ENH: Added new action that can download AMRFinderPlus database called fetch_amrfinderplus_db

[VinzentRisch]

solves #77

• Added new action that downloads the latest version of the AMRFinderPlus database and outputs it in an artifact of type AMRFinderPlusDatabase.

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 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/82/head:pr-82
git checkout pr-82
pip install -e .

2. Test it out!

 qiime amr fetch-amrfinderplus-db --o-amrfinderplus-db amrfinderplus_db.qza 

[VinzentRisch]

Hey can you have a look at this?
Only look at the new action and the tests that go with it, the new formats belong to another PR.

[ChristosMatzoros]

It runs as expected and the tests pass. Check some comments that I made.

[ChristosMatzoros]

Seems good to me!

[VinzentRisch]

Hi
I just changed the way _copy_all copies the files. Now it does not copy the files that are not needed for the database.

[ChristosMatzoros]

Seems good to me @VinzentRisch . Just a minor change in the comments.

[VinzentRisch]

Hi @ChristosMatzoros I changed the function copy_all slightly with a different regex. Could you run the function again to see if all works well?

[ChristosMatzoros]

Works fine!