Rhfogh xml yaml

.github/workflows/coverage_report.yml

@@ -1,8 +1,9 @@
+%YAML 1.2
 ---
 
 name: Coverage Report
 
-on:  # yamllint disable-line rule:truthy
+on:
   pull_request:
     types: [opened, reopened, synchronize]
     paths:
@@ -16,45 +17,44 @@ jobs:
 
     steps:
 
-    # yamllint disable-line rule:indentation
-    - uses: actions/checkout@v3
-
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v4
-      with:
-        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
-      uses: MishaKav/[email protected]
-      with:
-        repo-token: ${{ secrets.CI_TOKEN }}
-        pytest-coverage-path: ./pytest-coverage.txt
-        junitxml-path: ./pytest.xml
-        report-only-changed-files: true
-
-    - name: Check the output coverage
-      run: |
-        echo "Coverage Percantage - ${{ steps.coverage-comment.outputs.coverage }}"
-        echo "Coverage Warnings - ${{ steps.coverage-comment.outputs.warnings }}"
-        echo "Coverage Errors - ${{ steps.coverage-comment.outputs.errors }}"
-        echo "Coverage Failures - ${{ steps.coverage-comment.outputs.failures }}"
-        echo "Coverage Skipped - ${{ steps.coverage-comment.outputs.skipped }}"
-        echo "Coverage Tests - ${{ steps.coverage-comment.outputs.tests }}"
-        echo "Coverage Time - ${{ steps.coverage-comment.outputs.time }}"
+      - uses: actions/checkout@v3
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          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
+        uses: MishaKav/[email protected]
+        with:
+          repo-token: ${{ secrets.CI_TOKEN }}
+          pytest-coverage-path: ./pytest-coverage.txt
+          junitxml-path: ./pytest.xml
+          report-only-changed-files: true
+
+      - name: Check the output coverage
+        run: |
+          echo "Coverage Percantage - ${{ steps.coverage-comment.outputs.coverage }}"
+          echo "Coverage Warnings - ${{ steps.coverage-comment.outputs.warnings }}"
+          echo "Coverage Errors - ${{ steps.coverage-comment.outputs.errors }}"
+          echo "Coverage Failures - ${{ steps.coverage-comment.outputs.failures }}"
+          echo "Coverage Skipped - ${{ steps.coverage-comment.outputs.skipped }}"
+          echo "Coverage Tests - ${{ steps.coverage-comment.outputs.tests }}"
+          echo "Coverage Time - ${{ steps.coverage-comment.outputs.time }}"

.github/workflows/create-tag.yml

@@ -1,101 +1,101 @@
+%YAML 1.2
 ---
 
 name: Create/Update Tag
-on:  # yamllint disable-line rule:truthy
+on:
   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 }}
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v4
-      with:
-        python-version: "3.10"
+      - 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: |
+      - 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
+        # yamllint disable rule:line-length
+        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 ${{ secrets.PYPI }}
-        poetry publish
-    - name: Read package version
-      id: set-tag
-      # yamllint disable rule:line-length
-      run: |
-        pip install --upgrade pip
-        pip install toml
-        echo ::set-output name=tag_name::v$(python -c 'import toml; print(toml.load("./pyproject.toml")["tool"]["poetry"]["version"])')
-      # yamllint enable rule:line-length
+          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
-      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 }}"
-              });
+      - 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

@@ -1,3 +1,4 @@
+%YAML 1.2
 ---
 
 
@@ -6,9 +7,9 @@ name: "Pages"
 concurrency:
   group: "pages"
 
-on:  # yamllint disable-line rule:truthy
-  push:
-  pull_request:
+on:
+  push: null
+  pull_request: null
 
 jobs:
 

.github/workflows/pre-commit.yml

@@ -1,8 +1,9 @@
+%YAML 1.2
 ---
 
 name: Linting & Code Quality
 
-on:  # yamllint disable-line rule:truthy
+on:
   pull_request:
     types: [opened, reopened, synchronize]
 

.github/workflows/tests.yml

@@ -1,7 +1,8 @@
+%YAML 1.2
 ---
 
 name: Pytest
-on:  # yamllint disable-line rule:truthy
+on:
   pull_request:
     types: [opened, reopened, synchronize]
     paths:

.yamllint.yaml

@@ -9,3 +9,27 @@ rules:
   # Match line length to the one set by `black` the Python formatter
   line-length:
     max: 88
+
+  # octal values must start with 0o, numbers may not start with e.g. 01
+  # It is simpler, and costs nothing, to disallow values like `010`
+  # except as quoted strings
+  octal-values:
+    forbid-implicit-octal: true
+
+  # This bans implicit nulls, nulls must be explicit.
+  empty-values: enable
+
+  # With these settings, and `%YAML 1.2` in the file header, we have :
+  #
+  #  Booleans: true, false
+  #  None: null, Null, NULL
+  #  not-a-number: .NaN, .NAN, .nan
+  #  Infinity:  .Inf, .INF, .inf
+  #  Strings: On, ON, Off, OFF, YES, Yes, NO, No
+  #  Disallowed if not quoted: True, TRUE, False, FALSE
+  #
+  # Setting `truthy: disabled` would allow the disabled values, as Booleans
+  #
+  # If desired, you could ban unquoted infinity and not-a-number by
+  # float-values: forbind-int: true
+  # float-values: forbind-nan: true

conda-environment-dev.yml

@@ -1,3 +1,4 @@
+%YAML 1.2
 ---
 
 name: mxcubecore

mxcubecore/HardwareRepository.py

@@ -56,7 +56,7 @@
 yaml = YAML(typ="safe", pure=True)
 # The following are not needed for load, but define the default style.
 yaml.default_flow_style = False
-yaml.indent(mapping=4, sequence=4, offset=2)
+yaml.indent(mapping=2, sequence=4, offset=2)
 
 
 __copyright__ = """ Copyright © 2010 - 2020 by MXCuBE Collaboration """

mxcubecore/configuration/alba_xaloc13/beamline_config.yml

@@ -1,3 +1,4 @@
+%YAML 1.2
 ---
 
 # FIRST DRAFT of ALAB xaloc13 configuration. TO BE EDITED

mxcubecore/configuration/embl_hh_p14/beamline_config.yml

@@ -1,3 +1,4 @@
+%YAML 1.2
 ---
 
 # FIRST DRAFT of EMBL P14 configuration. TO BE EDITED

mxcubecore/configuration/esrf_id30a2/gphl-setup.yml

@@ -1,3 +1,4 @@
+%YAML 1.2
 ---
 
 _initialise_class: