Lint YAML files with yamllint

There is now a configuration file for `yamllint`
and a `pre-commit` hook.

The most straightforward linting issues were fixed.
The other ones are ignored and should be handled in the future.

.github/workflows/build_and_test.yml

@@ -1,16 +1,19 @@
+---
+
 name: Python build and test
 
-on: [push, pull_request]
+"on": [push, pull_request]
 
 jobs:
   build-linux:
     runs-on: ubuntu-latest
     strategy:
       max-parallel: 5
       matrix:
-        python-version: ["3.10"] #, "3.9", "3.10"]
+        python-version: ["3.10"]
 
     # Skip `pull_request` runs on local PRs for which `push` runs are already triggered
+    # yamllint disable-line rule:line-length
     if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository
 
     # Service containers to run with `container-job`

.github/workflows/bump_version_and_tag.yml

@@ -1,94 +1,98 @@
+---
+
+# yamllint disable rule:line-length
+
 name: Create/Update Tag
-on:
+"on":
   push:
     branches:
       - develop
 jobs:
   create-version-tag:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-      with:
-        token: ${{ secrets.CI_TOKEN }}
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v4
-      with:
-        python-version: "3.10"
-    - name: Update version
-      id: update-version
-      run: |
+      - uses: actions/checkout@v3
+        with:
+          token: ${{ secrets.CI_TOKEN }}
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Update version
+        id: update-version
+        run: |
+            pip install --upgrade pip
+            pip install poetry
+            poetry version minor
+            git config --global user.email "[email protected]"
+            git config --global user.name "Marcus Oskarsson"
+            git add -A
+            git commit -m "[skip ci] Bumped minor version"
+            git push -f
+            poetry build
+      - name: Publish package to PyPI
+        id: publish-pacakge
+        run: |
+          poetry config pypi-token.pypi ${{ secrets.PYPI }}
+          poetry publish
+      - name: Read package version
+        id: set-tag
+        run: |
           pip install --upgrade pip
-          pip install poetry
-          poetry version minor
-          git config --global user.email "[email protected]"
-          git config --global user.name "Marcus Oskarsson"
-          git add -A
-          git commit -m "[skip ci] Bumped minor version"
-          git push -f
-          poetry build
-    - name: Publish package to PyPI
-      id: publish-pacakge
-      run: |
-        poetry config pypi-token.pypi ${{ secrets.PYPI }}
-        poetry publish
-    - name: Read package version
-      id: set-tag
-      run: |
-        pip install --upgrade pip
-        pip install toml
-        echo ::set-output name=tag_name::v$(python -c 'import toml; print(toml.load("./pyproject.toml")["tool"]["poetry"]["version"])')
-    - name: Check tag exists
-      id: check-tag-exists
-      uses: actions/github-script@v6
-      env:
-        TAG: ${{ steps.set-tag.outputs.tag_name }}
-      with:
-        github-token: ${{ github.token }}
-        script: |
-          // https://github.com/mukunku/tag-exists-action
-          var exists = 'false';
-          try {
-              const getRefResponse = await github.rest.git.getRef({
-                  owner: context.repo.owner,
-                  repo: context.repo.repo,
-                  ref: "refs/tags/${{ steps.set-tag.outputs.tag_name }}"
-              });
+          pip install toml
+          echo ::set-output name=tag_name::v$(python -c 'import toml; print(toml.load("./pyproject.toml")["tool"]["poetry"]["version"])')
+      - name: Check tag exists
+        id: check-tag-exists
+        uses: actions/github-script@v6
+        env:
+          TAG: ${{ steps.set-tag.outputs.tag_name }}
+        with:
+          github-token: ${{ github.token }}
+          script: |
+            // https://github.com/mukunku/tag-exists-action
+            var exists = 'false';
+            try {
+                const getRefResponse = await github.rest.git.getRef({
+                    owner: context.repo.owner,
+                    repo: context.repo.repo,
+                    ref: "refs/tags/${{ steps.set-tag.outputs.tag_name }}"
+                });
 
-              if (getRefResponse.status === 200) {
-                  console.log("Tag was found");
-                  exists = 'true';
-              }
-          } catch(error) {
-              console.log("Tag was not found");
-          }
-          core.setOutput('exists', exists);
+                if (getRefResponse.status === 200) {
+                    console.log("Tag was found");
+                    exists = 'true';
+                }
+            } catch(error) {
+                console.log("Tag was not found");
+            }
+            core.setOutput('exists', exists);
 
-    - name: Update tag
-      uses: actions/github-script@v6
-      if: steps.check-tag-exists.outputs.exists == 'true'
-      env:
-        TAG: ${{ steps.set-tag.outputs.tag_name }}
-      with:
-        github-token: ${{ github.token }}
-        script: |
-          github.rest.git.updateRef({
-            owner: context.repo.owner,
-            repo: context.repo.repo,
-            ref: "refs/tags/${{ steps.set-tag.outputs.tag_name }}",
-            sha: context.sha
-          })
+      - name: Update tag
+        uses: actions/github-script@v6
+        if: steps.check-tag-exists.outputs.exists == 'true'
+        env:
+          TAG: ${{ steps.set-tag.outputs.tag_name }}
+        with:
+          github-token: ${{ github.token }}
+          script: |
+            github.rest.git.updateRef({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              ref: "refs/tags/${{ steps.set-tag.outputs.tag_name }}",
+              sha: context.sha
+            })
 
-    - name: Create tag
-      uses: actions/github-script@v6
-      if: steps.check-tag-exists.outputs.exists != 'true'
-      env:
-        TAG: ${{ steps.set-tag.outputs.tag_name }}
-      with:
-        github-token: ${{ github.token }}
-        script: |
-          github.rest.git.createRef({
-            owner: context.repo.owner,
-            repo: context.repo.repo,
-            ref: "refs/tags/${{ steps.set-tag.outputs.tag_name }}",
-            sha: context.sha
-          })
+      - name: Create tag
+        uses: actions/github-script@v6
+        if: steps.check-tag-exists.outputs.exists != 'true'
+        env:
+          TAG: ${{ steps.set-tag.outputs.tag_name }}
+        with:
+          github-token: ${{ github.token }}
+          script: |
+            github.rest.git.createRef({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              ref: "refs/tags/${{ steps.set-tag.outputs.tag_name }}",
+              sha: context.sha
+            })

.github/workflows/pages.yaml

@@ -6,7 +6,7 @@ name: "Pages"
 concurrency:
   group: "pages"
 
-on:
+"on":
   pull_request:
   push:
 

.github/workflows/ui.yml

@@ -1,6 +1,10 @@
+---
+
+# yamllint disable rule:line-length
+
 name: UI
 
-on: [push, pull_request]
+"on": [push, pull_request]
 
 jobs:
   format:

.pre-commit-config.yaml

@@ -1,11 +1,23 @@
+---
+
 default_language_version:
   python: python3.10
+
+
 repos:
+
+  - repo: https://github.com/adrienverge/yamllint
+    rev: v1.35.1
+    hooks:
+      - id: yamllint
+        args:
+          - --strict
+
   - repo: https://github.com/python-poetry/poetry
     rev: 1.5.0
     hooks:
       - id: poetry-check
-  #    - id: poetry-lock
+
   - repo: https://github.com/myint/autoflake
     rev: v1.6.0
     hooks:
@@ -17,11 +29,13 @@ repos:
           - --in-place
           - --remove-duplicate-keys
           - --ignore-pass-after-docstring
+
   - repo: https://github.com/psf/black
     rev: 22.8.0
     hooks:
-    - id: black
-      name: Black
+      - id: black
+        name: Black
+
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.3.0
     hooks:
@@ -37,18 +51,10 @@ repos:
         exclude: ^.drone\.yml|meta.yaml
       - id: mixed-line-ending
         args: ["--fix=lf"]
-  # - repo: https://github.com/PyCQA/isort
-  #   rev: 5.10.1
-  #   hooks:
-  #     - id: isort
-  #       name: Import Sort
-  #       args:
-  #         - --settings=.
+
   - repo: https://github.com/PyCQA/flake8
     rev: 4.0.1
     hooks:
-    - id: flake8
-      name: Flake8
-# Not using bugbear for now
-#      additional_dependencies: ["flake8-bugbear==22.9.11"]
-      exclude: (ui/|test/)
+      - id: flake8
+        name: Flake8
+        exclude: (ui/|test/)

.readthedocs.yaml

@@ -25,6 +25,7 @@ build:
     - "git fetch --unshallow || true"
     - "mamba env create --file conda-environment.yml --force"
     - "mamba run --name mxcubeweb poetry install --only=docs,main"
+    # yamllint disable-line rule:line-length
     - "(mamba run --name mxcubeweb redis-server &) && mamba run --name mxcubeweb python -m sphinx -T -E -b html -d _build/doctrees -c docs docs/source ${READTHEDOCS_OUTPUT}/html && mamba run --name mxcubeweb redis-cli shutdown"
 
 

.yamllint.yaml

@@ -0,0 +1,11 @@
+---
+
+extends: default
+
+ignore: |
+  ui/pnpm-lock.yaml
+
+rules:
+  # Match line length to the one set by `black` the Python formatter
+  line-length:
+    max: 88

conda-environment.yml

@@ -1,3 +1,5 @@
+---
+
 name: mxcubeweb
 
 channels:

meta.yaml

@@ -1,9 +1,10 @@
-{% set data = load_setup_py_data(setup_file="./setup.py",
-  from_recipe_dir=True) %}
+---
+
+# {% set data = load_setup_py_data(setup_file="./setup.py", from_recipe_dir=True) %}
 
 package:
-  name: {{ data.get('name') }}
-  version: {{ data.get('version') }}
+  name: {{data.get('name')}}
+  version: {{data.get('version')}}
 
 source:
   path: .
@@ -51,8 +52,8 @@ test:
     - {{data.get('name')}}
 
 about:
-  home: {{ data.get('url')}}
-  license: {{ data.get('license')}}
-  summary: {{ data.get('description')}}
-  author: {{ data.get('author')}}
-  description: {{ data.get('description')}}
+  home: {{data.get('url')}}
+  license: {{data.get('license')}}
+  summary: {{data.get('description')}}
+  author: {{data.get('author')}}
+  description: {{data.get('description')}}