Lint YAML files with yamllint

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

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

.github/workflows/coverage_report.yml

@@ -1,15 +1,22 @@
+---
+
 name: Coverage Report
-on:
+
+on:  # yamllint disable-line rule:truthy
   pull_request:
     types: [opened, reopened, synchronize]
     paths:
       - '**.py'
+
 jobs:
   pytest-coverage:
     runs-on: ubuntu-latest
     permissions:
       pull-requests: write
+
     steps:
+
+    # yamllint disable-line rule:indentation
     - uses: actions/checkout@v3
 
     - name: Set up Python 3.10
@@ -18,16 +25,20 @@ jobs:
         python-version: "3.10"
 
     - name: Install dependencies
+      # yamllint disable rule:line-length
       run: |
         sudo apt-get update && sudo apt-get install -y libsasl2-dev libldap2-dev libssl-dev
         python -m pip install --upgrade pip
         python -m pip install poetry --user
         python -m poetry install --extras=tango
+      # yamllint enable rule:line-length
 
     - name: Run and write pytest
+      # yamllint disable rule:line-length
       run: |
         set -o pipefail
         poetry run pytest --cov=mxcubecore --junitxml=pytest.xml --cov-report=term-missing:skip-covered | tee pytest-coverage.txt
+      # yamllint enable rule:line-length
 
     - name: Pytest coverage comment
       id: coverage-comment

.github/workflows/create-tag.yml

@@ -1,12 +1,15 @@
+---
+
 name: Create/Update Tag
-on:
+on:  # yamllint disable-line rule:truthy
   push:
     branches:
       - develop
 jobs:
   create-version-tag:
     runs-on: ubuntu-latest
     steps:
+    # yamllint disable-line rule:indentation
     - uses: actions/checkout@v3
       with:
         token: ${{ secrets.CI_TOKEN }}
@@ -34,10 +37,12 @@ jobs:
         poetry publish
     - name: Read package version
       id: set-tag
+      # yamllint disable rule:line-length
       run: |
         pip install --upgrade pip
         pip install toml
         echo ::set-output name=tag_name::v$(python -c 'import toml; print(toml.load("./pyproject.toml")["tool"]["poetry"]["version"])')
+      # yamllint enable rule:line-length
 
     - name: Check tag exists
       id: check-tag-exists

.github/workflows/pages.yaml

@@ -6,7 +6,7 @@ name: "Pages"
 concurrency:
   group: "pages"
 
-on:
+on:  # yamllint disable-line rule:truthy
   push:
   pull_request:
 

.github/workflows/pre-commit.yml

@@ -1,29 +1,37 @@
+---
+
 name: Linting & Code Quality
-on:
+
+on:  # yamllint disable-line rule:truthy
   pull_request:
     types: [opened, reopened, synchronize]
+
 jobs:
   pre-commit:
     runs-on: ubuntu-latest
+
     steps:
-    - uses: actions/checkout@v3
-
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v4
-      with:
-        python-version: "3.8"
-
-    - name: Install openldap
-      run: |
-        sudo apt-get update && sudo apt-get upgrade -y
-        sudo apt-get install -y libldap2-dev libsasl2-dev slapd ldap-utils tox lcov valgrind
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install poetry --user
-        python -m poetry install
-
-    - name: Run Pre-Commit
-      run: |
-        poetry run pre-commit run --all-files
+
+      - uses: actions/checkout@v3
+
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.8"
+
+      - name: Install openldap
+        # yamllint disable rule:line-length
+        run: |
+          sudo apt-get update && sudo apt-get upgrade -y
+          sudo apt-get install -y libldap2-dev libsasl2-dev slapd ldap-utils tox lcov valgrind
+        # yamllint enable rule:line-length
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install poetry --user
+          python -m poetry install
+
+      - name: Run Pre-Commit
+        run: |
+          poetry run pre-commit run --all-files

.github/workflows/tests.yml

@@ -1,5 +1,7 @@
+---
+
 name: Pytest
-on:
+on:  # yamllint disable-line rule:truthy
   pull_request:
     types: [opened, reopened, synchronize]
     paths:
@@ -19,6 +21,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
 
       - name: Install openldap
+        # yamllint disable-line rule:line-length
         run: sudo apt-get update && sudo apt-get install -y libldap2-dev libsasl2-dev slapd ldap-utils tox lcov valgrind
 
       - name: Install dependencies

.pre-commit-config.yaml

@@ -1,11 +1,22 @@
+---
+
 default_language_version:
   python: python3.8
+
 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:
@@ -17,19 +28,19 @@ 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:
       - id: trailing-whitespace
-        #
-        # Exclude files below from trailing-whitespace checks until we get around fixing them.
-        # This way we can check that all other files are trailing-whitespace clean in CI.
-        #
+        # Exclude files from trailing-whitespace checks until we get around fixing them.
+        # This way we can check that other files are trailing-whitespace clean in CI.
         exclude: |
             (?x)^(
                 mxcubecore/configuration/.*|
@@ -47,10 +58,8 @@ repos:
                 mxcubecore/HardwareObjects/ESRF/ID29XRFSpectrum\.py
             )$
       - id: end-of-file-fixer
-        #
-        # Exclude files below from end-of-file-fixer checks until we get around fixing them.
-        # This way we can check that all other files are end-of-file-fixer clean in CI.
-        #
+        # Exclude files from end-of-file-fixer checks until we get around fixing them.
+        # This way we can check that other files are end-of-file-fixer clean in CI.
         exclude: |
             (?x)^(
                 mxcubecore/configuration/.*|
@@ -60,26 +69,11 @@ repos:
             )$
       - id: check-case-conflict
       - id: check-merge-conflict
-        # exclude files where underlines are not distinguishable from merge conflicts
+        # Exclude files where underlines are not distinguishable from merge conflicts.
         exclude: /README\.rst$|^docs/.*\.rst$
       - id: check-symlinks
       - id: check-xml
       - id: check-yaml
         exclude: ^.drone\.yml
       - 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=.
-  #       exclude: (/__init__\.py$|deprecated/|mxcubecore/HardwareObjects/(ALBA|ASLS|DESY|EMBL|ESRF|LNLS|MAXIV|SOLEIL|ANSTO|Gphl|Arinax))
-  # - repo: https://github.com/PyCQA/flake8
-  #   rev: 4.0.1
-  #   hooks:
-  #   - id: flake8
-  #     name: Flake8
-  #     additional_dependencies: ["flake8-bugbear==22.9.11"]
-  #     exclude: (utils/pyispyb_client/|deprecated/|mxcubecore/HardwareObjects/(ALBA|ASLS|DESY|EMBL|ESRF|LNLS|MAXIV|SOLEIL|ANSTO|Gphl|Arinax))

.readthedocs.yaml

@@ -25,6 +25,7 @@ build:
     - "git fetch --unshallow || true"
     - "mamba env create --file conda-environment-dev.yml --force"
     - "mamba run --name mxcubecore poetry install --only=docs,main"
+    # yamllint disable-line rule:line-length
     - "mamba run --name mxcubecore sphinx-build -T -E -b html -c ./docs/ ./docs/source/ ${READTHEDOCS_OUTPUT}/html/"
 
 

.yamllint.yaml

@@ -0,0 +1,8 @@
+---
+
+extends: default
+
+rules:
+  # Match line length to the one set by `black` the Python formatter
+  line-length:
+    max: 88

conda-environment-dev.yml

@@ -1,3 +1,5 @@
+---
+
 name: mxcubecore
 channels:
   - conda-forge

mxcubecore/configuration/alba_xaloc13/beamline_config.yml

@@ -1,3 +1,8 @@
+---
+
+# yamllint disable rule:comments-indentation
+# yamllint disable rule:indentation
+
 # FIRST DRAFT of ALAB xaloc13 configuration. TO BE EDITED
 
 # The class to initialise, and init parameters
@@ -15,8 +20,8 @@ _initialise_class:
 # would need those added (e.g. the centring methods)
 #
 _objects:
-    # The !!o0map and the lines starting with '- ' give you an *orderd* dictionary
-    # And thus a reproducible loading order
+  # The !!o0map and the lines starting with '- ' give you an *orderd* dictionary
+  # And thus a reproducible loading order
   !!omap
     # The values are the file paths to the configuration file for the
     # object, relative to the configuration file path(s)
@@ -103,7 +108,7 @@ acquisition_limit_values:
         - 6000.0
     osc_range:         # (degrees)
         - -2165.0
-        -  2165.0
+        - 2165.0
     number_of_images:  # (int)
         - 1
         - 9999

mxcubecore/configuration/embl_hh_p14/beamline_config.yml

@@ -1,3 +1,5 @@
+---
+
 # FIRST DRAFT of EMBL P14 configuration. TO BE EDITED
 
 # The class to initialise, and init parameters
@@ -54,7 +56,7 @@ _objects:
     - image_tracking: image-tracking.xml
     - gphl_workflow: gphl-workflow.xml
     - gphl_connection: gphl-setup.xml
-#    - centring: centring.xml
+    # - centring: centring.xml
     # Analysis:
     - offline_processing: auto-processing.xml
     - online_processing: parallel-processing.xml
@@ -64,8 +66,8 @@ _objects:
     - ppu_control: ppu_control.xml
 # Non-object attributes:
 advanced_methods:
-  - MeshScan
-  - XrayCentering
+    - MeshScan
+    - XrayCentering
 tunable_wavelength: true
 disable_num_passes: false
 run_online_processing: true

mxcubecore/configuration/esrf_id30a2/gphl-setup.yml

@@ -1,3 +1,8 @@
+---
+
+# yamllint disable rule:comments
+# yamllint disable rule:comments-indentation
+# yamllint disable rule:line-length
 
 _initialise_class:
     class: mxcubecore.HardwareObjects.Gphl.GphlWorkflowConnection.GphlWorkflowConnection

mxcubecore/configuration/esrf_id30a2/gphl-workflow.yml

@@ -1,3 +1,10 @@
+---
+
+# yamllint disable rule:comments-indentation
+# yamllint disable rule:hyphens
+# yamllint disable rule:indentation
+# yamllint disable rule:line-length
+
 _initialise_class:
     class: mxcubecore.HardwareObjects.Gphl.GphlWorkflow.GphlWorkflow