Test O2 linter

.checkov.yml

@@ -0,0 +1,6 @@
+---
+# You can see all available properties here: https://github.com/bridgecrewio/checkov#configuration-using-a-config-file
+quiet: true
+skip-check:
+  - CKV_DOCKER_2
+  - CKV_GHA_7

.clang-format

@@ -24,6 +24,7 @@ ExperimentalAutoDetectBinPacking: false
 IndentCaseLabels: true
 IndentFunctionDeclarationAfterType: true
 IndentWidth:     2
+InsertNewlineAtEOF: true
 # It is broken on windows. Breaks all #include "header.h"
 ---
 Language:        Cpp

.github/labeler.yml

@@ -0,0 +1,68 @@
+---
+alice3:
+  - changed-files:
+      - any-glob-to-any-file: ['ALICE3/**']
+
+common:
+  - changed-files:
+      - any-glob-to-any-file: ['Common/**']
+
+infrastructure:
+  - changed-files:
+      - any-glob-to-any-file:
+          - '.clang-format'
+          - '.clang-tidy'
+          - '.flake8'
+          - '.github/**'
+          - '.checkov.yml'
+          - '.mega-linter.yml'
+          - 'cmake/**'
+          - 'CODEOWNERS'
+          - 'CPPLINT.cfg'
+          - 'dependencies/**'
+          - 'packaging/**'
+          - 'pyproject.toml'
+
+datamodel:
+  - changed-files:
+      - any-glob-to-any-file: ['DataModel/**', '*/DataModel/**']
+
+dpg:
+  - changed-files:
+      - any-glob-to-any-file: ['DPG/**']
+
+pwgcf:
+  - changed-files:
+      - any-glob-to-any-file: ['PWGCF/**', '*/PWGCF/**']
+
+pwgdq:
+  - changed-files:
+      - any-glob-to-any-file: ['PWGDQ/**', '*/PWGDQ/**']
+
+pwgem:
+  - changed-files:
+      - any-glob-to-any-file: ['PWGEM/**', '*/PWGEM/**']
+
+pwghf:
+  - changed-files:
+      - any-glob-to-any-file: ['PWGHF/**', '*/PWGHF/**']
+
+pwgje:
+  - changed-files:
+      - any-glob-to-any-file: ['PWGJE/**', '*/PWGJE/**']
+
+pwglf:
+  - changed-files:
+      - any-glob-to-any-file: ['PWGLF/**', '*/PWGLF/**', 'PWGMM/**', '*/PWGMM/**']
+
+pwgud:
+  - changed-files:
+      - any-glob-to-any-file: ['PWGUD/**', '*/PWGUD/**']
+
+trigger:
+  - changed-files:
+      - any-glob-to-any-file: ['EventFiltering/**']
+
+tutorial:
+  - changed-files:
+      - any-glob-to-any-file: ['Tutorials/**']

.github/workflows/clean-test.yml

@@ -0,0 +1,51 @@
+---
+name: Clean PR checks
+
+'on':
+  workflow_dispatch:
+    inputs:
+      pr:
+        description: PR number in this repo to be cleaned
+        type: string   # can't use number here
+        required: true
+      message:
+        description: Human-readable message displayed on the new pending status
+        type: string
+        required: false
+        default: ''
+
+      # Warning: GitHub limits the total number of inputs to 10, so a maximum of
+      # 8 checks is allowed here!
+      # Warning: the check_* keys are magic and must consist of the string
+      # "check_" followed by the applicable check name exactly. The
+      # "description" field is only the human-readable label for the input.
+      'check_build/O2Physics/o2/macOS-arm':
+        description: build/O2Physics/o2/macOS-arm
+        type: boolean
+        default: true
+
+      'check_build/O2Physics/o2/macOS':
+        description: build/O2Physics/o2/macOS
+        type: boolean
+        default: true
+
+      'check_build/O2Physics/o2':
+        description: build/O2Physics/o2
+        type: boolean
+        default: true
+
+permissions: {}
+
+jobs:
+  clean:
+    name: Clean PR checks
+    uses: alisw/ali-bot/.github/workflows/clean-pr-checks.yml@master
+    with:
+      owner: ${{ github.event.repository.owner.login }}
+      repo: ${{ github.event.repository.name }}
+      pr: ${{ github.event.inputs.pr }}
+      message: ${{ github.event.inputs.message }}
+      checks: ${{ toJSON(github.event.inputs) }}
+    permissions:
+      pull-requests: read  # to get last commit for pr (octokit/graphql-action)
+      statuses: write      # for set-github-status

.github/workflows/codeowner-self-approval.yml

@@ -13,7 +13,7 @@ permissions:
 
 jobs:
   approve:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     # Only run if the PR author enabled auto-merge, not someone else.
     # Also run if a new approval was created, as this affects whether we can
     # auto-approve. There is a risk of infinite loops here, though -- when we

.github/workflows/labeler.yml

@@ -0,0 +1,122 @@
+---
+name: "Pull Request Labeler"
+'on':
+  pull_request_target:
+    types: [opened, synchronize, reopened, edited]
+permissions: read-all
+
+jobs:
+  labeler:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      pull-requests: write
+    outputs:
+      labels: ${{ steps.labeler.outputs.all-labels }}
+    steps:
+      - name: Label the PR
+        id: labeler
+        uses: actions/labeler@v5
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          sync-labels: true
+  title-prefix-checker:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      pull-requests: write
+    needs: labeler
+    steps:
+      - name: Check the PR title prefix
+        id: check-prefix
+        env:
+          title: ${{ github.event.pull_request.title }}
+          labels: ${{ needs.labeler.outputs.labels }}
+        shell: python
+        run: |
+          import os
+          import re
+          import sys
+          title = os.environ['title']
+          labels = os.environ['labels']
+          tags = {
+              "infrastructure": "Infrastructure",
+              "common": "Common",
+              "alice3": "ALICE3",
+              "pwgcf": "PWGCF",
+              "pwgdq": "PWGDQ",
+              "pwgem": "PWGEM",
+              "pwghf": "PWGHF",
+              "pwgje": "PWGJE",
+              "pwglf": "PWGLF",
+              "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
+          # 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):
+              prefix_title = match.group(1)
+              words_prefix_title = prefix_title.replace(",", " ").replace("/", " ").split()
+              title_stripped = title[len(match.group()) :]
+              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()):
+                  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
+              else:
+                  print("::warning::No known tags found in the prefix.")
+                  if tags_relevant:
+                      replace_title = 1
+                      title_new = prefix_good + title
+          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}".')
+          else:
+              print("::notice::The PR title prefix is fine.")
+          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)
+      - name: Fix the PR title prefix
+        if: ${{ steps.check-prefix.outputs.replace == 1 }}
+        uses: the-wright-jamie/[email protected]
+        with:
+          repo-token: "${{ secrets.GITHUB_TOKEN }}"
+          base-branch-regex: master
+          error-on-fail: false
+          title-template: "${{ steps.check-prefix.outputs.title }}"
+          title-update-action: replace

.github/workflows/mega-linter.yml

@@ -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@v7
+        uses: oxsecurity/megalinter@v8.1.0
         env:
           # All available variables are described in documentation:
           # https://megalinter.io/configuration/
@@ -47,6 +47,16 @@ jobs:
           VALIDATE_ALL_CODEBASE: false
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
+      # Upload MegaLinter artifacts
+      - name: Archive production artifacts
+        uses: actions/upload-artifact@v4
+        if: success() || failure()
+        with:
+          name: MegaLinter reports
+          path: |
+            megalinter-reports
+            mega-linter.log
+
       # Create or delete the cleanup branch
       - name: Update cleanup branch
         if: ${{ github.event.repository.owner.login == 'AliceO2Group' }}

.github/workflows/o2-linter.yml

@@ -0,0 +1,30 @@
+---
+# Find issues in O2 code
+name: O2 linter
+
+'on': [pull_request, push]
+permissions: {}
+env:
+  MAIN_BRANCH: master
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  o2-linter:
+    name: O2 linter
+    runs-on: ubuntu-24.04
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # needed to get the full history
+      - name: Run tests
+        run: |
+          # Diff against the common ancestor of the source branch and the main branch.
+          readarray -t files < <(git diff --diff-filter d --name-only origin/${{ env.MAIN_BRANCH }}...)
+          [ ${{ github.event_name }} == 'pull_request' ] && options="-g"
+          # shellcheck disable=SC2086 # Ignore unquoted options.
+          python3 Scripts/o2_linter.py $options "${files[@]}"
+          echo "Tip: If you allow actions in your fork repository, O2 linter will run when you push commits."

ALICE3/Core/CMakeLists.txt

@@ -15,6 +15,14 @@ o2physics_add_library(ALICE3Core
                       PUBLIC_LINK_LIBRARIES O2::Framework O2Physics::AnalysisCore)
 
 o2physics_target_root_dictionary(ALICE3Core
-                                 HEADERS TOFResoALICE3.h
-                                         DelphesO2TrackSmearer.h
-                                 LINKDEF ALICE3CoreLinkDef.h)
+                      HEADERS TOFResoALICE3.h
+                              DelphesO2TrackSmearer.h
+                      LINKDEF ALICE3CoreLinkDef.h)
+
+o2physics_add_library(FastTracker
+                      SOURCES FastTracker.cxx
+                      PUBLIC_LINK_LIBRARIES O2::Framework O2Physics::AnalysisCore)
+
+o2physics_target_root_dictionary(FastTracker
+                      HEADERS FastTracker.h
+                      LINKDEF FastTrackerLinkDef.h)

ALICE3/Core/DetLayer.h

@@ -0,0 +1,52 @@
+// Copyright 2019-2020 CERN and copyright holders of ALICE O2.
+// See https://alice-o2.web.cern.ch/copyright for details of the copyright holders.
+// All rights not expressly granted are reserved.
+//
+// This software is distributed under the terms of the GNU General Public
+// License v3 (GPL Version 3), copied verbatim in the file "COPYING".
+//
+// In applying this license CERN does not waive the privileges and immunities
+// granted to it by virtue of its status as an Intergovernmental Organization
+// or submit itself to any jurisdiction.
+
+///
+/// \file   DetLayer.h
+/// \author David Dobrigkeit Chinellato
+/// \since  11/03/2021
+/// \brief  Basic struct to hold information regarding a detector layer to be used in fast simulation
+///
+
+#ifndef ALICE3_CORE_DETLAYER_H_
+#define ALICE3_CORE_DETLAYER_H_
+
+#include "TString.h"
+
+namespace o2::fastsim
+{
+
+struct DetLayer {
+  // TString for holding name
+  TString name;
+
+  // position variables
+  float r; // radius in centimeters
+  float z; // z dimension in centimeters
+
+  // material variables
+  float x0;   // radiation length
+  float xrho; // density
+
+  // resolution variables for active layers
+  float resRPhi; // RPhi resolution in centimeters
+  float resZ;    // Z resolution in centimeters
+
+  // efficiency
+  float eff; // detection efficiency
+
+  // layer type
+  int type; // 0: undefined/inert, 1: silicon, 2: gas/tpc
+};
+
+} // namespace o2::fastsim
+
+#endif // ALICE3_CORE_DETLAYER_H_