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Reapply "Merge branch 'develop' into feature/lynnt_ccnuefilter"
This reverts commit d5e3270.
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.github/pull_request_template.md

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## Description
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Please provide a detailed description of the changes this pull request introduces.
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$${\color{red}!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!}$$
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$${\color{red}\bf{\textrm{IMPORTANT UPDATE June 22nd 2025:}}}$$ If you are making a PR which is intended as a patch for the CURRENT production (which started in Spring 2025), you must make two PRs: one for develop and one for the production/v10_06_00 branch.
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$${\color{red}!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!}$$
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## Checklist
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- [ ] Added at least 1 label from [available labels](https://github.com/SBNSoftware/sbndcode/issues/labels?sort=name-asc).
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- [ ] Assigned at least 1 reviewer under `Reviewers`,
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- [ ] Assigned all contributers including yourself under `Assignees`
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- [ ] Linked any relevant issues under `Developement`
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- [ ] Does this PR affect CAF data format? If so, please assign a CAF maintainer ([PetrilloAtWork](https://github.com/PetrilloAtWork) or [JosiePaton](https://github.com/JosiePaton)) as additional reviewer.
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- [ ] Does this affect the standard workflow?
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- [ ] Is this PR a patch for the ongoing production? If so, separate PR must also be made for production/v10_06_00 branch!
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### Relevant PR links (optional)
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Does this PR require merging another PR in a different repository (such as sbnanobj/sbnobj etc.)?

CMakeLists.txt

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cmake_minimum_required(VERSION 3.20 FATAL_ERROR)
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set(${PROJECT_NAME}_CMAKE_PROJECT_VERSION_STRING 10.06.00.01)
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set(${PROJECT_NAME}_CMAKE_PROJECT_VERSION_STRING 10.06.01)
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find_package(cetmodules REQUIRED)
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project(sbndcode LANGUAGES CXX)
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README.md

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# sbndcode
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## Getting Started
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[SBN Young Guide](https://sbnsoftware.github.io/SBNYoung/SBNYoungIndex.html)

sbndcode/JobConfigurations/base/cafmakerjob_sbnd_data_base.fcl

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# change tools in sbn to have 2D TPC sim/sp input
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physics.producers.pandoraShowerRazzle.SimChannelLabel: "sptpc2d:gauss"
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physics.producers.pandoraTrackDazzle.SimChannelLabel: "sptpc2d:gauss"
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physics.producers.cnnid.WireLabel: "sptpc2d:gauss"
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# uncomment below lines to use DNN ROI SP for Razzle/Dazzle/CNNID
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#physics.producers.pandoraShowerRazzle.SimChannelLabel: "sptpc2d:dnnsp"
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#physics.producers.pandoraTrackDazzle.SimChannelLabel: "sptpc2d:dnnsp"
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#physics.producers.cnnid.WireLabel: "sptpc2d:dnnsp"
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### Calorimetry for data
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physics.producers.cnnid.PointIdAlg.CalorimetryAlg: @local::sbnd_calorimetryalgdata

sbndcode/JobConfigurations/standard/caf/cafmakerjob_sbnd.fcl

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physics.producers.pandoraShowerRazzle.SimChannelLabel: "simtpc2d:simpleSC"
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physics.producers.pandoraTrackDazzle.SimChannelLabel: "simtpc2d:simpleSC"
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physics.producers.cnnid.WireLabel: "simtpc2d:gauss"
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# uncomment below line for to use DNN ROI SP for CNNID scores
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#physics.producers.cnnid.WireLabel: "simtpc2d:dnnsp"
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physics.producers.vertexCharge.CaloAlg: @local::sbnd_calorimetryalgmc
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physics.producers.vertexStub.CaloAlg: @local::sbnd_calorimetryalgmc

sbndcode/JobConfigurations/standard/caf/cafmakerjob_sbnd_data_sce.fcl

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physics.producers.cafmaker.CRTSpacePointMatchLabel: "crtspacepointmatchingSCE"
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physics.producers.cafmaker.SBNDCRTTrackMatchLabel: "crttrackmatchingSCE"
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physics.producers.cafmaker.OpT0Label: "opt0finderSCE"
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physics.producers.cafmaker.TPCPMTBarycenterMatchLabel: "tpcpmtbarycentermatchingSCE"
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physics.producers.cafmaker.CVNLabel: "cvnSCE"
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physics.producers.cnnid.ClusterModuleLabel: "pandoraSCE"

sbndcode/JobConfigurations/standard/caf/cafmakerjob_sbnd_sce.fcl

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physics.producers.cafmaker.CRTHitMatchLabel: "pandoraSCETrackCRTHit"
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physics.producers.cafmaker.CRTTrackMatchLabel: "pandoraSCETrackCRTTrack"
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physics.producers.cafmaker.OpT0Label: "opt0finderSCE"
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physics.producers.cafmaker.TPCPMTBarycenterMatchLabel: "tpcpmtbarycentermatchingSCE"
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physics.producers.cafmaker.CVNLabel: "cvnSCE"
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physics.producers.cnnid.ClusterModuleLabel: "pandoraSCE"

sbndcode/JobConfigurations/standard/reco/reco1_data.fcl

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outputs.out1.SelectEvents: [ "reco1" ]
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physics.producers.gaushit.CalDataModuleLabel: "sptpc2d:gauss"
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# uncomment below 4 lines to run DNN ROI finding SP
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#physics.producers.sptpc2d.wcls_main.outputers: ["wclsFrameSaver:spsaver" , "wclsFrameSaver:dnnsaver"]
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#physics.producers.sptpc2d.wcls_main.structs.use_dnnroi: true
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#physics.producers.sptpc2d.wcls_main.structs.nchunks: 2 # should match training config
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#physics.producers.sptpc2d.wcls_main.structs.tick_per_slice: 4 # should match training config
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# uncomment below line to run DNN ROI finding SP for reco
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#physics.producers.gaushit.CalDataModuleLabel: "sptpc2d:dnnsp"

sbndcode/JobConfigurations/standard/standard_detsim_sbnd.fcl

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]
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}
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}
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# uncomment below 4 lines to run DNN ROI finding SP
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# physics.producers.simtpc2d.wcls_main.outputers: ["wclsDepoFluxWriter:postdrift", "wclsFrameSaver:spsaver", "wclsFrameSaver:dnnsaver"] # "wclsFrameSaver:simdigits" <- by default, do not save RawDigits. Uncomment this line to save RawDigits and set
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# physics.producers.simtpc2d.wcls_main.structs.use_dnnroi: true
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# physics.producers.simtpc2d.wcls_main.structs.nchunks: 2 # should match training config
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# physics.producers.simtpc2d.wcls_main.structs.tick_per_slice: 4 # should match training config

sbndcode/JobConfigurations/standard/standard_reco1_sbnd.fcl

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#outputs table overrides
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outputs.out1.dataTier: "reconstructed"
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outputs.out1.outputCommands: [@sequence::outputs.out1.outputCommands, @sequence::sbnd_reco1_drops]
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# uncomment below line to run DNN ROI finding SP for reco -- must have run DNN ROI finding in detsim stage
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#physics.producers.gaushit.CalDataModuleLabel: "simtpc2d:dnnsp"

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