MAINT: Changed all imports from types-genomics to types

[VinzentRisch]

Blocked by qiime2/q2-types#309
Solves #49

• Changed all imports from q2-types-genomics to q2-types
• Updated Readme to include new qiime2 distribution 2024.2

Set up an environment

CONDA_SUBDIR=osx-64 mamba create -yn q2-amr \
  -c conda-forge -c bioconda -c defaults \
  -c https://packages.qiime2.org/qiime2/2024.2/shotgun/released/ -c qiime2 \
  qiime2 q2cli q2templates q2-types 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/50/head:pr-50
git checkout pr-50
pip install -e .

2. Download test files
   Download test files: mags.qza, card_db.qza

3. Test it out!

qiime amr annotate-mags-card --i-mag mags.qza --i-card-db /Users/rischv/Documents/data/card_database/wildcard/card_db.qza --output-dir amr_pr-50

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (f03527e) 93.30% compared to head (34b6030) 93.30%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #50      +/-   ##
==========================================
- Coverage   93.30%   93.30%   -0.01%     
==========================================
  Files          18       18              
  Lines        1061     1060       -1     
==========================================
- Hits          990      989       -1     
  Misses         71       71              

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[ChristosMatzoros]

Dear @VinzentRisch,

I reviewed and executed the code with the changes introduced in this PR, specifically the transition of imports from q2-types-genomics to q2-type. Upon execution, I can confirm that the code runs as expected without any errors. Additionally, I have verified that all instances of q2-types-genomics in the codebase have been successfully updated to q2-types. The changes are implemented correctly, and I did not find any oversight regarding the replacement of q2-types-genomics with q2-types. I recommend merging this PR.