v0.7.0 Release

[ktmeaton]

v0.7.0 - Recursive Recombinants

Reviews

• [ ] @ConnorChato

  • [ ] Pull Release Documentation reviewed.
  • [ ] Test Summary Package reviewed.
  • [ ] Tests (continuous integration) reviewed.

• [x] @TheZetner

  • [x] Pull Release Documentation reviewed.
  • [x] Test Summary Package reviewed.
  • [x] Tests (continuous integration) reviewed.

• [ ] @AndreaTy

  • [ ] Pull Release Documentation reviewed.
  • [ ] Test Summary Package reviewed.
  • [ ] Tests (continuous integration) reviewed.

Edits

• [ ] @keaton:
  • [ ] Clarify the difference between a lineage and sublineage change.
  • [ ] Clarify what the node/lineage names mean in the sankey diagrams (ex. cluster_id)

Notes

This is a minor release aimed towards a nextclade dataset upgrade from 2022-10-27 to 2023-01-09 which adds nomenclature for newly designated recombinants XBH - XBP. This release also adds initial support for the detection of "recursive recombination" including XBL and XBN which are recombinants of XBB.

A comprehensive test summary report can be downloaded directly with: ncov-recombinant_v0.6.1_v0.7.0.zip or viewed at the following link once the release is complete.

Documentation

• Issue #24: Create documentation on Read The Docs

Dataset

• Issue #210: Handle numeric strain names.

Resources

• Issue #185: Simplify creation of the pango-lineage nomenclature phylogeny to use the lineage_notes.txt file and the pango_aliasor library.

sc2rf

• Issue #195: Add bypass to intermission allele ratio for edge cases.
• Issue #204: Add special handling for XBB sequenced with ARTIC v4.1 and dropout regions.
• Issue #205: Add new column parents_conflict to indicate whether the reported lineages from covSPECTRUM conflict with the reported parental clades from `sc2rf.
• Issue #213: Add XBK to auto-pass lineages.
• Issue #222: Add new parameter --gisaid-access-key to sc2rf and sc2rf_recombinants.
• Issue #229: Fix bug where auto-pass lineages are missing when exclude_negatives is set to true.
• Issue #231: Fix bug where 'null' lineages in covSPECTRUM caused error in sc2rf postprocess.
• The order of the postprocessing.py was rearranged to have more comprehensive details for auto-pass lineages.
• Add XAN to auto-pass lineages.

Plot

• Issue #209: Restrict the palette for rbd_level to the range of 0:12.
• Issue #218: Fix bug concerning data fragmentation with large numbers of sequences.
• Issue #221: Remove parameter --singletons in favor of --min-cluster-size to control cluster size in plots.
• Issue #224: Fix bug where plot crashed with extremely large datasets.
• Combine plot and plot_historical into one snakemake rule. Also at custom pattern plot_NX (ex. plot_N10) to adjust min cluster size.

Report

• Combine report and report_historical into one snakemake rule.

Validate

• Issue #225: Fix bug where false negatives passed validation because the status column wasn't checked.

Designated Lineages

• Issue #217: XBB.1.5
• Issue #196: XBF
• Issue #206: XBG
• Issue #196: XBH
• Issue #199: XBJ
• Issue #213: XBK
• Issue #219: XBL
• Issue #215: XBM
• Issue #197: XBN

Proposed Lineages

• Issue #203: proposed1305
• Issue #208: proposed1340
• Issue #212: proposed1425
• Issue #214: proposed1440
• Issue #216: proposed1444
• Issue #220: proposed1576

Continuous Integration

• Issue #223: Change CI mamba version to fix setup-miniconda failure

Commits

• c279f1e4 docs: add changelog for v0.7.0
• 2964b4a1 docs: update notes to include 1576 proposed issue
• fdc874ab docs: add test summary package for v0.7.0
• 3f3d4438 docs: update docs v0.7.0
• 78696b36 script: add bug fix to sc2rf postprocess for #231
• 403777a0 script: lint plotting script
• 2a09c783 script: fix sc2rf postprocess bug in duplicate removal
• d44d5f90 data: add XBP to controls-gisaid
• 4293439c profile: add controls-gisaid to virusseq builds
• 91d6fb89 defaults: update nextclade dataset to 2023-02-01
• 630b2cd5 resources: update
• 49e6f598 profile: add virusseq profile
• 7e586d1d script: add extra logic for auto-passing lineages
• 0ebe5e9c script: fix bug in report where it didn't check that plots existed
• 25b2f243 docs: update developers guide
• 914d933f defaults: add XBN to controls-gisaid and validation
• 8eaf08a9 data: restore controls-gisaid strain list
• fa123009 script: defragment plot for 218
• 5f24f695 dataset: update controls-gisaid strain list
• efc5aab7 defaults: update validation to fix XBH dropout
• See CHANGELOG.md for additional commits.

[ktmeaton]

Something has gone wrong and a merge was created. I'm going to try and revert it.

[ktmeaton]

This was a pretty astonishing series of mistakes that led to this. Overall, I wasn't diligent about double-checking what branch I was on, or which git commands failed.

# First mistake, when using depth 1, I was missing the dev branch
git clone --depth 1 https://github.com/ktmeaton/ncov-recombinant
# Second mistake, this pull applied the changes from v0.7.0 to my master branch
# Also, I should have used the dev branch not the v0.7.0 tag
git pull origin v0.7.0
# Third mistake, I should have checked out the dev branch not the v0.7.0 tag
# Checking out the tag failed (from --depth 1) and I was still on master and didn't notice
git checkout v0.7.0
# Adding the edits to the TSP from my local machine
git add docs/testing_summary_package/ncov-recombinant_v0.6.1_v0.7.0.html
# Fourth mistake: pre-commit linting hooks were not installed, so HTML wasn't linted and raised CI error
git commit -m "docs: update tsp with lineage change and cluster_id note"
# Fifth mistake: I should have checked which branch I was on before pushing, this pushed to main.
git push

This is how I fixed the mistake:

1. On master, checkout the previous version (v0.6.1): git checkout v0.6.1
2. Force push to master: git push -f origin master
3. Checkout dev properly: git checkout dev
4. Add the TSP updates to dev.
5. Create a new redo PR #238.