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add occupancy banks and bookkeeping class #1469

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1 change: 0 additions & 1 deletion .github-ci.yaml
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5 changes: 4 additions & 1 deletion .github/dependabot.yml
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Expand Up @@ -19,7 +19,10 @@ updates:
prefix: "build(deps)"
ignore:
- dependency-name: "org.jlab:groot" # since version numbers are not in order
- dependency-name: "org.ejml:ejml-simple" # keep version the same as `j4ml:j4ml-clas12:jar:0.9-SNAPSHOT`; see pull requests #636 and #632
- dependency-name: "net.objecthunter:exp4j" # pinned for dependency convergence
- dependency-name: "org.ejml:ejml-simple" # pinned for dependency convergence
- dependency-name: "org.apache.commons:commons-lang3" # pinned for dependency convergence
- dependency-name: "org.slf4j:slf4j-api" # pinned for dependency convergence
- dependency-name: "org.openjfx:javafx-base"
versions: [">= 24"] # version 24 requires JAVA_VERSION 22+
- dependency-name: "org.openjfx:javafx-graphics"
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70 changes: 45 additions & 25 deletions .github/workflows/ci.yml
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Expand Up @@ -61,7 +61,7 @@ jobs:
runs-on: macos-latest
steps:
- uses: actions/checkout@v7
- uses: actions/setup-java@v5.7.0
- uses: actions/setup-java@v6.0.1
with:
java-version: ${{ env.JAVA_VERSION }}
distribution: ${{ env.java_distribution }}
Expand All @@ -72,7 +72,7 @@ jobs:
- name: build
run: |
./build-coatjava.sh --lfs --no-progress -T${{ env.nthreads }}
./bin/install-clara -b -c ./coatjava ./clara
./bin/install-clara -c ./coatjava ./clara
- name: tar # tarball to preserve permissions
run: |
tar czvf coatjava.tar.gz coatjava
Expand All @@ -91,7 +91,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v7
- uses: actions/setup-java@v5.7.0
- uses: actions/setup-java@v6.0.1
with:
java-version: ${{ env.JAVA_VERSION }}
distribution: ${{ env.java_distribution }}
Expand All @@ -102,7 +102,7 @@ jobs:
- name: build
run: |
./build-coatjava.sh --lfs --no-progress -T${{ env.nthreads }}
./bin/install-clara -b -c ./coatjava ./clara
./bin/install-clara -c ./coatjava ./clara
- name: tar # tarball to preserve permissions
run: |
tar czvf coatjava.tar.gz coatjava
Expand All @@ -115,6 +115,26 @@ jobs:
coatjava.tar.gz
clara.tar.gz

dependency_info:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v7
- name: Set up JDK
uses: actions/setup-java@v6.0.1
with:
java-version: ${{ env.JAVA_VERSION }}
distribution: ${{ env.java_distribution }}
# NOTE: do not use `cache: maven` here, so stale `_remote.repositories` data aren't read
- name: build
run: |
./build-coatjava.sh --no-aux --no-progress --quiet -T${{ env.nthreads }}
- name: collect info
run: libexec/dependency-info.rb
- name: print dependency trees
run: cat target/info/trees.txt
- name: print dependency repository sources
run: cat target/info/repos.yaml

# tests
#############################################################################

Expand All @@ -137,7 +157,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v7
- uses: actions/setup-java@v5.7.0
- uses: actions/setup-java@v6.0.1
with:
java-version: ${{ matrix.JAVA_VERSION }}
distribution: ${{ env.java_distribution }}
Expand All @@ -161,7 +181,7 @@ jobs:
steps:
- uses: actions/checkout@v7
- name: Set up JDK
uses: actions/setup-java@v5.7.0
uses: actions/setup-java@v6.0.1
with:
java-version: ${{ env.JAVA_VERSION }}
distribution: ${{ env.java_distribution }}
Expand All @@ -170,7 +190,7 @@ jobs:
with:
name: build_ubuntu-latest
- name: untar build
run: tar xzvf coatjava.tar.gz
run: tar xzf coatjava.tar.gz
- name: spotbugs
run: ./build-coatjava.sh --spotbugs --no-maps --no-progress

Expand All @@ -180,7 +200,7 @@ jobs:
steps:
- uses: actions/checkout@v7
- name: Set up JDK
uses: actions/setup-java@v5.7.0
uses: actions/setup-java@v6.0.1
with:
java-version: ${{ env.JAVA_VERSION }}
distribution: ${{ env.java_distribution }}
Expand All @@ -194,7 +214,7 @@ jobs:
path: |
clas_018779.evio.00001
- name: untar build
run: tar xzvf coatjava.tar.gz
run: tar xzf coatjava.tar.gz
- name: run test
run: |
ls -lhtr
Expand All @@ -209,7 +229,7 @@ jobs:
steps:
- uses: actions/checkout@v7
- name: Set up JDK
uses: actions/setup-java@v5.7.0
uses: actions/setup-java@v6.0.1
with:
java-version: ${{ env.JAVA_VERSION }}
distribution: ${{ env.java_distribution }}
Expand All @@ -224,11 +244,11 @@ jobs:
clas_018779.evio.00001
- name: untar build
run: |
tar xzvf clara.tar.gz
tar xzvf coatjava.tar.gz
tar xzf clara.tar.gz
tar xzf coatjava.tar.gz
- run: ls
- name: run test
run: ./bin/run-clara -y ./etc/services/rgd-clarode.yml -t 4 -n 500 -c ./clara -o ./tmp ./clas_018779.evio.00001
run: ./bin/run-clara -y ./etc/services/data-ai.yaml -t 4 -n 500 -c ./clara -o ./tmp ./clas_018779.evio.00001
- name: ls tmp
run: ls -lhtr tmp
- name: rename
Expand Down Expand Up @@ -267,7 +287,7 @@ jobs:
steps:
- uses: actions/checkout@v7
- name: Set up JDK
uses: actions/setup-java@v5.7.0
uses: actions/setup-java@v6.0.1
with:
java-version: ${{ env.JAVA_VERSION }}
distribution: ${{ env.java_distribution }}
Expand All @@ -277,8 +297,8 @@ jobs:
name: build_${{ matrix.runner }}
- name: untar build
run: |
tar xzvf coatjava.tar.gz
tar xzvf clara.tar.gz
tar xzf coatjava.tar.gz
tar xzf clara.tar.gz
- name: run test
run: |
git lfs install
Expand All @@ -295,7 +315,7 @@ jobs:
steps:
- uses: actions/checkout@v7
- name: Set up JDK
uses: actions/setup-java@v5.7.0
uses: actions/setup-java@v6.0.1
with:
java-version: ${{ env.JAVA_VERSION }}
distribution: ${{ env.java_distribution }}
Expand All @@ -305,8 +325,8 @@ jobs:
name: build_macos
- name: untar build
run: |
tar xzvf coatjava.tar.gz
tar xzvf clara.tar.gz
tar xzf coatjava.tar.gz
tar xzf clara.tar.gz
- name: run test
run: |
git lfs install
Expand All @@ -320,7 +340,7 @@ jobs:
steps:
- uses: actions/checkout@v7
- name: Set up JDK
uses: actions/setup-java@v5.7.0
uses: actions/setup-java@v6.0.1
with:
java-version: ${{ env.JAVA_VERSION }}
distribution: ${{ env.java_distribution }}
Expand All @@ -333,7 +353,7 @@ jobs:
with:
name: build_ubuntu-latest
- name: untar build
run: tar xzvf coatjava.tar.gz
run: tar xzf coatjava.tar.gz
- name: test run-groovy
run: coatjava/bin/run-groovy validation/advanced-tests/test-run-groovy.groovy

Expand All @@ -343,7 +363,7 @@ jobs:
steps:
- uses: actions/checkout@v7
- name: Set up JDK
uses: actions/setup-java@v5.7.0
uses: actions/setup-java@v6.0.1
with:
java-version: ${{ env.JAVA_VERSION }}
distribution: ${{ env.java_distribution }}
Expand All @@ -355,7 +375,7 @@ jobs:
with:
name: build_ubuntu-latest
- name: untar build
run: tar xzvf coatjava.tar.gz
run: tar xzf coatjava.tar.gz
- name: hipo2npz
run: ./coatjava/bin/hipo2npz rec.hipo rec.npz
- name: hipo2npz-dump
Expand Down Expand Up @@ -384,7 +404,7 @@ jobs:
path: pages/jacoco
### javadoc
- name: set up JDK
uses: actions/setup-java@v5.7.0
uses: actions/setup-java@v6.0.1
with:
java-version: ${{ env.JAVA_VERSION }}
distribution: ${{ env.java_distribution }}
Expand Down Expand Up @@ -440,7 +460,7 @@ jobs:
mv coatjava{,-${{ env.TAG_NAME }}}
tar czf coatjava-${{ env.TAG_NAME }}{.tar.gz,}
- name: release
uses: softprops/action-gh-release@v3.0.2
uses: softprops/action-gh-release@v3.0.3
with:
files: coatjava-${{ env.TAG_NAME }}.tar.gz
- name: open issue if failed
Expand Down
6 changes: 5 additions & 1 deletion .gitignore
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Expand Up @@ -8,6 +8,11 @@ target
tmp
/common-tools/clas-io/src/main/java/org/jlab/io/banks

# data files
*.evio
*.hipo
!/etc/data/test/*.hipo

# deployment
/myLocalMvnRepo
/coatjava-*.tar.gz
Expand Down Expand Up @@ -50,7 +55,6 @@ hs_err_pid*

# no log files:
*.log
*.evio

bin/evio2hipotest
export.sh
14 changes: 7 additions & 7 deletions .gitlab-ci.yml
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Expand Up @@ -172,16 +172,16 @@ clara:
dependencies: [build,download]
script:
- tar -xzf clara.tar.gz
- run-clara -v -c $CLARA_HOME -t 4 -y ./etc/services/rgd-clarode.yml -n 30 -o out $EVIOFILE
- run-clara -v -c $CLARA_HOME -t 4 -y ./etc/services/data-ai.yaml -n 30 -o out $EVIOFILE
- mv out/rec_$EVIOFILE.hipo claroded.hipo

profile:
extends: .clon
allow_failure: true
script:
- ./clara/plugins/clas12/libexec/profile -e cpu run-clara -c ./clara -y ./etc/services/rgd-clarode.yml -o tmp1 -t 16 -l $EVIOFILE
- ./clara/plugins/clas12/libexec/profile -e alloc run-clara -c ./clara -y ./etc/services/rgd-clarode.yml -o tmp2 -t 16 -l $EVIOFILE
- ./clara/plugins/clas12/libexec/profile -e lock run-clara -c ./clara -y ./etc/services/rgd-clarode.yml -o tmp3 -t 16 -l $EVIOFILE
- ./clara/plugins/clas12/libexec/profile -e cpu -o _clara -- run-clara -c ./clara -y ./etc/services/data-ai.yaml -o tmp1 -t 16 -l $EVIOFILE
- ./clara/plugins/clas12/libexec/profile -e alloc -o _clara -- run-clara -c ./clara -y ./etc/services/data-ai.yaml -o tmp2 -t 16 -l $EVIOFILE
- ./clara/plugins/clas12/libexec/profile -e lock -o _clara -- run-clara -c ./clara -y ./etc/services/data-ai.yaml -o tmp3 -t 16 -l $EVIOFILE
artifacts:
when: always
expire_in: 1 week
Expand All @@ -192,12 +192,12 @@ scaling:
extends: .clon
allow_failure: true
script:
- ./clara/plugins/clas12/libexec/scaling -c ./clara -y ./etc/services/rgd-clarode.yml -t 8,12,18,24 $EVIOFILE
- ./clara/plugins/clas12/libexec/scaling -c ./clara -y ./etc/services/data-ai.yaml -t 8,12,18,24 $EVIOFILE
artifacts:
when: always
expire_in: 1 week
paths:
- scaling.svg
- scaling*.svg

pages:
stage: deploy
Expand All @@ -207,7 +207,7 @@ pages:
- cp -r pages public
- mkdir public/perf
- cp asprof*.html public/perf
- cp scaling.svg public/perf
- cp scaling*.svg public/perf
pages: true
artifacts:
expire_in: 1 week
Expand Down
24 changes: 24 additions & 0 deletions Makefile
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@@ -0,0 +1,24 @@
# this is a simple Makefile meant for developers' convenience
# - it only has the most common build commands we use
# - for any other build command, please use `./build-coatjava.sh`

# convert `make` arg `-j#` -> `mvn` arg `-T#`, if provided
JOBS := $(patsubst -j%,%,$(filter -j%,$(MAKEFLAGS)))
THREADS := $(if $(strip $(JOBS)),-T$(JOBS),)

BUILD := ./build-coatjava.sh

.PHONY: default all clean clara

.DEFAULT_GOAL := default

default:
$(BUILD) $(THREADS)

clean:
$(BUILD) --clean $(THREADS)

clara:
$(BUILD) --clara $(THREADS)

all: clara
16 changes: 4 additions & 12 deletions bin/install-clara
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Expand Up @@ -71,13 +71,12 @@ trap cleanup EXIT
# Configure:
debug=0
args=()
usage="Usage: install-clara [-v] [-b] [-c COATJAVA] [-f CLARA] [-g GRAPES] PATH"
usage="Usage: install-clara [-v] [-c COATJAVA] [-f CLARA] [-g GRAPES] PATH"
info="""
- The default CLARA / GRAPES versions are $clara / $grapes
- COATJAVA can also be specified as a local installation directory
- If the COATJAVA version is not specified, it will try to auto-detect it.
- [-v adds verbosity and disables cleanup]
- [-b builds clara from source]"""
- [-v adds verbosity and disables cleanup]"""

while [[ $# -gt 0 ]]
do
Expand All @@ -86,7 +85,6 @@ do
-f) clara="$2" && shift && shift ;;
-c) coatjava="$2" && shift && shift ;;
-g) grapes="$2" && shift && shift ;;
-b) build=1 && shift ;;
-v) let debug=$debug+1 && shift ;;
-*|--*) echo -e "$usage\n\nUnknown option: $1" && exit 1 ;;
*) args+=("$1") && shift ;;
Expand Down Expand Up @@ -126,14 +124,8 @@ tmp_dir=$(cd $tmp_dir && pwd)
cd $tmp_dir

# CLARA:
if ! [ -z ${build+x} ]
then
echo -e "\nBuilding CLARA from source ..."
build_clara $PWD/clara-cre
else
echo -e "\nRetrieving CLARA version $clara ..."
get https://clasweb.jlab.org/clas12offline/distribution/clara/clara-cre-$clara.tar.gz
fi
echo -e "\nBuilding CLARA from source ..."
build_clara $PWD/clara-cre

# COATJAVA:
if ! compgen -G "$coatjava/lib/clas/coat-libs-*.jar" > /dev/null
Expand Down
10 changes: 0 additions & 10 deletions bin/postprocess2
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7 changes: 0 additions & 7 deletions bin/run-groovy
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@@ -1,11 +1,4 @@
#!/bin/bash

. `dirname $0`/../libexec/env.sh groovy

echo """
****************************************
* Running COATJAVA Groovy Script *
****************************************
"""

groovy -cp "$JYPATH" "$@"
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