#!/bin/bash

set -e

mkdir ~/.basespace

cp test/dotbasespace/*.bash ~/.basespace

cp test/dotbasespace/*.json ~/.basespace

cd data

curl -O https://s3.amazonaws.com/basespace-sdk-unit-test-data/BC-12_S12_L001_R2_001.fastq.gz

cd ..

# ...

cat test/dotbasespace/unit_tests.cfg | sed "s/__ACCESS_TOKEN__/$ACCESS_TOKEN/" > ~/.basespace/unit_tests.cfg

cp ~/.basespace/unit_tests.cfg ~/.basespace/default.cfg

pip install pyflakes

echo

echo "Static analysis warnings from pyflakes:"

echo

# exclude doc directory because those files are auto-generated

# the "|| true" at the end causes CI not to fail. In future

# you could remove that if you want pyflakes warnings to break the build.

find . \( -path ./doc -o -path ./src/build \) -prune -o -name '*.py' -print | xargs pyflakes || true

# TODO add stricter flake8 checking here

# (checks for proper formatting of code in compliance with PEP8)

echo

echo "Unit test output:"

echo

python test/unit_tests.py

exit $?