Merge pull request #361 from JeffersonLab/v2.3.x

Release v2.3.x

Author: wdconinc

.dockerignore

@@ -1,3 +1,19 @@
-build
-map_directory
+# install destinations
+bin/*
+lib/*
+share/*
+
+# develop directories
+.git/*
+build/*
+
+# large content
+rootfiles/*
+
+# large directory
+# but cheaper to copy than download
+#map_directory/*
+
+# large content
+*.root
 

.gitignore

@@ -1,8 +1,19 @@
 images
 
+# random seed files
+G4Master_run*.rndm
+G4Worker?_run*.rndm
+G4Worker?_run*evt*.rndm
+run*evt*.rndm
+currentEvent.rndm
+currentRun.rndm
+
 # output from createHTML
 _remoll_*.html
 
+# Jupyter checkpoints
+.ipynb_checkpoints
+
 # backups etc
 *~
 *.swp
@@ -11,7 +22,7 @@ _remoll_*.html
 *.DS_Store
 
 #ignore doxygen files for now
-doc
+Doxygen
 
 #ignore libraries and helper files
 *.so
@@ -49,6 +60,7 @@ log
 #ignore project files for eclipse
 .cproject
 .project
+.settings
 
 #ignore build type file
 .buildtype
@@ -62,3 +74,11 @@ sample_gdml.*
 #ignore log files
 *.log
 callgrind.*
+
+# jekyll
+_site
+.sass-cache
+.jekyll-cache
+.jekyll-metadata
+vendor
+Gemfile.lock

.travis.yml

@@ -2,52 +2,68 @@ sudo: required
 services:
 - docker
 
-script:
-- docker build -t jeffersonlab/remoll .
-- for suite in load validate overlap ; do
-    docker run --rm -t jeffersonlab/remoll scripts/tests/test_geometries.sh ${suite} ;
-  done
-- for suite in unit ; do
-    docker run --rm -t jeffersonlab/remoll scripts/tests/test_macros.sh ${suite} ;
-  done
-- for suite in commit release ; do
-    docker run -t jeffersonlab/remoll sh -c "
-      scripts/tests/test_macros.sh ${suite} &&
-      scripts/tests/targz_macros.sh ${suite} &&
-      scripts/tests/watermark.sh ${suite}
-    " || exit 1 ;
-    docker cp $(docker ps -l -q):"/jlab/remoll/remolltest.*.*.log.tar.gz" . ;
-    docker cp $(docker ps -l -q):"/jlab/remoll/remolltest.*.*.root.tar.gz" . ;
-    docker cp $(docker ps -l -q):"/jlab/remoll/remolltest.*.*.analysis.log.tar.gz" . ;
-    docker cp $(docker ps -l -q):"/jlab/remoll/remolltest.*.*.analysis.pdf.tar.gz" . ;
-    docker cp $(docker ps -l -q):"/jlab/remoll/remolltest.*.*.analysis.root.tar.gz" . ;
-    docker cp $(docker ps -l -q):"/jlab/remoll/rootfiles_tests_*_*_analysis.pdf" . ;
-    docker rm $(docker ps -l -q) ;
-  done
-
-after_success:
-- docker login -u "$DOCKER_USERNAME" -p "$DOCKER_PASSWORD";
-- if [ "$TRAVIS_BRANCH" == "master" ]; then
-    docker tag jeffersonlab/remoll jeffersonlab/remoll:latest && docker push jeffersonlab/remoll:latest ;
-  else
-    docker tag jeffersonlab/remoll jeffersonlab/remoll:$TRAVIS_BRANCH && docker push jeffersonlab/remoll:$TRAVIS_BRANCH ;
-  fi
+jobs:
+  include:
+    - stage: build docker image
+      script:
+      - docker build -t jeffersonlab/remoll:$TRAVIS_BRANCH .
+      - echo "$DOCKER_PASSWORD" | docker login -u "$DOCKER_USERNAME" --password-stdin ;
+        if [ "${TRAVIS_PULL_REQUEST}" == "false" ]; then
+          if [ "$TRAVIS_BRANCH" == "master" ]; then
+            docker tag jeffersonlab/remoll:$TRAVIS_BRANCH jeffersonlab/remoll:latest ;
+            docker push jeffersonlab/remoll:latest ;
+            docker tag jeffersonlab/remoll:latest jeffersonlab/remoll:$TRAVIS_BRANCH ;
+          else
+            docker push jeffersonlab/remoll:$TRAVIS_BRANCH ;
+          fi
+        fi
+    - stage: tests
+      script:
+      - for suite in load validate overlap ; do
+          echo "=== scripts/tests/test_geometries.sh ${suite} ===" ;
+          mkdir -p ${PWD}/logfiles ${PWD}/rootfiles ;
+          time docker run --rm -v ${PWD}/rootfiles:/jlab/remoll/rootfiles -v ${PWD}/logfiles:/jlab/remoll/logfiles -t jeffersonlab/remoll:$TRAVIS_BRANCH sh -c "
+            scripts/tests/test_geometries.sh ${suite}
+          " ;
+        done ;
+        ls -al ${PWD}/logfiles ${PWD}/rootfiles
+    - script:
+      - for suite in unit ; do
+          echo "=== scripts/tests/test_macros.sh ${suite} ===" ;
+          mkdir -p ${PWD}/logfiles ${PWD}/rootfiles ;
+          time docker run --rm -v ${PWD}/rootfiles:/jlab/remoll/rootfiles -v ${PWD}/logfiles:/jlab/remoll/logfiles -t jeffersonlab/remoll:$TRAVIS_BRANCH sh -c "
+            scripts/tests/test_macros.sh ${suite}
+        " ;
+        done ;
+        ls -al ${PWD}/logfiles ${PWD}/rootfiles
+    - script:
+      - for suite in commit ; do
+          echo "=== scripts/tests/test_macros.sh ${suite} ===" ;
+          mkdir -p ${PWD}/logfiles ${PWD}/rootfiles ;
+          time docker run --rm -v ${PWD}/rootfiles:/jlab/remoll/rootfiles -v ${PWD}/logfiles:/jlab/remoll/logfiles -t jeffersonlab/remoll:$TRAVIS_BRANCH sh -c "
+            scripts/tests/test_macros.sh ${suite} &&
+            scripts/tests/targz_macros.sh ${suite} &&
+            scripts/tests/watermark.sh ${suite}
+          " ;
+        done ;
+        ls -al ${PWD}/logfiles ${PWD}/rootfiles
 
 notifications:
-  slack: jlab12gev:PVp0QYADLTXmFdicK6WXkTGN
+  slack:
+    secure: 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
 
 deploy:
   provider: releases
   api_key:
     secure: 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
   file_glob: true
   file:
-  - "remolltest.*.*.log.tar.gz"
-  - "remolltest.*.*.root.tar.gz"
-  - "remolltest.*.*.analysis.log.tar.gz"
-  - "remolltest.*.*.analysis.pdf.tar.gz"
-  - "remolltest.*.*.analysis.root.tar.gz"
-  - "rootfiles_tests_*_*_analysis.pdf"
+  - "logfiles/remoll.*.*.log.tar.gz"
+  - "logfiles/remoll.*.*.analysis.log.tar.gz"
+  - "rootfiles/remoll.*.*.root.tar.gz"
+  - "rootfiles/remoll.*.*.analysis.root.tar.gz"
+  - "rootfiles/remoll.*.*.analysis.pdf.tar.gz"
+  - "rootfiles/remoll_*_*_analysis_book.pdf"
   skip_cleanup: true
   on:
     repo: JeffersonLab/remoll

CMakeLists.txt

@@ -2,7 +2,7 @@
 # Setup the project
 #
 cmake_minimum_required(VERSION 3.5)
-project(remoll VERSION 0.1 LANGUAGES CXX)
+project(remoll VERSION 0.1 LANGUAGES CXX C)
 
 # Disallow in-source builds
 if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
@@ -305,33 +305,70 @@ set(REMOLL_LOCATION /group/halla/www/hallaweb/html/12GeV/Moller/downloads/remoll
 set(REMOLL_DOWNLOADS http://hallaweb.jlab.org/12GeV/Moller/downloads/remoll/)
 set(REMOLL_MAP_DIR ${PROJECT_SOURCE_DIR}/map_directory)
 if(EXISTS ${REMOLL_LOCATION})
+  message(STATUS "Copying files directly from directory...")
   set(REMOLL_DOWNLOADS file://${REMOLL_LOCATION})
+else()
+  message(STATUS "Fieldmaps will be downloaded from web...")
 endif()
 file(DOWNLOAD
-     ${REMOLL_DOWNLOADS}/blockyUpstream_rm_1.1.txt
-     ${REMOLL_MAP_DIR}/blockyUpstream_rm_1.1.txt
-     EXPECTED_MD5 3e2338e1ba74b03da37545e98931f5f3)
+     ${REMOLL_DOWNLOADS}/hybridJLAB.txt
+     ${REMOLL_MAP_DIR}/hybridJLAB.txt
+     EXPECTED_MD5 c2da18fd7ab80cc4abe7eafc487963dc
+     )
 file(DOWNLOAD
-     ${REMOLL_DOWNLOADS}/blockyHybrid_rm_3.0.txt
-     ${REMOLL_MAP_DIR}/blockyHybrid_rm_3.0.txt
-     EXPECTED_MD5 b4bfef8f362e0df66f166b4e76a6847e)
+     ${REMOLL_DOWNLOADS}/upstreamJLAB_1.25.txt
+     ${REMOLL_MAP_DIR}/upstreamJLAB_1.25.txt
+     EXPECTED_MD5 af06ed35516c17640e89ba3aa0f5b200
+     )
+file(DOWNLOAD
+     ${REMOLL_DOWNLOADS}/hybridJLAB_v2.txt
+     ${REMOLL_MAP_DIR}/hybridJLAB_v2.txt
+     EXPECTED_MD5 4a0d1abc9b80cf5f2c3dd495a1133e26
+     )
+file(DOWNLOAD
+     ${REMOLL_DOWNLOADS}/segmentedJLAB_v2.txt
+     ${REMOLL_MAP_DIR}/segmentedJLAB_v2.txt
+     EXPECTED_MD5 2a21b540f6496e3f554302f369646bbb
+     )
+file(DOWNLOAD
+     ${REMOLL_DOWNLOADS}/upstreamJLAB_v2.txt
+     ${REMOLL_MAP_DIR}/upstreamJLAB_v2.txt
+     EXPECTED_MD5 bed73f2ea44135c52222bc8e767e1954
+     )
 install(FILES
-     ${REMOLL_MAP_DIR}/blockyHybrid_rm_3.0.txt
-     ${REMOLL_MAP_DIR}/blockyUpstream_rm_1.1.txt
+     ${REMOLL_MAP_DIR}/hybridJLAB.txt
+     ${REMOLL_MAP_DIR}/upstreamJLAB_1.25.txt
+     ${REMOLL_MAP_DIR}/hybridJLAB_v2.txt
+     ${REMOLL_MAP_DIR}/segmentedJLAB_v2.txt
+     ${REMOLL_MAP_DIR}/upstreamJLAB_v2.txt
      DESTINATION ${CMAKE_INSTALL_DATADIR}/remoll)
 if(ADDITIONAL_FIELDS)
   message(STATUS "Ensuring additional fields are available")
+  file(DOWNLOAD
+     ${REMOLL_DOWNLOADS}/blockyUpstream_rm_1.1.txt
+     ${REMOLL_MAP_DIR}/blockyUpstream_rm_1.1.txt
+     EXPECTED_MD5 3e2338e1ba74b03da37545e98931f5f3
+     )
+  file(DOWNLOAD
+     ${REMOLL_DOWNLOADS}/blockyHybrid_rm_3.0.txt
+     ${REMOLL_MAP_DIR}/blockyHybrid_rm_3.0.txt
+     EXPECTED_MD5 b4bfef8f362e0df66f166b4e76a6847e
+     )
   file(DOWNLOAD
      ${REMOLL_DOWNLOADS}/upstreamSymmetric_sensR_0.1.txt
      ${REMOLL_MAP_DIR}/upstreamSymmetric_sensR_0.1.txt
-     EXPECTED_MD5 849d9dc5abab0842fc13fef7f4918648)
+     EXPECTED_MD5 849d9dc5abab0842fc13fef7f4918648
+     )
   file(DOWNLOAD
      ${REMOLL_DOWNLOADS}/hybridSymmetric_sensR_0.1.txt
      ${REMOLL_MAP_DIR}/hybridSymmetric_sensR_0.1.txt
-     EXPECTED_MD5 78fad2ffa5b5ae129df11bdf0ce25333)
+     EXPECTED_MD5 78fad2ffa5b5ae129df11bdf0ce25333
+     )
   install(FILES
-     ${REMOLL_MAP_DIR}/upstreamSymmetric_sensR_0.0.txt
-     ${REMOLL_MAP_DIR}/hybridSymmetric_sensR_0.0.txt
+     ${REMOLL_MAP_DIR}/blockyHybrid_rm_3.0.txt
+     ${REMOLL_MAP_DIR}/blockyUpstream_rm_1.1.txt
+     ${REMOLL_MAP_DIR}/upstreamSymmetric_sensR_0.1.txt
+     ${REMOLL_MAP_DIR}/hybridSymmetric_sensR_0.1.txt
      DESTINATION ${CMAKE_INSTALL_DATADIR}/remoll)
 else()
   message(STATUS "Download additional fields with '-DADDITIONAL_FIELDS=ON'.")

Dockerfile

@@ -1,36 +1,61 @@
-FROM jeffersonlab/jlabce:2.3
+# Instructions for building remoll, a Docker image for the MOLLER experiment.
+#
+# Instructions for building the remoll image: 
+#   docker build -t jeffersonlab/remoll:latest .
+# Instructions for building the remoll image without cache: 
+#   docker build --no-cache -t jeffersonlab/remoll:latest .
+# Sharing the remoll image on DockerHub: 
+#   docker push jeffersonlab/remoll:latest
+#
+# Running the container with docker:
+#   docker run --rm -it jeffersonlab/remoll:latest remoll macros/runexample.mac
+#
+# Running the container with singularity:
+#   singularity build --disable-cache --fix-perms --sandbox remoll:latest docker-daemon://jeffersonlab/remoll:latest
+#   singularity run remoll:latest remoll macros/runexample.mac
+# Note: building a sandbox image may not work on all filesystem or on
+# hyperlinked directories. Make sure you are in an actual directory with:
+#   cd `readlink -f .`
+#
+
+FROM jeffersonlab/jlabce:2.3-mt
 
 # Install libgcj and pdftk
-RUN wget https://copr.fedorainfracloud.org/coprs/robert/gcj/repo/epel-7/robert-gcj-epel-7.repo -P /etc/yum.repos.d && \
-    wget https://copr.fedorainfracloud.org/coprs/robert/pdftk/repo/epel-7/robert-pdftk-epel-7.repo -P /etc/yum.repos.d && \
-    yum install -y pdftk ghostscript
+RUN wget -q https://copr.fedorainfracloud.org/coprs/robert/gcj/repo/epel-7/robert-gcj-epel-7.repo -P /etc/yum.repos.d && \
+    wget -q https://copr.fedorainfracloud.org/coprs/robert/pdftk/repo/epel-7/robert-pdftk-epel-7.repo -P /etc/yum.repos.d && \
+    yum install -q -y pdftk ghostscript
 
+# Add Tini entry point
+ENV TINI_VERSION v0.19.0
+ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /tini
+RUN chmod +x /tini
+
+# Set JLab CE version
 ENV JLAB_VERSION=2.3
 ENV JLAB_ROOT=/jlab
-ENV JLAB_SOFTWARE=/jlab/2.3/Linux_CentOS7.2.1511-x86_64-gcc4.8.5
 
+# Set remoll location
 ENV REMOLL=/jlab/remoll
 
-WORKDIR $REMOLL
-
 # Compile remoll
-ADD . .
-RUN source $JLAB_ROOT/$JLAB_VERSION/ce/jlab.sh && \
+WORKDIR $REMOLL
+COPY . .
+RUN source /etc/profile && \
     mkdir -p $REMOLL/build && \
     pushd $REMOLL/build && \
     cmake .. && \
     make -j$(nproc) && \
-    make install
+    make install && \
+    make clean
+
+# Environment through /etc/profile
+RUN ln -sf $REMOLL/bin/remoll.csh /etc/profile.d/remoll.csh
+RUN ln -sf $REMOLL/bin/remoll.sh /etc/profile.d/remoll.sh
 
-# Create environment point bash script
-RUN echo '#!/bin/bash'                                >  /entrypoint.sh && \
-    echo 'unset OSRELEASE'                            >> /entrypoint.sh && \
-    echo 'source $JLAB_ROOT/$JLAB_VERSION/ce/jlab.sh' >> /entrypoint.sh && \
-    echo 'export PATH=${REMOLL}/bin:${PATH}'          >> /entrypoint.sh && \
-    echo 'export REMOLL=${REMOLL}'                    >> /entrypoint.sh && \
-    echo 'cd $REMOLL && exec "$@"'                    >> /entrypoint.sh && \
-    chmod +x /entrypoint.sh
+# Override JLab CE environment for container use
+COPY docker/jlab.sh /jlab/${JLAB_VERSION}/ce/jlab.sh
 
-ENTRYPOINT ["/entrypoint.sh"]
+# Entry point loads the environment
+ENTRYPOINT ["/tini", "--", "bash", "-c", "source /etc/profile && \"$@\"", "-s"]
 
-CMD ["build/remoll","-h"]
+CMD ["remoll"]