Merge pull request #171 from bigbio/dev #110

	name: Conda Build

	on: [push, pull_request]

	jobs:
	build:
	runs-on: ubuntu-latest

	steps:
	- name: Checkout repository
	uses: actions/checkout@v2

	- name: Set up Miniconda
	uses: conda-incubator/setup-miniconda@v2
	with:
	auto-update-conda: true
	python-version: 3.8
	channels: conda-forge,defaults,bioconda

	- name: Create conda environment
	run: conda env create -f environment.yml

	- name: Activate conda environment
	run: \|
	source $CONDA/etc/profile.d/conda.sh
	conda activate sdrf-pipelines
	shell: bash

	- name: Install conda-build
	run: \|
	source $CONDA/etc/profile.d/conda.sh
	conda activate sdrf-pipelines
	conda install -n sdrf-pipelines conda-build anaconda-client
	shell: bash -l {0}

	- name: Activate conda environment and build package
	run: \|
	source $CONDA/etc/profile.d/conda.sh
	conda activate sdrf-pipelines
	conda build recipe
	PACKAGE_PATH=$(find /usr/share/miniconda/envs/sdrf-pipelines/conda-bld/noarch/ -name "sdrf-pipelines-*.tar.bz2" \| head -n 1)
	conda install --offline "$PACKAGE_PATH"
	shell: bash -l {0}

	- name: Test the installed package
	run: \|
	conda activate sdrf-pipelines
	parse_sdrf --help
	shell: bash -l {0}

	- name: Test validation of SDRF file
	run: \|
	conda activate sdrf-pipelines
	parse_sdrf validate-sdrf --sdrf_file tests/data/reference/PDC000126/PDC000126.sdrf.tsv
	shell: bash -l {0}

	- name: Test validation of SDRF file with cache only
	run: \|
	conda activate sdrf-pipelines
	parse_sdrf validate-sdrf --sdrf_file tests/data/reference/PDC000126/PDC000126.sdrf.tsv --use_ols_cache_only
	shell: bash -l {0}

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