Merge branch 'main' into mx2-and-yh

JeffersonLab · Dec 12, 2024 · afd8ad6 · afd8ad6
2 parents 8a2095a + 25e852b
commit afd8ad6
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -389,7 +389,7 @@ jobs:
             -Dtest_data_file=$(pwd)/test_data.hipo       \
             -Dtest_num_events=${{ env.num_events }}      \
             -Dtest_output_dir=$(pwd)/validation_results  \
-            -Dtest_multithreading=${{ env.num_threads }} \
+            -Dtest_num_threads=${{ env.num_threads }}    \
             ${{ matrix.opts }}
       - name: dump all build options
         run: meson configure iguana_build --no-pager
@@ -413,6 +413,7 @@ jobs:
       - run: tree iguana
       ### run tests
       - name: meson test
+        if: ${{ matrix.id != 'documentation' }}
         working-directory: iguana_build
         run: |
           if [ "${{ env.verbose_test }}" = "true" ]; then
@@ -423,26 +424,26 @@ jobs:
           fi
       ### run benchmarks
       - name: benchmark algorithms
-        if: ${{ matrix.id == 'coverage' }} # use the coverage job's GITHUB_STEP_SUMMARY
+        if: ${{ matrix.id == 'cpp' && inputs.id == 'linux-latest' }}
         run: |
           for suite in single_threaded memoize; do
             meson test --benchmark --suite $suite -C iguana_build | tee benchmark_$suite.txt
           done
           iguana_src/.github/make-benchmark-table.rb benchmark_{single_threaded,memoize}.txt | xargs -0 -I{} echo {} >> $GITHUB_STEP_SUMMARY
       ### coverage
-      # - name: coverage
-      #   if: ${{ matrix.id == 'coverage' }}
-      #   run: |
-      #     ninja -C iguana_build coverage-html
-      #     ninja -C iguana_build coverage-text
-      #     mv iguana_build/meson-logs/coveragereport coverage-report
-      #     echo '### Coverage Report' >> $GITHUB_STEP_SUMMARY
-      #     echo '```' >> $GITHUB_STEP_SUMMARY
-      #     cat iguana_build/meson-logs/coverage.txt >> $GITHUB_STEP_SUMMARY
-      #     echo '```' >> $GITHUB_STEP_SUMMARY
-      #     echo '' >> $GITHUB_STEP_SUMMARY
-      #     echo '- for details, see the `coverage-report` artifact' >> $GITHUB_STEP_SUMMARY
-      #     echo '- to compare to the report from the `main` branch, see <https://jeffersonlab.github.io/iguana/coverage-report>' >> $GITHUB_STEP_SUMMARY
+      - name: coverage
+        if: ${{ matrix.id == 'coverage' }}
+        run: |
+          ninja -C iguana_build coverage-html
+          ninja -C iguana_build coverage-text
+          mv iguana_build/meson-logs/coveragereport coverage-report
+          echo '### Coverage Report' >> $GITHUB_STEP_SUMMARY
+          echo '```' >> $GITHUB_STEP_SUMMARY
+          cat iguana_build/meson-logs/coverage.txt >> $GITHUB_STEP_SUMMARY
+          echo '```' >> $GITHUB_STEP_SUMMARY
+          echo '' >> $GITHUB_STEP_SUMMARY
+          echo '- for details, see the `coverage-report` artifact' >> $GITHUB_STEP_SUMMARY
+          echo '- to compare to the report from the `main` branch, see <https://jeffersonlab.github.io/iguana/coverage-report>' >> $GITHUB_STEP_SUMMARY
       ### test relocatability
       - name: test relocatability
         if: ${{ matrix.id == 'cpp' }} # don't bother re-running santizers, etc.
@@ -511,13 +512,13 @@ jobs:
           name: meson_logs_${{ matrix.id }}
           retention-days: 5
           path: iguana_build/meson-logs
-      # - name: upload coverage artifacts
-      #   uses: actions/upload-artifact@v4
-      #   if: ${{ matrix.id == 'coverage' }}
-      #   with:
-      #     name: coverage-report
-      #     retention-days: 5
-      #     path: coverage-report
+      - name: upload coverage artifacts
+        uses: actions/upload-artifact@v4
+        if: ${{ matrix.id == 'coverage' }}
+        with:
+          name: coverage-report
+          retention-days: 5
+          path: coverage-report
       - name: upload validator artifacts
         uses: actions/upload-artifact@v4
         if: ${{ matrix.id == 'cpp' }}
@@ -551,18 +552,18 @@ jobs:
         with:
           name: doc_doxygen
           path: doxygen
-      # - name: download coverage report
-      #   uses: actions/download-artifact@v4
-      #   with:
-      #     name: coverage-report
-      #     path: coverage-report
+      - name: download coverage report
+        uses: actions/download-artifact@v4
+        with:
+          name: coverage-report
+          path: coverage-report
       - run: tree
       - name: collect
         run: |
           mkdir pages
           cp iguana_src/.github/pages-index.html pages/index.html
           mv doxygen pages/
-      # - run: mv coverage-report pages/
+      - run: mv coverage-report pages/
       - run: tree
       - uses: actions/upload-pages-artifact@v3
         with:

diff --git a/.github/workflows/linux.yml b/.github/workflows/linux.yml
@@ -36,7 +36,7 @@ jobs:
           ],
           "include": [
             { "id": "cpp",                 "CC": "gcc",   "CXX": "g++",     "opts": "-Dbuildtype=release -Dz_require_root=true   -Dtest_validator_all_stats=true"  },
-            { "id": "coverage",            "CC": "gcc",   "CXX": "g++",     "opts": "-Dbuildtype=release -Dz_require_root=true   -Db_coverage=true"     },
+            { "id": "coverage",            "CC": "gcc",   "CXX": "g++",     "opts": "-Dbuildtype=release -Dz_require_root=true   -Db_coverage=true  -Dz_test_multithreading=false" },
             { "id": "documentation",       "CC": "gcc",   "CXX": "g++",     "opts": "-Dbuildtype=release -Dz_require_root=true   -Dinstall_documentation=true" },
             { "id": "address-sanitizer",   "CC": "clang", "CXX": "clang++", "opts": "-Dbuildtype=debug   -Dz_require_root=true   -Db_sanitize=address   -Db_lundef=false -Db_pie=true" },
             { "id": "thread-sanitizer",    "CC": "clang", "CXX": "clang++", "opts": "-Dbuildtype=debug   -Dz_require_root=true   -Db_sanitize=thread    -Db_lundef=false -Db_pie=true" },

diff --git a/meson.options b/meson.options
@@ -11,9 +11,10 @@ option('test_data_file',           type: 'string',  value: '',    description: '
 option('test_num_events',          type: 'string',  value: '10',  description: 'Number of events from `test_data_file` to test')
 option('test_output_dir',          type: 'string',  value: '',    description: 'Output directory for tests. Must be an absolute path. If unspecified, tests will still run, but will not produce output files.')
 option('test_validator_all_stats', type: 'boolean', value: false, description: 'If true, use all statistics for validators, rather than `test_num_events`')
-option('test_multithreading',      type: 'integer', value: 4, min: 0, description: 'run multithreading tests with this many threads (use 0 for hardware max)')
+option('test_num_threads',         type: 'integer', value: 4, min: 0, description: 'run multithreading tests with this many threads (use 0 for hardware max)')
 
 # expert options: the defaults should be reasonable for a local installation; different values may be preferred for installation in common areas
 option('z_install_envfile',     type: 'boolean', value: true,  description: 'Install a sourceable environment variable file')
 option('z_require_root',        type: 'boolean', value: false, description: 'Fail if ROOT is not found')
 option('z_require_rcdb',        type: 'boolean', value: false, description: 'Fail if RCDB is not found')
+option('z_test_multithreading', type: 'boolean', value: true,  description: 'Enable multithreading tests')
diff --git a/meson/ubsan.supp b/meson/ubsan.supp
@@ -1,6 +1,16 @@
 # https://github.com/gavalian/hipo/issues/49
-alignment:hipo::structure::getFloatAt
+alignment:hipo::structure::getIntAt
 alignment:hipo::structure::getShortAt
+alignment:hipo::structure::getByteAt
+alignment:hipo::structure::getFloatAt
 alignment:hipo::structure::getDoubleAt
-alignment:hipo::structure::putDoubleAt
+alignment:hipo::structure::getLongAt
+alignment:hipo::structure::getStringAt
+
 alignment:hipo::structure::putIntAt
+alignment:hipo::structure::putShortAt
+alignment:hipo::structure::putByteAt
+alignment:hipo::structure::putFloatAt
+alignment:hipo::structure::putDoubleAt
+alignment:hipo::structure::putLongAt
+alignment:hipo::structure::putStringAt
diff --git a/src/iguana/algorithms/clas12/PhotonGBTFilter/Algorithm.h b/src/iguana/algorithms/clas12/PhotonGBTFilter/Algorithm.h
@@ -38,7 +38,7 @@ namespace iguana::clas12 {
       void Run(hipo::banklist& banks) const override;
       void Stop() override;   
 
-      /// **Method**: Applies forward detector cut using REC::Particle Theta
+      /// Applies forward detector cut using REC::Particle Theta
       /// @param theta lab angle of the particle with respect to the beam direction (radians)
       /// @returns `true` if the particle's theta is within the forward detector coverage, `false` otherwise
       bool ForwardDetectorFilter(float const theta) const;
@@ -66,14 +66,14 @@ namespace iguana::clas12 {
         double ecout_m2v = 0;
       }; 
 
-      /// **Method**: Applies pid purity cuts to photons, compatible to how the GBT models are trained
+      /// Applies pid purity cuts to photons, compatible to how the GBT models are trained
       /// @param E energy of the photon
       /// @param Epcal energy the photon has deposited in the pre-shower calorimeter
       /// @param theta lab angle of the photon with respect to the beam direction (radians)
       /// @returns `true` if the photon passes the pid purity cuts, `false` otherwise
       bool PidPurityPhotonFilter(float const E, float const Epcal, float const theta) const;
 
-      /// **Action function**: Classifies the photon for a given event as signal or background
+      /// Classifies the photon for a given event as signal or background
       /// @param particleBank the REC::Particle hipo bank
       /// @param caloBank the REC::Calorimeter hipo bank
       /// @param calo_map the std::map<> of calorimeter data for the event, indexed by pindex
@@ -83,32 +83,32 @@ namespace iguana::clas12 {
       bool Filter(hipo::bank const &particleBank, hipo::bank const &caloBank, std::map<int, PhotonGBTFilter::calo_row_data> calo_map, int const row, int const runnum) const;
 
 
-      /// **Method**: Calls the appropriate CatBoost model for the given run group, classifying the photon of interest
+      /// Calls the appropriate CatBoost model for the given run group, classifying the photon of interest
       /// @param input_data the input features of the model
       /// @param runnum the run number associated to the event
       /// @returns `true` if the 
       bool ClassifyPhoton(std::vector<float> const &input_data, int const runnum) const;
 
 
-      /// **Method**: Gets calorimeter data for particles in the event
+      /// Gets calorimeter data for particles in the event
       /// @param bank the bank to get data from
       /// @returns a map with keys as particle indices (pindex) and values as calo_row_data structs
       std::map<int, PhotonGBTFilter::calo_row_data> GetCaloMap(hipo::bank const &bank) const;
 
 
-      /// **Method**: Gets the calorimeter vector for a particle in the event
+      /// Gets the calorimeter vector for a particle in the event
       /// @param crd data struct of a single REC::Calorimeter's row data
       /// @returns a ROOT::Math::XYZVector with the coordinates of the particle in the calorimeter
       ROOT::Math::XYZVector GetParticleCaloVector(PhotonGBTFilter::calo_row_data calo_row) const;
 
 
-      /// **Method**: Gets the mass of a particle given its PID
+      /// Gets the mass of a particle given its PID
       /// @param pid the particle ID to get the mass for
       /// @returns the mass of the particle in GeV; returns -1.0 if the PID is not recognized
       double GetMass(int pid) const;
 
 
-      /// **Method**: Gets the model function for the run number
+      /// Gets the model function for the run number
       /// @param runnum the run of the associated event
       /// @returns GBT function for the run period
       std::function<double(std::vector<float> const &)> getModelFunction(int runnum) const;

diff --git a/src/iguana/algorithms/example/ExampleAlgorithm/Algorithm.h b/src/iguana/algorithms/example/ExampleAlgorithm/Algorithm.h
@@ -83,7 +83,7 @@ namespace iguana::example {
       // #   - `Transform` for a transformation type algorithm, such as momentum corrections
       // #   - `Create` for a creation type algorithm, such as inclusive kinematic (x, Q2, etc.) reconstruction
       // ############################################################################
-      /// **Action function**: checks if the PDG `pid` is positive;
+      /// @action_function{scalar filter} checks if the PDG `pid` is positive;
       /// this is an example action function, please replace it with your own
       /// @param pid the particle PDG to check
       /// @returns `true` if `pid` is positive

diff --git a/src/iguana/tests/meson.build b/src/iguana/tests/meson.build
@@ -57,31 +57,33 @@ foreach algo : algo_dict
       )
 
       # multithreaded tests
-      foreach concurrency_model : [ 'memoize' ] # note: we used to have more, so leave this array in case we want more
-        multithreading_args = [
-          'multithreading',
-          '-j', get_option('test_multithreading').to_string(),
-          '-m', concurrency_model,
-          '-V', # vary run number
-        ]
-        test(
-          '-'.join(['multithreading', concurrency_model, test_name_algo]),
-          test_exe,
-          suite: [ 'algorithm', 'multithreading', concurrency_model ],
-          args: multithreading_args + [ '-n', get_option('test_num_events') ] + test_args,
-          is_parallel: false,
-          env: project_test_env,
-          timeout: 0,
-        )
-        benchmark(
-          '-'.join(['benchmark', f'multithreading_@concurrency_model@', test_name_algo]),
-          test_exe,
-          suite: [ 'algorithm', 'multithreading', concurrency_model ],
-          args: multithreading_args + [ '-n', '0' ] + test_args, # benchmark all the events
-          env: project_test_env,
-          timeout: 0,
-        )
-      endforeach
+      if get_option('z_test_multithreading')
+        foreach concurrency_model : [ 'memoize' ] # note: we used to have more, so leave this array in case we want more
+          multithreading_args = [
+            'multithreading',
+            '-j', get_option('test_num_threads').to_string(),
+            '-m', concurrency_model,
+            '-V', # vary run number
+          ]
+          test(
+            '-'.join(['multithreading', concurrency_model, test_name_algo]),
+            test_exe,
+            suite: [ 'algorithm', 'multithreading', concurrency_model ],
+            args: multithreading_args + [ '-n', get_option('test_num_events') ] + test_args,
+            is_parallel: false,
+            env: project_test_env,
+            timeout: 0,
+          )
+          benchmark(
+            '-'.join(['benchmark', f'multithreading_@concurrency_model@', test_name_algo]),
+            test_exe,
+            suite: [ 'algorithm', 'multithreading', concurrency_model ],
+            args: multithreading_args + [ '-n', '0' ] + test_args, # benchmark all the events
+            env: project_test_env,
+            timeout: 0,
+          )
+        endforeach
+      endif
 
     endif