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UI cleanup: remove progress steps, fix hero header text visibility
Ashkan Taghipour (The University of Western Australia) +1: Claude Opus 4.6- Remove non-clickable progress step buttons from top of page (progress_html component, _build_progress_html, CSS classes) - Fix hero header text color: Gradio theme was overriding white text with dark color on the dark background. Added !important to ensure title, subtitle, and stat labels are visible. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>ca4b089 -
Improve Genome Explorer heatmap: angle x-axis labels, limit tick count
Ashkan Taghipour (The University of Western Australia) +1: Claude Opus 4.6X-axis genomic position labels were overlapping. Fixed by rotating labels -45 degrees, limiting to ~20 ticks, reducing font size, and adding bottom margin for the angled text. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>1e42f44 -
Fix Your Report tab: remove duplicate outputs causing Gradio error
Ashkan Taghipour (The University of Western Australia) +1: Claude Opus 4.6The generate report callback had final_download_json and final_download_csv each listed twice in outputs (value + visibility). Gradio 6.x does not allow duplicate components in outputs. Fixed by using gr.File(value, visible) to set both in a single return value, reducing outputs from 7 to 5. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>9fc7d91 -
Replace broken multiselect with single-select + Add/Clear buttons
Ashkan Taghipour (The University of Western Australia) +1: Claude Opus 4.6Gradio 6.5.1 multiselect dropdown is unreliable. Replaced with: - Single-select dropdown to pick one line at a time - "Add to party" button to add selected line to party list - "Clear party" button to reset - Visible "Party members" textbox showing current selections This matches the backpack pattern used in Quest 2/4 which works reliably. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>1185c9e -
Fix party dropdown: add filterable=True, handle multiselect value types
Ashkan Taghipour (The University of Western Australia) +1: Claude Opus 4.6- Add filterable=True to party_dropdown for reliable Gradio 6.x rendering - Fix on_party_dropdown to handle None, str, and list values from Gradio multiselect (list("string") would split into individual characters) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>7ef3f1b -
Fix Protein World performance: replace 55k-item dropdown with textbox
Ashkan Taghipour (The University of Western Australia) +1: Claude Opus 4.6The gene dropdown with 55,512 choices caused the browser to hang. Replaced with: - A textbox where users type a gene ID and press Enter or click Load - A small "pick from backpack" dropdown showing only pinned genes - A hidden dropdown for Gene Card "Show Protein" button integration All pin callbacks now also sync the backpack picker choices. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>16c6db2 -
Fix Compare button: show comparison plot after clicking Compare
Ashkan Taghipour (The University of Western Australia) +1: Claude Opus 4.6The plot was invisible because the callback output the figure and True to the same component (overwriting), and True is not valid for setting visibility in Gradio 6.x. Now returns gr.Plot(value=fig, visible=True). Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>f01b448 -
Fix Genetic Landscape: add party selection dropdown, improve cluster explanation
Ashkan Taghipour (The University of Western Australia) +1: Claude Opus 4.6- Replace broken lasso/click selection (unsupported in Plotly 3D) with a multi-select dropdown for choosing party members to compare - Wire party dropdown → state.selected_party → Compare button - Add explanation of why there are 3 clusters (KMeans silhouette=0.649) - Improve header and accordion text with clear user guidance Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>3e00bd5 -
Improve Protein World UX: add pin button, backpack display, clear guidance
Ashkan Taghipour (The University of Western Australia) +1: Claude Opus 4.6- Add "Pin this gene to Backpack" button directly in Quest 4 - Show backpack contents in Quest 4, synced with Quest 2 and Gene Card - Rewrite header and labels to explain what proteins are and how pinning works - Fix misleading dropdown label to "Select a gene to inspect" Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>45410eb
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Fix Gradio 6.x compatibility for HF Spaces
Ashkan Taghipour (The University of Western Australia)- Move theme/css from gr.Blocks() to launch() per Gradio 6 API - Set ssr_mode=False to prevent localhost-access crash on HF Spaces - Add 11 Gradio 6 compatibility tests4965d2c -
UI overhaul: immersive chapter-based experience
Ashkan Taghipour (The University of Western Australia)- Rename tabs: Origins, Genetic Landscape, Gene Universe, Genome Explorer, Protein World, Your Report - Load 3D UMAP embedding for true 3D scatter visualization - Add country filter dropdown on Origins tab (replaces global filters accordion) - Remove global filters accordion - Update progress stepper labels - Add new precomputed artifacts: 3D embedding, sunburst hierarchy, polar layout, radar axes - Update UMAP callback to use 3D Scatter3d - Upgrade Gradio SDK version to 6.5.114ba315 -
Fix HF Spaces deployment: pin pydantic, update sdk, clean deps
Ashkan Taghipour (The University of Western Australia)- Pin pydantic==2.10.6 in requirements.txt to fix the 'No API found' error caused by pydantic/ASGI incompatibility on HF Spaces - Update sdk_version from 5.9.1 to 5.29.0 for better stability - Remove unused runtime dependencies (scipy, scikit-learn, umap-learn, biopython, pyfaidx, Pillow, reportlab) that are only needed for offline precomputation, reducing build time and install failures - Fix SelectData callback in treasure table: use properly typed function instead of lambda to receive gr.SelectData event correctly4b345ed -
Initial deploy: Pigeon Pea Pangenome Atlas
Ashkan Taghipour (The University of Western Australia)16e4ad5 -
initial commit
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