ENH: Adding AMRFinderPlusAnnotation type

[VinzentRisch]

solves #85

• Added new type SampleData[AMRFinderPlusAnnotations] to be used with SampleData[MAGs] annotation.
• Added new type FeatureData[AMRFinderPlusAnnotation] to be used with FeatureData[Sequence] annotation.

Set up an environment

CONDA_SUBDIR=osx-64 mamba create -yn q2-amr \
  -c https://packages.qiime2.org/qiime2/2024.2/shotgun/released/ \
  -c qiime2 -c conda-forge -c bioconda -c defaults \
  qiime2 q2cli q2templates q2-types rgi tqdm jellyfish ncbi-amrfinderplus

conda activate q2-amr
conda config --env --set subdir osx-64

pip install --no-deps --force-reinstall \
  git+https://github.com/misialq/rgi.git@py38-fix \
  git+https://github.com/bokulich-lab/q2-amr.git

Run it locally

1. First, clone the repo and checkout the PR branch:

git clone https://github.com/bokulich-lab/q2-amr.git
cd q2-amr
git fetch origin pull/86/head:pr-86
git checkout pr-86
pip install -e .

Download test data:
PR-86.zip

2. Test it out!

qiime tools import --input-path sample_data --output-path amr_annotations.qza --type "SampleData[AMRFinderPlusAnnotations]"
qiime tools import --input-path feature_data --output-path amr_annotation.qza --type "FeatureData[AMRFinderPlusAnnotation]"

[ChristosMatzoros]

The code looks great and everything works as expected!!

[VinzentRisch]

Hi @misialq
Can you merge this one for me too?
And can you remove those checks that are not needed anymore so i can merge the PRs by myself? The checks are still there also on newly created PRs.

[misialq]

Hey @VinzentRisch, I finally figured why all these check were always appearing on all of your PRs and fixed it - from now on, only the two should be visible. What I am wondering, though, is why the coverage report does not show up here (or anywhere else?) - can you please investigate? I'm merging this one in the meantime.

[misialq]

Oh, and let's stop using the `` ticks in commit names/PR titles - it breaks our CI 😅

[VinzentRisch]

On the topic of CI bugs. @misialq
I think revert commits also break the CI
see here: https://github.com/bokulich-lab/q2-amr/actions/runs/9807765273/job/27082173410?pr=86#step:4:12
Or is it something else?

[misialq]

Yeah, it seems so... my suspicion is that the additional quotation marks " in the revert commit message may have something to do with that...