sequencing update #194

	name: growth rate calc

	on:
	push:
	branches: [ "master" ]

	jobs:
	testsuite:
	runs-on: ubuntu-latest
	defaults:
	run:
	shell: bash

	steps:
	- name: Check out repository code
	uses: actions/checkout@main
	with:
	repo-token: ${{ secrets.GITHUB_TOKEN }}

	- name: Setup for conda
	uses: conda-incubator/setup-miniconda@v2
	with:
	auto-update-conda: true
	channels: bioconda,conda-forge
	channel-priority: true
	python-version: 3.7
	activate-environment: test

	- name: Install
	shell: bash -l {0}
	run: \|
	conda install -n base conda-libmamba-solver
	conda config --set solver libmamba
	conda config --add channels bioconda
	conda config --add channels conda-forge
	conda install freyja pandas
	python calc_relgrowthrates.py

	# add and push changes
	if [[($(git status rel_growth_rates.csv --porcelain \| wc -c) -ne 0)]]; then
	git config --local user.name "$GITHUB_ACTOR"
	git config --local user.email "[email protected]"
	git add rel_growth_rates.csv
	git commit -m "growth rate calc"
	git push origin master
	else
	echo "no change to growth rate estimate"
	fi;

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