💚:bug::snake: Fix bug for 0 passing predictions

[evanroyrees]

💚⬆️ Pin scikit-learn to >=1.3 :snake::art: Replace conda commands with mamba in Makefile :fire::arrow_down: Remove hdbscan (now available in scikit-learn >= 1.3)

HDBSCAN has been failing in pytests and this seems to be an artifact of hdbscan being integrated into scikit-learn.

Some of these issues have cropped up in the past few weeks (https://github.com/scikit-learn-contrib/hdbscan/issues/600).

scikit-learn is now pinned to >=1.3 as this is the earliest release of HDBSCAN being available via sklearn.cluster.HDBSCAN

The run_hdscan function has now been updated according to the API that was adopted in the sklearn library.

PR checklist

• [x] This comment contains a description of changes (with reason).
• [x] If you've fixed a bug or added code that should be tested, add tests!
• [x] Have you followed the pipeline conventions in the contribution docs

[codecov[bot]]

Codecov Report

Patch coverage: 30.66% and project coverage change: -0.29% :warning:

Comparison is base (6637426) 27.59% compared to head (bc34fae) 27.31%. Report is 46 commits behind head on dev.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## dev #341 +/- ## ========================================== - Coverage 27.59% 27.31% -0.29% ========================================== Files 45 50 +5 Lines 5349 5730 +381 ========================================== + Hits 1476 1565 +89 - Misses 3873 4165 +292 ``` | [Flag](https://app.codecov.io/gh/KwanLab/Autometa/pull/341/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab) | Coverage Δ | | |---|---|---| | [unittests](https://app.codecov.io/gh/KwanLab/Autometa/pull/341/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab) | `27.31% <30.66%> (-0.29%)` | :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. | [Files Changed](https://app.codecov.io/gh/KwanLab/Autometa/pull/341?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://app.codecov.io/gh/KwanLab/Autometa/pull/341?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://app.codecov.io/gh/KwanLab/Autometa/pull/341?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://app.codecov.io/gh/KwanLab/Autometa/pull/341?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://app.codecov.io/gh/KwanLab/Autometa/pull/341?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://app.codecov.io/gh/KwanLab/Autometa/pull/341?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://app.codecov.io/gh/KwanLab/Autometa/pull/341?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://app.codecov.io/gh/KwanLab/Autometa/pull/341?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/lca.py](https://app.codecov.io/gh/KwanLab/Autometa/pull/341?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab#diff-YXV0b21ldGEvdGF4b25vbXkvbGNhLnB5) | `9.37% <19.04%> (+0.57%)` | :arrow_up: | | [autometa/taxonomy/gtdb.py](https://app.codecov.io/gh/KwanLab/Autometa/pull/341?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/common/utilities.py](https://app.codecov.io/gh/KwanLab/Autometa/pull/341?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab#diff-YXV0b21ldGEvY29tbW9uL3V0aWxpdGllcy5weQ==) | `23.35% <37.50%> (+0.65%)` | :arrow_up: | | ... and [11 more](https://app.codecov.io/gh/KwanLab/Autometa/pull/341?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=KwanLab) | |

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[chasemc]

May need to look at hdbscan in tests e.g. https://github.com/KwanLab/Autometa/blob/8ebd7a703fb16e384adede3ae5fd58539c66db43/tests/environment.yml#L14