gregcaporaso / q2-this-is-a-test

q2-plugin-template

A skeleton for QIIME 2 plugins.

To use this template for a new plugin creation, you'll first need to create a new plugin repo by clicking the Use this template button. Fill out the new repository name and description. Following that initial setup, in your new plugin repo you still need to adjust the following elements:

• exchange this_is_a_test and plugin-name with the name of your plugin
• adjust all the required fields in setup.py and plugin_setup.py
• adjust the Greg Caporaso in all the copyright headers and the license file
• add versioneer support for version management:
  • install versioneer (link) into any python environment: pip install versioneer
  • from the project directory, run versioneer install to create/modify all the required files
  • add the # flake8: noqa flag on top of the versioneer.py file for the file to be ignore by lint checks

Enjoy!

Development using Dev Containers (Visual Studio Code)

To streamline the plugin development process, you can use support for Docker containers built into VS Code in a form of Dev Containers (see here for more information). In this approach a Docker container will be created and configured (using the provided specification) and your VS Code environment will be attached to this container where you can continue developing as usual. You only need to specify which version of QIIME 2 you want to use (see below) and the respective Docker image will be pulled and used to create the container.

The elements you need to use the QIIME 2 devcontainer are:

• container spec located under .devcontainer.json in your project directory
• requirements.txt file listing all the project-specific conda dependencies that should be installed in the environment
• prep-dev-container section in the Makefile

The only parts that you should need to modify are the packages listed in the requirements.txt file. If you are setting up Dev Containers in an already existing repo you will need to copy the files/section listed above. Once you have your requirements ready follow those steps to get started:

1. Install VS Code (if needed) and enable launch from command line (see here for macOS instructions).
2. In your terminal, navigate to the repo you want to open in the devcontainer and execute:

   export QIIME_VERSION=2022.2 && code .

   Replace 2022.2 with the version of QIIME 2 that you would like to use. While it is possible to open those containers without going through the terminal, it is required in our setup to define the desired QIIME version.
3. When prompted, reopen the folder in a Dev Container by clicking on "Reopen in container".
4. The Docker image will be pulled (happens only once per image) and the corresponding container will be created and configured - this may take a few minutes.
5. Once container configuration is finished you should be good to go: you can start developing as usual. The conda environment in the container is already configured and should have your plugin installed inside.

Development with git hooks and setting up a dev environment

To make your life a bit easier, you can use git hooks to automate certain tasks while working with Git (see here for more details). Here, we are making use of the pre-commit tool which allows us to configure all the hooks in one place. The pre-commit hook configured here will automatically run linting and formatting tasks before any commit (i.e. on git commit). In the configuration file you will see that the pre-push hook is commented-out - it is just more complicated to configure an environment for running that hook (given all the different conda dependencies that the plugin/QIIME 2 may have).

To set up your dev environment, including the hooks, simply run make dev in an existing conda environment - this will install all the required tooling. You don't need to do anything else - the hooks will be automatically executed whenever you commit.

Note: If, for whatever reason, you need to skip the hooks, you can append the --no-verify flag to the git command - the hooks won't be executed.