📝🎨 Add Bioconda project url to setup.py
🎨 Add toast when browser storage limits are reached (issue #11)
:art::memo: Move favicon to automappa/assets
:arrow_up::art: Add geom-median to environment.yml
:art: Add get_clusters_geom_medians(...) to celery tasks
:arrow_up::art: Bump VERSION to 2.2.0
:see_no_evil: Add data to .gitignore

…ome-tab

…bitmq) for task-queue

Add TODOs for WIP next steps... To be checked before merge into develop

🎨🐛 Prevent samples-store data from being overwritten on initial callback
🎨 samples-store data now persistent with local session
🎨 Refactor some variables in MAG refinement
🎨 WIP

…zation

… MetaData.table.keys()

Should now be able to 🔥 remove all of the data stores to track the fileupload table_id... 🔥

🐳🌻🐘🎨 Add docker-services: celery, flower, prometheus, grafana, redis, rabbitmq
🎨🔥 Remove environment/*.env files. Consolidate to .env with corresponding prefixes
🎨 Change pydantic models built on BaseSettings in automappa.settings to use only .env with env_prefix
🎨🌻 Add working configuration of celery task-queue with redis backend and rabbitMQ broker
📝 Add resources/references for misc. links used during debugging/troubleshooting
⬆️ Add flower. Move celery[redis] to pip install section of environment.yml
🎨 black formatting to serializers and change server.upload_folder root to server.root_upload_folder
🎨 blak formatting to home.py

🎨 dbc.Select(...) are now populated with values from db tables
🐛🎨 Investigate whether serializer.get_uploaded_files_table() is functional (TODO)
🐳 Add commented out arg to create_engine(..., pre_pool_ping: Optional[bool]) and db settings
🐳 Add PRE_POOL_PING to .env

🔥 Remove (now deprecated) stores
🎨 Add serialization of a hash-refinement table when hash-binning file is uploaded (respective to hash-binning)
🎨 Remove --debug arg from parser. Move statement to .env (now handle read with automappa.settings.server.debug
🔥 remove unused imports in index.py
🎨 Move samples stores from home.py to index.py
Add dbc.InputGroup(...) with selects for binning, markers and metagenome
🎨 Add dbc.Button(...) to save table-ids in 'selected-tables-store' to be read from mag_refinement.py
🎨🐛 Continue refactor of get_scatterplot_2d(...) to use other embedding methods
🎨 Add get_marker_symbols(...) to tasks.py and automappa.utils.markers (WIP currently being used to *expensively* generate symbols during 2d scatterplot creation

🔥 Remove unused (commented out) argparse args
🔥🎨🐳 Update automappa-web service command to not use removed argparse args

Will still need to ensure this is working once celery tasks are implemented

🐛🔥 Fix sankey diagram subsetting bug where selections would not render
🎨 Change MAG-specific completeness/purity boxplot to barplot
🎨 Rename save_to_db(...) to file_to_db(...) in serializer
🎨 Add metric_barplot(...) func to automappa.utils.figures

- 🐳🎨 Add mem_limit: 4GB to automappa-web service
- 🎨🐛 Remove ability for user to navigate to other tabs when no data has been uploaded/selected
- 🎨 Disable 'Refine mags' button if data has not been selected
- 🎨 Add DataTable(...) to visualize the currently loaded datasets
- 🎨 Change server settings import so it is clear that the server setting are imported and not the server
- 🎨🥕 Silence numba and h5py loggers in mag_refinement.py (beginnings of celery task-queue tasks implementation)
 - 🎨 Add logger to automappa.tasks
- 🐛 Fix logger emitted message during refinement data serialization to postgres db

…g methods

🎨🐛 Need to replace kmers.embed(...) method in tasks.py to include n_jobs=1 when autometa 2.0.4 release is out
🎨🥦 Add celeryconfig
🎨🥦 Add working kmer freq. analysis parallelize pipeline for use in task-queue
🎨 Add use of pydantic.BaseModel in models.py of SampleTables, KmerTable, AnnotationTable and misc. others (WIP)
🎨 Add construction of SeqIO.SeqRecords when retrieving metagenome from table using new func, get_metagenome_seqrecords(...)
🎨 Refactor get_contig_marker_counts(...)
🎨 Refactor get_marker_symbols(...) in markers.py
🎨🔥 Remove hard-coded values in automappa.utils.figures.get_embedding_traces_df(...)
🎨 Parse selected_data_tables as SampleTables.parse_raw(selected_data_tables) for shared data
🎨 Add tasks button to home.py
🎨 Replace typehints for selected_data_tables to Json[SampleTables]

🎨 Fetch data from postgres service
🎨🥦 Retrieve scatterplot-2d coordinates from celery task-queue results (selected from auto-generated dropdown)
🎨🌻 Add flower configuration env variable to settings.py
🎨 generate product of all combinations of kmer pipeline params (kmer_size, norm_method, embed_method) for 2d-coords retrieval
🎨🐎🐛 Retrieve mag summary data from SampleTables properties instead of using get_table(...)
🔥🐛 Remove default value of 'cluster' for mag_summary_cluster_col_dropdown
🎨🔥 Remove unnecessary nested lists of Input(...) in mag_summary callbacks
🎨 Add long_callback_manager to app (WIP: currently not being used)
🎨 Add handling of kmer param titles and metagenome annotation titles to format_axis_title(...) in figures.py
🎨🐳🐰 Change rabbitmq image from latest to 3.10.1-management-alpine (w/port) to use amqp management UI

📝 Move misc. markdown docs to docs directory

🐳 Ignore .vscode for docker context
🐳 Install mamba and prune prior to env update

💚🐎 Add dash-extensions to enable caching
🔥 Reduce kmer tasks to am_clr norm method and kmer_size of 5 (bhsne, densmap and umap embeddings)

Turn off debug mode by default

🔥 Change clone of `home-tab` branch to `develop` branch

🐳📺🎨 Automappa web app with home tab for data upload

- 🥦 Add task-queue for pre/post-processing tasks with celery
- 🟥 Add Redis service for celery backend
- 🐰 Add RabbitMQ service for celery broker
- 🐘 Add PostgreSQL for data ingestion
- 🌷 Add Flower for celery task-queue monitoring
- 🐍🎨 Add Pydantic for data models
- 🐳 Add docker-compose file to orchestrate Automappa services

* 🎨 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