Merge branch 'master' into feature-antin-cex-output-variables

Author: FabiolaLP

.clang-format

@@ -47,11 +47,11 @@ IncludeCategories:
     Priority: 2
     CaseSensitive: true
   # O2Physics, non-PWG
-  - Regex: ^(<|")(Common|ALICE3|DPG|EventFiltering|Tools|Tutorials)/.*\.h
+  - Regex: ^(<|")(Common|ALICE3|DPG|EventFiltering|PID|Tools|Tutorials)/.*\.h
     Priority: 3
     CaseSensitive: true
   # O2
-  - Regex: ^(<|")(Algorithm|CCDB|Common[A-Z]|DataFormats|DCAFitter|Detectors|EMCAL|FDD|Field|Framework|FT0|FV0|GlobalTracking|GPU|ITS|MathUtils|MCH|MFT|MID|PHOS|PID|ReconstructionDataFormats|SimulationDataFormat|TOF|TPC|ZDC).*/.*\.h
+  - Regex: ^(<|")(Algorithm|CCDB|Common[A-Z]|DataFormats|DCAFitter|Detectors|EMCAL|FDD|Field|Framework|FT0|FV0|GlobalTracking|GPU|ITS|MathUtils|MCH|MFT|MID|PHOS|ReconstructionDataFormats|SimulationDataFormat|TOF|TPC|ZDC).*/.*\.h
     Priority: 4
     CaseSensitive: true
   # ROOT
@@ -93,6 +93,7 @@ IncludeCategories:
   # rest
   - Regex: .*
     Priority: 100
+    CaseSensitive: true
 SpaceBeforeAssignmentOperators: true
 SpaceBeforeParens: ControlStatements
 SpaceInEmptyParentheses: false

.clang-tidy

@@ -1,21 +1,146 @@
+---
+Checks:
+  # - clang-analyzer-* # enabled by default
+  # - clang-diagnostic-* # enabled by default
+  - -clang-diagnostic-unknown-pragmas
+  - bugprone-*
+  - -bugprone-assert-side-effect
+  - -bugprone-bad-signal-to-kill-thread
+  - -bugprone-bitwise-pointer-cast
+  - -bugprone-bool-pointer-implicit-conversion
+  - -bugprone-compare-pointer-to-member-virtual-function
+  - -bugprone-crtp-constructor-accessibility
+  - -bugprone-easily-swappable-parameters # Too sensitive
+  - -bugprone-forwarding-reference-overload
+  - -bugprone-implicit-widening-of-multiplication-result # Specific cases irrelevant in this repo
+  - -bugprone-lambda-function-name
+  - -bugprone-no-escape
+  - -bugprone-posix-return
+  - -bugprone-signal-handler
+  - -bugprone-signed-char-misuse # Specific use cases. Probably very rare.
+  - -bugprone-spuriously-wake-up-functions
+  - -bugprone-suspicious-stringview-data-usage # Probably harmless in this repo
+  - -bugprone-unused-raii
+  - cppcoreguidelines-avoid-const-or-ref-data-members
+  - cppcoreguidelines-avoid-goto
+  - cppcoreguidelines-avoid-non-const-global-variables
+  - cppcoreguidelines-init-variables
+  - cppcoreguidelines-macro-usage
+  - cppcoreguidelines-misleading-capture-default-by-value
+  - cppcoreguidelines-missing-std-forward
+  - cppcoreguidelines-prefer-member-initializer
+  - cppcoreguidelines-pro-bounds-array-to-pointer-decay
+  - cppcoreguidelines-pro-type-const-cast
+  - cppcoreguidelines-pro-type-cstyle-cast
+  - cppcoreguidelines-pro-type-member-init
+  - cppcoreguidelines-pro-type-reinterpret-cast
+  - cppcoreguidelines-pro-type-static-cast-downcast
+  - cppcoreguidelines-pro-type-union-access
+  - cppcoreguidelines-rvalue-reference-param-not-moved
+  - cppcoreguidelines-slicing
+  - cppcoreguidelines-virtual-class-destructor
+  - google-default-arguments
+  # - google-explicit-constructor # triggered for O2 columns
+  - google-global-names-in-headers
+  # - misc-const-correctness # to be checked
+  - misc-header-include-cycle
+  - misc-include-cleaner
+  - misc-misplaced-const
+  - misc-redundant-expression
+  - misc-unconventional-assign-operator
+  - misc-unused-alias-decls
+  - misc-unused-parameters
+  - misc-unused-using-decls
+  - modernize-avoid-bind
+  - modernize-avoid-c-arrays
+  - modernize-concat-nested-namespaces
+  - modernize-deprecated-headers
+  - modernize-make-shared
+  - modernize-make-unique
+  - modernize-redundant-void-arg
+  - modernize-return-braced-init-list
+  - modernize-use-auto
+  - modernize-use-default-member-init
+  - modernize-use-designated-initializers
+  - modernize-use-equals-default
+  - modernize-use-equals-delete
+  - modernize-use-nodiscard
+  - modernize-use-nullptr
+  - modernize-use-override
+  - modernize-use-starts-ends-with
+  - performance-for-range-copy
+  - performance-implicit-conversion-in-loop
+  - performance-inefficient-algorithm
+  - performance-inefficient-string-concatenation
+  - performance-inefficient-vector-operation
+  - performance-move-const-arg
+  - performance-no-automatic-move
+  - performance-trivially-destructible
+  - performance-type-promotion-in-math-fn
+  - performance-unnecessary-copy-initialization
+  - performance-unnecessary-value-param # slow
+  - readability-avoid-unconditional-preprocessor-if
+  - readability-braces-around-statements
+  - readability-const-return-type
+  - readability-container-contains
+  - readability-container-data-pointer
+  - readability-container-size-empty
+  - readability-delete-null-pointer
+  - readability-duplicate-include
+  - readability-else-after-return
+  - readability-enum-initial-value
+  - readability-implicit-bool-conversion
+  - readability-inconsistent-declaration-parameter-name
+  - readability-misplaced-array-index
+  - readability-non-const-parameter
+  - readability-redundant-access-specifiers
+  - readability-redundant-casting
+  - readability-redundant-control-flow
+  - readability-redundant-declaration
+  - readability-redundant-member-init
+  - readability-redundant-preprocessor
+  - readability-redundant-string-cstr
+  - readability-redundant-string-init
+  - readability-reference-to-constructed-temporary
+  - readability-simplify-boolean-expr
+  - readability-static-definition-in-anonymous-namespace
+  - readability-string-compare
+  - readability-suspicious-call-argument
+# Select which of the enabled checks should be reported as errors instead of warnings.
+WarningsAsErrors: >-
+  *,
+  -readability-braces-around-statements,
+  -readability-suspicious-call-argument,
+  -modernize-*,
+  -readability-*,
 CheckOptions:
+  modernize-avoid-c-arrays.AllowStringArrays: true
+  # Common tolerated conversions
+  bugprone-narrowing-conversions.WarnOnFloatingPointNarrowingConversion: false
+  bugprone-narrowing-conversions.WarnOnIntegerNarrowingConversion: false
+  bugprone-narrowing-conversions.WarnOnIntegerToFloatingPointNarrowingConversion: false
+  readability-implicit-bool-conversion.AllowLogicalOperatorConversion: true
+  readability-implicit-bool-conversion.AllowPointerConditions: true
+  # Some data model structs are missing some special functions by design.
+  cppcoreguidelines-special-member-functions.AllowMissingMoveFunctions: true
   # 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 }
+  readability-identifier-naming.ClassCase: CamelCase
+  readability-identifier-naming.ClassMemberPrefix: m
+  readability-identifier-naming.ConceptCase: CamelCase
+  readability-identifier-naming.ConstexprVariableCase: CamelCase
+  readability-identifier-naming.EnumCase: CamelCase
+  readability-identifier-naming.EnumConstantCase: CamelCase
+  readability-identifier-naming.EnumConstantIgnoredRegexp: "^k?[A-Z][a-zA-Z0-9_]*$" # Allow "k" prefix and non-trailing underscores in PDG names.
+  readability-identifier-naming.FunctionCase: camelBack
+  readability-identifier-naming.MacroDefinitionCase: UPPER_CASE
+  readability-identifier-naming.MacroDefinitionIgnoredRegexp: "^[A-Z][A-Z0-9_]*_$" # Allow the trailing underscore in header guards.
+  readability-identifier-naming.MemberCase: camelBack
+  readability-identifier-naming.NamespaceCase: lower_case
+  readability-identifier-naming.ParameterCase: camelBack
+  readability-identifier-naming.StructCase: CamelCase
+  readability-identifier-naming.TemplateParameterCase: CamelCase
+  readability-identifier-naming.TypeAliasCase: CamelCase
+  readability-identifier-naming.TypedefCase: CamelCase
+  readability-identifier-naming.TypeTemplateParameterCase: CamelCase
+  readability-identifier-naming.VariableCase: camelBack
+...

.github/workflows/labeler.yml

@@ -16,7 +16,7 @@ jobs:
     steps:
       - name: Label the PR
         id: labeler
-        uses: actions/labeler@v6
+        uses: actions/labeler@v7
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           sync-labels: true

.github/workflows/mega-linter.yml

@@ -23,7 +23,7 @@ jobs:
     steps:
       # Git Checkout
       - name: Checkout Code
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
         with:
           # Checkout the HEAD of the PR instead of the merge commit.
           ref: ${{ github.event.pull_request.head.sha }}
@@ -32,13 +32,14 @@ jobs:
           fetch-depth: 0
           # So we can use secrets.ALIBUILD_GITHUB_TOKEN to push later.
           persist-credentials: false
+          allow-unsafe-pr-checkout: true # needed for pull_request_target
 
       # MegaLinter
       - name: MegaLinter
         id: ml
         # You can override MegaLinter flavor used to have faster performances
         # More info at https://megalinter.io/flavors/
-        uses: oxsecurity/megalinter@v9.4.0
+        uses: oxsecurity/megalinter@v10.0.0
         env:
           # All available variables are described in documentation:
           # https://megalinter.io/configuration/

.github/workflows/o2-linter.yml

@@ -30,10 +30,11 @@ jobs:
           echo BRANCH_HEAD="$branch_head" >> "$GITHUB_ENV"
           echo BRANCH_BASE="$branch_base" >> "$GITHUB_ENV"
       - name: Checkout Code
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
         with:
           ref: ${{ env.BRANCH_HEAD }}
           fetch-depth: 0 # needed to get the full history
+          allow-unsafe-pr-checkout: true # needed for pull_request_target
       - name: Run tests
         id: linter
         run: |

.github/workflows/stale.yml

@@ -13,7 +13,7 @@ jobs:
   stale:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/stale@v10
+      - uses: actions/stale@v11
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           stale-pr-message: 'This PR has not been updated in the last 30 days. Is it still needed? Unless further action is taken, it will be closed in 5 days.'

.mega-linter.yml

@@ -19,13 +19,13 @@ DISABLE_LINTERS:
   - PYTHON_FLAKE8
   - PYTHON_ISORT
   - REPOSITORY_DEVSKIM
-  - REPOSITORY_GITLEAKS
-  - REPOSITORY_KICS
+  - REPOSITORY_OSV_SCANNER
   - REPOSITORY_SECRETLINT
   - REPOSITORY_TRIVY
   - YAML_PRETTIER
   - YAML_V8R
 DISABLE_ERRORS_LINTERS: # If errors are found by these linters, they will be considered as non blocking.
+  - ACTION_ZIZMOR
   - PYTHON_BANDIT # The bandit check is overly broad and complains about subprocess usage.
 SHOW_ELAPSED_TIME: true
 FILEIO_REPORTER: false
@@ -40,5 +40,5 @@ PYTHON_RUFF_CONFIG_FILE: pyproject.toml
 CPP_CPPLINT_FILE_EXTENSIONS: [".C", ".c", ".c++", ".cc", ".cl", ".cpp", ".cu", ".cuh", ".cxx", ".cxx.in", ".h", ".h++", ".hh", ".h.in", ".hpp", ".hxx", ".inc", ".inl", ".macro"]
 CPP_CLANG_FORMAT_FILE_EXTENSIONS: [".C", ".c", ".c++", ".cc", ".cl", ".cpp", ".cu", ".cuh", ".cxx", ".cxx.in", ".h", ".h++", ".hh", ".h.in", ".hpp", ".hxx", ".inc", ".inl", ".macro"]
 CPP_CPPCHECK_FILE_EXTENSIONS: [".C", ".c", ".c++", ".cc", ".cl", ".cpp", ".cu", ".cuh", ".cxx", ".cxx.in", ".h", ".h++", ".hh", ".h.in", ".hpp", ".hxx", ".inc", ".inl", ".macro"]
-CPP_CPPCHECK_ARGUMENTS: --language=c++ --std=c++20 --check-level=exhaustive --suppressions-list=cppcheck_config
-REPOSITORY_GITLEAKS_PR_COMMITS_SCAN: true
+CPP_CPPCHECK_ARGUMENTS: --language=c++ --std=c++20 --enable=style --check-level=exhaustive --suppressions-list=cppcheck_suppressions --inline-suppr --force
+ACTION_ZIZMOR_UNSECURED_ENV_VARIABLES: [GITHUB_TOKEN]

ALICE3/CMakeLists.txt

@@ -12,6 +12,7 @@
 
 add_subdirectory(Core)
 # add_subdirectory(DataModel)
+add_subdirectory(ML)
 add_subdirectory(Tasks)
 add_subdirectory(TableProducer)
 add_subdirectory(Macros)

ALICE3/Core/Decayer.h

@@ -19,6 +19,7 @@
 #ifndef ALICE3_CORE_DECAYER_H_
 #define ALICE3_CORE_DECAYER_H_
 
+#include "ALICE3/Core/OTFParticle.h"
 #include "ALICE3/Core/TrackUtilities.h"
 
 #include <CommonConstants/PhysicsConstants.h>
@@ -60,28 +61,27 @@ class Decayer
     const double ctau = o2::constants::physics::LightSpeedCm2S * particleInfo->Lifetime(); // cm
     const double betaGamma = particle.p() / mass;
     const double rxyz = -betaGamma * ctau * std::log(1 - u);
-    double vx, vy, vz;
     double px, py, e;
 
     if (!charge) {
-      vx = particle.vx() + rxyz * (particle.px() / particle.p());
-      vy = particle.vy() + rxyz * (particle.py() / particle.p());
-      vz = particle.vz() + rxyz * (particle.pz() / particle.p());
+      mVx = particle.vx() + rxyz * (particle.px() / particle.p());
+      mVy = particle.vy() + rxyz * (particle.py() / particle.p());
+      mVz = particle.vz() + rxyz * (particle.pz() / particle.p());
       px = particle.px();
       py = particle.py();
     } else {
       o2::track::TrackParCov track;
       o2::math_utils::CircleXYf_t circle;
       o2::upgrade::convertOTFParticleToO2Track(particle, track, pdgDB);
 
-      float sna, csa;
+      float sna{}, csa{};
       track.getCircleParams(mBz, circle, sna, csa);
       const double rxy = rxyz / std::sqrt(1. + track.getTgl() * track.getTgl());
       const double theta = rxy / circle.rC;
 
-      vx = ((particle.vx() - circle.xC) * std::cos(theta) - (particle.vy() - circle.yC) * std::sin(theta)) + circle.xC;
-      vy = ((particle.vy() - circle.yC) * std::cos(theta) + (particle.vx() - circle.xC) * std::sin(theta)) + circle.yC;
-      vz = particle.vz() + rxyz * (particle.pz() / track.getP());
+      mVx = ((particle.vx() - circle.xC) * std::cos(theta) - (particle.vy() - circle.yC) * std::sin(theta)) + circle.xC;
+      mVy = ((particle.vy() - circle.yC) * std::cos(theta) + (particle.vx() - circle.xC) * std::sin(theta)) + circle.yC;
+      mVz = particle.vz() + rxyz * (particle.pz() / track.getP());
 
       px = particle.px() * std::cos(theta) - particle.py() * std::sin(theta);
       py = particle.py() * std::cos(theta) + particle.px() * std::sin(theta);
@@ -124,25 +124,33 @@ class Decayer
       o2::upgrade::OTFParticle particle;
       TLorentzVector dau = *decay.GetDecay(i);
       particle.setPDG(pdgCodesDaughters[i]);
-      particle.setVxVyVz(vx, vy, vz);
+      particle.setVxVyVz(mVx, mVy, mVz);
       particle.setPxPyPzE(dau.Px(), dau.Py(), dau.Pz(), dau.E());
+      particle.setBitOn(o2::upgrade::DecayerBits::ProducedByDecayer);
       decayProducts.push_back(particle);
     }
 
     return decayProducts;
   }
 
+  // Setters
+  void setBField(const double b) { mBz = b; }
   void setSeed(const int seed)
   {
     mRand3.SetSeed(seed);   // For decay length sampling
     gRandom->SetSeed(seed); // For TGenPhaseSpace
   }
 
-  void setBField(const double b) { mBz = b; }
+  // Getters
+  float getSecondaryVertexX() const { return static_cast<float>(mVx); }
+  float getSecondaryVertexY() const { return static_cast<float>(mVy); }
+  float getSecondaryVertexZ() const { return static_cast<float>(mVz); }
+  float getDecayRadius() const { return static_cast<float>(std::hypot(mVx, mVy)); }
 
  private:
-  TRandom3 mRand3;
-  double mBz;
+  double mBz{20.}; // kG
+  double mVx{-1.}, mVy{-1.}, mVz{-1.};
+  TRandom3 mRand3{};
 };
 
 } // namespace upgrade