Version 0.4, release candidate 3

• refactored search interface (fixes #218, #219, #220, #195 and others, thanks @GopiGugan and @RouxCil!)
• search by lineage, #161
• export beadplot as SVG, #251
• move between beads with arrow keys
• visual feedback for loading large beadplots
• fixes #239
• restored scrollbar for beadplot panel

Version 0.4, release candidate 2

• forgot to add d3-scale.js to repo, colour legends were not rendering for webserver
• fixes #241, timetree residuals for divergence from strict clock were highly variable because these were based on a single "representative genome" per lineage - a low divergence genome may be sampled by chance
• fixes #242, sped up processing of cluster data JSON (bottleneck in edgelist parsing routine)

Version 0.4, release candidate 1

• moved several functions from batch.py to new script batch_utils.py for access from local.py, #202
• build_timetree now returns standardized residuals to measure departure from molecular clock by lineage, #213
• JSON and Newick outputs are now automatically timestamped
• dbstats.json now carries lineage-specific information for colouring the tree, #213
• added --dry-run parameter for testing batch script (prevents upload of data files to webserver)
• moved several files to temporary deprecated folder
• removed unused reference sequence data files
• updated VCF to version 4, #214
• removed unused filter_fasta() function from treetime.py
• filtering genomes using both lower and upper quantiles of Poisson distribution, #228
• added colour legends for time-scaled tree plot
• beadplot SVG now dynamically redrawn to scale with window size
• moved most JS from index.html to new file covizu.js
• added FileSaver.js to enable users to download trees, #174
• refactored data structures to be more compact, #208
• search interface refactoring in progress

Version 0.3, release candidate 2

Improvements to front-end:

• added help text
• clusters in time-tree now properly scaled to time axis
• page load animation
• added scp calls to batch.py
• replaced <details> elements with jQuery-UI tab interface

Version 0.3, release candidate 1

Complete refactoring of backend to utilize GISAID provisioning feed instead of querying database

• reduced memory consumption of consensus tree generating function in clustering.py
• no longer writing symmetric differences out to temporary files
• replaced Python multiprocessing Pool with MPI via mpi4py for calculating bootstrap distances, NJ trees
• streaming genome sequences to minimap2 instead of writing to filesystem
• new file gisaid_utils.py
• incorporated verbosity levels into Callback, also reporting MPI thread ids

Version 0.2, release candidate 2

• revised frontend to conform to GISAID requirements
  • added acknowledgements popup
  • added GISAID data usage footer text
  • added logo
• implemented API to retrieve originating and submitting lab info, displays as pop-up
• tooltips now flip in response to relative location of cursor on page
• simplified tooltip content (rounding genetic distances, reduced line breaks)
• using divs for page layout instead of table

Version 0.2, release candidate 1

• added main workflow script batch.py
• converted to module, wrote setup.py script, moved scripts to covizu subdir
• gotoh2 is now deprecated in favour of minimap2
• wrote pangorider.py script to provide programmatic access to pangolearn
• no longer clustering genomes using hierarchical clustering and t-SNE - dropped in favour of Pangolin lineages as the emergent standard
• no longer using R to generate beadplot data - now implemented beadplot.py
• implemented symmetric difference computation of distance matrices, neighbor joining
• implemented custom consensus tree function
• wrote custom algorithm to convert consensus tree to beadplot after collapsing polytomies and short branches
• now cleaning up temporary files during execution to avoid flooding the filesystem
• pulling genome data directly from sqlite3 database instead of exporting a FASTA file
• implemented Callback function for nice progress monitoring on command line
• filtering outliers based on molecular clock (assuming Poisson distribution around expectation)
• implemented search interface
• too many other bug fixes and improvements to count

First production release, release candidate 1

• implemented search interface
• displaying sequence level information in info column
• implemented tool tips