Daily Component Tests and Migrations #462

	name: Daily Component Tests and Migrations

	on:
	schedule:
	- cron: "0 9 * * *"

	jobs:
	build:
	name: Daily Component Tests and Migrations (Python ${{ matrix.python-version }})
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: [3.7]
	fail-fast: false
	steps:
	- uses: conda-incubator/setup-miniconda@v2
	with:
	miniconda-version: 'latest'
	auto-update-conda: true
	python-version: ${{ matrix.python-version }}
	channels: conda-forge,bioconda
	activate-environment: anvio_env
	- name: "Set up the conda environment"
	shell: bash -l {0}
	run: \|
	conda info -a
	conda install -y "mamba >=0.24.0"
	mamba install -y python=${{ matrix.python-version }} sqlite prodigal idba mcl muscle=3.8.1551 hmmer diamond blast megahit spades bowtie2 tbb=2020.3 bwa graphviz "samtools >=1.9" trimal iqtree trnascan-se fasttree
	mamba install -y -c conda-forge r-stringi=1.7.8
	mamba install -y r-base r-tidyverse r-optparse r-stringi r-magrittr r-reshape2
	Rscript -e 'install.packages("BiocManager", repos="https://cran.rstudio.com"); BiocManager::install("qvalue")'
	- uses: actions/checkout@v2
	- name: "Install anvi'o from the codebase"
	shell: bash -l {0}
	run: \|
	pip install .
	- name: "Run component tests for general metagenomics tasks"
	shell: bash -l {0}
	run: \|
	anvi-self-test --suite metagenomics-full --no-interactive
	- name: "Run component tests for metabolism framework"
	shell: bash -l {0}
	run: \|
	anvi-self-test --suite metabolism --no-interactive
	- name: "Migrate ancient anvi'o databases"
	shell: bash -l {0}
	run: \|
	anvi-self-test --suite database-migrations

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