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Change Alpha Diversity Metric #635

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Change Alpha Diversity Metric

Change Alpha Diversity Metric #635

Workflow file for this run

.github/workflows/main.yml at c0cb8a9
name: microsetta-interface CI
on:
pull_request:
push:
branches:
- master
jobs:
lint:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: set up python 3.7
uses: actions/setup-python@v1
with:
python-version: 3.7
- name: lint it
run: python -m pip install --upgrade pip
- name: lint
run: |
pip install -q flake8
flake8 microsetta_interface
test:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: Setup for conda
uses: conda-incubator/setup-miniconda@v2
with:
auto-update-conda: true
python-version: 3.7
- name: Install
shell: bash -l {0}
run: |
conda create --yes -n test-microsetta-interface python=3.7
conda activate test-microsetta-interface
conda install --yes --file ci/conda_requirements.txt
pip install -r ci/pip_requirements.txt
pip install -e . --no-deps
- name: Test
shell: bash -l {0}
run: |
conda activate test-microsetta-interface
pytest
integration:
runs-on: ubuntu-latest
# Service containers to run with `runner-job`
services:
# Label used to access the service container
postgres:
# Docker Hub image
image: postgres:13.4
env:
POSTGRES_DB: ag_test
POSTGRES_USER: postgres
POSTGRES_PASSWORD: postgres
# Set health checks to wait until postgres has started
options: >-
--health-cmd pg_isready
--health-interval 10s
--health-timeout 5s
--health-retries 5
ports:
# based on https://github.com/actions/example-services/blob/master/.github/workflows/postgres-service.yml#L44-L72
- 5432/tcp
steps:
# Downloads a copy of the code in your repository before running CI tests
- name: Check out repository code
uses: actions/checkout@v2
- name: Setup for conda
uses: conda-incubator/setup-miniconda@v2
with:
auto-update-conda: true
python-version: 3.7
- name: Install
env:
BRANCH: ${{ github.base_ref == 'master-overhaul' && 'master-overhaul' || 'master' }}
shell: bash -l {0}
run: |
echo Branch: $BRANCH
conda create --yes -n microsetta-interface python=3.7
conda activate microsetta-interface
conda install --yes --file ci/conda_requirements.txt
pip install -r ci/pip_requirements.txt
python setup.py compile_catalog
pip install -e . --no-deps
git clone -b $BRANCH --single-branch https://github.com/biocore/microsetta-private-api.git
pushd microsetta-private-api
pgport=${{ job.services.postgres.ports[5432] }}
sed -i "s/self.port = 5432/self.port = $pgport/" microsetta_private_api/config_manager.py
# PGPASSWORD is read by pg_restore, which is called by the build_db process.
export PGPASSWORD=postgres
conda create --yes -n microsetta-private-api python=3.7
conda activate microsetta-private-api
conda install --yes --file ci/conda_requirements.txt
pip install -r ci/pip_requirements.txt
pip install -e . --no-deps
# establish database state
python microsetta_private_api/LEGACY/build_db.py
popd
- name: Run integration tests
shell: bash -l {0}
run: |
conda activate microsetta-private-api
pushd microsetta-private-api
sed -i 's/"debug": true,/"debug": true, "disable_authentication": true,/' microsetta_private_api/server_config.json
python microsetta_private_api/server.py &
sleep 10 # give time to start up
popd
conda activate microsetta-interface
redis-server --daemonize yes
source keys_for_testing.sh
python microsetta_interface/tests/test_integration.py 2> >(tee -a stderr.log >&2)
# make sure we did not skip tests, which would indicate a failure in
# the harness. this test will produce an exit status of 1 if the
# test suite reports skipped tests
[[ $(tail -n 1 stderr.log | grep skipped) == "" ]];