Merge branch 'main' into WilfS/feature_nestedTubes

.github/workflows/container.yml

@@ -0,0 +1,60 @@
+name: Build Docker Image
+
+on:
+  schedule:
+    - cron: '0 4 * * *' # Everyday at 4am UTC
+  push:
+    branches: [ main ]
+    tags: 
+      - "v*.*.*"
+  workflow_dispatch:
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    # Don't let forks build containers
+    if: github.repository == 'rat-pac/ratpac-two'
+    permissions: 
+      packages: write
+      contents: read
+      attestations: write
+      id-token: write
+    steps:
+      - name: Docker meta
+        id: meta
+        uses: docker/metadata-action@v5
+        with:    
+          images: |
+            ratpac/ratpac-two
+            ghcr.io/${{ github.repository }}
+          # generate Docker tags based on the following events/attributes
+          # Using default, which should generate tags for branchs and `nightly`
+          # tags: |
+          #   type=schedule
+          #   type=ref,event=branch
+          #   type=ref,event=workflow_dispatch
+          #   type=semver,pattern={{raw}}
+          #   type=sha
+      -
+        name: Login to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - 
+        name: Login to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      -
+        name: Build and push
+        id: push
+        uses: docker/build-push-action@v5
+        with:
+          file: containers/Dockerfile
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/rattests-template.yml

@@ -0,0 +1,41 @@
+on:
+  workflow_call:
+    inputs:
+      rattest-name:
+        required: true
+        type: string
+
+jobs:
+  rattest:
+    runs-on: ubuntu-latest
+    container: 
+      image: ratpac/ratpac-two:latest-base
+      options: --user root
+    steps:
+    - name: Get build cache
+      id: cache
+      uses: actions/cache/restore@v4
+      with:
+        path: ratpac2
+        key: ${{ github.sha }}-install
+    - name: Run rattest 
+      working-directory: ratpac2
+      shell: bash
+      run: |
+        source /ratpac-setup/env.sh
+        source ../ratpac2/ratpac.sh
+        rattest -t test/full/${{ inputs.rattest-name }}
+      id: test
+      continue-on-error: true
+    - name: upload-result
+      uses: actions/upload-artifact@v4
+      with:
+        name: ${{ inputs.rattest-name }}-result
+        if-no-files-found: error
+        path: |
+          ratpac2/test/full/${{ inputs.rattest-name }}/*.png
+          ratpac2/test/full/${{ inputs.rattest-name }}/*.html
+    - name: check-test-result
+      if: steps.test.outcome != 'success'
+      run: exit 1 
+

.github/workflows/rattests.yml

@@ -0,0 +1,42 @@
+name: rattests
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    container: 
+      image: ratpac/ratpac-two:latest-base
+      options: --user root
+    steps:
+    - name: Checkout Ratpac2
+      uses: actions/checkout@v4
+      with:
+        path: ratpac2
+    - name: Build Ratpac2
+      working-directory: ratpac2
+      shell: bash
+      run: |
+        source /ratpac-setup/env.sh
+        make -j$(nproc)
+    - name: Cache build output
+      id: cache
+      uses: actions/cache/save@v4
+      with:
+        key: ${{ github.sha }}-install
+        path: ratpac2
+
+  acrylic_attenuation:
+    needs: build
+    uses: ./.github/workflows/rattests-template.yml
+    with:
+      rattest-name: acrylic_attenuation
+
+  fitcentroid:
+    needs: build
+    uses: ./.github/workflows/rattests-template.yml
+    with:
+      rattest-name: fitcentroid

.gitignore

@@ -19,6 +19,7 @@ src/core/Config.hh
 
 *.log
 *.root
+!test/full/*/standard.root
 *.heprep
 .DS_Store
 *.gif
@@ -28,7 +29,14 @@ src/core/Config.hh
 
 .idea/
 .vscode/
+.cache/
+compile_commands.json
 doc/_build/
+doc/doxygen
 .pytest_cache*
 ratpac.*sh
 RatpacConfig.cmake
+
+# rattest outputs 
+test/full/*/*.png 
+test/full/*/*.html

.readthedocs.yml

@@ -2,7 +2,7 @@
 version: 2
 
 build:
-  os: "ubuntu-20.04"
+  os: "ubuntu-22.04"
   tools:
     python: "3.11"
 

CMakeLists.txt

@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 3.11...3.14)
-project(ratpac VERSION 2.1.3
+project(ratpac VERSION 2.3.0
                 DESCRIPTION "RAT-PAC"
                 LANGUAGES C CXX)
 
@@ -78,9 +78,12 @@ else()
 endif()
 include(${ROOT_USE_FILE})
 
-find_package(Geant4 REQUIRED COMPONENTS qt)
+find_package(Geant4 REQUIRED)
+find_package(Geant4 QUIET OPTIONAL_COMPONENTS qt)
 include(${Geant4_USE_FILE})
 include_directories(${Geant4_INCLUDE_DIRS})
+include_directories(${CLHEP_INCLUDE_DIRS})
+include_directories(${XercesC_INCLUDE_DIRS})
 
 find_package(Threads REQUIRED)
 
@@ -136,6 +139,9 @@ install(DIRECTORY models/ DESTINATION ${RATSHARE}/models
 install(DIRECTORY python/ DESTINATION ${RATSHARE}/python
   PATTERN "python/*")
 
+# Install rattest executable
+install(PROGRAMS python/rattest.py DESTINATION bin RENAME rattest)
+
 # Install the macro files
 install(DIRECTORY macros/ DESTINATION ${RATSHARE}/macros
   PATTERN "macros/*")

Makefile

@@ -4,7 +4,7 @@ build_directory := build
 install_directory := $(PWD)/install
 
 all:
-	ln -sf ../../cformat.sh ./.git/hooks/pre-commit
+	ln -sf $(PWD)/cformat.sh $(shell git rev-parse --git-common-dir)/hooks/pre-commit
 	cmake . -B$(build_directory) -DCMAKE_INSTALL_PREFIX=$(install_directory)
 	cmake --build $(build_directory) -- $(MAKEFLAGS)
 	cmake --install $(build_directory) &> /dev/null

README.md

@@ -1,27 +1,67 @@
 # Ratpac-two
+
 [![Documentation Status](https://readthedocs.org/projects/ratpac/badge/?version=latest)](https://ratpac.readthedocs.io/en/latest/?badge=latest)
 
 [![Build RatpacExperiment](https://github.com/rat-pac/ratpac-two/actions/workflows/build-experiment.yml/badge.svg)](https://github.com/rat-pac/ratpac-two/actions/workflows/build-experiment.yml)
 
 [![clang-format Check](https://github.com/rat-pac/ratpac-two/actions/workflows/check-format.yml/badge.svg)](https://github.com/rat-pac/ratpac-two/actions/workflows/check-format.yml)
 
-[ratpac.readthedocs.io](ratpac.readthedocs.io)
+[![Build Docker Image](https://github.com/rat-pac/ratpac-two/actions/workflows/latest-container.yml/badge.svg?branch=main&event=deployment)](https://github.com/rat-pac/ratpac-two/actions/workflows/latest-container.yml)
+
+[ratpac.readthedocs.io](https://ratpac.readthedocs.io)
+
+## Quick Start with containers
+
+The easiest way to get started with ratpac-two is via containers. The latest
+builds can be found on
+[dockerhub](https://hub.docker.com/r/ratpac/ratpac-two/tags) or on
+[ghcr.io](https://github.com/rat-pac/ratpac-two/pkgs/container/ratpac-two).
+
+On HPC platforms, apptainer/singularity containers are a better option than
+docker containers. To create these, run
+
+```sh
+apptainer pull ratpac2.sif docker://ratpac/ratpac-two:main
+```
+
+To enter the container:
+
+```sh
+apptainer run [-B /disks/to/mount] ratpac2.sif
+```
+
 ## Installation
-Installation requires [ROOT 6.25+](https://root.cern.ch), 
+
+Installation requires [ROOT 6.25+](https://root.cern.ch),
 [Geant4 11.0+](https://geant4.web.cern.ch/), and [cmake 3.22+](https://cmake.org/)
 
-Install using cmake
+For development, the following are also required:
 
-    $ cmake . -Bbuild
-    $ cmake --build build -- -j$(nproc)
+- clang-format: major version 14. _other major versions are known to produce
+different outputs that will result in failed checks_
 
-If you want to install the code, just add
+The most well-supported way of installing ratpac-two is via the [ratpac-setup
+script](https://github.com/rat-pac/ratpac-setup). Follow the instruction will
+produce a standalone directory that includes all dependencies. You can also
+check this repo for the best-tested minor versions of each dependency.
+
+A convenience Makefile exists to automate the above process, simply type `make`.
+
+Install using cmake:
 
-    $ cmake --build build . --target install -j$(nproc)
+``` sh
+    cmake . -Bbuild
+    cmake --build build -- -j$(nproc)
+```
 
-A convenience Makefile exists to automate the above process.
+If you want to install the code, just add
+
+``` sh
+    cmake --build build . --target install -j$(nproc)
+```
 
 ## Usage
+
 Ratpac-two compiles as a library which can be extended for specific experiment
 use cases. The library can be accessed through CMake using
 `find_package(Ratpac)`.
@@ -32,6 +72,7 @@ against the ratpac library, and any specific additions to the C++ framework
 should exist outside of the main repository.
 
 ## About
+
 Ratpac-two is a refactor of ratpac which makes the necessary changes to compile
 with modern versions of GCC and is compatible with the latest Geant4 and ROOT
 versions. This version of Ratpac is not backwards compatible with the previous

cformat.sh

@@ -11,7 +11,7 @@ fi
 
 echo "Checking formatting..."
 changes=0
-for file in $(find ./src \( -name "*.cc" -o -name "*.hh" -o -name "*.icc" -o -name "*.cpp" -o -name "*.hpp" \)); do
+for file in $(find ./src ./test \( -name "*.cc" -o -name "*.hh" -o -name "*.icc" -o -name "*.cpp" -o -name "*.hpp" -o -name "*.C" \)); do
     retval=$(clang-format -style=file -n -Werror $file)
     if [ $? -eq 1 ]; then
         echo "Formatting $file"

containers/Dockerfile

@@ -1,13 +1,13 @@
-FROM ratpac/ratpac-two:base
-LABEL maintainer="Morgan Askins <maskins@berkeley.edu>"
+FROM ratpac/ratpac-two:latest-base
+LABEL maintainer="James Shen <[email protected].edu>"
 
 SHELL ["/bin/bash", "-c"]
 
 USER ratuser
 
 WORKDIR /ratpac-setup
 
-RUN ./setup.sh --only ratpac -j6
+RUN ./setup.sh --only ratpac -j$(nproc)
 RUN cd ratpac && cmake --install build && cd ..
 
 RUN sed -i '1s/^/#!\/bin\/bash\n/' /ratpac-setup/env.sh