Merge branch 'main' into 1179-neural-network-inference-for-roman-pots

eic · Oct 31, 2024 · 90ee0e5 · 90ee0e5
2 parents ff41aa0 + 6a948d5
commit 90ee0e5
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diff --git a/.github/lsan.supp b/.github/lsan.supp
@@ -5,3 +5,4 @@ leak:edm4hep::*::createBuffers
 leak:libActsCore.so
 leak:libCling.so
 leak:libCore.so
+leak:libJANA.so
diff --git a/.github/workflows/linux-eic-shell.yml b/.github/workflows/linux-eic-shell.yml
@@ -210,7 +210,7 @@ jobs:
         path: clang_tidy_fixes.yml
         if-no-files-found: ignore
     - name: Suggest clang-tidy fixes as PR comments
-      uses: platisd/[email protected].0
+      uses: platisd/[email protected].1
       if: ${{ github.event_name == 'pull_request' }}
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
@@ -764,20 +764,19 @@ jobs:
         if_no_artifact_found: warn
     - name: Compare to previous artifacts
       uses: eic/run-cvmfs-osg-eic-shell@main
-      if: steps.download_previous_artifact.outputs.found_artifact == 'true'
       with:
         platform-release: "${{ env.platform }}:${{ env.release }}"
         setup: "/opt/detector/epic-${{ env.detector-version }}/bin/thisepic.sh"
         run: |
-          export PYTHONPATH=$HOME/.local/lib/python3.10/site-packages:$PYTHONPATH
           mkdir capybara-reports
           mkdir new
           ln -sf ../rec_${{ matrix.particle }}_1GeV_20GeV_${{ matrix.detector_config }}.edm4eic.root new/
-          capybara bara ref/rec_${{ matrix.particle }}_1GeV_20GeV_${{ matrix.detector_config }}.edm4eic.root new/rec_${{ matrix.particle }}_1GeV_20GeV_${{ matrix.detector_config }}.edm4eic.root
+          # using nullglob to ensure ref/* does not fail
+          shopt -s nullglob
+          capybara bara ref/*rec_${{ matrix.particle }}_1GeV_20GeV_${{ matrix.detector_config }}.edm4eic.root new/rec_${{ matrix.particle }}_1GeV_20GeV_${{ matrix.detector_config }}.edm4eic.root
           mv capybara-reports rec_${{ matrix.particle }}_1GeV_20GeV_${{ matrix.detector_config }}
           touch .rec_${{ matrix.particle }}_1GeV_20GeV_${{ matrix.detector_config }}
     - uses: actions/upload-artifact@v4
-      if: steps.download_previous_artifact.outputs.found_artifact == 'true'
       with:
         name: rec_${{ matrix.particle }}_1GeV_20GeV_${{ matrix.detector_config }}.capy
         path: |
@@ -965,21 +964,19 @@ jobs:
         if_no_artifact_found: warn
     - name: Compare to previous artifacts
       uses: eic/run-cvmfs-osg-eic-shell@main
-      if: steps.download_previous_artifact.outputs.found_artifact == 'true'
       with:
         platform-release: "${{ env.platform }}:${{ env.release }}"
         setup: "/opt/detector/epic-${{ env.detector-version }}/bin/thisepic.sh"
         run: |
-          pip install 'pygithub>=2' 'bokeh>=3'
-          export PYTHONPATH=$HOME/.local/lib/python3.10/site-packages:$PYTHONPATH
           mkdir capybara-reports
           mkdir new
           ln -sf ../rec_dis_${{matrix.beam}}_minQ2=${{matrix.minq2}}_${{ matrix.detector_config }}.edm4eic.root new/
-          capybara bara ref/rec_dis_${{matrix.beam}}_minQ2=${{matrix.minq2}}_${{ matrix.detector_config }}.edm4eic.root new/rec_dis_${{matrix.beam}}_minQ2=${{matrix.minq2}}_${{ matrix.detector_config }}.edm4eic.root
+          # using nullglob to ensure ref/* does not fail
+          shopt -s nullglob
+          capybara bara ref/*rec_dis_${{matrix.beam}}_minQ2=${{matrix.minq2}}_${{ matrix.detector_config }}.edm4eic.root new/rec_dis_${{matrix.beam}}_minQ2=${{matrix.minq2}}_${{ matrix.detector_config }}.edm4eic.root
           mv capybara-reports rec_dis_${{matrix.beam}}_minQ2=${{matrix.minq2}}_${{ matrix.detector_config }}
           touch .rec_dis_${{matrix.beam}}_minQ2=${{matrix.minq2}}_${{ matrix.detector_config }}
     - uses: actions/upload-artifact@v4
-      if: steps.download_previous_artifact.outputs.found_artifact == 'true'
       with:
         name: rec_dis_${{matrix.beam}}_minQ2=${{matrix.minq2}}_${{ matrix.detector_config }}.capy
         path: |

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -2,7 +2,7 @@ ci:
     skip: [clang-format]
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.6.0
+  rev: v5.0.0
   hooks:
   - id: end-of-file-fixer
   - id: trailing-whitespace

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -150,13 +150,10 @@ set(CMAKE_INSTALL_RPATH
 set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
 
 # Check and print what JANA2 is used
-find_package(JANA 2.0.8 REQUIRED)
+find_package(JANA REQUIRED)
 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}")
-add_compile_definitions(HAVE_PODIO)
-# TODO: NWB: Do this correctly in JANA via target_compile_definitions for v2.1.1
-# TODO: NWB: Maybe we want these to be prefixed, e.g. JANA2_HAVE_PODIO
 
 # Algorithms
 find_package(algorithms 1.0.0 REQUIRED Core)

diff --git a/docs/howto/use_docker.md b/docs/howto/use_docker.md
@@ -8,7 +8,7 @@ The containers are released both for docker and singularity. Singularity images
 - [Docker Hub](https://hub.docker.com/u/eicweb)
 - CVMFS path (available at BNL and JLab):
   ```
-  singularity run /cvmfs/singularity.opensciencegrid.org/eicweb/jug_xl:nightly
+  singularity run /cvmfs/singularity.opensciencegrid.org/eicweb/eic_xl:nightly
   ```
 
 ### Images structure:
@@ -19,7 +19,7 @@ The containers are released both for docker and singularity. Singularity images
 
 - **debian_base** - is a container generic base container based on amd64/debian:testing
 - **jug_dev** - have all major HENP packages such as ROOT, Geant4 and DD4HEP but without detector and reconstruction. The image is used for testing purposes and automation.
-- **jug_xl** - intended to be used to run simulation and work on detectors for users. jug_dev + full simulation packages
+- **eic_xl** - intended to be used to run simulation and work on detectors for users. jug_dev + full simulation packages
 
 
 
@@ -39,7 +39,7 @@ So testing is the precursor to the next release version.
 
 **TL;DR;**
 
-Now it is recommended to use: ```eicweb/jug_xl:nightly```
+Now it is recommended to use: ```eicweb/eic_xl:nightly```
 
 
 ## Run in docker
@@ -50,13 +50,13 @@ Containers are available at eicweb namespace at
 To download or update the container:
 
 ```bash
-docker pull eicweb/jug_xl:nightly
+docker pull eicweb/eic_xl:nightly
 ```
 
 Running docker (minimal and probably useless):
 
 ```bash
-docker run -it --rm eicweb/jug_xl:nightly
+docker run -it --rm eicweb/eic_xl:nightly
 ```
 
 
@@ -113,7 +113,7 @@ You can bind any directory on your system to docker image by using **-v** flag:
 Convenient place inside docker image is `/mnt/` directory. Full example:
 
 ```bash
-docker run -it -v /home/user/eic/data:/mnt/data --rm eicweb/jug_xl:nightly
+docker run -it -v /home/user/eic/data:/mnt/data --rm eicweb/eic_xl:nightly
 ls /mnt/data
 ```
 
@@ -133,7 +133,7 @@ ls /mnt/data
 With debugging enabled and all ports open:
 
 ```
-docker run -it --rm --cap-add=SYS_PTRACE --security-opt seccomp=unconfined eicweb/jug_xl:nightly
+docker run -it --rm --cap-add=SYS_PTRACE --security-opt seccomp=unconfined eicweb/eic_xl:nightly
 ```
 
 
@@ -146,7 +146,7 @@ The setup depends on particular tool:
 - [Visual Studio Code docker remote debugging](https://code.visualstudio.com/docs/remote/remote-overview)
 - [CLion docker toolchain](https://www.jetbrains.com/help/clion/clion-toolchains-in-docker.html)
 
-> Use `\usr\local\bin\cmake` as cmake path, when configuring IDEs with jug_xl image
+> Use `\usr\local\bin\cmake` as cmake path, when configuring IDEs with eic_xl image
 
 ![vscode-docker](vscode_docker.png ':size=800')
 
@@ -166,7 +166,7 @@ You can use X11 natively (as natively as possible) with this docker image in you
 To use graphics, make sure you are in an X11 session and run the following command:
 
 ```bash
-docker run -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix --rm -it --user $(id -u) eicweb/jug_xl:nightly
+docker run -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix --rm -it --user $(id -u) eicweb/eic_xl:nightly
 ```
 
 There might be issues with user id on systems like JLab farms.
@@ -179,7 +179,7 @@ Make sure VcXsrv is whitelisted in the Windows firewall when prompted.
 Start VcXsrv with 'allow from any origin' flag
 
 ```bash
-docker run --rm -it -e LIBGL_ALWAIS_INDIRECT=1 -e DISPLAY=10.0.75.1:0 eicweb/jug_xl:nightly
+docker run --rm -it -e LIBGL_ALWAIS_INDIRECT=1 -e DISPLAY=10.0.75.1:0 eicweb/eic_xl:nightly
 ```
 
 > 10.0.75.1 address corresponds to the network configuration in docker settings
@@ -208,7 +208,7 @@ This will start XQuartz and whitelist your local IP address.
 Finally, you can start up docker with the following command:
 
 ```
-docker run --rm -it -v /tmp/.X11-unix:/tmp/.X11-unix -e DISPLAY=$ip:0 eicweb/jug_xl:nightly
+docker run --rm -it -v /tmp/.X11-unix:/tmp/.X11-unix -e DISPLAY=$ip:0 eicweb/eic_xl:nightly
 ```
 
 
@@ -221,7 +221,7 @@ action needed. For the most optimal experience, you can install your software to
 ``/usr/local`` is a symlink to ``/opt/view``).
 
 ```
-FROM eicweb/jug_xl:nightly
+FROM eicweb/eic_xl:nightly
 RUN apt-get update \
     && export DEBIAN_FRONTEND=noninteractive \
     && apt-get -y install git gdb

diff --git a/docs/howto/use_singularity.md b/docs/howto/use_singularity.md
@@ -88,10 +88,10 @@ For farms like at BNL or JLab the images are automatically replicated to
 CVMS:
 
 ```bash
-/cvmfs/singularity.opensciencegrid.org/eicweb/jug_xl*
+/cvmfs/singularity.opensciencegrid.org/eicweb/eic_xl*
 
 # example to run
-singularity run /cvmfs/singularity.opensciencegrid.org/eicweb/jug_xl:nightly
+singularity run /cvmfs/singularity.opensciencegrid.org/eicweb/eic_xl:nightly
 ```
 
 ### eic-shell explained
@@ -106,7 +106,7 @@ singularity like:
 # $PREFIX here is where you installed everything (by default where install.sh executed)
 export EIC_SHELL_PREFIX=...
 export SINGULARITY_BINDPATH=/home
-singularity exec $PREFIX/local/lib/jug_xl-nightly.sif eic-shell $@
+singularity exec $PREFIX/local/lib/eic_xl-nightly.sif eic-shell $@
 ```
 
 The **eic-shell** inside the container loads the proper environment and

diff --git a/docs/tutorial/02-work-environment.md b/docs/tutorial/02-work-environment.md
@@ -24,7 +24,7 @@ curl --location https://get.epic-eic.org | bash
 # or, if /cvmfs is available:
 # n.b. on JLab ifarm you may need to do 'module load singularity/3.9.5' first
 
-singularity exec /cvmfs/singularity.opensciencegrid.org/eicweb/jug_xl:nightly eic-shell
+singularity exec /cvmfs/singularity.opensciencegrid.org/eicweb/eic_xl:nightly eic-shell
 
 ```
 Once inside the eic-shell, you should source the geometry setup script since this is not done by default.