GitHub¶

List files in active PRs¶

To apply repository-wide automated changes (such as formatting) in active repositories, it is useful to list files in active PRs to minimize the impact of such changes.

The GitHub CLI can be used to obtain such information. The following extracts information, in JSON format, about 100 open PRs:

gh pr list -L 100 --json number,updatedAt,createdAt,title

jq can then be used to interact with the JSON output.

To extract the list of PR numbers with updates after a certain date one can use the folloiwng query:

gh pr list -L 500 --json number,updatedAt,createdAt,title \
  | jq '[.[] | select(.updatedAt > ("2025-07-01"))]' \
  | jq '.[] | .number'

With the PR numbers at hand, one can list the modified files in each PR using [gh] again:

gh pr diff --name-only <PR_NUMBER>

Credits

This workflow was originally developed by Egor Marin, who helped with the automatic formatting of the whole MDAnalysis code base.

Secret files¶

GitHub Actions might require a secret file. Such file could be stored encrypted in the GitHub repository and the decryption passphrase can be stored as a GitHub Secret.

Encrypting Secret File with GPG¶

Encrypt file with GPG:

gpg --symmetric --cipher-algo AES256 FILE

The passphrase used at this step is required to decrypt the file and can be stored as a GitHub Secret.

Decryption Secret File¶

#!/bin/sh

mkdir $HOME/secrets

gpg --quiet --batch --yes --decrypt --passphrase="$SECRET_PASSPHRASE" \
    --output $HOME/secrets/FILE FILE.gpg

The shell script has to be executable when pushed to GitHub:

chmod +x decrypt_secret.sh

GitHub Action¶

name: Decrypt Secret File

on: push

jobs:
  my-job:
    name: Decrypt Secret File
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2
      - name: Decrypt Secret File
        run: ./.github/scripts/decrypt_secret.sh
        env:
          SECRET_PASSPHRASE: ${{ secrets.SECRET_PASSPHRASE }}