1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
|
#!/bin/bash
#
# Runs tests in a sandboxed environment that loosely replicates the GitHub Actions
# environment.
set -euo pipefail
# Conda functions are not exported into a new bash environment by default, so we
# need to source the conda profile script from the current conda installation.
# This script expects PS1 to be defined, so we set it to an empty value.
export PS1=
conda_dir=$(conda info --base)
source "${conda_dir}/etc/profile.d/conda.sh"
ENV_NAME="test-augur"
# Install mamba if not available to avoid Conda solver issues
if [[ ! -e "`which mamba`" ]]; then
echo Installing Mamba
conda install --yes -n base -c conda-forge mamba
fi
# Install Augur from the current directory into a new conda environment.
echo Setting up Conda test environment with mamba
mamba create --yes --quiet -n ${ENV_NAME} -c conda-forge -c bioconda augur
conda activate ${ENV_NAME}
python3 -m pip install .[dev]
# Run unit and functional tests.
echo Running tests
./run_tests.sh || true
# Clean up the temporary environment.
echo Cleaning up
conda deactivate
conda env remove -n ${ENV_NAME}
|
