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CONTRIBUTING.md

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Contributing

Setup for General Development

  • Fork and clone this repo, e.g. using the instructions at GitHub: Fork a repo
    • Navigate to neksa/mutagene, click the Fork button at the top right
    • git clone https://github.com/<your_github_username>/mutagene.git
    • cd mutagene
    • git remote add upstream https://github.com/neksa/mutagene.git
    • Keep your fork in sync using the instructions at GitHub: Syncing a fork
  • Use your package manager of choice to install pipenv
  • Create a new pipenv environment
    • e.g., if you need to specify a python executable: pipenv install --python=/usr/bin/python3.7
  • Install the package in development mode using setup.py
    • pipenv run python setup.py develop

Adding Features or Fixing Bugs

  • Create and check out a feature or bugfix branch
    • e.g., git checkout -b feature/motif_extension
  • Add and commit your changes
  • Update README.md when needed
  • Add a description of your changes to CHANGELOG.md
  • Ensure all tests are passing, as described below
  • Submit a pull request to the upstream repo with a description of your changes
  • Ensure the new branch is mergeable

Testing

  • Write additional tests to cover new features as necessary
  • Please make sure that all tests pass when running pytest
  • Our tests make use of the pytest-securestore plugin to store credentials for connecting to an instance of JFrog Artifactory that stores test articles. In order to run tests using pytest, it is necessary to set the following environment variables:
    • SECURE_STORE_FILE=./pytest-secure.yml.aes
    • SECURE_STORE_PASSWORD=contact Alexander Goncearenco or Steven Handy for instructions
    • To add a test article to Artifactory, update the TEST_FILE_MAP dictionary in the file tests/cli/cli_test_utils.py
    • If you wish to use your own Artifactory repository, the test scripts can obtain the articles from their original sources and upload them to your Artifactory repository. See pytest-secure.yml.template for the required format for a file to contain your connection information.
    • To encrypt your YAML file, use the following commands in a pipenv run python interpreter:
      • import pyAesCrypt
      • pyAesCrypt.encryptFile('./<your_artifactory_creds_file>.yml', './<your_artifactory_creds_file>.yml.aes', '<your_encryption_password>', (64 * 1024))
  • Run the tests using pytest
    • pipenv run pytest --secure-store-filename=$SECURE_STORE_FILE --secure-store-password=$SECURE_STORE_PASSWORD tests