#Annoplot #dataviz development was briefly resumed this month to implement more dynamism in generation of legends. Previous status found here:

https://beige.party/@beadsland/115902402815167705

As Voices of Solaria discord server has been deleted, talky bot project has been retired, dropping total line count by a little more than 800. Nonetheless, another two hundred or so lines have been added through work on Annoplot and chart scripts, including:

• revisions to variants parentage tracing, tree normalization and bundling logic and legend subheaders

• providing for complete removal of all helper artists when removing legend

• reworking of legend build process to dynamically reconfigure until fits available space

• tweaks to legend title wrapping, tile emboss treatments, organization and naming of bubbles

• improvements to process of ancestry digging for footnotes and determining footnote candidates

• updates to devpie (this #datavis) mirrored legends, to take advantage of dynamic legend build process

Having finally gotten all the kinks out of the latest #annoplot chart, gonna finally break my fast for the day.

Chart and #annoplot library now further revised to more fully address sparsity of #CDC data.

Most recent dataset, updated Friday, shows four XFG lineages, reflecting variants broken out by CDC in recent months, together outpacing growth of parent and remaining siblings.

Meanwhile, Nimbus 1.8.1 / PQ family still holding out at near a twelfth of total estimated share.

Note that, in absence of robust data from states, CDC has given up modeling historical estimates, instead giving only shares of reported sequences.

Raj's dashboard, updated three weeks ago, showed Stratus dynasty with diversified XFG.3 family at plurality, accounting for still over a fifth of all samples, with XFG.14 already over a tenth.

GISAID data for the most recent three-plus-week period was dominated by paltry submissions from New York (146 sequences), followed by Minnesota (129), California (39), Illinois (38), Massachusetts (33), and Nebraska (27).

❖ #ThisIsOurPolio #variants #CovidIsNotOver #dataviz #datavis

#Annoplot #dataviz development has been temporarily suspended as of October, but for maintenance.

December maintenance included tweaking legend, ancestry in legend footnotes, and data import.

Work in November consisted primarily of work on #Buoy:

https://hcommons.social/@beadsland/115743279428734786

Now also on hold following multiple household emergencies.

Ultimate plan, after finishing up buoy, is to resume overdue refactoring of tiop libraries for variants #datavis chart, and then finally refactoring legacy levels chart into tiop and #Annoplot library.

At some point between now and the heat death of the universe, may even write up style guide and publish Annoplot under some license or another.

#Annoplot #dataviz development has been temporarily suspended as of October, but for maintenance:

https://hcommons.social/@beadsland/115295487903892225

November maintenance included: accommodating less frequently updated GISAID data; tweaking of etalicizing to parents; revising captions, footnotes, and alt-text generation for #datavis; and tweaking title wrapping in legend.

Buoy work continued until mid November, accounting for another 500 lines, when also put on hold. Hopefully will resume in January:

https://hcommons.social/@beadsland/115522549953210771

Work included: fleshing out pretty-printed logging; extensive refactoring; cleaning up derivative class mutations and pagination process; better handling of historical cutoffs, to allow for interruptions due to netbreaks; graceful shutdown and progress indicator behavior; debugging; refinement of refresh behavior; velocity-based scoring method for prioritizing what to reboost; redesign of parallel data-based pagination.

#Annoplot #dataviz development has been temporarily suspended as of October, after only about fifty lines added since last round of work in September:

https://hcommons.social/@beadsland/115295487903892225

Work in first week of October focused on:

* support for #datavis of partial periods of GISAID data
* tweaks to scrim and suds implementations
* revisions to captions to reflect current events

Work in first week of November focused on development of Buoy, a tool for floating self-boosted posts periodically, as a function of other posting behavior:

https://hcommons.social/@beadsland/115522549953210771

This added about 400 lines, plus another 50 lines to duplicate existing hotmods library:

https://hcommons.social/@beadsland/115522621038530696

Took it easy this month, recovering from seasonal booster. Thus, only a hundred more lines for #AnnoPlot #dataviz project since last round of work in August:

https://hcommons.social/@beadsland/115123231252276843

Work in September focused on:

* clarification of winter ancestries in legend footnotes
* restoring variant peak tracking from biweekly CDC data
* some more previously deferred refactoring
* preliminary work to allow for partial variants #datavis orchard chart bar between periods
* tweaking utility script to accommodate legacy variant namespace clash
* debugging and conforming usage
* clarification of language in caption

Another four hundred lines for #AnnoPlot #dataviz project since last round of work in July:

https://hcommons.social/@beadsland/114969608143508746

Work in August focused on:

• preliminary integration of adornments flank prototype
• tweak emboss hemming
• bugfixes, semantics, linting, error checking, and logging tweaks
• extensive previously deferred refactoring
• correctly format warnings captured by chirp
• rework alt-text for dominant families

In absence of CDC estimates:

• expand and debug proxy GISAID tooling into subsequent periods
• break out diversified branches in proxy columns
• rework of scrims and scrim titles, legend title and inner tick labels

Also, with regards to devpie #datavis:

• resolve collisions for wedge auto text
• smaller text treatments for wedge emboss
• resolve edge cases and improving efficiency
• add shell scripts to line tallies
• rework to determine cutoff, smoosh and slice wedges dynamically
• option to specify day count

Another three hundred lines for #AnnoPlot #dataviz project since last round of work in June:

https://hcommons.social/@beadsland/114788341947558989

Work in July focused on:

• streamline variants #datavis alt-text generation
• extensive refactoring across multiple annoplot and tiop modules
• build out option for using GISAID for tree chart, in lieu of recent estimates
• prototype dynamic offsets for flanking artists

With other tasks including:

• refine flattening of variants lineages
• resume TODO tracking
• tweak log messages in various methods
• tweak title adornment overhang
• tweak legend to better accommodate footnotes
• address data import issues
• tweak inclusion of ancestor variants on legend
• conform throughout to non-specific reporting periods
• add option for dropping most recent period
• migrate hatchmask suppression for scrim periods
• bugfixing of paragraph artist
• copy editing and revisions of captions
• tweak captions to better reflect runtime options
• tweak emboss edge collision detection

Another two hundred lines for #AnnoPlot #dataviz project since last round of work in May:
https://hcommons.social/@beadsland/114634070336715545

Work in June included:

• refine, expand and refactor variant legend #datavis footnotes
• correct representation of negative growth in share
• refactor and improve reversible dict
• streamline handling of chained clusters
• refactor, expand and debug footnote peaks methods
• refine and refactor alt-text pruning cascade
• refactoring in multiple additional submodules
• tweaks to this devpie chart
• fix errors import and inline presentation of GISAID data
• fix error in dot-hatch trigger
• tweak legend headers and family grouping
• prepare for handling of CDC's announced change in reporting periods
• resolve collisions for new clusters and common names
• preserve legend entries for significant GISAID variants

Two weeks ago, Mike Honey noted that there are three recombinants that have arrived on Doppelgänger spike proteins, namely XFJ, XFM, and XFP:

https://aus.social/@mike_honey_/114611686572899925

Last week, Xu Zhu (HT D. Focosi) identified a superset of recombinants that have all arrived at a pairing of LF.7's NTD with RBD from elsewhere, namely: XFC, XFG, XFH, XFJ, XFM, XFN and XFP:

https://x.com/dfocosi/status/1931351676880879856

Above variants chart #AnnoPlot script is now updated to favor grouping by such emerging clusters preferentially over grouping by legacy ancestors.

As a reminder, recombinants happen when more than one virus strain is actively replicating in the same organism.

Here, that means two simultaneous infections, from different sources, finding a home in the same person.

When #PublicHealth is a priority, this should be a rare occurrence.

There are seven unique recombinants identified in this new cluster, alone.

❖ #ThisIsOurPolio #Covid #Covid19 #SARS2 #variants #CovidIsNotOver #CovidIsAirborne #dataviz #datavis

Have a short list of refactorings and improvements still want to make to variants chart and #AnnoPlot libraries in support of same...

After which, will be able to move on to rebuilding legacy hospital capacity chart into a fuller suite of AnnoPlot mapping tools...

With goal of using those tools to map out continental fire and smoke data...

Assuming any such data is publicly available by the time am ready to embark on that project...

All the while confident that, were we ever to get H5N1 pandemic data, the existing variants tooling would be ready for repurposing.

Put in an intensive week of work preparing #AnnoPlot project variants chart for adequately representing the Nimbus strain, on the off chance that the CDC bothered to break same out in their data drop today.

Only for #CDC to punt on releasing any data this week, for reasons of an "issue with the software".

K.

https://hcommons.social/@beadsland/114639885219714547

Another four hundred lines for #AnnoPlot #dataviz project since last round of work in March:

https://hcommons.social/@beadsland/114475406737012154

Work in May/early June included:

• tweaks to this pie chart, chirp logging, annoplot legend classes and newspaper columns orphan control;

• tweaks to variants #datavis: tree constructor process, alt-text pruning internals, legend subclass, tree constructor methods, name collisions and recombinant lineage assignments, family groupings and legend headers, variant mocking, title overhang, tile embossing, growth calculation, and captions, all including significant refactoring;

• migration of bug to legend footer, and build out of prioritized legend footnotes for prominent lineages and recombinants, including recombinant chains, with calculation and approximation of historical peaks, and pruning for space constraints of both alt-text and footer proper.

Another hundred lines for #AnnoPlot #dataviz project in March:

https://hcommons.social/@beadsland/113977456216970296

Work in March included:

• accommodating less frequent updates to GISAID data
• debug flattening in preparation for tilt
• mixin for checking orientation and helper class for rotation and mirroring
• rework and refactor tilt calculations for inline bubble charts
• refactor degrees str method to helper class and consolidate older asdegrees util method

Holiday programming ticked over another hundred lines for #AnnoPlot #dataviz project since last update:

https://hcommons.social/@beadsland/113842033121034976

Variants was last #datavis being updated. May be the end.

Work in last month includes:

• auto-generated alt-text for variants chart
• rework of markdown utility module
• runtime-option aware captions
• prelim devpie alt-text generation
• tweaks to variant bundling, cluster ancestry & recombinant assignment; also emboss hemming, GISAID import, and footnote plumbing.

Gave myself some programming time as a holiday treat. Added ~300 lines to #AnnoPlot #dataviz project since last update:

https://hcommons.social/@beadsland/113711696418854256

In our post-data era, only variants #datavis is still actively being updated.

Work in last month includes:

• tweaks to variant bundling, family grouping, cluster ancestry & recombinant assignment
• footnote on legend
• auto-generated alt-text for variants chart
• rework of markdown utility module
• tweaks to GISAID imports, bubbles & tile embossing

Have been only debug maintenance mode since our last update. No appreciable increase in #AnnoPlot line count:

https://hcommons.social/@beadsland/113586957042066086

In our post-data era, only variants #dataviz is still actively being updated.

Maintenance includes: further refining GISAID data imports, correct assignment of cluster lineages, including recombinant children of cluster variants, and conforming to upgraded python version.

Unfortunately, ongoing fires in personal life means little time for #datavis programming.

Have been only debug maintenance mode since our last update. No appreciable increase in #AnnoPlot line count:

https://hcommons.social/@beadsland/113456689508810628

In our post-data era, only variants #dataviz is still actively being updated.

Maintenance includes: managing GISAID data imports, further refining legend criteria, revisions & corrections to naming tables, & properly pinning subvariants of clusters to progenitor lineages.

Unfortunately, ongoing fires in personal life means little time for #datavis programming.

Once again, have only had opportunity to add hundred or so lines to #AnnoPlot project since the last update:

https://hcommons.social/@beadsland/113218241027273518

In our post-data era, only variants #dataviz is still actively being updated.

Maintenance includes: cosmetic tweaks to bubbles and embossing; tweaks to label order, bundle logic, and legend families; debugging cluster and recombinants parent tracing; & general refactoring.

Unfortunately, ongoing fires in personal life means little time for #datavis programming.