Merge branch 'main' of github.com:eic/EICrecon into lgpl-license

.github/workflows/doxygen.yml

@@ -11,26 +11,29 @@ jobs:
     container:
       image: alpine:latest
       volumes:
-      - /home/runner/work/_temp:/home/runner/work/_temp
+        - /home/runner/work/_temp:/home/runner/work/_temp
       # FIXME hard-coded: see https://github.com/actions/upload-pages-artifact/pull/14
     steps:
-    - uses: actions/checkout@v2
-    - run: |
-        apk add doxygen graphviz
-        doxygen Doxyfile
-    - uses: actions/upload-artifact@v3
-      with:
-        name: docs
-        path: html/
-        if-no-files-found: error
-    - run: |
-        apk add tar bash
+      - uses: actions/checkout@v2
+      - run: |
+          apk add doxygen graphviz
+          doxygen Doxyfile        
+          cp -r docs publishing_docs
+          mv html publishing_docs/doxygen
+      - uses: actions/upload-artifact@v3
+        with:
+          name: docs
+          path: publishing_docs/
+          if-no-files-found: error
+      - run:
+
+          apk add tar bash
         # FIXME bash not really required: see https://github.com/actions/upload-pages-artifact/pull/14
-    - uses: actions/upload-pages-artifact@v1
-      if: github.ref == 'refs/heads/main'
-      with:
-        path: html/
-        retention-days: 7
+      - uses: actions/upload-pages-artifact@v1
+        if: github.ref == 'refs/heads/main'
+        with:
+          path: publishing_docs/
+          retention-days: 7
 
   deploy-docs:
     needs: build-docs
@@ -43,6 +46,6 @@ jobs:
       url: ${{ steps.deployment.outputs.page_url }}
     runs-on: ubuntu-latest
     steps:
-    - name: Deploy to GitHub Pages
-      id: deployment
-      uses: actions/deploy-pages@v1
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v1

.github/workflows/linux-eic-shell.yml

@@ -14,24 +14,41 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  build-test:
+  build-gcc:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - uses: cvmfs-contrib/github-action-cvmfs@v2
     - uses: eic/run-cvmfs-osg-eic-shell@main
       with:
         platform-release: "jug_xl:nightly"
-        setup: /opt/detector/epic-nightly/setup.sh
         run: |
           # install this repo
-          cmake -B build -S . \
-            -DDETECTOR_LIBS_EPIC=/opt/detector/epic-nightly/lib/libepic.so \
-            -DDETECTOR_LIBS_IP6=/opt/detector/epic-nightly/lib/libip6.so
+          CC=gcc CXX=g++ cmake -B build -S .
           cmake --build build -- install
     - uses: actions/upload-artifact@v3
       with:
-        name: build-eic-shell-epic-nightly
+        name: build-gcc-eic-shell
+        path: |
+          .
+          !src/
+        if-no-files-found: error
+
+  build-clang:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: cvmfs-contrib/github-action-cvmfs@v2
+    - uses: eic/run-cvmfs-osg-eic-shell@main
+      with:
+        platform-release: "jug_xl:nightly"
+        run: |
+          # install this repo
+          CC=clang CXX=clang++ cmake -B build -S .
+          cmake --build build -- install
+    - uses: actions/upload-artifact@v3
+      with:
+        name: build-clang-eic-shell
         path: |
           .
           !src/

.gitignore

@@ -7,6 +7,7 @@ src/services/io/podio/datamodel_glue.h
 include/*
 plugins/*
 build/*
+install/*
 
 ##### C++ basic gitignore #####
 
@@ -149,3 +150,9 @@ lib/
 
 /tests
 /build
+
+src/tools/default_flags_table/__pycache__/
+
+src/tools/default_flags_table/calibrations/
+
+src/tools/default_flags_table/fieldmaps/

CMakeLists.txt

@@ -27,7 +27,7 @@
 
 cmake_minimum_required(VERSION 3.16)
 
-project(EICRecon VERSION 0.0.0)
+project(EICRecon VERSION 0.2.3)
 
 # Make C++17 a default
 if(NOT "${CMAKE_CXX_STANDARD}")
@@ -63,6 +63,27 @@ message(STATUS "${CMAKE_PROJECT_NAME}: JANA2 CMake   : ${JANA_DIR}")
 message(STATUS "${CMAKE_PROJECT_NAME}: JANA2 includes: ${JANA_INCLUDE_DIR}")
 message(STATUS "${CMAKE_PROJECT_NAME}: JANA2 library : ${JANA_LIBRARY}")
 
+# PODIO, EDM4HEP, EDM4EIC event models
+find_package(podio REQUIRED)
+find_package(EDM4HEP REQUIRED)
+find_package(EDM4EIC REQUIRED)
+set(EDM4EIC_INCLUDE_DIR ${EDM4EIC_DIR}/../../include)
+
+# DD4Hep is required for the most of the part
+find_package(DD4hep REQUIRED)
+
+# ACTS
+find_package(Acts REQUIRED COMPONENTS Core PluginIdentification PluginTGeo PluginDD4hep)
+set(Acts_VERSION_MIN "19.0.0")
+set(Acts_VERSION "${Acts_VERSION_MAJOR}.${Acts_VERSION_MINOR}.${Acts_VERSION_PATCH}")
+if(${Acts_VERSION} VERSION_LESS ${Acts_VERSION_MIN}
+        AND NOT "${Acts_VERSION}" STREQUAL "9.9.9")
+    message(FATAL_ERROR "Acts version ${Acts_VERSION_MIN} or higher required, but ${Acts_VERSION} found")
+endif()
+set(Acts_INCLUDE_DIRS ${Acts_DIR}/../../../include ${ActsDD4hep_DIR}/../../../include )
+
+# CERN ROOT
+find_package(ROOT REQUIRED)
 
 # Set it ON for additional CMake printout
 set(EICRECON_VERBOSE_CMAKE OFF)
@@ -78,15 +99,16 @@ list (APPEND CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/cmake)   # Find Find<Modules>
 # ------------------------------------------------------------------
 print_grand_header("    B U I L D   E I C R E C O N   P A R T S    ")
 # ------------------------------------------------------------------
+add_subdirectory( src/services )
 add_subdirectory( src/algorithms )
 add_subdirectory( src/benchmarks )
 add_subdirectory( src/detectors )
 add_subdirectory( src/examples )
 add_subdirectory( src/global )
 add_subdirectory( src/scripts )
-add_subdirectory( src/services )
 add_subdirectory( src/tests )
 add_subdirectory( src/utilities )
+add_subdirectory( src/tools/default_flags_table )
 
 
 

README.md

@@ -5,22 +5,14 @@ The repository contains reconstruction source code for the EPIC detector. It's f
 is to take real or simulated data and reconstruct it into physical values
 for later analysis.
 
+- [Documentation website](https://eic.github.io/EICrecon/#/)
+- [Getting started instruction with eic-shell](https://eic.github.io/EICrecon/#/get-started/eic-shell)
+
+
 If you are new to EIC software then you should start with the tutorials which
 can be found here:
 [https://indico.bnl.gov/category/443/](https://indico.bnl.gov/category/443/)
 
-A preliminary tutorial on JANA2 is being developed here:
-[https://faustus123.github.io/tutorial-jana2](https://faustus123.github.io/tutorial-jana2/index.html)
-
-
-## Table of contents
-1. [Getting started with eic-shell](./docs/Use_with_eic_shell.md)
-2. [Creating a user plugin (custom histograms/trees)](./docs/HowTo_make_plugin.md)
-3. [Adding a factory (algorithm)](./docs/HowTo_add_factory.md)
-4. [Contributing and Conventions](./CONTRIBUTING.md)
-5. [Logging](./docs/Logging.md)
-6. [Manual Build instructions](./docs/Manual_Build.md)
-   * [Installation via EDPM](./docs/EDPM.md)
-7. [Tracking implementation](./docs/tracking_implementation.md)
-
+A preliminary tutorial on JANA2 
+[is being developed here](https://eic.github.io/EICrecon/#/tutorial/01-introduction)
 

cmake/jana_plugin.cmake

@@ -18,8 +18,6 @@ macro(plugin_add _name)
 
     # include logging by default
     find_package(spdlog REQUIRED)
-    find_package(fmt REQUIRED)
-    set(fmt_INCLUDE_DIR ${fmt_DIR}/../../../include)
 
     # include ROOT by default
     find_package(ROOT REQUIRED)
@@ -29,7 +27,6 @@ macro(plugin_add _name)
     target_include_directories(${_name}_plugin PUBLIC ${CMAKE_SOURCE_DIR}/src)
     target_include_directories(${_name}_plugin SYSTEM PUBLIC ${JANA_INCLUDE_DIR} )
     target_include_directories(${_name}_plugin SYSTEM PUBLIC ${ROOT_INCLUDE_DIRS} )
-    target_include_directories(${_name}_plugin SYSTEM PUBLIC ${fmt_INCLUDE_DIR} )
     set_target_properties(${_name}_plugin PROPERTIES PREFIX "" OUTPUT_NAME "${_name}" SUFFIX ".so")
     target_link_libraries(${_name}_plugin ${JANA_LIB} spdlog::spdlog)
 
@@ -42,7 +39,6 @@ macro(plugin_add _name)
         add_library(${_name}_library STATIC "")
 	    target_include_directories(${_name}_library PUBLIC ${CMAKE_SOURCE_DIR}/src)
         target_include_directories(${_name}_library SYSTEM PUBLIC ${JANA_INCLUDE_DIR} )
-        target_include_directories(${_name}_library SYSTEM PUBLIC ${fmt_INCLUDE_DIR} )
         set_target_properties(${_name}_library PROPERTIES PREFIX "lib" OUTPUT_NAME "${_name}" SUFFIX ".a")
         target_link_libraries(${_name}_library ${JANA_LIB} spdlog::spdlog)
 
@@ -153,3 +149,84 @@ macro(plugin_glob_all _name)
     print_file_names("  " ${HEADER_FILES})  # Prints header files
 
 endmacro()
+
+
+# Adds dd4hep for a plugin
+macro(plugin_add_dd4hep _name)
+
+    if(NOT DD4hep_FOUND)
+        find_package(DD4hep REQUIRED)
+    endif()
+
+    plugin_include_directories(${_name} SYSTEM PUBLIC ${DD4hep_INCLUDE_DIRS})
+    plugin_link_libraries(${_name} DD4hep::DDCore DD4hep::DDRec)
+
+endmacro()
+
+
+# Adds ACTS tracking package for a plugin
+macro(plugin_add_acts _name)
+
+    if(NOT Acts_FOUND)
+        find_package(Acts REQUIRED COMPONENTS Core PluginIdentification PluginTGeo PluginJson PluginDD4hep)
+        set(Acts_VERSION_MIN "19.0.0")
+        set(Acts_VERSION "${Acts_VERSION_MAJOR}.${Acts_VERSION_MINOR}.${Acts_VERSION_PATCH}")
+        if(${Acts_VERSION} VERSION_LESS ${Acts_VERSION_MIN}
+                AND NOT "${Acts_VERSION}" STREQUAL "9.9.9")
+            message(FATAL_ERROR "Acts version ${Acts_VERSION_MIN} or higher required, but ${Acts_VERSION} found")
+        endif()
+
+        set(Acts_INCLUDE_DIRS ${Acts_DIR}/../../../include ${ActsDD4hep_DIR}/../../../include )
+    endif()
+
+    # Add include directories (works same as target_include_directories)
+    plugin_include_directories(${PLUGIN_NAME} SYSTEM PUBLIC ${Acts_INCLUDE_DIRS})
+
+    # Add libraries (works same as target_include_directories)
+    plugin_link_libraries(${PLUGIN_NAME} ActsCore ActsPluginIdentification ActsPluginTGeo ActsPluginJson ActsPluginDD4hep)
+endmacro()
+
+# Adds podio, edm4hep, edm4eic for a plugin
+macro(plugin_add_event_model _name)
+
+    if(NOT podio_FOUND)
+        find_package(podio REQUIRED)
+    endif()
+
+    if(NOT EDM4HEP_FOUND)
+        find_package(EDM4HEP REQUIRED)
+    endif()
+
+    if(NOT EDM4EIC_FOUND)
+        find_package(EDM4EIC REQUIRED)
+        set(EDM4EIC_INCLUDE_DIR ${EDM4EIC_DIR}/../../include)
+    endif()
+
+    # Add include directories
+    # (same as target_include_directories but for both plugin and library)
+    plugin_include_directories(${PLUGIN_NAME} SYSTEM PUBLIC ${podio_INCLUDE_DIR} ${EDM4EIC_INCLUDE_DIR} ${EDM4HEP_INCLUDE_DIR})
+
+    # Add libraries
+    # (same as target_include_directories but for both plugin and library)
+    plugin_link_libraries(${PLUGIN_NAME}
+            EDM4EIC::edm4eic
+            EDM4HEP::edm4hep
+            )
+endmacro()
+
+
+# Adds cern ROOT for a plugin
+macro(plugin_add_cern_root _name)
+
+    if(NOT ROOT_FOUND)
+        #find_package(ROOT REQUIRED COMPONENTS Core Tree Hist RIO EG)
+        find_package(ROOT REQUIRED)
+    endif()
+
+    # Add include directories
+    plugin_include_directories(${PLUGIN_NAME} SYSTEM PUBLIC ${ROOT_INCLUDE_DIRS} )
+
+    # Add libraries
+    #plugin_link_libraries(${PLUGIN_NAME} ${ROOT_LIBRARIES} EDM4EIC::edm4eic algorithms_digi_library algorithms_tracking_library ROOT::EG)
+    plugin_link_libraries(${PLUGIN_NAME} ${ROOT_LIBRARIES})
+endmacro()

docs/.gitignore

@@ -0,0 +1,4 @@
+node_modules/
+.cache/
+public
+.idea/

docs/README.md

@@ -0,0 +1,7 @@
+# EICrecon
+
+**JANA based reconstruction for the EPIC detector**
+
+<img src="demo.png" style="max-height: 300px"/>
+
+

docs/_sidebar.md

@@ -0,0 +1,26 @@
+* [Home](/)
+* Getting started    
+    * [EIC shell (recommended)](get-started/eic-shell.md)
+    * [Manual build](get-started/manual-build.md)
+    * [EDPM](get-started/edpm.md)
+* HowTo
+    * [Make Plugin](howto/make_plugin.md)
+    * [Add Factory](howto/add_factory.md)
+* Design
+    * [Flags&Env](design/common_flags_env.md)
+    * [Cmake](design/cmake.md)
+    * [Logging](design/logging.md)
+    * [Tracking](design/tracking.md)
+    * [Particle Matching](design/particle_matching.md)
+    * [Gaudi Algorithms](design/gaudi-algorithms.md)
+* Tutorials 
+    * [Introduction](tutorial/01-introduction.md)
+    * [Work environment](tutorial/02-work-environment.md)
+    * [End user plugin](tutorial/03-end-user-plugin.md)
+    * [Factory](tutorial/04-factory.md)
+    * [Contributing](tutorial/05-contributing.md)
+* Misc
+    * [References](misc/references.md)
+    * [This website](misc/this_website.md)   
+* Table flags
+    * [Table flags](table_flags/flags.md)