Updating a package on bioconda

Suppose:

• You have a package that has already been released on bioconda
• You have implemented a bugfix or other update and pushed to master (or equivalent branch) in the GitHub repository
• You have tagged the update as a Release on GitHub (and, optionally, obtained a DOI using Zenodo)

Read this first: bioconda-bot will update your package automatically

In most cases, you will not need to act. The bioconda-bot webpage will detect your new version release, and package it up accordingly.

You will receive an email from notifications@github.com in the name of Bioconda Bot, which will provide details of the pull request it has already created on your behalf.

The kind people who maintain bioconda will review the changes and merge when the required standards are met.

Manually updating your package

• See also:
  • Initial local setup of bioconda

1: Fork bioconda-recipes to your GitHub account

Create or update an existing fork of the bioconda-recipes repository on GitHub in your account

• Click here to create the fork

2: Get a current local fork of bioconda-recipes

Clone, or update your local copy of your fork of bioconda-recipes repository.

git clone git@github.com:<YOUR_GITHUB_USERNAME>/bioconda-recipes.git

3: Set the upstream remote

Go into the repository and set the upstream remote to be the official bioconda repository:

cd bioconda-recipes
git remote add upstream https://github.com/bioconda/bioconda-recipes.git

4: Sync local and remote repositories

Make sure the local fork is up to date with the remote repositories

git checkout master          # change to master branch
git pull upstream master     # get changes from official repository
git push origin master       # push changes to your fork

5: Create and checkout a new branch for this package update

Name the branch update_<package> where <package> is the package name.

git checkout -b update_<package>

6: Edit your package recipe to point to the new release

Change to the package recipe directory and edit with your preferred editor.

cd recipes/<package>

• Edit the meta.yaml file to update elements for the new version of the package.
  • Update the version variable:
    • {% set version = "<NEW_VERSION>" %}
    • Updating the version variable should mean that the source: url: is updated automatically (so long as the versions correspond to our standard version naming scheme)
  • Update the hash:
    • sha256: <HASH>
    • To get the sha256 hash on macOS, use shasum -a 256 <PATH_TO_FILE> on the .tar.gz file downloaded from the GitHub release.
  • If this is not the first meta.yaml file you’ve edited for this release, increment the build: number: value by one.
  • If necessary, update requirements: host: to add or remove the necessary packages (one per line)

7: Push your modified files to your own fork

Change to the recipes directory and add your modified files

cd ..
git add <package>

• Push to your fork

git push

8: Create a pull request from your fork

Go to your GitHub repo at https://github.com/<YOUR_GITHUB_USERNAME>/bioconda-recipes

• Change to the branch you just created
• Click on the corresponding Pull Request button, and follow the online instructions
• Go to the official repository’s Pull Requests page and locate your PR.
  • When this goes green (gets a green tick) the tests have been passed. If there is a red cross, more attention is needed to the update.
  • If the tests have been passed, open your pull request and select a reviewer. If they approve your changes, the PR will be merged, and the new package version will be available.

9: Only after merging: delete your branch

Checkout the master branch, then delete the update_<package> branch locally.

git checkout master
git branch -d update_<package>

- Delete the `update_<package>` branch on the remote repository
- Sync your fork to the remote master, and update your fork on `GitHub`:

git checkout master
git pull upstream master
git push origin master

10: Congratulations, you’re done!

But have you updated pypi yet?