├── .github ├── pull_request_template.md └── workflows │ ├── end-to-end-tests.yml │ └── pylint.yml ├── .gitignore ├── .gitmodules ├── CONTRIBUTING.md ├── DBINSTALL.md ├── Dockerfile.backend ├── Dockerfile.frontend ├── INSTALL.md ├── LICENSE ├── README.md ├── batch.py ├── config ├── .pylintrc ├── config.js ├── cypress.config.js ├── dbconfig.js └── pm2.config.js ├── convert_json.py ├── covizu ├── __init__.py ├── beadplot.py ├── clustering.py ├── data │ ├── NC_045512.fa │ └── README.md ├── deprecated │ ├── ChunkyBot.py │ ├── autobot.py │ ├── db_utils.py │ └── pangorider.py ├── hunepi │ ├── infections_increasing_model_comparisons.rds │ └── num_infections_model_comparisons.rds ├── minimap2.py ├── treetime.py └── utils │ ├── __init__.py │ ├── batch_utils.py │ ├── gisaid_utils.py │ ├── pangolin_utils.py │ ├── progress_utils.py │ └── seq_utils.py ├── css ├── driver.min.css └── style.css ├── cypress ├── e2e │ ├── beadplot.empty.js │ ├── beadplot.spec.cy.js │ ├── covizu.old.js │ ├── covizu.spec.cy.js │ └── utils.spec.cy.js ├── support │ ├── commands.js │ └── e2e.js └── videos │ └── covizu.spec.cy.js.mp4 ├── data └── mut_annotations.json ├── data_test ├── README.md ├── clusters.json ├── dbstats.json ├── mut_annotations.json ├── timetree.nwk └── xbbtree.nwk ├── dbmanager.js ├── dbmanager_test.js ├── doc ├── backend.md ├── beadplot.png ├── build-timetree.mmd ├── build-timetree.svg ├── covizu.Rmd ├── covizu.html ├── frontend-system-diagram.mmd ├── frontend-system-diagram.svg ├── make-beadplots.mmd ├── make-beadplots.svg ├── process-feed.mmd └── process-feed.svg ├── docker-compose.yml ├── globalVariables.js ├── img ├── Loading_icon_cropped.gif ├── antibody.png ├── bat.png ├── blue_triangle.png ├── green_pentagon.png ├── orange_star.png ├── purple_square.jpeg ├── red_circle.png └── search.png ├── index-es.html ├── index-fr.html ├── index-zh.html ├── index.html ├── js ├── FileSaver.LICENSE.md ├── FileSaver.js ├── beadplot.js ├── covizu.js ├── d3-save-svg.LICENSE.txt ├── d3-save-svg.min.js ├── d3-scale.js ├── d3.js ├── drawtree.js ├── driver.LICENSE.md ├── driver.min.js ├── gisaid │ ├── README.md │ ├── gisaid.css │ ├── gisaid.js │ └── popup.html ├── jquery.js ├── phylo.js ├── search.js └── utils.js ├── local.py ├── mongodb_scripts ├── createUsers.js ├── deleteUsers.js └── updateDatabase.js ├── package.json ├── run-server.sh ├── scripts ├── db_backup.py ├── mut_annotation_edit.py └── tidyClusters.R ├── server.js ├── server ├── parseCluster.js ├── phylo.js └── utils.js ├── setup.py └── tests ├── NC_Test.fa ├── __init__.py ├── test_batch_utils.py ├── test_beadplot.py ├── test_clustering.py ├── test_gisaid_utils.py ├── test_install.py ├── test_seq_utils.py ├── test_timetree.py ├── test_tree1.nwk └── test_tree2.nwk /.github/pull_request_template.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PoonLab/covizu/HEAD/.github/pull_request_template.md 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