Refactor with fixes, features and improved directory structure #39
Conversation
This file contains 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
Significantly simplified code base with modular components that are each passed their own page's app (DashBlueprint) components and layouts are standardized to use render function that may receive the app with or without arguments :fire: Remove (now) unnecessary index.py :arrow_up: Pin dash-extensions to first major release :arrow_up: Pin dash to 2.10 :arrow_up: Add dash-mantine-components :arrow_up: Add dash-iconify TODO: Use tools in dash-mantine and dash-iconify libs for improved aesthetic
🎨 change default server debug setting to False
🐳 Add quotes around ports per docker-compose spec 🐛🔥 Remove extra id in norm_method_dropdown component 📝🔥 Fix typos and add details in CONTRIBUTING 🔥 Remove unused .py pages in pages dir 🎨 Update layout of home components
🎨 style buttons using dash-mantine-components
🎨🔥 Refactor refine_mags_inputs_groups by extracting selects for easier layout and styling 🎨🔥 Add icons to not found page and remove unnecessary text 🎨 rename id variables for modal and its close buttons 🎨 restyle modal
🔥 Remove settings banner component to isolate its components for easier layout and styling 🎨 Refactor marker symbols legend to use icons rather than naming shapes 🎨 Restyle save selections and settings buttons
🎨 Add selection callback for rendering contig connections cytoscape
🎨 Add REDIS_BACKEND details to .env
🎨 Add specific backend params to Serverside(..., backend=...) from automappa.data.db import {redis,file_system}_backend
🔥 Remove unnecessary serializers script in utils
🎨 Change default z-axis for 3D-scatterplot to coverage
⬆️ pin dash-mantine-components to 0.12 in env using pip rather than conda 🔥 Remove unused binning store 🎨 Change navigation to use dmc.NavLink 🎨 Add icons in page registry with blueprints
🔥 Remove pandas series from boxplot figures
🎨 Replace many of the Dropdowns in Offcanvas with RadioGroup Radio options (less clicks for the user)
📝 Add documentation for tasks in CONTRIBUTING and reference tasks README.md 🥕 Add minimum working example for task submission, progress display for a task status badge 🥕 Add structure for passing queue around from __main__ to page layouts 🥕 Add task discovery for home page task in celeryconfig.py
🐳🐍 Replace base image of miniforge with mambaforge 🐛 Update Makefile to remove correct image name for celery queue
🎨 Notification system tells user of current state of tasks processing 🐛🎨 Move dcc.Store(...) within respective du.Upload component 🎨 Add tasks store for getting tasks statuses 🐰🥕 Add tasks in home for handling sample data ingestion
🎨 Add MIMAG cluster count computations 🎨 Add metadata to sample data card info 🐛 Replace na values from cluster col during contig loader pre-processing
🎨 replace Length Sum units from kbp to mbp
evanroyrees
added
bug
This was referenced Jul 21, 2023
evanroyrees
added a commit
that referenced
this pull request
Jul 26, 2023
⬆️🎨 Bump VERSION to 2.2.0 * Refactor with fixes, features and improved directory structure (#39) * 🎨 Apply black formatting * 🎨⬆️🤠 refactor to use dash-extensions DashBlueprints * Significantly simplified code base with modular components that are each passed their own page's app (DashBlueprint) * components and layouts are standardized to use render function that may receive the app with or without arguments * 🔥 Remove (now) unnecessary index.py * ⬆️ Pin dash-extensions to first major release * ⬆️ Pin dash to 2.10 * ⬆️ Add dash-mantine-components * ⬆️ Add dash-iconify * 📝 Add contributing docs * 🎨🐛📝🐳 Fix docs, prop id and docker specs * 🐳 Add quotes around ports per docker-compose spec * 📝🎨🔥 add Development resources 🎨🔥 Add icons to not found page and remove unnecessary text * 🎨 Refactor mag refinement page components * 🎨 Refactor marker symbols legend to use icons rather than naming shapes * 🎨 Restyle save selections and settings buttons * 🎨 Refactor mag-refinement offsettings canvas components * 🎨 Add minimum example contig_cytoscape component * 🎨 Add specific backend configurations * 🎨 Add REDIS_BACKEND details to .env * 🎨 Add specific backend params to Serverside(..., backend=...) from automappa.data.db import {redis,file_system}_backend * 📝🔥 Refactor dash components to DashProxy components * ⬆️ pin dash-mantine-components to 0.12 in env using pip rather than conda * 🎨 Add icons in page registry with blueprints * 🎨 Add coverage range slider component * 🎨 Add Refinement model to track contig cluster refinements * 🎨 Implement data source to connect MAG refinements table * 🎨 Add methods to get latest user refinements contig headers * 🎨 Add interaction b/w coverage range slider and scatterplot2d * 🎨 Connect download refinements button to data source * 🎨 Hide MAG refinements switch is now disabled when there are no user refinements that have been made * 🎨 Refinements table has been styled with new timestamp string and removed 'initial_cluster' column * 🎨 Refinements table now only retrieves user refinements (i.e. excludes initial clusters) * 🎨 Add refinements clear button * Add working data source for completeness/purity boxplot * 🎨 Add minimal working AgGrid for MAG Summary * 🎨 Replace dbc.Offcanvas with dmc.Drawer * 🎨 Replace many of the Dropdowns in Offcanvas with RadioGroup Radio options (less clicks for the user) * 🥕🐰 Add logic for modular task-queue * 📝 Add documentation for tasks in CONTRIBUTING and reference tasks README.md * 🥕 Add minimum working example for task submission, progress display for a task status badge * 🥕 Add task discovery for home page task in celeryconfig.py * 🐳🐍 Replace base image of miniforge with mambaforge * 🥕🎨 Notification system tells user of current state of tasks processing * 🐛🎨 Move dcc.Store(...) within respective du.Upload component * 🎨 Add tasks store for getting tasks statuses * 🐰🥕 Add tasks in home for handling sample data ingestion * 🎨 Add mag length sum computations * 🎨 Add MIMAG cluster count computations * 🎨 Add metadata to sample data card info * 🐛 Replace na values from cluster col during contig loader pre-processing * 🎨🔥 Add sample removal feature * 🎨 Affix settings and save mag buttons * 📝 Update docs for release 2.2
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.
No description provided.