Release 2.2.0

[evanroyrees]

Release 2.2.0

🐚 Additional autometa workflows

• Addition of workflow where only required inputs are reads and assembly
• autometa.sh and autometa-large-data-mode.sh now require taxa_routine as an input parameter (choices are "ncbi" or "ncbi_gtdb". Autometa workflow now contains an optional sub-workflow where binning is guided by GTDB taxonomy after retrieving bacteria and archaea classified using the NCBI database.

TaxonomyDatabase

:snake: GTDB taxonomy integration to use within Autometa's taxon-binning and genome-binning workflows.

TL;DR

Abstraction of taxonomy databases using TaxonomyDatabase abstract base class with required abstractmethods.

This is currently implemented for both the NCBI and GTDB taxonomy database. Future taxonomy database integrations should follow the format from the TaxonomyDatabase class.

CAMI formatter

Binning validation/benchmarking utilities added/updated such as formatting autometa binning results into biobox format

Misc

• 💚 Fix pytest requirements in GH actions
• :bug:⬇️ pin scipy and joblib to avoid hdbscan import error
• :snake:🤫 Fix deprecated pandas method invocation in bedtools.py

[codecov[bot]]

Codecov Report

Base: 27.72% // Head: 27.62% // Decreases project coverage by -0.10% :warning:

Coverage data is based on head (1f5773f) compared to base (f514de8). Patch coverage: 26.00% of modified lines in pull request are covered.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #300 +/- ## ========================================== - Coverage 27.72% 27.62% -0.11% ========================================== Files 47 50 +3 Lines 5406 5734 +328 ========================================== + Hits 1499 1584 +85 - Misses 3907 4150 +243 ``` | Flag | Coverage Δ | | |---|---|---| | unittests | `27.62% <26.00%> (-0.11%)` | :arrow_down: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab#carryforward-flags-in-the-pull-request-comment) to find out more. | [Impacted Files](https://codecov.io/gh/KwanLab/Autometa/pull/300?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab) | Coverage Δ | | |---|---|---| | [autometa/binning/large\_data\_mode.py](https://codecov.io/gh/KwanLab/Autometa/pull/300/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab#diff-YXV0b21ldGEvYmlubmluZy9sYXJnZV9kYXRhX21vZGUucHk=) | `0.00% <0.00%> (ø)` | | | [autometa/config/databases.py](https://codecov.io/gh/KwanLab/Autometa/pull/300/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab#diff-YXV0b21ldGEvY29uZmlnL2RhdGFiYXNlcy5weQ==) | `0.00% <0.00%> (ø)` | | | [autometa/config/utilities.py](https://codecov.io/gh/KwanLab/Autometa/pull/300/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab#diff-YXV0b21ldGEvY29uZmlnL3V0aWxpdGllcy5weQ==) | `25.00% <ø> (ø)` | | | [autometa/validation/benchmark.py](https://codecov.io/gh/KwanLab/Autometa/pull/300/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab#diff-YXV0b21ldGEvdmFsaWRhdGlvbi9iZW5jaG1hcmsucHk=) | `0.00% <0.00%> (ø)` | | | [autometa/validation/cami.py](https://codecov.io/gh/KwanLab/Autometa/pull/300/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab#diff-YXV0b21ldGEvdmFsaWRhdGlvbi9jYW1pLnB5) | `0.00% <0.00%> (ø)` | | | [autometa/taxonomy/majority\_vote.py](https://codecov.io/gh/KwanLab/Autometa/pull/300/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab#diff-YXV0b21ldGEvdGF4b25vbXkvbWFqb3JpdHlfdm90ZS5weQ==) | `13.53% <11.53%> (+0.83%)` | :arrow_up: | | [autometa/binning/summary.py](https://codecov.io/gh/KwanLab/Autometa/pull/300/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab#diff-YXV0b21ldGEvYmlubmluZy9zdW1tYXJ5LnB5) | `41.48% <18.18%> (-0.38%)` | :arrow_down: | | [autometa/taxonomy/gtdb.py](https://codecov.io/gh/KwanLab/Autometa/pull/300/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab#diff-YXV0b21ldGEvdGF4b25vbXkvZ3RkYi5weQ==) | `21.01% <21.01%> (ø)` | | | [autometa/taxonomy/lca.py](https://codecov.io/gh/KwanLab/Autometa/pull/300/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab#diff-YXV0b21ldGEvdGF4b25vbXkvbGNhLnB5) | `9.37% <22.22%> (+0.57%)` | :arrow_up: | | [autometa/common/utilities.py](https://codecov.io/gh/KwanLab/Autometa/pull/300/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab#diff-YXV0b21ldGEvY29tbW9uL3V0aWxpdGllcy5weQ==) | `23.35% <33.33%> (+0.65%)` | :arrow_up: | | ... and [11 more](https://codecov.io/gh/KwanLab/Autometa/pull/300/diff?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab) | | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab)

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