Testing skbio against QIIME 2 to ensure integrity and/or identify breaking points

[qiyunzhu]

This issue documents the procedures of testing skbio against QIIME 2 to see if anything may break. The procedures follow the QIIME 2 development documentation. @wasade @mortonjt @mataton

Create a QIIME 2 development environment (adjust the command for shotgun and macos versions).

wget https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-amplicon-ubuntu-latest-conda.yml
conda env create -n qiime2-amplicon-dev --file qiime2-amplicon-ubuntu-latest-conda.yml
rm qiime2-amplicon-ubuntu-latest-conda.yml
conda activate qiime2-amplicon-dev

Clone codebases of all QIIME 2 core plugins (can be listed by qiime info), and make sure their tests pass in the original environment.

plugins="alignment composition cutadapt dada2 deblur demux diversity diversity-lib emperor feature-classifier feature-table fragment-insertion longitudinal metadata phylogeny quality-control quality-filter rescript sample-classifier taxa types vsearch"
for plugin in $plugins; do
  git clone https://github.com/qiime2/q2-$plugin.git
  cd q2-$plugin
  make dev
  make test
  cd ..
done

Install a certain skbio development version. This will override even if some libraries are bond by an older skbio version.

pip install --no-deps --force-reinstall git+https://github.com/account_name/scikit-bio.git@branch_name

Run all tests again with the updated skbio.

for plugin in $plugins; do
  cd q2-$plugin
  make test
  cd ..
done

Functional test: Navigate to the QIIME 2 tutorials webpage. Select relevant tutorials and follow. In particular, the "“Moving Pictures” tutorial - Multiple Interface Edition" tutorial provides Python API codes, which one can copy & paste into a Python script to facilitate automated test.