Merge branch 'AliceO2Group:master' into at2024

Author: pkurash

.clang-format

@@ -39,7 +39,60 @@ PenaltyBreakFirstLessLess: 120
 PenaltyBreakString: 1000
 PenaltyExcessCharacter: 1000000
 PenaltyReturnTypeOnItsOwnLine: 200
-SortIncludes: false
+SortIncludes: CaseSensitive
+IncludeBlocks: Regroup
+IncludeCategories:
+  # O2Physics, PWG
+  - Regex: ^(<|")PWG[A-Z]{2}/.*\.h
+    Priority: 2
+    CaseSensitive: true
+  # O2Physics, non-PWG
+  - Regex: ^(<|")(Common|ALICE3|DPG|EventFiltering|Tools|Tutorials)/.*\.h
+    Priority: 3
+    CaseSensitive: true
+  # O2
+  - Regex: ^(<|")(Algorithm|CCDB|Common[A-Z]|DataFormats|DCAFitter|Detectors|EMCAL|Field|Framework|FT0|FV0|GlobalTracking|GPU|ITS|MathUtils|MFT|MCH|MID|PHOS|PID|ReconstructionDataFormats|SimulationDataFormat|TOF|TPC|ZDC).*/.*\.h
+    Priority: 4
+    CaseSensitive: true
+  # ROOT
+  - Regex: ^(<|")(T[A-Z]|Math/|Roo[A-Z])[[:alnum:]/]+\.h
+    Priority: 5
+    CaseSensitive: true
+  # known third-party: KFParticle
+  - Regex: ^(<|")KF[A-Z][[:alnum:]]+\.h
+    Priority: 6
+    CaseSensitive: true
+  # known third-party: FastJet
+  - Regex: ^(<|")fastjet/
+    Priority: 6
+    CaseSensitive: true
+  # known third-party: ONNX runtime
+  - Regex: ^(<|")onnxruntime
+    Priority: 6
+    CaseSensitive: true
+  # incomplete path to DataModel
+  - Regex: ^(<|").*DataModel/
+    Priority: 1
+    CaseSensitive: true
+  # other third-party
+  - Regex: ^(<|")([[:alnum:]_]+/)+[[:alnum:]_]+\.h
+    Priority: 6
+    CaseSensitive: true
+  # other local-looking file
+  - Regex: ^".*\.
+    Priority: 1
+    CaseSensitive: true
+  # C system
+  - Regex: ^(<|")[[:lower:]_]+\.h(>|")
+    Priority: 102
+    CaseSensitive: true
+  # C++ system
+  - Regex: ^(<|")[[:lower:]_/]+(>|")
+    Priority: 101
+    CaseSensitive: true
+  # rest
+  - Regex: .*
+    Priority: 100
 SpaceBeforeAssignmentOperators: true
 SpaceBeforeParens: ControlStatements
 SpaceInEmptyParentheses: false

.clang-tidy

@@ -1,3 +1,21 @@
 CheckOptions:
-  - key: CheckPathRegex
-    value: '.*/O2/.*'
+  # Naming conventions
+  - { key: readability-identifier-naming.ClassCase, value: CamelCase }
+  - { key: readability-identifier-naming.ClassMemberPrefix, value: m }
+  - { key: readability-identifier-naming.ConceptCase, value: CamelCase }
+  - { key: readability-identifier-naming.ConstexprVariableCase, value: CamelCase }
+  - { key: readability-identifier-naming.EnumCase, value: CamelCase }
+  - { key: readability-identifier-naming.EnumConstantCase, value: CamelCase }
+  - { key: readability-identifier-naming.EnumConstantIgnoredRegexp, value: "^k?[A-Z][a-zA-Z0-9_]*$" }  # Allow "k" prefix and non-trailing underscores in PDG names.
+  - { key: readability-identifier-naming.FunctionCase, value: camelBack }
+  - { key: readability-identifier-naming.MacroDefinitionCase, value: UPPER_CASE }
+  - { key: readability-identifier-naming.MacroDefinitionIgnoredRegexp, value: "^[A-Z][A-Z0-9_]*_$" }  # Allow the trailing underscore in header guards.
+  - { key: readability-identifier-naming.MemberCase, value: camelBack }
+  - { key: readability-identifier-naming.NamespaceCase, value: lower_case }
+  - { key: readability-identifier-naming.ParameterCase, value: camelBack }
+  - { key: readability-identifier-naming.StructCase, value: CamelCase }
+  - { key: readability-identifier-naming.TemplateParameterCase, value: CamelCase }
+  - { key: readability-identifier-naming.TypeAliasCase, value: CamelCase }
+  - { key: readability-identifier-naming.TypedefCase, value: CamelCase }
+  - { key: readability-identifier-naming.TypeTemplateParameterCase, value: CamelCase }
+  - { key: readability-identifier-naming.VariableCase, value: camelBack }

.git-blame-ignore-revs

@@ -0,0 +1,10 @@
+---
+# Dependabot configuration
+# Reference: https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

.github/dependabot.yml

@@ -1,69 +1,89 @@
 ---
-alice3:
+infrastructure:
   - changed-files:
-      - any-glob-to-any-file: ['ALICE3/**']
+      - any-glob-to-any-file:
+          - ".checkov.yml"
+          - ".clang-format"
+          - ".clang-tidy"
+          - ".flake8"
+          - ".git-blame-ignore-revs"
+          - ".github/**"
+          - ".gitignore"
+          - ".mega-linter.yml"
+          - ".pre-commit-config.yaml"
+          - "cmake/**"
+          - "CMakeLists.txt"
+          - "CODEOWNERS"
+          - "COPYING"
+          - "cppcheck_config"
+          - "CPPLINT.cfg"
+          - "dependencies/**"
+          - "o2linter_config"
+          - "packaging/**"
+          - "pyproject.toml"
+          - "README.md"
 
-common:
+datamodel:
   - changed-files:
-      - any-glob-to-any-file: ['Common/**']
+      - any-glob-to-any-file: ["DataModel/**", "**/DataModel/**"]
 
-infrastructure:
+alice3:
   - changed-files:
-      - any-glob-to-any-file:
-          - '.clang-format'
-          - '.clang-tidy'
-          - '.flake8'
-          - '.github/**'
-          - '.checkov.yml'
-          - '.mega-linter.yml'
-          - '.pre-commit-config.yaml'
-          - 'cmake/**'
-          - 'CODEOWNERS'
-          - 'CPPLINT.cfg'
-          - 'dependencies/**'
-          - 'packaging/**'
-          - 'pyproject.toml'
+      - any-glob-to-any-file: ["ALICE3/**"]
 
-datamodel:
+common:
   - changed-files:
-      - any-glob-to-any-file: ['DataModel/**', '*/DataModel/**']
+      - any-glob-to-any-file: ["Common/**"]
 
 dpg:
   - changed-files:
-      - any-glob-to-any-file: ['DPG/**']
+      - any-glob-to-any-file: ["DPG/**"]
 
 pwgcf:
   - changed-files:
-      - any-glob-to-any-file: ['PWGCF/**', '*/PWGCF/**']
+      - any-glob-to-any-file: ["PWGCF/**", "*/PWGCF/**"]
 
 pwgdq:
   - changed-files:
-      - any-glob-to-any-file: ['PWGDQ/**', '*/PWGDQ/**']
+      - any-glob-to-any-file: ["PWGDQ/**", "*/PWGDQ/**"]
 
 pwgem:
   - changed-files:
-      - any-glob-to-any-file: ['PWGEM/**', '*/PWGEM/**']
+      - any-glob-to-any-file: ["PWGEM/**", "*/PWGEM/**"]
 
 pwghf:
   - changed-files:
-      - any-glob-to-any-file: ['PWGHF/**', '*/PWGHF/**']
+      - any-glob-to-any-file: ["PWGHF/**", "*/PWGHF/**"]
 
 pwgje:
   - changed-files:
-      - any-glob-to-any-file: ['PWGJE/**', '*/PWGJE/**']
+      - any-glob-to-any-file: ["PWGJE/**", "*/PWGJE/**"]
 
 pwglf:
   - changed-files:
-      - any-glob-to-any-file: ['PWGLF/**', '*/PWGLF/**', 'PWGMM/**', '*/PWGMM/**']
+      - any-glob-to-any-file:
+          ["PWGLF/**", "*/PWGLF/**", "PWGMM/**", "*/PWGMM/**"]
+
+pwgmm:
+  - changed-files:
+      - any-glob-to-any-file: ["PWGMM/**", "*/PWGMM/**"]
 
 pwgud:
   - changed-files:
-      - any-glob-to-any-file: ['PWGUD/**', '*/PWGUD/**']
+      - any-glob-to-any-file: ["PWGUD/**", "*/PWGUD/**"]
+
+scripts:
+  - changed-files:
+      - any-glob-to-any-file: ["Scripts/**"]
+
+tools:
+  - changed-files:
+      - any-glob-to-any-file: ["Tools/**"]
 
 trigger:
   - changed-files:
-      - any-glob-to-any-file: ['EventFiltering/**']
+      - any-glob-to-any-file: ["EventFiltering/**"]
 
 tutorial:
   - changed-files:
-      - any-glob-to-any-file: ['Tutorials/**']
+      - any-glob-to-any-file: ["Tutorials/**"]

.github/labeler.yml

@@ -16,7 +16,7 @@ jobs:
     steps:
       - name: Label the PR
         id: labeler
-        uses: actions/labeler@v5
+        uses: actions/labeler@v6
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           sync-labels: true
@@ -41,73 +41,73 @@ jobs:
           labels = os.environ['labels']
           tags = {
               "infrastructure": "Infrastructure",
+              "scripts": "Scripts",
+              "tools": "Tools",
               "common": "Common",
+              "trigger": "Trigger",
+              "dpg": "DPG",
+              "tutorial": "Tutorial",
               "alice3": "ALICE3",
               "pwgcf": "PWGCF",
               "pwgdq": "PWGDQ",
               "pwgem": "PWGEM",
               "pwghf": "PWGHF",
               "pwgje": "PWGJE",
               "pwglf": "PWGLF",
+              "pwgmm": "PWGMM",
               "pwgud": "PWGUD",
-              "dpg": "DPG",
-              "trigger": "Trigger",
-              "tutorial": "Tutorial",
           }
           print(f'PR title: "{title}"')
           print(f'PR labels: "{labels}"')
           tags_relevant = [tags[label] for label in tags if label in labels.split(",")]
           print("Relevant title tags:", ",".join(tags_relevant))
-          passed = True
-          prefix_good = ",".join(tags_relevant)
-          prefix_good = f"[{prefix_good}] "
-          print(f"Generated prefix: {prefix_good}")
-          replace_title = 0
-          title_new = title
+          prefix_generated = ",".join(tags_relevant)
+          prefix_generated = f"[{prefix_generated}] "
+          print(f"Generated prefix: {prefix_generated}")
+          found_tags = False
+          title_new = title.strip()
           # If there is a prefix which contains a known tag, check it for correct tags, and reformat it if needed.
           # If there is a prefix which does not contain any known tag, add the tag prefix.
           # If there is no prefix, add the tag prefix.
-          if match := re.match(r"\[?(\w[\w, /\+-]+)[\]:]+ ", title):
+          if match := re.match(r" *\[?(\w[\w,/\+\- ]+)[\]: ]+ ", title):
               prefix_title = match.group(1)
               words_prefix_title = prefix_title.replace(",", " ").replace("/", " ").split()
-              title_stripped = title[len(match.group()) :]
+              title_stripped = title[len(match.group()) :].strip()
               print(f'PR title prefix: "{prefix_title}" -> tags: {words_prefix_title}')
               print(f'Stripped PR title: "{title_stripped}"')
               if any(tag in words_prefix_title for tag in tags.values()):
+                  found_tags = True
+                  passed = True
                   for tag in tags.values():
                       if tag in tags_relevant and tag not in words_prefix_title:
                           print(f'::error::Relevant tag "{tag}" not found in the prefix of the PR title.')
                           passed = False
                       if tag not in tags_relevant and tag in words_prefix_title:
                           print(f'::error::Irrelevant tag "{tag}" found in the prefix of the PR title.')
                           passed = False
-                  # Format a valid prefix.
-                  if passed:
-                      prefix_good = ",".join(w for w in prefix_title.replace(",", " ").split() if w)
-                      prefix_good = f"[{prefix_good}] "
-                      print(f"::notice::Reformatted prefix: {prefix_good}")
-                      if match.group() != prefix_good:
-                          replace_title = 1
-                          title_new = prefix_good + title_stripped
+                  if not passed:
+                      print("::error::Problems were found in the PR title prefix.")
+                      print('::notice::Use the form "tags: title" or "[tags] title".')
+                      sys.exit(1)
+                  # Form a valid title with the existing prefix.
+                  prefix_good = ",".join(w for w in prefix_title.replace(",", " ").split() if w)
+                  prefix_good = f"[{prefix_good}] "
+                  print(f'::notice::Reformatted prefix: "{prefix_good}"')
+                  title_new = prefix_good + title_stripped
               else:
                   print("::warning::No known tags found in the prefix.")
-                  if tags_relevant:
-                      replace_title = 1
-                      title_new = prefix_good + title
+                  title_new = " ".join((*match.group().split(), title_stripped))
           else:
               print("::warning::No valid prefix found in the PR title.")
-              if tags_relevant:
-                  replace_title = 1
-                  title_new = prefix_good + title
-          if not passed:
-              print("::error::Problems were found in the PR title prefix.")
-              print('::notice::Use the form "tags: title" or "[tags] title".')
-              sys.exit(1)
-          if replace_title:
-              print("::warning::The PR title prefix with tags needs to be added or adjusted.")
-              print(f'::warning::New title: "{title_new}".')
+          if not found_tags and tags_relevant:
+              title_new = prefix_generated + title_new.strip()
+          replace_title = 0
+          if title_new == title:
+              print("::notice::The PR title is fine.")
           else:
-              print("::notice::The PR title prefix is fine.")
+              replace_title = 1
+              print("::warning::The PR title needs to be adjusted.")
+              print(f'::warning::New title: "{title_new}".')
           with open(os.environ["GITHUB_OUTPUT"], "a", encoding="utf-8") as fh:
               print(f"replace={replace_title}", file=fh)
               print(f"title={title_new}", file=fh)

.github/workflows/labeler.yml

@@ -23,7 +23,7 @@ jobs:
     steps:
       # Git Checkout
       - name: Checkout Code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           # Checkout the HEAD of the PR instead of the merge commit.
           ref: ${{ github.event.pull_request.head.sha }}
@@ -38,7 +38,7 @@ jobs:
         id: ml
         # You can override MegaLinter flavor used to have faster performances
         # More info at https://megalinter.io/flavors/
-        uses: oxsecurity/megalinter@v8.3.0
+        uses: oxsecurity/megalinter@v9.3.0
         env:
           # All available variables are described in documentation:
           # https://megalinter.io/configuration/
@@ -49,7 +49,7 @@ jobs:
 
       # Upload MegaLinter artifacts
       - name: Archive production artifacts
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         if: success() || failure()
         with:
           name: MegaLinter reports