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MMEDs Tests

add basic test for new workflow #1346

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add basic test for new workflow

add basic test for new workflow #1346

Workflow file for this run

.github/workflows/tests.yml at f9ca99d
name: MMEDs Tests
on: [push
]
jobs:
run-tests-complex:
runs-on: ubuntu-22.04
defaults:
run:
shell: bash -l {0}
steps:
- uses: actions/checkout@v2
- name: Set up Python 3.9
uses: actions/setup-python@v2
with:
python-version: 3.9
- name: Set PYTHONPATH
run: echo "PYTHONPATH=." >> $GITHUB_ENV
- name: Install packages
run: python -m pip install pip==24.0; pip install cryptography; pip install jupyter_client==6.1.12; pip install ipython_genutils==0.2.0; pip install nbconvert==5.6.1; pip install rpy2; pip install ipykernel; pip install pandas==1.2.3; pip install pillow; pip install -U Jinja2==3.0; pip install coverage;
- name: install pandoc
run: sudo apt-get install pandoc;
- name: Start MySQL
run: sudo systemctl start mysql.service;
- name: MySQL Setup
run: mysql -u root -proot < setup.sql
- name: Start MongoDB
uses: supercharge/mongodb-github-action@1.12.0
with:
mongodb-version: '6.0'
- name: Server data setup
run: mkdir /home/runner/mmeds_server_data; mkdir /home/runner/conda_envs; mkdir -p /home/runner/conda_env_files/pheniqs; mkdir -p /home/runner/.modules/modulefiles; cp -r ./test_files /home/runner/mmeds_server_data/.; cp ./mmeds/resources/mmeds_stats.yaml /home/runner/mmeds_server_data/.; cp -r ./modules/* /home/runner/.modules/modulefiles/.; cp -r ./conda_env_files/* /home/runner/conda_env_files/.; mkdir /home/runner/mmeds_server_data/taxonomic_databases; touch /home/runner/mmeds_server_data/taxonomic_databases/dummy_classifier.qza;
- name: Python install
run: sudo python setup.py install --verbose; pip install wheel; pip install git+https://github.com/clemente-lab/mmeds-meta@$GITHUB_REF_NAME;
#- name: install jupyter
#run: conda env create -f ./conda_env_files/jupyter_env-github.yaml -p /home/runner/conda_envs/jupyter;
- name: add bioconda channel for qiime
run: conda config --append channels conda-forge --append channels bioconda --append channels defaults
- name: install qiime
run: conda env create -f ./conda_env_files/qiime2-2020.8_env.yaml -p /home/runner/conda_envs/qiime2-2020.8
#- name: install R
#run: sudo apt install dirmngr gnupg apt-transport-https ca-certificates software-properties-common; sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9; sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/'; sudo apt install r-base;
#- name: install R dependencies
#run: sudo Rscript -e 'install.packages("GGally",dependencies=TRUE)'; sudo Rscript -e 'install.packages("ggrepel",dependencies=TRUE)'; sudo Rscript -e 'install.packages("RColorBrewer",dependencies=TRUE)'; sudo Rscript -e 'install.packages("ggplot2",dependencies=TRUE)';
- name: install pheniqs
run: conda env create -f ./conda_env_files/pheniqs_env.yaml -p /home/runner/conda_envs/pheniqs
- name: install latex
run: conda env create -f ./conda_env_files/latex_env.yaml -p /home/runner/conda_envs/latex
- name: Unit Tests
run: |
coverage run --parallel-mode --concurrency=multiprocessing ./mmeds/tests/unit/test.py analysis demultiplex;
- uses: actions/upload-artifact@v4
with:
name: summary-pdf-output
path: /home/runner/mmeds_server_data/test_files/test_study/Qiime2_0/summary/mkstapylton@gmail.com-mattS-qiime2.pdf
- name: Upload Unit coverage
uses: codecov/codecov-action@v4
with:
token: ${{ secrets.CODECOV_TOKEN }}
run-tests-simple:
runs-on: ubuntu-22.04
steps:
- uses: actions/checkout@v2
- name: Set up Python 3.9
uses: actions/setup-python@v2
with:
python-version: 3.9
- name: Install packages
run: python -m pip install pip==24.0; sudo apt-get install tidy environment-modules -y; pip install cryptography; pip install coverage;
- name: Set PYTHONPATH
run: echo "PYTHONPATH=." >> $GITHUB_ENV
- name: Start MySQL
run: sudo systemctl start mysql.service;
- name: MySQL Setup
run: mysql -u root -proot < setup.sql
- name: Start MongoDB
uses: supercharge/mongodb-github-action@1.12.0
with:
mongodb-version: '6.0'
- name: Server data setup
run: mkdir /home/runner/mmeds_server_data; mkdir /home/runner/conda_envs; mkdir -p /home/runner/conda_env_files/pheniqs; mkdir -p /home/runner/.modules/modulefiles; cp -r ./test_files /home/runner/mmeds_server_data/.; cp ./mmeds/resources/mmeds_stats.yaml /home/runner/mmeds_server_data/.; cp -r ./modules/* /home/runner/.modules/modulefiles/.; cp -r ./conda_env_files/* /home/runner/conda_env_files/.; mkdir /home/runner/mmeds_server_data/taxonomic_databases; touch /home/runner/mmeds_server_data/taxonomic_databases/dummy_classifier.qza;
- name: Python install
run: sudo python setup.py install --verbose; pip install wheel; pip install git+https://github.com/clemente-lab/mmeds-meta@$GITHUB_REF_NAME;
- name: Install GraphViz
run: sudo apt-get install graphviz
- name: install pheniqs
run: conda env create -f ./conda_env_files/pheniqs_env.yaml -p /home/runner/conda_envs/pheniqs
- name: Unit Tests
run: |
coverage run --parallel-mode --concurrency=multiprocessing ./mmeds/tests/unit/test.py adder authentication database documents error formatter tools uploader util validate spawn snakemake;
- name: Upload Unit coverage
uses: codecov/codecov-action@v4
with:
token: ${{ secrets.CODECOV_TOKEN }}
- name: Server Tests
run: |
pytest --cov=mmeds -W ignore::DeprecationWarning -W ignore::FutureWarning -s --durations=0 ./mmeds/tests/watcher/test_watcher.py&
sleep 1;
pytest --cov=mmeds -W ignore::DeprecationWarning -W ignore::FutureWarning -s ./mmeds/tests/server/test_server.py -x --durations=0;
- name: Upload Server Coverage
uses: codecov/codecov-action@v4
with:
token: ${{ secrets.CODECOV_TOKEN }}
- name: Metadata Tests
run: pytest --cov=mmeds -W ignore::DeprecationWarning -W ignore::FutureWarning -s ./mmeds/tests/metadata/test_error_metadata.py;
- name: Load File Action
if: failure()
id: read_file
uses: guibranco/github-file-reader-action-v2@latest
with:
path: "/home/runner/mmeds_server_data/MMEDS_log.txt"
- name: Print MMEDS Logs
if: failure()
run: echo "${{ steps.read_file.outputs.contents }}"