Changes

Add GitHub actions to CI (#1020)

* Don't default CMake presets to "debug"

* Rename CI presets

* Use CMake BUILD_TESTING to decide to add testing tree

This allows more granularity for building unit tests or just testing the apps

* First iteration of GHA CI

* Integrate style workflow

* Try again

* Fix things, thanks vscode

* Fix exclusion

* Disable clang-format, try different docker url

* REVERTME: single job

* Run as root

see https://github.com/actions/checkout/issues/956

```
Post job cleanup.
/usr/bin/docker exec  8a93ca44215e080743610d80ccea33c624f5d3fce1aa4038cd018c06b13a75a6 sh -c "cat /etc/*release | grep ^ID"
node:internal/fs/utils:347
    throw err;
    ^

Error: EACCES: permission denied, open '/__w/_temp/_runner_file_commands/save_state_56877b46-0efb-448b-8122-6d4d35217f1e'
    at Object.openSync (node:fs:590:3)
    at Object.writeFileSync (node:fs:2202:35)
    at Object.appendFileSync (node:fs:2264:6)
    at Object.issueFileCommand (/__w/_actions/actions/checkout/v3/dist/index.js:2950:8)
    at Object.saveState (/__w/_actions/actions/checkout/v3/dist/index.js:2867:31)
    at Object.8647 (/__w/_actions/actions/checkout/v3/dist/index.js:2326:10)
    at __nccwpck_require__ (/__w/_actions/actions/checkout/v3/dist/index.js:18256:43)
    at Object.2565 (/__w/_actions/actions/checkout/v3/dist/index.js:146:34)
    at __nccwpck_require__ (/__w/_actions/actions/checkout/v3/dist/index.js:18256:43)
    at Object.9210 (/__w/_actions/actions/checkout/v3/dist/index.js:1141:36) {
  errno: -13,
  syscall: 'open',
  code: 'EACCES',
  path: '/__w/_temp/_runner_file_commands/save_state_56877b46-0efb-448b-8122-6d4d35217f1e'
}
```

* Introspect

* Try a different shell

* Source the fucking profile perhaps since it might ignore entrypoint

* No source I guess

* use github env, run tests

* Try to fix environment

* Try again

* Fix (I think?) openmp variables for celer-sim app

* Disable GPU tests at configure time if CELER_DISABLE_DEVICE

* Automatically skip device tests if CELER_DISABLE_DEVICE

* Update versions

* Use std allocateor rather than pinned when no device is available

* Use MPI max numprocs when setting NP default

github runner only has 2

* Disable more tests when GPU unavailable

* fixup! Use std allocateor rather than pinned when no device is available

* Enable all jobs

* Support root disabling (and initialization) from error handler

* Disable device tests if device is disabled at runtime

* Fix thread count for celer-sim with ROOT

* REVERTME: disable all but one ROCM image

* Downgrade to checkout v3

* Fix rocm json and jenkins build names

* Fix root/shared options

* fixup! Disable device tests if device is disabled at runtime

* Fix json

* Dubious ownership

* Fix CELERITAS_TEST_VERBOSE

* Fix matrix and tag fetch

* Try fetch depth

* Try single fetch depth, and fix use of accel example

* Try more fetch depth

* Add ld flags

* Disable example builds that don't currently work

* Fix syntax errors

* Add vecgeom-reldb and fix asan diabling

* Disable reldeb example too

* Remove to-dos

* Exclude changes to rst/md in check

* REVERTME: don't disable device

* Revert "REVERTME: don't disable device"

This reverts commit fbdea2d4d6572875e2c0f71af9cb3e1c6d5b8f71.

* Update 'special' annotations

* Add conflict between hip+assertions and update CI matrix

* Remove profile source and update working dirs

* Update documentation

* Fix image selection and parallelism

* fixup! Fix image selection and parallelism

* Reverse ordering so fine-grained is first

Refactor ParticleState and ParticleParams to SoA (#1012)

* Refactor ParticleState and ParticleParams to SoA

* Removed ParticleRecord

* rename enum

* rename particleparams data member

* change underlying type of MatterType, support Quantity for LdgSpan, use LdgSpan as collection storage when possible

* Move stable_decal_constant to celeritas::constants

---------

Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>

Use Celeritas error and output handling in celer-g4 app (#1013)

* Add convenience functino for getting number of threads from geant4 run manager

* Add log messages

* Add `to_color_code` for logger levels

* Move g4 exception disabling to GeantUtils

* Add additional diagnostics to g4-only output registry

* Use Celeritas error handling and logging for celer-g4

* Add scoped profiling to actual run

* Fix no-geant4 inline functions

* Add field validation

* Pass more data instead of using global static

* Mark manager thread from local logger to distinguish from global CELER_LOG

* Fix recursive mutex deadlock

Use consistent energy intervals for model applicability and selection (#1015)

* Use consistent energy intervals for model applicability and selection

* Add check for SB upper limit and update limit in combined brems interactor

---------

Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>

Fix unchecked merge train wreck (#1021)

* REVERTME: disable other builds

* Source profile in examples

* Add a metabuild for pulls and a workflow

* Fix stable_decay_constant

* Update OpaqueId struct since ParticleRecord no longer exists

* Update workflow names

* Address feedback

Refactor vecgeom setup in preparation for surface support (#1017)

* Move vecgeom verbosity environment fetching to free function

* Add functions for checking vecgeom build tpe

* Add simple cms vecgeom test

* Add scoped limit saver to clean up vecgeom params

* Update Vecgeom.test.cc

Fixup

---------

Co-authored-by: Guilherme Lima <mrguilima@users.noreply.github.com>

Add support for VecGeom surface model (#1016)

* Add option to use AdePT's surface navigator

* Adding the surface data transfer to the GPU

* New file SurfNavigator.h

* Fix SurfNavigator.hh and add GPU transfer and cleanup of surface data

* Renaming VecgeomParams.cu as VecgeomParams.surface.cu

* Refactored geometry setup and teardown with some surface model tests passing

* Rename static function to match member function

* Cleanup commented out code

* Fix compilation for CUDA disabled + vecgeom 2.x HEAD

* Make teardown_surface_tracking_device() a VecgeomParams' member function

* Add required header

* Rename build_surface_trk_device() as setup_surface_trk_device()

* Fix CUDA=OFF build

* Revert rearrangement

* use separate header for surface stuff

* Rearrange things again

* Fix no-cuda build

* Fix missing cuda manager local variable

* Minor formatting

* Improve some of the preprocessor ugliness

* Always build volume tracking for gpu vecgeom

* Update comments

---------

Co-authored-by: Seth R Johnson <johnsonsr@ornl.gov>

Fix CI for "push" events (#1022)

* REVERTME

* Disambiguate concurrency and improve names

* Revert "REVERTME"

This reverts commit 7e44f514f4ca84f0a20c1dc2fa788780ef93de67.

* Improve PR name and revert push name to default

* Add detail

* REVERTME: fail push, succeed after wait pr

* Revert "REVERTME: fail push, succeed after wait pr"

This reverts commit 20bfb9341ee0cc24e827edae5f522a1f4c34eeeb.

* Split merge queue into separate workflow

Use default field driver options in celer-g4 test (#1024)

Add G4SD "simple calorimeter" that outputs to JSON (#1014)

Fix duplicate libvecgeom.a in some components' build (#1027)

Optimize data access through ORANGE visitors (#1018)

* use span API of Collection instead of raw pointers

* Simplify return type, add assert, rename

* simplify indexing

* fix range construction

* update TransformVisitor

* rename range

* constness in array operators, fix issue with make_array temporary

* change storagespan for surfaces

* simplify make_array declaration, doc

* update surface constructor

Update cmake presets for Zeus (#1028)

Simplify data access for host collections (#1029)

* add CollectionTraits for ldg-supported type and host memspace

* fix collection test

* cleanup

Add multithread exception support and logging to Geant4 app (#1026)

* Revert "Use Celeritas error handling and logging for celer-g4"

This reverts commit 8bab436fe7a5c28173aaaaf70a090a8b20e8fe17.

* Add multiexception handler

* Add documentation to MEH

* Fix read-after-destroy for Geant4 exceptions

Storing RuntimeError after G4Exception exited results in a dangling pointer to the temporary stream used to construct the abbreviated filename.

* Fix AbortRun argument

* Lowercase accessors to avoid class/member function symbol conflict

Update Celeritas CMake defaults and add documentation build (#1030)

* Update crusher to use amd 5.6 toolchain
* Update cloc script
* Build with amd 5.6 on frontier
* Allow default CMake config options to change based on available version
* Default to disabling tests, demos, and debug
* Add documentation workflow
* Build and upload developer documentation
* Fix documentation
* Fix doxygen build and add 'doc' as required for release branch

Hotfix: CUDA 12.3.52 build error (#1033)

I think there's a compiler bug because AllItemsT definitely can't be
constructed from two values...
```
scale/external/celeritas/src/orange/transform/TransformVisitor.hh(127): error: more than one operator "[]" matches these operands:
            function "celeritas::Collection<T, W, M, I>::operator[](celeritas::Collection<T, W, M, I>::ItemRangeT) const [with T=celeritas::real_type, W=celeritas::Ownership::const_reference, M=celeritas::MemSpace::device, I=celeritas::OpaqueId<celeritas::real_type, celeritas::size_type>]" (declared at line 301 of /home/vmuser/build/rnsd/scale/external/celeritas/src/corecel/data/Collection.hh)
            function "celeritas::Collection<T, W, M, I>::operator[](celeritas::Collection<T, W, M, I>::AllItemsT) const [with T=celeritas::real_type, W=celeritas::Ownership::const_reference, M=celeritas::MemSpace::device, I=celeritas::OpaqueId<celeritas::real_type, celeritas::size_type>]" (declared at line 305 of /home/vmuser/build/rnsd/scale/external/celeritas/src/corecel/data/Collection.hh)
            operand types are: const celeritas::TransformVisitor::Reals [ {...} ]
      return T{reals_[{data_offset, data_offset + size}]};
                     ^
```

Add preflight github action (#1032)

* Add 'local' preflight build
* Use older gcc 8/clang 10 on older ubuntu system
* Add environment variables for CC/CXX
* Install g++ and don't error on warning
* Use an artificial git tag to give cache hits within the same PR and avoid meaningless SHAs

Release v0.4.0 (#1031)

* Add pull request template and document labels

* Add pull request template for releases

* Fix documentation

* Update latex pdf header to include institutions

* Move rst file locations

* Add release documentation

Fix Jenkins CI build and ccache use (#1036)

* Line wrap pull request
* Build local on 'develop' as well for ccache reasons
* Reset jenkins: use newer presets from workflow
* Update git-describe when buliding a branch
* Rename build-local to build-fast

Write celer-g4 input to output file or screen (#1034)

* Add command-line options for dumping default celer-g4 JSON
* Output required celer-g4 JSON variables
* Improve output of 'unset' primary generator distributions
* Write run input to celer-g4 output file
* Fix defaults being in 1-element array

 Open Update Perlmutter CMake profile and env script (#1041)

REVERT LATER: disable HIP for now