Merge pull request #8 from qiime2/linting-action

start adding linter

Author: Oddant1

.github/scripts/lint.py

@@ -0,0 +1,67 @@
+import os
+import re
+import sys
+import yaml
+import requests
+
+
+DIR = 'plugins'
+
+KEY_SET = set(['owner', 'name', 'branch', 'docs'])
+ENV_FILE_REGEX = '.*-qiime2-.*-20[0-9][0-9]\.([1-9]|1[0-2])\.yml'
+GITHUB_BASE_URL = "https://api.github.com"
+
+env_urls = []
+
+GITHUB_TOKEN = sys.argv[1]
+GITHUB_BASE_URL = 'https://api.github.com'
+
+
+def lint(yml):
+    # Assert corrrect keys
+    assert set(yml.keys()) == KEY_SET
+
+    # Get the docs URL assert 200
+    response = requests.get(yml['docs'])
+    assert response.status_code == 200
+
+    # Put together the owner/name:branch
+    url = f'{GITHUB_BASE_URL}/repos/{yml['owner']}/{yml['name']}/contents/environment-files'
+    headers = {
+        'Authorization': f'token: {GITHUB_TOKEN}',
+        'X-GitHub-Api-Version': '2022-11-28'
+    }
+    query_params = {
+        'owner': yml['owner'],
+        'repo': yml['name'],
+        'ref': yml['branch'],
+        'path': '/environment-files/'
+    }
+
+    # Get all files in the /environment-files/ folder
+    response = requests.get(url, headers=headers, params=query_params)
+    envs = response.json()
+
+    # If the file matches the regex to be a QIIME 2 environment-file then keep
+    # track of its download URL
+    for env in envs:
+        if re.search(ENV_FILE_REGEX, env['name']) is not None:
+            env_urls.append(env['download_url'])
+
+
+if __name__ == "__main__":
+    GITHUB_TOKEN = sys.argv[1]
+    files = sys.argv[2:]
+
+    for file in files:
+        head, tail = os.path.split(file)
+        file_name, file_ext = os.path.splitext(tail)
+
+        # We only care about files added to the plugins dir
+        if head == DIR:
+            with open(file, 'r') as fh:
+                yml = yaml.safe_load(fh)
+                lint(yml)
+
+    with open(os.environ['GITHUB_OUTPUT'], 'a') as fh:
+        fh.write(f'ENV_FILES={env_urls}\n')

.github/workflows/lint-pr.yml

@@ -0,0 +1,84 @@
+name: lint-pr
+
+# Run on PR changing files in plugins dir against main
+on:
+  pull_request:
+    branches:
+      - 'main'
+    paths:
+      - '/plugins/**'
+
+jobs:
+  lint-yml:
+    runs-on: ubuntu-latest
+    outputs:
+      ENV_FILES: ${{ steps.lint.outputs.ENV_FILES }}
+
+    steps:
+      # Checkout new commit and prior HEAD
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 2
+
+      # Get diff
+      # This feels odd to me got it from
+      # https://docs.github.com/en/actions/writing-workflows/choosing-what-your-workflow-does/workflow-commands-for-github-actions#multiline-strings
+      - name: Get Diff
+        run: |
+          {
+            echo 'DIFF<<EOF'
+            git diff --name-only HEAD~ HEAD
+            echo EOF
+          } >> "$GITHUB_ENV"
+
+      # Lint all plugins/** files in diff (filtering of diff occurs in Python)
+      # Also gets all env files in added plugins for env testing
+      - name: Lint Yml and Get Env Files
+        id: lint
+        run: python .github/scripts/lint.py ${{ secrets.GITHUB_TOKEN }} $DIFF
+
+  # Install all envs found and at least make sure `qiime info` runs
+  # TODO: Make this attempt to run pytest?
+  test-envs:
+    needs: lint-yml
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-13]
+        url: ${{ fromJSON(needs.lint-yml.outputs.ENV_FILES) }}
+    runs-on: ${{ matrix.os }}
+    env:
+      prefix: ./test
+
+    steps:
+      - name: Set up Miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: ''
+          architecture: 'x64'
+          auto-activate-base: true
+          miniconda-version: 'latest'
+
+      # Hacky stff to make it so I can activate the conda env for testing
+      - name: Set up Test Environment
+        env:
+          url: ${{ matrix.url }}
+        run: |
+          conda env create -y -p ${{ env.prefix }} -f $url
+          mkdir -p ${{ env.prefix }}/etc
+          cat <<EOF > '${{ env.prefix }}/etc/activate.sh'
+            . "$CONDA/etc/profile.d/conda.sh"
+            conda activate '${{ env.prefix }}'
+          EOF
+          chmod +x 'test/etc/activate.sh'
+
+      - name: Test
+        run: |
+          source ${{ env.prefix }}/etc/activate.sh
+          conda activate ${{ env.prefix }}
+          qiime info
+
+# Grab the target repo and validate it?
+  # Description?
+  # README?
+  # Env files?