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CHANGELOG

Development

Commits

v0.2.8

Notes

  1. Add Jupyter Notebook for processing BEAST output.
  2. Updates to Root-To-Tip Regression and Geographic.
  3. Update and sync all metadata files.
  4. Separated auspice output into beast/ml datasets.
  5. Add beast timetrees to auspice.

Commits

v0.2.7

Notes

  1. Add mugration to workflow.
  2. Upgrade auspice to 2.25.1
  3. Remove old Jupyter Notebooks
  4. Curate host metadata.
  5. Consolidate visualization to auspice notebook.

Pull Requests

Commits

v0.2.6

Notes

  1. Put project specific results in seperate repository.
  2. Added 2020 Latvia samples to database, mark as low coverage for now.
  3. Move log directory to within results.
  4. Remove xml tree output from notebooks.
  5. Create scripts to backup, restore, and clean projects.
  6. Remove plot_table rules and script.
  7. Only include visual files into the report.
  8. Put config files inside the associated project directory.
  9. Update function identify_local_sample to use database.
  10. Environment addition: augur, cartopy, ffpmeg, snp-dists, bokeh.
  11. Create Pairwise SNP matrix.
  12. Remove results folder from docs.
  13. Create new output folder collect for detect snp density.
  14. Remove US Kim strain, mark as laboratory manipulation.
  15. Clean snp density files from version control.
  16. Add country to continent mapping for metadata.
  17. Improvements to plotting missing data and filtering log.
  18. Change all metadata column names to lowercase.
  19. Changed from TreeTime to LSD2.
  20. Included rules to prepare for BEAST.
  21. Jupyter Notebooks pertaining to TreeTime are not used.

Pull Requests

Commits

v0.2.5

Notes

  1. Separate mugration notebook into model and plot.
  2. Add a heatmap test, output to misc.
  3. Create a new rule to generate locus coverage.
  4. Remove output directory of eager rule.
  5. Make a list of target genes
  6. Hard code target genes into ref locus bed
  7. Move ref locus bed to reference
  8. Create gene by gene coverage.
  9. Analyze both coverage and depth of loci.
  10. Compare gene to plasmid coverage (pla, pPCP1)
  11. Apply a coverage filter for pPCP1 plasmid.
  12. Add locus coverage info to nexus tree.
  13. Created spreadmaps for branch major.

Pull Requests

Commits

v0.2.4

Notes

  1. Update coord_x and coord_y in clock_model.
  2. Save timetrees and divtrees for all relevant methods.
  3. Mugration working for all attributes individually.
  4. Changed mugration to work with timetree object input.
  5. Start version tagging auspice visualizations.

Commits

  • 58dd2e11 update notes, changelog, and auspice json for v0.2.4
  • 46d3d1fc fixed mugration by making sure to copy tree div
  • e886d001 working mugration for Country
  • 1cdf4259 working mugration for Branch_Number
  • 7ea625a6 save timetrees and divtrees for all relevant methods
  • 0723ae41 update coord_x and coord_y in clock_model
  • 3d7890ee prepare notes for development post-v0.2.3
  • 4dee9cd2 update CHANGELOG for v0.2.3

v0.2.3

Notes

  1. Experiment with relaxed clock parameters.
  2. Experiment with marginal likelihood parameters.
  3. Experiment with the coalescent parameters.
  4. Catch bad lower confidence bounds.
  5. Think about snippy_dir in rule eager...

Pull Requests

Commits

  • 51adae7d update notes for v0.2.3
  • fc418ff6 Merge pull request #3 from ktmeaton/dev
  • 0f8f57db excellent timetree marginal parameters
  • 181f944c add comments to nexus for clock_model
  • 18a7b0e8 checkpoint with working but unstable marginal estimate
  • ab3f9116 add comments to nexus for parse_tree
  • c33bd646 slack:0.1, blm: joint, tc:def, time_marginal:def
  • b34519fb slack:0.5, blm: joint, tc:def, time_marginal:def
  • 4158f9a4 first pass at timetree marginal parameters
  • 1bd08990 Merge pull request #2 from ktmeaton/dev

v0.2.2

Notes

  1. Add entropy to augur.
  2. Add mugration models to augur.
  3. Add clock model to augur.
  4. Add clock lengths to augur.
  5. Add date confidence to augur.
  6. Scatterplot of taxa vs rtl for treemmer.
  7. Prune tree, dataframe, and alignment with treemmer.
  8. Confirm pruning consistency between tree, dataframe, and alignment (n=247).
  9. Plot tree comparison.
  10. Checkpoint before clock modelling in BEAST.
  11. Use pickle to save objects of Jupyter notebooks.
  12. New jupyter notebooks for post-phylo.
  13. Put jupyter notebook output into results.
  14. Think about snippy_dir in rule eager...

Pull Requests

Commits

v0.2.1

Notes

  1. Automate commit history.
  2. Automate release notes.
  3. Automate CHANGELOG updates.

Commits

  • f30964b8 disable singularity from install testing
  • 4aa4cdca release log has truncated commits and changelog has full
  • d039c749 automatically create changelog
  • 36b672fd don't run full CI on ver tags
  • 6d726288 refine CI workflows to pushes on master or dev
  • 46e443f4 fix dockerfile path for release
  • 6aaaa5e7 automate release on ver tags
  • ec5504ad automate commit notes
  • 023214c8 update notes for v0.2.1
  • 35ab58cb provide config file for flake8 in lint CI
  • 8857dcc1 add treemmer notebook results
  • f862d441 disable singularity from CI
  • d136168a add treemmer and ete3 to env
  • 05aa4ce8 update workflow for multiqc eager dir
  • 59e94d4b update augur and auspice export for confidence
  • 9d73947a separate the augur and auspice json
  • 730002b7 update branch_support notebook and output
  • 419cbdb8 update parse_tree notebook and output
  • fa522bb9 auto publish auspice files and use clock filter in parse_tree
  • ceffb5f8 split timetree into model and plot
  • e56adb70 split timetree into model and plot

v0.2.0

Pull Requests

Commits

v0.1.4

Commits

v0.1.3

Commits

v0.1.2

Commits

v0.1.1

Commits

v0.1.0

Commits