BUG: Fixes JSON file detection bug in heatmap visualizer

[VinzentRisch]

This PR was created to fix #37.

• The heatmap visualizer has to copy all JSON files from the annotation artifact to one directory and rename the files in the process.
• The files where missing the .json extension after the renaming and because of this were not detected.
• Now the .json is added to the destination path, what resolved the issue
• Added comments to the heatmap visualizer.

Set up an environment

CONDA_SUBDIR=osx-64 mamba create -yn q2-amr \
  -c conda-forge -c bioconda -c qiime2 -c defaults \
  -c https://packages.qiime2.org/qiime2/2023.9/shotgun/released/ \
  qiime2 q2cli q2templates q2-types q2-types-genomics rgi

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 \

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/38/head:pr-38
git checkout pr-38
pip install -e .

2. Download test file amr_annotations.qza

3. Test it out!

 qiime amr heatmap --i-amr-annotation amr_annotations.qza --o-visualization heatmap.qzv

Should look like this:

[VinzentRisch]

Hey @Sann5 :) can you give this a review.
Super small bug and everything should run smoothly.
And please tell me if the environment setup and PR checkout works fine, I have tested it myself but no one else has tried it before. 🙂

[codecov-commenter]

Codecov Report

Attention: 1 lines in your changes are missing coverage. Please review.

Comparison is base (68f5ddb) 93.35% compared to head (ebe425f) 93.35%.

Files	Patch %	Lines
q2_amr/card/heatmap.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##             main      #38   +/-   ##
=======================================
  Coverage   93.35%   93.35%           
=======================================
  Files          18       18           
  Lines        1054     1054           
=======================================
  Hits          984      984           
  Misses         70       70           

☔ View full report in Codecov by Sentry.
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[Sann5]

@VinzentRisch in the Set up an environment section is it not redundant to pip install q2-amr from git when in the next step it is cloned and installed manually?

[VinzentRisch]

Yeah that is true. I'll remove it :)

[Sann5]

• ✅ Env setup worked
• ✅ Visualizer runs locally
• ✅ Test pass locally
• ✅ Code looks good to me

Overall it all looks good to me :)

[VinzentRisch]

Thanks :)