Merge branch 'dev' into MFTSup_Sept2019

Author: rpezzi

.travis.yml

@@ -9,16 +9,53 @@ matrix:
   include:
     - os: linux
       dist: xenial
-      env: TOOL=clang-format
+      env: JOB=clang-format
       addons:
         apt:
           sources:
             - llvm-toolchain-xenial-8
           packages:
             - clang-format-8
       compiler: clang
+      script: |
+        if [ "$TRAVIS_PULL_REQUEST" != "false" ]; then
+          BASE_COMMIT=$(git rev-parse $TRAVIS_BRANCH)
+          echo "Running clang-format-8 against branch $TRAVIS_BRANCH, with hash $BASE_COMMIT"
+          COMMIT_FILES=$(git diff --name-only $BASE_COMMIT | grep -ivE 'LinkDef|Utilities/PCG/')
+          RESULT_OUTPUT="$(git-clang-format-8 --commit $BASE_COMMIT --diff --binary `which clang-format-8` $COMMIT_FILES)"
+
+          for x in $COMMIT_FILES; do
+            case $x in
+              *.h|*.cxx)
+                # We remove the header from the diff as it contains +++ then
+                # we only select the added lines to check for the long ones.
+                # We do not need to check for the lines which have been removed
+                # and we do not want to check for the lines which were not changed
+                # to avoid extra work.
+                # 120 characters are allowed, meaning the error should start with 122,
+                # to allow for the starting + at the end of the line.
+                git diff $x | tail -n +5 | grep -e '^+' | grep '.\{122,\}' && { echo "Line longer than 120 chars in $x." && exit 1; } || true ;;
+              *.hxx|*.cc|*.hpp) echo "$x uses non-allowed extension." && exit 1 ;;
+              *) ;;
+            esac
+          done
+
+          if [ "$RESULT_OUTPUT" == "no modified files to format" ] \
+            || [ "$RESULT_OUTPUT" == "clang-format did not modify any files" ] ; then
+            echo "clang-format passed."
+            exit 0
+          else
+            echo "clang-format failed."
+            echo "To reproduce it locally please run"
+            echo -e "\tgit checkout $TRAVIS_BRANCH"
+            echo -e "\tgit-clang-format --commit $BASE_COMMIT --diff --binary $(which clang-format)"
+            echo "$RESULT_OUTPUT"
+            exit 1
+          fi
+        fi
     - os: linux
-      env: TOOL=doxygen
+      dist: bionic
+      env: JOB=doxygen
       addons:
         apt:
           packages:
@@ -28,59 +65,16 @@ matrix:
             - doxygen-gui
             - graphviz
             - cmake
+      script: |
+        cat > CMakeLists.txt <<\EOF
+        add_subdirectory(doc)
+        EOF
+        cmake .
+        make doc
       deploy:
         provider: pages
         skip_cleanup: true
         github_token: $GITHUB_API_TOKEN # Set in travis-ci.org dashboard
         local_dir: doc/html
         on:
           branch: dev
-script: |
-    if [[ $TOOL == "doxygen" ]]; then
-      cat > CMakeLists.txt <<\EOF
-      add_subdirectory(doc)
-    EOF
-      # This is required because of differences between doxygen and github
-      # markdown syntax for code blocks. The committed code should use
-      # the github flavour and we generate the doxygen one on the fly.
-      git grep -l '^```[a-zA-Z]' | xargs sed -i .old -e 's|```\([a-zA-Z][a-zA-Z]*\)|\n```{.\1}\n|g;s|[.]bash|.sh|g;s|```|~~~~~~~|g'
-      find . -name "*.old" -delete
-      cmake .
-      make doc
-    elif [[ $TOOL == "clang-format" ]]; then
-      if [ "$TRAVIS_PULL_REQUEST" != "false" ]; then
-        BASE_COMMIT=$(git rev-parse $TRAVIS_BRANCH)
-        echo "Running clang-format-8 against branch $TRAVIS_BRANCH, with hash $BASE_COMMIT"
-        COMMIT_FILES=$(git diff --name-only $BASE_COMMIT | grep -ivE 'LinkDef|Utilities/PCG/')
-        RESULT_OUTPUT="$(git-clang-format-8 --commit $BASE_COMMIT --diff --binary `which clang-format-8` $COMMIT_FILES)"
-
-        for x in $COMMIT_FILES; do
-          case $x in
-            *.h|*.cxx)
-              # We remove the header from the diff as it contains +++ then
-              # we only select the added lines to check for the long ones.
-              # We do not need to check for the lines which have been removed
-              # and we do not want to check for the lines which were not changed
-              # to avoid extra work.
-              # 120 characters are allowed, meaning the error should start with 122,
-              # to allow for the starting + at the end of the line.
-              git diff $x | tail -n +5 | grep -e '^+' | grep '.\{122,\}' && { echo "Line longer than 120 chars in $x." && exit 1; } || true ;;
-            *.hxx|*.cc|*.hpp) echo "$x uses non-allowed extension." && exit 1 ;;
-            *) ;;
-          esac
-        done
-
-        if [ "$RESULT_OUTPUT" == "no modified files to format" ] \
-          || [ "$RESULT_OUTPUT" == "clang-format did not modify any files" ] ; then
-          echo "clang-format passed."
-          exit 0
-        else
-          echo "clang-format failed."
-          echo "To reproduce it locally please run"
-          echo -e "\tgit checkout $TRAVIS_BRANCH"
-          echo -e "\tgit-clang-format --commit $BASE_COMMIT --diff --binary $(which clang-format)"
-          echo "$RESULT_OUTPUT"
-          exit 1
-        fi
-      fi
-    fi

Algorithm/README.md

@@ -1,3 +1,7 @@
+<!-- doxy
 \page refAlgorithm Module 'Algorithm'
+/doxy -->
+
+# Algorithm
 
 A description of this module is not yet available.

Framework/ArrowTests/CMakeLists.txt Analysis/CMakeLists.txtFramework/ArrowTests/CMakeLists.txt renamed to Analysis/CMakeLists.txt

@@ -8,8 +8,7 @@
 # granted to it by virtue of its status as an Intergovernmental Organization or
 # submit itself to any jurisdiction.
 
-o2_add_test(01
-            SOURCES test/test_Arrow01.cxx
-            COMPONENT_NAME arrow
-            PUBLIC_LINK_LIBRARIES arrow::arrow_shared
-            LABELS arrow)
+#add_subdirectory(Core)
+#add_subdirectory(Tools)
+#add_subdirectory(Tasks)
+add_subdirectory(Tutorials)

Framework/AnalysisTutorial/CMakeLists.txt Analysis/Tutorials/CMakeLists.txtFramework/AnalysisTutorial/CMakeLists.txt renamed to Analysis/Tutorials/CMakeLists.txt

@@ -25,6 +25,11 @@ o2_add_executable(track-iteration
                   PUBLIC_LINK_LIBRARIES O2::Framework
                   COMPONENT_NAME AnalysisTutorial)
 
+o2_add_executable(full-track-iteration
+                  SOURCES src/fullTrackIteration.cxx
+                  PUBLIC_LINK_LIBRARIES O2::Framework
+                  COMPONENT_NAME AnalysisTutorial)
+
 o2_add_executable(collision-tracks-iteration
                   SOURCES src/collisionTracksIteration.cxx
                   PUBLIC_LINK_LIBRARIES O2::Framework
@@ -35,6 +40,11 @@ o2_add_executable(new-collections
                   PUBLIC_LINK_LIBRARIES O2::Framework
                   COMPONENT_NAME AnalysisTutorial)
 
+o2_add_executable(associated-derived
+                  SOURCES src/associatedExample.cxx
+                  PUBLIC_LINK_LIBRARIES O2::Framework
+                  COMPONENT_NAME AnalysisTutorial)
+
 o2_add_executable(dynamic-columns
                   SOURCES src/dynamicColumns.cxx
                   PUBLIC_LINK_LIBRARIES O2::Framework
@@ -44,3 +54,8 @@ o2_add_executable(histograms
                   SOURCES src/histograms.cxx
                   PUBLIC_LINK_LIBRARIES O2::Framework
                   COMPONENT_NAME AnalysisTutorial)
+
+o2_add_executable(filters
+                  SOURCES src/filters.cxx
+                  PUBLIC_LINK_LIBRARIES O2::Framework
+                  COMPONENT_NAME AnalysisTutorial)

Analysis/Tutorials/src/associatedExample.cxx

@@ -0,0 +1,76 @@
+// Copyright CERN and copyright holders of ALICE O2. This software is
+// distributed under the terms of the GNU General Public License v3 (GPL
+// Version 3), copied verbatim in the file "COPYING".
+//
+// See http://alice-o2.web.cern.ch/license for full licensing information.
+//
+// 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.
+#include "Framework/runDataProcessing.h"
+#include "Framework/AnalysisTask.h"
+#include "Framework/AnalysisDataModel.h"
+
+namespace o2::aod
+{
+namespace etaphi
+{
+DECLARE_SOA_COLUMN(Eta, etas, float, "fEta");
+DECLARE_SOA_COLUMN(Phi, phis, float, "fPhi");
+DECLARE_SOA_COLUMN(Pt, pts, float, "fPt");
+} // namespace etaphi
+DECLARE_SOA_TABLE(EtaPhi, "AOD", "ETAPHI",
+                  etaphi::Eta, etaphi::Phi);
+DECLARE_SOA_TABLE(EtaPhiPt, "AOD", "ETAPHIPT",
+                  etaphi::Eta, etaphi::Phi, etaphi::Pt);
+} // namespace o2::aod
+
+using namespace o2;
+using namespace o2::framework;
+
+// This is a very simple example showing how to iterate over tracks
+// and create a new collection for them.
+// FIXME: this should really inherit from AnalysisTask but
+//        we need GCC 7.4+ for that
+struct ATask {
+  Produces<aod::EtaPhi> etaphi;
+  Produces<aod::EtaPhiPt> etaphipt;
+
+  void process(aod::Tracks const& tracks)
+  {
+    for (auto& track : tracks) {
+      float phi = asin(track.snp()) + track.alpha() + static_cast<float>(M_PI);
+      float eta = log(tan(0.25f * static_cast<float>(M_PI) - 0.5f * atan(track.tgl())));
+      float pt = 1.f / track.signed1Pt();
+      etaphi(eta, phi);
+      etaphipt(eta, phi, pt);
+    }
+  }
+};
+
+struct BTask {
+  void process(aod::Collision const& collision, soa::Join<aod::Tracks, aod::EtaPhi> const& extTracks)
+  {
+    //    LOG(INFO) << "TF: " << collision.timeframeID() << std::endl;
+    LOG(INFO) << "Rows: " << extTracks.asArrowTable()->num_rows() << std::endl;
+    for (auto& track : extTracks) {
+      LOGF(INFO, "(%f, %f) - (%f, %f)", track.eta(), track.phi(), track.etas(), track.phis());
+    }
+  }
+};
+
+struct CTask {
+  void process(aod::Collision const& collision, soa::Concat<aod::EtaPhi, aod::EtaPhiPt> const& concatenated)
+  {
+    //    LOG(INFO) << "TF: " << collision.timeframeID() << std::endl;
+    LOG(INFO) << "Rows: " << concatenated.asArrowTable()->num_rows() << std::endl;
+  }
+};
+
+WorkflowSpec defineDataProcessing(ConfigContext const&)
+{
+  return WorkflowSpec{
+    adaptAnalysisTask<ATask>("produce-etaphi"),
+    adaptAnalysisTask<BTask>("consume-etaphi"),
+    adaptAnalysisTask<CTask>("consume-etaphi-twice")};
+}

…utorial/src/collisionTracksIteration.cxx …torials/src/collisionTracksIteration.cxxFramework/AnalysisTutorial/src/collisionTracksIteration.cxx renamed to Analysis/Tutorials/src/collisionTracksIteration.cxx Framework/AnalysisTutorial/src/collisionTracksIteration.cxx renamed to Analysis/Tutorials/src/collisionTracksIteration.cxx

@@ -21,7 +21,7 @@ DECLARE_SOA_COLUMN(Alpha, alpha, float, "fAlpha");
 DECLARE_SOA_DYNAMIC_COLUMN(Eta, eta, [](float tgl) { return log(tan(0.25 * M_PI - 0.5 * atan(tgl))); });
 DECLARE_SOA_DYNAMIC_COLUMN(Phi, phi, [](float snp, float alpha) { return asin(snp) + alpha + M_PI; });
 } // namespace etaphi
-DECLARE_SOA_TABLE(EtaPhis, "RN2", "ETAPHI",
+DECLARE_SOA_TABLE(EtaPhis, "AOD", "ETAPHI",
                   etaphi::Tgl, etaphi::Snp, etaphi::Alpha,
                   etaphi::Eta<etaphi::Tgl>,
                   etaphi::Phi<etaphi::Snp, etaphi::Alpha>);

…/AnalysisTutorial/src/dynamicColumns.cxx Analysis/Tutorials/src/dynamicColumns.cxxFramework/AnalysisTutorial/src/dynamicColumns.cxx renamed to Analysis/Tutorials/src/dynamicColumns.cxx Framework/AnalysisTutorial/src/dynamicColumns.cxx renamed to Analysis/Tutorials/src/dynamicColumns.cxx

@@ -0,0 +1,60 @@
+// Copyright CERN and copyright holders of ALICE O2. This software is
+// distributed under the terms of the GNU General Public License v3 (GPL
+// Version 3), copied verbatim in the file "COPYING".
+//
+// See http://alice-o2.web.cern.ch/license for full licensing information.
+//
+// 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.
+#include "Framework/runDataProcessing.h"
+#include "Framework/AnalysisTask.h"
+#include "Framework/AnalysisDataModel.h"
+
+namespace o2::aod
+{
+namespace etaphi
+{
+DECLARE_SOA_COLUMN(Eta, eta, float, "fEta");
+DECLARE_SOA_COLUMN(Phi, phi, float, "fPhi");
+} // namespace etaphi
+DECLARE_SOA_TABLE(EtaPhi, "AOD", "ETAPHI",
+                  etaphi::Eta, etaphi::Phi);
+} // namespace o2::aod
+
+using namespace o2;
+using namespace o2::framework;
+using namespace o2::framework::expressions;
+
+// This is a very simple example showing how to iterate over tracks
+// and create a new collection for them.
+// FIXME: this should really inherit from AnalysisTask but
+//        we need GCC 7.4+ for that
+struct ATask {
+  Produces<aod::EtaPhi> etaphi;
+
+  void process(aod::Tracks const& tracks)
+  {
+    for (auto& track : tracks) {
+      etaphi(track.phi(), track.eta());
+    }
+  }
+};
+
+struct BTask {
+  Filter ptFilter = (aod::etaphi::phi > 1.f) && (aod::etaphi::phi < 2.f);
+
+  void process(soa::Filtered<aod::EtaPhi> const& etaPhis)
+  {
+    for (auto& etaPhi : etaPhis) {
+      LOGF(INFO, "(%f, 1 < %f < 2)", etaPhi.eta(), etaPhi.phi());
+    }
+  }
+};
+
+WorkflowSpec defineDataProcessing(ConfigContext const&)
+{
+  return WorkflowSpec{
+    adaptAnalysisTask<ATask>("produce-etaphi"),
+    adaptAnalysisTask<BTask>("consume-etaphi")};
+}

Analysis/Tutorials/src/filters.cxx

@@ -0,0 +1,43 @@
+// Copyright CERN and copyright holders of ALICE O2. This software is
+// distributed under the terms of the GNU General Public License v3 (GPL
+// Version 3), copied verbatim in the file "COPYING".
+//
+// See http://alice-o2.web.cern.ch/license for full licensing information.
+//
+// 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.
+#include "Framework/runDataProcessing.h"
+#include "Framework/AnalysisTask.h"
+
+#include <TFile.h>
+#include <TH1F.h>
+
+using namespace o2;
+using namespace o2::framework;
+
+// Another example
+// FIXME: this should really inherit from AnalysisTask but
+//        we need GCC 7.4+ for that
+struct ATask {
+  void init(InitContext&)
+  {
+    count = 0;
+  }
+
+  void process(soa::Join<aod::Tracks, aod::TracksExtra> const& fullTracks)
+  {
+    for (auto& track : fullTracks) {
+      LOGF(info, "%d, %f %f", count, track.alpha(), track.tpcSignal());
+      count++;
+    }
+  }
+
+  size_t count = 2016927;
+};
+
+WorkflowSpec defineDataProcessing(ConfigContext const&)
+{
+  return WorkflowSpec{
+    adaptAnalysisTask<ATask>("track-iteration-tutorial")};
+}