📝🎨 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