FIX: Pandas deprecations

[adamovanja]

This PR ensures forward compatibility with pandas v2.0 and maintains usablility with pandas version <2.0. It fixes #160.

Note on testing:
The below test should fail when installing q2-fondue from channel "https://packages.qiime2.org/qiime2/2023.2/tested/" as currently described in the main channel README.md file (and done in the Docker image). The test works without errors when using the updated code.
Using q2-fondue from channel "https://packages.qiime2.org/qiime2/2023.7/tested/" the code works independently (code from main channel or this PR).

• Follow the instructions to install the minimal conda environment in the README.md file.
• Fetch both sequence and metadata for a defined accession ID (e.g. test A below) and/or fetch accession IDs from a query of your choice.

Test A:

echo -e "id\nERR1698166" > file.tsv
qiime tools import  \
	--type NCBIAccessionIDs  \
	--input-path file.tsv  \
	--output-path file.qza
qiime fondue get-all  \
	--i-accession-ids file.qza  \
	--p-email your_email@somewhere.com  \
	--p-retries 0  \
	--output-dir file-output  \
	--verbose

Note before merging

• Before merging this PR, we should update the Docker image and the link in the README.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (4943f83) 98.64% compared to head (6bd23d2) 98.74%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #161      +/-   ##
==========================================
+ Coverage   98.64%   98.74%   +0.09%     
==========================================
  Files          29       29              
  Lines        3035     3031       -4     
==========================================
- Hits         2994     2993       -1     
+ Misses         41       38       -3     

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[lina-kim]

How interesting! Thanks for looking into and resolving this @adamovanja. Docker image has been updated and runs successfully.

Just wondering, how come the 2023.9 tag of q2-fondue is filed under the 2023.7 QIIME 2 release according to the package directory?

[adamovanja]

thanks for the updated Docker image @lina-kim.

As for your tag-release question, I think @misialq is the better source to answer this question since he has kindly kept track of Q2 releases and tags for now.

[lina-kim]

Looks great, thanks @adamovanja! Also runs successfully with this code + pandas v2.0.3 (in a container with qiime2, q2-types, and q2cli v2023.2).