developer_docs

Development

Welcome to Cromshell's development document, here you will find instructions on setting up your environment and other relevant material for contributing to Cromshell.

Getting Started

Cromshell development requires python3 (>=.7) to be installed, afterwards the Cromshell development environment can be set up by the following steps:

1. Pull cromshell git repository

    git clone [email protected]:broadinstitute/cromshell.git
    cd cromshell
    git checkout cromshell_2.0
    git checkout -b <your initial>_<name of your new branch>

2. Create a virtual python environment

    python3 -mvenv venv
    . venv/bin/activate
    pip install --upgrade pip
    pip install -r dev-requirements.txt
    pip install -e .

After following the above development environment setup steps, cromshell should have been added to your path. Run cromshell --help to confirm installation.

> cromshell --help
Usage: cromshell [OPTIONS] COMMAND [ARGS]...

  Cromshell is a script for submitting workflows to a cromwell server and
  monitoring / querying their results.

Setup Cromshell configuration files

If Cromshell determines ~/.cromshell does not exist it will automatically create a hidden directory containing configuration files after running on of its sub commands.

1. Run

    cromshell-alpha version

The following directory and files should be created

    > ~/.cromshell
            all.workflow.database.tsv
            cromshell_config.json

• all.workflow.database.tsv : Tab-delimited file listing all workflows executed by the user
• cromshell_config.json : Configuration file for cromshell

2. Edit the cromshell_config file so that the desired Cromwell server is being used, for example:

{
  "cromwell_server": "http://localhost:8000",
  "requests_timeout": 5
}

You can set the "cromwell_server" to an existing server or create a local one temproraly using a docker container, then setting the config to http://localhost:8000 like in the example above. The command below can be used to create a Cromwell version 67 server container.

	docker run -d -p 8000:8000 broadinstitute/cromwell:67 server

How do these configurations affect your cromshell1.0 configs?
Cromshell2.0 uses the same all.workflow.database.tsv as cromshell1, thus it will read-write to the same file. The cromshell_config.json file is new in cromshell2.0, changes to this file will not affect your cromshell1.0 settings.

Development Steps

Now that you have set up your Cromshell environment, you can start adding and testing new commands and features. There are three main steps to follow:

1. Add a command or feature to the codebase
2. Add unit and integration tests for the added scripts
3. Run test and linting scripts

Once you have a functional command or feature with all of its unit/integration tests successfully completing, then you can push your changes to the cromshell branch for review.

Best Practices

When styling your code use the following site

• A well formatted function will have
  • Lower case name with underscores as spaces
  • Use type hint where-ever possible
  • Includes a doc string describing the function and parameters.

def alias_exists(alias_name: str, submission_file: str) -> bool:
   """
   Check if alias name already exists in submission file
   :param alias_name: Alternate string identifier for workflow submission
   :param submission_file: Path to cromshell submission file
   :return:
   """
   ...

• Have a goal to make unit tests for every new function added.

Versioning

We use bumpversion to maintain version numbers. DO NOT MANUALLY EDIT ANY VERSION NUMBERS.

Our versions are specified by a 3 number semantic version system (https://semver.org/):

major.minor.patch

To update the version with bumpversion do the following:

bumpversion PART where PART is one of:

• major
• minor
• patch

This will increase the corresponding version number by 1.