removal of 'conda' from the installers may affect environments where conda is preferred; please ensure that this change is intentional and consistent with deployment practices.

installers_to_use = ['mamba', 'pip']

[Copilot]

Pull Request Overview

Updates following the BTEP presentation to bump template versions, improve plot performance and styling, add normalization toggles to the Phenotype Clustering pipeline, and consolidate environment/install scripts.

• Bumped parent template version in templateConfig.json
• Swapped go.Scatter to go.Scattergl for faster scatter rendering
• Added normalization options, aspect‐ratio fixes, and font size adjustments in Pheno_Cluster
• Removed old environment.yml and revised installer scripts
• Updated startup hook and platform detection logic

Reviewed Changes

Copilot reviewed 13 out of 13 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
templateConfig.json	Bump parentTemplateVersion from 0.176.0 to 0.192.0.
pages2/robust_scatter_plotter.py	Swapped Scatter to Scattergl for WebGL‐based rendering.
pages2/Pheno_Cluster_b.py	Added normalization toggles, sizing tweaks, and aspect‐ratio fixes; updated function signature.
pages2/Pheno_Cluster_a.py	Applied aspect‐ratio fix to UMAP plots.
install_missing_packages.py	Removed conda fallback from installer list.
environment.yml	Deleted entire file (migrating to meta.yaml).
app_top_of_page.py & Multiplex_Analysis_Web_Apps.py	Switched platform check from "nidap.nih.gov" to "foundry-artifacts".
.streamlit/pages.toml	Entire file removed.
.hooks/startup.sh	Uninstalled pip/mamba install commands.
.envs/maestro/meta.yaml	Introduced new consolidated conda/pip recipe.

Comments suppressed due to low confidence (6)

.hooks/startup.sh:9

• All essential pip and mamba install commands were removed, which may prevent required dependencies from being installed during startup; verify that startup.sh still installs necessary packages.

pip install scikit-learn streamlit-extras squidpy split-file-reader st-pages dill pympler objsize

.streamlit/pages.toml:1

• The pages.toml file has been completely removed, which will break custom Streamlit page navigation; confirm that page configuration is intentionally migrated or updated.

[[pages]]

pages2/Pheno_Cluster_b.py:98

• The 'plot_column' parameter is no longer used in the function body; consider removing it or integrating its use to avoid confusion.

def phenocluster__plot_diff_intensity_2(adata, groups, method, n_genes, plot_column, normalize_total, log_normalize, z_normalize, cluster_group):

pages2/Pheno_Cluster_b.py:98

• [nitpick] The function name uses a double underscore which can be confusing and violates typical Python naming conventions; consider renaming to use a single underscore or a more descriptive name.

def phenocluster__plot_diff_intensity_2(adata, groups, method, n_genes, plot_column, normalize_total, log_normalize, z_normalize, cluster_group):

environment.yml:1

• The 'environment.yml' file has been deleted; ensure that its removal is intentional and that environment management is consolidated in meta.yaml.

-   -dependencies:

install_missing_packages.py:71

• Removing 'conda' from installers_to_use removes a fallback option if mamba isn't available; consider re-adding 'conda' as a fallback installer.

installers_to_use = ['mamba', 'pip']

[Copilot]

The docstring for 'platform_is_nidap' still refers to checking for NIDAP, but the logic checks for 'foundry-artifacts'; update the docstring to reflect the current check.

[andrew-weisman]

Approved as long as the bugs from the 7/29/25 meeting are addressed so we're sure this is a fully functional version. Is that the case @djsmith17? Thanks for taking the initiative.