Release v2.2.0

[priesgo]

Changes

Major

• Added Pangolin lineage defining mutations. Add parser for the data coming from pangolin constellations, add model to hold the data in the DB, annotate the mutations tables with lineages

Minor

• Update the documentation to prepare custom references for CoVigator pipeline
• Update CoVigator paper citation
• Remove effect column from mutations tables

[codecov[bot]]

Codecov Report

Patch coverage: 98.65% and project coverage change: +2.42 :tada:

Comparison is base (5582535) 83.17% compared to head (7da34a9) 85.59%.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #122 +/- ## ========================================== + Coverage 83.17% 85.59% +2.42% ========================================== Files 46 48 +2 Lines 4238 4964 +726 ========================================== + Hits 3525 4249 +724 - Misses 713 715 +2 ``` | [Impacted Files](https://app.codecov.io/gh/TRON-Bioinformatics/covigator/pull/122?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=TRON-Bioinformatics) | Coverage Δ | | |---|---|---| | [covigator/dashboard/figures/figures.py](https://app.codecov.io/gh/TRON-Bioinformatics/covigator/pull/122?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=TRON-Bioinformatics#diff-Y292aWdhdG9yL2Rhc2hib2FyZC9maWd1cmVzL2ZpZ3VyZXMucHk=) | `100.00% <ø> (ø)` | | | [covigator/dashboard/figures/recurrent\_mutations.py](https://app.codecov.io/gh/TRON-Bioinformatics/covigator/pull/122?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=TRON-Bioinformatics#diff-Y292aWdhdG9yL2Rhc2hib2FyZC9maWd1cmVzL3JlY3VycmVudF9tdXRhdGlvbnMucHk=) | `21.67% <0.00%> (ø)` | | | [covigator/dashboard/tabs/recurrent\_mutations.py](https://app.codecov.io/gh/TRON-Bioinformatics/covigator/pull/122?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=TRON-Bioinformatics#diff-Y292aWdhdG9yL2Rhc2hib2FyZC90YWJzL3JlY3VycmVudF9tdXRhdGlvbnMucHk=) | `36.55% <0.00%> (ø)` | | | [covigator/database/queries.py](https://app.codecov.io/gh/TRON-Bioinformatics/covigator/pull/122?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=TRON-Bioinformatics#diff-Y292aWdhdG9yL2RhdGFiYXNlL3F1ZXJpZXMucHk=) | `73.46% <95.74%> (+3.34%)` | :arrow_up: | | [covigator/tests/unit\_tests/test\_queries.py](https://app.codecov.io/gh/TRON-Bioinformatics/covigator/pull/122?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=TRON-Bioinformatics#diff-Y292aWdhdG9yL3Rlc3RzL3VuaXRfdGVzdHMvdGVzdF9xdWVyaWVzLnB5) | `89.33% <97.82%> (+2.04%)` | :arrow_up: | | [covigator/references/lineage\_annotation.py](https://app.codecov.io/gh/TRON-Bioinformatics/covigator/pull/122?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=TRON-Bioinformatics#diff-Y292aWdhdG9yL3JlZmVyZW5jZXMvbGluZWFnZV9hbm5vdGF0aW9uLnB5) | `99.46% <99.46%> (ø)` | | | [covigator/\_\_init\_\_.py](https://app.codecov.io/gh/TRON-Bioinformatics/covigator/pull/122?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=TRON-Bioinformatics#diff-Y292aWdhdG9yL19faW5pdF9fLnB5) | `100.00% <100.00%> (ø)` | | | [covigator/accessor/abstract\_accessor.py](https://app.codecov.io/gh/TRON-Bioinformatics/covigator/pull/122?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=TRON-Bioinformatics#diff-Y292aWdhdG9yL2FjY2Vzc29yL2Fic3RyYWN0X2FjY2Vzc29yLnB5) | `97.14% <100.00%> (-0.08%)` | :arrow_down: | | [covigator/database/database.py](https://app.codecov.io/gh/TRON-Bioinformatics/covigator/pull/122?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=TRON-Bioinformatics#diff-Y292aWdhdG9yL2RhdGFiYXNlL2RhdGFiYXNlLnB5) | `64.06% <100.00%> (+1.76%)` | :arrow_up: | | [covigator/database/model.py](https://app.codecov.io/gh/TRON-Bioinformatics/covigator/pull/122?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=TRON-Bioinformatics#diff-Y292aWdhdG9yL2RhdGFiYXNlL21vZGVsLnB5) | `98.82% <100.00%> (+0.06%)` | :arrow_up: | | ... and [5 more](https://app.codecov.io/gh/TRON-Bioinformatics/covigator/pull/122?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=TRON-Bioinformatics) | |

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