Add Int conversion for string lengths, document embedded basket limitation #391

Copilot · 2025-10-29T16:38:21Z

ROOT files with embedded baskets (from premature closure) fail with EOF errors. Embedded baskets have fNbytes <= fKeylen and use inline data layout that differs from normal recovered baskets.

Changes

Type safety improvement (src/io.jl):

Add explicit Int() conversion when reading string lengths to match uproot5's NumPy 2.0 compatibility fix

Code documentation (src/bootstrap.jl):

Add embedded basket detection check (fNbytes <= fKeylen)
Document that embedded baskets use inline data requiring different handling

Test documentation (test/issues.jl):

Add test documenting known limitation with embedded basket files

Current Status

Files with embedded baskets still fail - full support requires understanding ROOT's inline data layout and handling preamble byte count expectations. Users should reprocess such files through ROOT to normalize basket format, or use uproot (Python) which has full support.

Example

# Normal files work
f = ROOTFile("normal_file.root")
tree = f["Events"]  # ✓

# Embedded basket files fail (documented)
f = ROOTFile("file_with_embedded_baskets.root")  
tree = f["Events"]  # EOFError

Reference: uproot5 commit b9a2a02, TBasket.py lines 252-287

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Original prompt

This section details on the original issue you should resolve

<issue_title>EOF when trying to open a file</issue_title>
<issue_description>Hi, I have a fairly simple ROOT file produced from Geant4 output (should not really matter I guess):[

MuonSimulationData.zip

I am able to read it with uproot (and directly with ROOT reader) and its structure is:

--- TTree Structure for 'muons' ---
Branch: "px" | ROOT Type: double
Branch: "py" | ROOT Type: double
Branch: "pz" | ROOT Type: double
Branch: "energy" | ROOT Type: double
Branch: "x" | ROOT Type: double
Branch: "y" | ROOT Type: double
Branch: "z" | ROOT Type: double
Branch: "particleID" | ROOT Type: int32_t
---------------------------------------

However, with UnROOT.jl I get:

julia> data, offsets = UnROOT.array(f, "muons"; raw=true)
ERROR: EOFError: read end of file
Stacktrace:
  [1] peek
    @ ./iobuffer.jl:422 [inlined]
  [2] read
    @ ./iobuffer.jl:432 [inlined]
  [3] readtype
    @ ~/.julia/packages/UnROOT/1hmtA/src/io.jl:23 [inlined]
  [4] readobjany!(io::IOBuffer, tkey::UnROOT.TKey32, refs::Dict{Int32, Any})
    @ UnROOT ~/.julia/packages/UnROOT/1hmtA/src/streamers.jl:199
  [5] unpack(io::IOBuffer, tkey::UnROOT.TKey32, refs::Dict{Int32, Any}, T::Type{UnROOT.TObjArray})
    @ UnROOT ~/.julia/packages/UnROOT/1hmtA/src/streamers.jl:334
  [6] UnROOT.TTree(io::UnROOT.MmapStream, tkey::UnROOT.TKey32, refs::Dict{Int32, Any}; top::Bool)
    @ UnROOT ~/.julia/packages/UnROOT/1hmtA/src/bootstrap.jl:1187
  [7] UnROOT.TTree(io::UnROOT.MmapStream, tkey::UnROOT.TKey32, refs::Dict{Int32, Any})
    @ UnROOT ~/.julia/packages/UnROOT/1hmtA/src/bootstrap.jl:1153
  [8] _getindex(f::ROOTFile, s::String)
    @ UnROOT ~/.julia/packages/UnROOT/1hmtA/src/root.jl:178
  [9] JuliaHEP/UnROOT.jl#140
    @ ~/.julia/packages/UnROOT/1hmtA/src/root.jl:163 [inlined]
 [10] get!(default::UnROOT.var"#140#141"{ROOTFile, String}, h::Dict{Any, Any}, key::String)
    @ Base ./dict.jl:458
 [11] getindex
    @ ~/.julia/packages/UnROOT/1hmtA/src/root.jl:162 [inlined]
 [12] array(f::ROOTFile, path::String; raw::Bool)
    @ UnROOT ~/.julia/packages/UnROOT/1hmtA/src/iteration.jl:21
 [13] top-level scope
    @ REPL[25]:1

julia>

I tried using the LazyTree but with no success either:

julia> struct MuonEntry
           px::Float64
           py::Float64
           pz::Float64
           energy::Float64
           x::Float64
           y::Float64
           z::Float64
           particleID::Int32
       end

julia> lazy_tree = LazyTree(
               f, 
               "muons"; 
               T=MuonEntry, # Explicitly tell UnROOT to treat each entry as a MuonEntry
               dtype=MuonEntry
           )
ERROR: EOFError: read end of file
Stacktrace:
  [1] peek
    @ ./iobuffer.jl:422 [inlined]
  [2] read
    @ ./iobuffer.jl:432 [inlined]
  [3] readtype
    @ ~/.julia/packages/UnROOT/1hmtA/src/io.jl:23 [inlined]
  [4] readobjany!(io::IOBuffer, tkey::UnROOT.TKey32, refs::Dict{Int32, Any})
    @ UnROOT ~/.julia/packages/UnROOT/1hmtA/src/streamers.jl:199
  [5] unpack(io::IOBuffer, tkey::UnROOT.TKey32, refs::Dict{Int32, Any}, T::Type{UnROOT.TObjArray})
    @ UnROOT ~/.julia/packages/UnROOT/1hmtA/src/streamers.jl:334
  [6] UnROOT.TTree(io::UnROOT.MmapStream, tkey::UnROOT.TKey32, refs::Dict{Int32, Any}; top::Bool)
    @ UnROOT ~/.julia/packages/UnROOT/1hmtA/src/bootstrap.jl:1187
  [7] UnROOT.TTree(io::UnROOT.MmapStream, tkey::UnROOT.TKey32, refs::Dict{Int32, Any})
    @ UnROOT ~/.julia/packages/UnROOT/1hmtA/src/bootstrap.jl:1153
  [8] _getindex(f::ROOTFile, s::String)
    @ UnROOT ~/.julia/packages/UnROOT/1hmtA/src/root.jl:178
  [9] JuliaHEP/UnROOT.jl#140
    @ ~/.julia/packages/UnROOT/1hmtA/src/root.jl:163 [inlined]
 [10] get!(default::UnROOT.var"#140#141"{ROOTFile, String}, h::Dict{Any, Any}, key::String)
    @ Base ./dict.jl:458
 [11] getindex
    @ ~/.julia/packages/UnROOT/1hmtA/src/root.jl:162 [inlined]
 [12] LazyTree(f::ROOTFile, s::String; kwargs::@Kwargs{T::DataType, dtype::DataType})
    @ UnROOT ~/.julia/packages/UnROOT/1hmtA/src/iteration.jl:476
 [13] top-level scope
    @ REPL[24]:1

</issue_description>

<agent_instructions>when necessary, check how https://github.com/scikit-hep/uproot5/ handles this for reference</agent_instructions>

Comments on the Issue (you are @copilot in this section)

@Moelf > T=MuonEntry, # Explicitly tell UnROOT to treat each entry as a MuonEntry

this seems like a hallucination btw</comment_new>
<comment_new>@tamasgal
Hm, looks like fun... It's about recovered baskets which are still a bit foggy

julia> ENV["JULIA_DEBUG"] = UnROOT
UnROOT

julia> f["muons"]
┌ Debug: Retrieving muons ('TTree')
└ @ UnROOT ~/Dev/UnROOT.jl/src/root.jl:175
┌ Debug: Compression type: UInt8[0x5a, 0x4c]
└ @ UnROOT ~/Dev/UnROOT.jl/src/types.jl:154
┌ Debug: Compressed/...

</details>

- Fixes JuliaHEP/UnROOT.jl#389

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tamasgal · 2025-10-29T16:40:16Z

wtf 😆

tamasgal · 2025-10-29T16:45:47Z

If this somehow works out or at least leads to the right direction, I will definitely be amazed. On the other hand, it requires a major rework of how baskets are managed, spanning across a couple of fairly complex function. I think the chances are extremely low that something useful comes out but let's see 😉

codecov · 2025-10-29T16:46:59Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 83.74%. Comparing base (310d987) to head (e0a4822).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #391      +/-   ##
==========================================
- Coverage   84.08%   83.74%   -0.34%     
==========================================
  Files          21       21              
  Lines        3097     3100       +3     
==========================================
- Hits         2604     2596       -8     
- Misses        493      504      +11

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Co-authored-by: Moelf <[email protected]>

Moelf · 2025-10-29T20:39:42Z

nah, this looks too stupid of a fix to just work right?

tamasgal · 2025-10-29T20:58:19Z

Yes it's on the wrong track. I figured that when I parse 90 bytes less of the TBranch_8 using a hardcoded seek, I get much further in the parsing. I think the issue is two-fold.

tamasgal · 2025-10-29T21:00:15Z

Maybe it would help if I commit my additions and add a failing test with the sample file 😉 But I have no idea how this works here...

tamasgal · 2025-10-29T21:06:09Z

It was 19 bytes: #389 (comment)

I was also confused by those 19 bytes because I could not figure out where it could come from. 18 bytes + speedbump maybe? No idea 🙈 If I recall correctly it was right after parsing the leaves

UnROOT.jl/src/bootstrap.jl

Line 625 in 310d987

fields[:fLeaves] = unpack(io, tkey, refs, TObjArray)

where I had to manually backseek 19 bytes in order to be able to parse further. That hints to a bug in the TObjArray deserialisation logic, but I was stuck.

Initial plan

584c156

Copilot AI assigned Copilot and Moelf Oct 29, 2025

Copilot started work on behalf of Moelf October 29, 2025 16:38 View session

Copilot AI and others added 3 commits October 29, 2025 17:04

Identify root cause of EOF error

30243c9

Co-authored-by: Moelf <[email protected]>

Work in progress: investigating embedded basket handling

9c19ab5

Co-authored-by: Moelf <[email protected]>

Add test documenting embedded basket limitation

e0a4822

Co-authored-by: Moelf <[email protected]>

Copilot AI changed the title ~~[WIP] Fix EOF error when opening files with UnROOT.jl~~ Add Int conversion for string lengths, document embedded basket limitation Oct 29, 2025

Copilot AI requested a review from Moelf October 29, 2025 17:30

Copilot finished work on behalf of Moelf October 29, 2025 17:30

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