WIP: UBT straws#1169
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📝 WalkthroughWalkthroughThis PR replaces the UpstreamTagger detector's fixed-box geometry with a full parametric straw detector implementation. The detector now reads configuration from YAML, accumulates energy loss across multiple steps in ChangesUpstreamTagger Parametric Straw Detector Implementation
Sequence Diagram(s)sequenceDiagram
participant SimSetup as Sim Setup
participant ShipGeo as ShipGeo Module
participant GeometryConfig as geometry_config.py
participant ShipDetConf as shipDet_conf.py
participant UpstreamTagger as ROOT.UpstreamTagger
participant MC as MC Engine
SimSetup->>ShipGeo: Define z-positions
ShipGeo-->>SimSetup: TrackStation, UBTStation1-4
SimSetup->>GeometryConfig: Create config with z-positions
GeometryConfig-->>SimSetup: c.UpstreamTagger, c.UBTStation1
SimSetup->>ShipDetConf: configure(run, ship_geo)
ShipDetConf->>ShipDetConf: configure_upstreamTagger(yaml, ship_geo)
ShipDetConf->>UpstreamTagger: UpstreamTagger(medium)
UpstreamTagger->>UpstreamTagger: Initialize fMedium
ShipDetConf->>UpstreamTagger: SetzPositions(UBTStation1.z)
ShipDetConf->>UpstreamTagger: SetApertureArea(w, h, l)
ShipDetConf->>UpstreamTagger: SetStrawDiameter(outer, wall)
ShipDetConf->>UpstreamTagger: SetStrawPitch(pitch, offset)
ShipDetConf->>UpstreamTagger: SetDeltazLayer(delta_z)
ShipDetConf->>UpstreamTagger: SetDeltazView(delta_z_view)
ShipDetConf->>UpstreamTagger: SetStereoAngle(angle)
ShipDetConf->>UpstreamTagger: SetWireThickness(thickness)
ShipDetConf->>UpstreamTagger: SetFrameMaterial(material)
UpstreamTagger->>UpstreamTagger: ConstructGeometry()
UpstreamTagger-->>ShipDetConf: Detector ready
MC->>UpstreamTagger: ProcessHits(vol) for each step
UpstreamTagger->>UpstreamTagger: fELoss += gMC->Edep()
UpstreamTagger->>UpstreamTagger: volName = gMC->CurrentVolName()
UpstreamTagger->>UpstreamTagger: subDetID = detPieces(volName)
UpstreamTagger-->>MC: Hit created with subDetID
Estimated code review effort🎯 4 (Complex) | ⏱️ ~45 minutes Suggested reviewers
🚥 Pre-merge checks | ✅ 2 | ❌ 3❌ Failed checks (2 warnings, 1 inconclusive)
✅ Passed checks (2 passed)
✏️ Tip: You can configure your own custom pre-merge checks in the settings. ✨ Finishing Touches🧪 Generate unit tests (beta)
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Actionable comments posted: 8
Caution
Some comments are outside the diff and can’t be posted inline due to platform limitations.
⚠️ Outside diff range comments (1)
UpstreamTagger/UpstreamTagger.cxx (1)
117-140:⚠️ Potential issue | 🟠 Major | ⚡ Quick win
subDetIDis computed and then discarded.Line 119 derives the Y/U/V/plastic ID, but
AddHit()still only receivesuniqueId. As a result, the newUpstreamTaggerHit::fSubDetIDpath never gets populated, so downstream code cannot distinguish which UBT subdetector produced the hit.🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@UpstreamTagger/UpstreamTagger.cxx` around lines 117 - 140, The code computes subDetID via detPieces(volName) but never uses it, so UpstreamTaggerHit::fSubDetID remains unset; modify the hit-creation path to pass subDetID into the hit (either extend AddHit to accept a subDetID parameter or set the hit's fSubDetID after creation), updating the call site in UpstreamTagger.cxx where AddHit(fEventID, fTrackID, uniqueId, ...) is invoked and any related constructors/factories that produce UpstreamTaggerHit so the hit's fSubDetID is populated with the computed subDetID.
🧹 Nitpick comments (1)
python/geometry_config.py (1)
425-431: ⚡ Quick winRemove the checked-in merge markers.
These commented
<<<<<<<,=======,>>>>>>>lines make the selected UBT geometry harder to trust during later edits.Cleanup
- # <<<<<<< HEAD c.UpstreamTagger.BoxZ = 2.0 * u.cm # Z dimension (thickness) c.UpstreamTagger.Z_Position = -25.400 * u.m + c.decayVolume.z # Relative position of UBT to decay vessel centre - # ======= - # c.UpstreamTagger.BoxZ = 16.0 * u.cm # Z dimension (thickness) - # c.UpstreamTagger.Z_Position = -25.400 * u.m + c.decayVolume.z # Relative position of UBT to decay vessel centre - # >>>>>>> mymaster🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@python/geometry_config.py` around lines 425 - 431, Remove the leftover merge conflict markers and the alternate commented block so the UpstreamTagger settings are unambiguous: delete the lines containing "<<<<<<<", "=======", ">>>>>>>" and the commented-out alternative BoxZ/Z_Position entries, leaving only the intended assignments for c.UpstreamTagger.BoxZ and c.UpstreamTagger.Z_Position (e.g., BoxZ = 2.0 * u.cm and Z_Position = -25.400 * u.m + c.decayVolume.z).
🤖 Prompt for all review comments with AI agents
Verify each finding against the current code and only fix it if needed.
Inline comments:
In `@geometry/media.geo`:
- Around line 2205-2208: The material definition for WReWire claims
"Tunsten-Rhenium 75/25" but uses fractions 0.97 0.03; update the definition so
the actual composition matches the label (or vice versa). Locate the WReWire
block and either change the composition numbers from "0.97 0.03" to "0.75 0.25"
to reflect 75% W / 25% Re, or change the comment/label to the correct ratio that
matches the existing fractions; ensure any dependent documentation or variable
names that reference WReWire remain consistent.
In `@geometry/ubt_config.yaml`:
- Around line 2-13: The UBT config is missing the frame_material key required by
UpstreamTagger::ConstructGeometry() which calls
ShipGeo::InitMedium(f_frame_material); add a "frame_material" entry inside the
UBT block (e.g., frame_material: <validMediumName>) so f_frame_material is
non-empty and matches an existing medium name known to ShipGeo::InitMedium;
ensure the value exactly matches the material identifier used elsewhere in the
project.
In `@macro/run_simScript.py`:
- Around line 349-350: The file log severity is currently forced to fatal via
ROOT.gInterpreter.ProcessLine('fair::Logger::SetFileSeverity("fatal");'), which
hides non-fatal diagnostics needed for postmortem; change the code to set
fair::Logger::SetFileSeverity("debug") (or a less restrictive level) when
running in debug mode (e.g., when --debug is enabled) and keep the more
restrictive level otherwise, and ensure this conditional mirrors any
console-only verbosity settings like fair::Logger::SetVerbosity so file and
console logging reflect the chosen debug flag.
- Around line 758-761: ROOT.gErrorIgnoreLevel is being changed globally before
the overlap check and never restored; scope the suppression to only the
overlap-checking block by saving the current level, setting
ROOT.gErrorIgnoreLevel = ROOT.kFatal only while options.check_overlaps and the
overlap code (the block under the if options.check_overlaps) runs, then restore
the saved value immediately after that block so subsequent operations (file
filtering, muon discrimination, tree/event processing) use the original error
level.
In `@python/shipDet_conf.py`:
- Around line 464-472: Remove the leftover merge-conflict markers and
commented-out alternate implementation in the upstream tagger block: delete the
conflict markers (<<<<<<< HEAD, =======, >>>>>>> mymaster) and the redundant
commented lines referencing upstreamTagger, UpstreamTagger.SetZposition, and
SetBoxDimensions, leaving the single intended call
configure_upstreamTagger(os.path.join(os.environ["FAIRSHIP"], "geometry",
"ubt_config.yaml"), ship_geo) intact so only the active configure_upstreamTagger
usage remains.
- Line 502: The file currently sets exclusionList = ["TargetStation"] which
forces skipping TargetStation during run.AddModule(...) and can alter
physics/geometry; change this so TargetStation is not unconditionally
excluded—either initialize exclusionList to an empty list or make adding
"TargetStation" conditional (e.g., based on a config flag or environment
variable) and update any code paths that reference exclusionList and
run.AddModule to respect that conditional logic (look for the exclusionList
variable and the run.AddModule(...) call sites to apply the change).
In `@python/ShipGeo.py`:
- Around line 15-20: zPositions() is broken: it references sys without import,
treats ShipGeo as iterable and uses eval for attribute access; fix by importing
sys at top, retrieving the main module via sys.modules["__main__"], locating the
ShipGeo class/object on that module (e.g., getattr(main, "ShipGeo")), iterating
its attributes via dir() or vars(ShipGeo).items(), and replacing
eval("ShipGeo."+x+".z") with safe attribute access using
getattr(getattr(ShipGeo, x) or attribute object, "z", None) (use hasattr/getattr
checks) so you only print entries that actually have a numeric z attribute in
the ShipGeo namespace.
In `@UpstreamTagger/UpstreamTagger.cxx`:
- Around line 288-291: The geometry placement currently ignores the stored
det_zPos/SetZposition and uses T_station_z directly; change the node creation in
the UpstreamTagger constructor (where TGeoVolume* vol is created and
top->AddNode is called) to use the detector's stored Z position (det_zPos or the
value set by SetZposition, and/or the config value c.UpstreamTagger.Z_Position
from python/geometry_config.py) instead of the raw T_station_z; ensure any code
that updates SetZposition also updates the translation used for AddNode (or
recompute T_station_z from det_zPos before adding the node) so callers that only
set det_zPos get the correct placement.
---
Outside diff comments:
In `@UpstreamTagger/UpstreamTagger.cxx`:
- Around line 117-140: The code computes subDetID via detPieces(volName) but
never uses it, so UpstreamTaggerHit::fSubDetID remains unset; modify the
hit-creation path to pass subDetID into the hit (either extend AddHit to accept
a subDetID parameter or set the hit's fSubDetID after creation), updating the
call site in UpstreamTagger.cxx where AddHit(fEventID, fTrackID, uniqueId, ...)
is invoked and any related constructors/factories that produce UpstreamTaggerHit
so the hit's fSubDetID is populated with the computed subDetID.
---
Nitpick comments:
In `@python/geometry_config.py`:
- Around line 425-431: Remove the leftover merge conflict markers and the
alternate commented block so the UpstreamTagger settings are unambiguous: delete
the lines containing "<<<<<<<", "=======", ">>>>>>>" and the commented-out
alternative BoxZ/Z_Position entries, leaving only the intended assignments for
c.UpstreamTagger.BoxZ and c.UpstreamTagger.Z_Position (e.g., BoxZ = 2.0 * u.cm
and Z_Position = -25.400 * u.m + c.decayVolume.z).
🪄 Autofix (Beta)
Fix all unresolved CodeRabbit comments on this PR:
- Push a commit to this branch (recommended)
- Create a new PR with the fixes
ℹ️ Review info
⚙️ Run configuration
Configuration used: Organization UI
Review profile: CHILL
Plan: Pro
Run ID: c7a8b28a-3c79-4435-a6e3-6471dd9ff1c2
📒 Files selected for processing (10)
UpstreamTagger/UpstreamTagger.cxxUpstreamTagger/UpstreamTagger.hUpstreamTagger/UpstreamTaggerHit.cxxUpstreamTagger/UpstreamTaggerHit.hgeometry/media.geogeometry/ubt_config.yamlmacro/run_simScript.pypython/ShipGeo.pypython/geometry_config.pypython/shipDet_conf.py
| // Tunsten-Rhenium 75/25 wire | ||
| WReWire 2 183.84 186.207 74. 75. 19.3 0.97 0.03 | ||
| 0 1 20. 0.001 | ||
| 0 |
There was a problem hiding this comment.
WReWire does not match its stated composition.
The comment says this is a 75/25 tungsten-rhenium wire, but the mixture is defined with 0.97 0.03 fractions. That is a very different material budget, so either the label or the numbers need to be corrected before this is used in simulation.
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.
In `@geometry/media.geo` around lines 2205 - 2208, The material definition for
WReWire claims "Tunsten-Rhenium 75/25" but uses fractions 0.97 0.03; update the
definition so the actual composition matches the label (or vice versa). Locate
the WReWire block and either change the composition numbers from "0.97 0.03" to
"0.75 0.25" to reflect 75% W / 25% Re, or change the comment/label to the
correct ratio that matches the existing fractions; ensure any dependent
documentation or variable names that reference WReWire remain consistent.
| UBT: | ||
| width: 50 # Aperture width (x) in cm (half length) | ||
| height: 150 # Aperture height (y) in cm (half length) | ||
| wire_thickness: 0.0025 # Sense wire thickness in cm | ||
| wall_thickness: 0.0015 # Straw wall thickness in cm | ||
| outer_straw_diameter: 0.5 # in cm | ||
| straw_pitch: 0.6 # Distance (y) between straws in a layer in cm | ||
| y_layer_offset: 0.25 # Offset (y) of straws between layers in cm | ||
| delta_z_layer: 0.433 # Distance (z = sqrt(3)/2 * D) between layers in cm | ||
| delta_z_view: 6 # Distance (z) between stereo views in cm | ||
| view_angle: 15 # Stereo angle in degree | ||
| station_length: 32 # (z = outer_straw_diameter + delta_z_layer + delta_z_view + space for plastic) in cm (half length) |
There was a problem hiding this comment.
This config is missing the frame material required by ConstructGeometry().
UpstreamTagger::ConstructGeometry() unconditionally calls ShipGeo::InitMedium(f_frame_material) and builds the frame with that medium. Without a frame_material entry here, the medium name stays empty and the new geometry path is reachable failure in this PR.
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.
In `@geometry/ubt_config.yaml` around lines 2 - 13, The UBT config is missing the
frame_material key required by UpstreamTagger::ConstructGeometry() which calls
ShipGeo::InitMedium(f_frame_material); add a "frame_material" entry inside the
UBT block (e.g., frame_material: <validMediumName>) so f_frame_material is
non-empty and matches an existing medium name known to ShipGeo::InitMedium;
ensure the value exactly matches the material identifier used elsewhere in the
project.
| ROOT.gInterpreter.ProcessLine('fair::Logger::SetFileSeverity("fatal");') | ||
| ROOT.gInterpreter.ProcessLine('fair::Logger::SetVerbosity("verylow");') |
There was a problem hiding this comment.
🧩 Analysis chain
🌐 Web query:
`In the current FairRoot/FairLogger version used by this project, what is the exact behavior of:
- fair::Logger::SetFileSeverity(...)
- fair::Logger::SetConsoleSeverity(...)
- fair::Logger::SetVerbosity(...)
Does SetFileSeverity("fatal") suppress all non-fatal messages written to file even when console severity is set to debug/debug1/debug2?`
💡 Result:
In the current FairRoot/FairLogger (FairLogger v2.3.2 as of 2026-03-17), fair::Logger::SetFileSeverity(severity) sets the minimum severity threshold for the file sink independently of other sinks. Similarly, fair::Logger::SetConsoleSeverity(severity) sets the threshold for the console sink. fair::Logger::SetVerbosity(verbosity) sets the verbosity level, which controls the detail/format of output (e.g., high/medium/low, affecting timestamps, file/line info) but does not alter severity thresholds. SetFileSeverity("fatal") sets the file sink to only log FATAL messages and higher (typically the highest severity; lower severities like debug/info are suppressed for file output). This suppression is independent of console settings. Thus, even if console severity is "debug" (or debug1/debug2 equivalents), non-fatal messages (e.g., debug, info) will not be written to the file—only fatal ones will. "fatal" logs the chosen severity and above; lower severities are filtered per sink. FairLogger wrapper (FairRoot's FairLogger.h) calls these methods and uses IsLogNeeded(fair::Severity) to check before logging, respecting per-sink thresholds.
Citations:
- 1: https://github.com/FairRootGroup/FairLogger
- 2: https://fairrootgroup.github.io/FairRoot/html/d5/de4/FairLogger_8h_source.html
- 3: https://fairrootgroup.github.io/FairRoot/html/db/da1/classFairLogger.html
- 4: https://github.com/eic/EicRoot/blob/master/fairtools/FairLogger.h
File logging suppresses non-fatal messages needed for crash triage.
Line 349 sets file severity to fatal, which suppresses all non-fatal messages (debug, info, warning) in file output according to FairLogger's independent per-sink severity behavior. This means even when --debug is passed (which only affects console output), the file log remains silent except for fatal events—losing context needed to debug failures like the CI Geant4 abort.
Adjust the file severity based on debug mode (e.g., SetFileSeverity("debug") when debug is enabled) to preserve non-fatal diagnostics for postmortem analysis.
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.
In `@macro/run_simScript.py` around lines 349 - 350, The file log severity is
currently forced to fatal via
ROOT.gInterpreter.ProcessLine('fair::Logger::SetFileSeverity("fatal");'), which
hides non-fatal diagnostics needed for postmortem; change the code to set
fair::Logger::SetFileSeverity("debug") (or a less restrictive level) when
running in debug mode (e.g., when --debug is enabled) and keep the more
restrictive level otherwise, and ensure this conditional mirrors any
console-only verbosity settings like fair::Logger::SetVerbosity so file and
console logging reflect the chosen debug flag.
| def zPositions(): | ||
| main = sys.modules["__main__"] | ||
| if hasattr(main, "ShipGeo"): | ||
| for x in ShipGeo: | ||
| if hasattr(eval("ShipGeo." + x), "z"): | ||
| print(x, "z=", eval("ShipGeo." + x + ".z")) |
There was a problem hiding this comment.
zPositions() is currently broken.
It uses sys without importing it, iterates over ShipGeo even though the class is not iterable, and relies on eval() for plain attribute access.
Proposed fix
+import sys
+
def zPositions():
main = sys.modules["__main__"]
- if hasattr(main, "ShipGeo"):
- for x in ShipGeo:
- if hasattr(eval("ShipGeo." + x), "z"):
- print(x, "z=", eval("ShipGeo." + x + ".z"))
+ for name, value in vars(main).items():
+ if isinstance(value, ShipGeo) and hasattr(value, "z"):
+ print(name, "z=", value.z)🧰 Tools
🪛 GitHub Check: static-analysis
[failure] 18-18: Pyrefly not-iterable
Type type[ShipGeo] is not iterable
[failure] 16-16: Pyrefly unknown-name
Could not find name sys
🪛 Ruff (0.15.12)
[error] 16-16: Undefined name sys
(F821)
[error] 19-19: Use of possibly insecure function; consider using ast.literal_eval
(S307)
[error] 20-20: Use of possibly insecure function; consider using ast.literal_eval
(S307)
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.
In `@python/ShipGeo.py` around lines 15 - 20, zPositions() is broken: it
references sys without import, treats ShipGeo as iterable and uses eval for
attribute access; fix by importing sys at top, retrieving the main module via
sys.modules["__main__"], locating the ShipGeo class/object on that module (e.g.,
getattr(main, "ShipGeo")), iterating its attributes via dir() or
vars(ShipGeo).items(), and replacing eval("ShipGeo."+x+".z") with safe attribute
access using getattr(getattr(ShipGeo, x) or attribute object, "z", None) (use
hasattr/getattr checks) so you only print entries that actually have a numeric z
attribute in the ShipGeo namespace.
| TGeoVolume* vol = new TGeoVolume(nmstation, statbox, med); | ||
| // z-translate the station to its (absolute) position | ||
| top->AddNode(vol, statnb, | ||
| new TGeoTranslation(0, floor_offset / 2., T_station_z)); |
There was a problem hiding this comment.
SetZposition() no longer affects the built geometry.
The public API still stores det_zPos, and python/geometry_config.py still defines c.UpstreamTagger.Z_Position, but this placement uses T_station_z directly. Any caller that only sets the detector Z will now get a silently misplaced UBT.
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.
In `@UpstreamTagger/UpstreamTagger.cxx` around lines 288 - 291, The geometry
placement currently ignores the stored det_zPos/SetZposition and uses
T_station_z directly; change the node creation in the UpstreamTagger constructor
(where TGeoVolume* vol is created and top->AddNode is called) to use the
detector's stored Z position (det_zPos or the value set by SetZposition, and/or
the config value c.UpstreamTagger.Z_Position from python/geometry_config.py)
instead of the raw T_station_z; ensure any code that updates SetZposition also
updates the translation used for AddNode (or recompute T_station_z from det_zPos
before adding the node) so callers that only set det_zPos get the correct
placement.
olantwin
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olantwin
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Some first comments, I'll review further later.
There was a problem hiding this comment.
Can we discuss changing the default log level and verbosity separately?
| # <<<<<<< HEAD | ||
| c.UpstreamTagger.BoxZ = 2.0 * u.cm # Z dimension (thickness) | ||
| c.UpstreamTagger.Z_Position = -25.400 * u.m + c.decayVolume.z # Relative position of UBT to decay vessel centre | ||
| # ======= | ||
| # c.UpstreamTagger.BoxZ = 16.0 * u.cm # Z dimension (thickness) | ||
| # c.UpstreamTagger.Z_Position = -25.400 * u.m + c.decayVolume.z # Relative position of UBT to decay vessel centre | ||
| # >>>>>>> mymaster |
There was a problem hiding this comment.
There's an unresolved merge conflict here.
| # <<<<<<< HEAD | ||
| configure_upstreamTagger(os.path.join(os.environ["FAIRSHIP"], "geometry", "ubt_config.yaml"), ship_geo) | ||
| # ======= | ||
| # upstreamTagger = ROOT.UpstreamTagger("UpstreamTagger", ROOT.kTRUE) | ||
| # upstreamTagger.SetZposition(ship_geo.UpstreamTagger.Z_Position) | ||
| # upstreamTagger.SetBoxDimensions( | ||
| # ship_geo.UpstreamTagger.BoxX, ship_geo.UpstreamTagger.BoxY, ship_geo.UpstreamTagger.BoxZ | ||
| # >>>>>>> mymaster | ||
| # ) |
There was a problem hiding this comment.
Another unresolved merge conflict
| run.SetField(fMagField) | ||
|
|
||
| exclusionList = [] | ||
| exclusionList = ["TargetStation"] |
There was a problem hiding this comment.
This should not be excluded by default.
There was a problem hiding this comment.
🧹 Nitpick comments (1)
python/shipDet_conf.py (1)
268-268: 💤 Low valueAdd type hints for consistency with peer functions.
Other
configure_*functions in this file have type annotations. Consider adding them here for consistency:-def configure_upstreamTagger(yaml_file, ship_geo): +def configure_upstreamTagger(yaml_file: str, ship_geo) -> None:🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the rest with a brief reason, keep changes minimal, and validate. In `@python/shipDet_conf.py` at line 268, Add type hints to the configure_upstreamTagger function signature to match the pattern used by other configure_* functions in the file. Add type annotations for the yaml_file parameter and the ship_geo parameter, as well as specify the return type of the function. Review the existing configure_* functions in the same file to determine the appropriate types to use for consistency.
🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
Nitpick comments:
In `@python/shipDet_conf.py`:
- Line 268: Add type hints to the configure_upstreamTagger function signature to
match the pattern used by other configure_* functions in the file. Add type
annotations for the yaml_file parameter and the ship_geo parameter, as well as
specify the return type of the function. Review the existing configure_*
functions in the same file to determine the appropriate types to use for
consistency.
ℹ️ Review info
⚙️ Run configuration
Configuration used: Organization UI
Review profile: CHILL
Plan: Pro
Run ID: 6feea647-0cb6-48b5-93cd-df61f02931ff
📒 Files selected for processing (4)
UpstreamTagger/UpstreamTagger.hmacro/run_simScript.pypython/geometry_config.pypython/shipDet_conf.py
💤 Files with no reviewable changes (1)
- UpstreamTagger/UpstreamTagger.h
🚧 Files skipped from review as they are similar to previous changes (2)
- python/geometry_config.py
- macro/run_simScript.py
3 participants
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