Support BSON and JLD2 file formats #19

Copilot · 2026-01-13T20:43:38Z

Rebased on master ✅

Successfully rebased JLD2 support on top of the current master branch (commit 904f01a) which includes the major API refactoring from PR #20.

Changes Made

Added JLD2 dependency to Project.toml
Updated source code to support both BSON and JLD2 formats
- File format determined by extension (.bson or .jld2)
- Proper error handling for unsupported extensions
- JLD2 uses String keys for metadata (version, whenrun, runtime, output)
Updated docstrings to mention both supported formats
Added comprehensive tests
- JLD2 function form tests (save/load)
- JLD2 macro form tests (@cache with .jld2)
- Error handling tests for unsupported extensions

Compatibility with New API

The implementation works with the refactored API from master:

cache() function now includes metadata by default (was cachemeta())
Both BSON and JLD2 save metadata: version, whenrun, runtime, output
@cache macro works with both formats
bson_mod parameter supported for BSON module loading

Testing

All 70 tests pass including:

Original BSON tests (macro and function forms)
New JLD2 tests (macro and function forms)
Error handling for unsupported file extensions
Module loading tests for both formats

Original prompt

This section details on the original issue you should resolve

<issue_title>Support other filetypes via FileIO</issue_title>
<issue_description>We currently use BSON directly, but other packages may provide better support in some cases.

For example, it seems like JLD2 may support arbitrary types better than BSON: https://juliaio.github.io/JLD2.jl/dev/

Perhaps it would have resolved some issues with saving BigInts that I was running into in one of my projects.

BSON also has some other limitations: JuliaIO/BSON.jl#20

At the same time, I seem to be seeing slightly smaller file sizes for BSON in some cases.

All in all, this suggests that some added flexibility here could be nice, which I think can be accomplished via FileIO. Added flexibility may even make it possible to use other formats (e.g., MAT.jl) in some cases for some amount of interoperability.

Some care will be needed to check that loading from within a module still works (e.g., for loading from Pluto).

It would also be great if this can be done in a non-breaking way, i.e., the saved file when using BSON is the same as before. This will probably require providing the option to pass kwargs to the save and load functions (to enable passing mod for BSON), which may be handy to have in general anyway.</issue_description>

<agent_instructions>The PR should use the save and load functions from FileIO.jl, which looks like
save(FILENAME, Dict("ans" => ans))
load(FILENAME)
and forward keyword arguments (e.g., mod for BSON) along to them (though it may require some updates to BSON...).

The PR should also add tests for BSON.jl, JLD2.jl, and MAT.jl, and add some examples to the README.</agent_instructions>

Comments on the Issue (you are @copilot in this section)
@dahong67 Some more discussion about JLD2: https://discourse.julialang.org/t/a-future-for-jld2/42958/57

Fixes Add support for JLD2 #12

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dahong67 · 2026-01-13T21:33:53Z

@copilot let's drop FileIO since some filetypes (e.g., PNG) don't actually make much sense for the general purpose caching we are doing (where we want to be able to store "arbitrary" Julia objects). And saving outputs to application-specific formats is probably best left to actually just using FileIO (or the relevant file saving/loading packages) directly.

Instead, let's stick with just BSON and JLD2. Filenames with other extensions should error.

Also, let's not include MAT since it doesn't seem to be able to round-trip data (e.g., in my testing it seemed to turn NamedTuples into Dicts). Makes sense, since that's not really its purpose.

…sions Co-authored-by: dahong67 <9384655+dahong67@users.noreply.github.com>

Copilot · 2026-01-13T21:44:12Z

@copilot let's drop FileIO since some filetypes (e.g., PNG) don't actually make much sense for the general purpose caching we are doing (where we want to be able to store "arbitrary" Julia objects). A...

Done! Removed FileIO dependency and now using BSON and JLD2 directly. Files with unsupported extensions (anything other than .bson or .jld2) now error with a clear message. Removed MAT support as it doesn't round-trip data properly. All tests pass. (650e6b0)

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codecov · 2026-01-13T21:54:20Z

Codecov Report

❌ Patch coverage is 93.18182% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 96.05%. Comparing base (e977fd8) to head (4053b6f).
⚠️ Report is 15 commits behind head on master.

Files with missing lines	Patch %	Lines
src/CacheVariables.jl	93.18%	3 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##            master      #19      +/-   ##
===========================================
- Coverage   100.00%   96.05%   -3.95%     
===========================================
  Files            1        1              
  Lines           43       76      +33     
===========================================
+ Hits            43       73      +30     
- Misses           0        3       +3

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dahong67

Okay, I'll do some work on this now

dahong67 · 2026-01-14T12:58:35Z

@copilot please add tests to get coverage back to 100%

…dling, and cachemeta Co-authored-by: dahong67 <9384655+dahong67@users.noreply.github.com>

Copilot · 2026-01-14T13:11:18Z

@copilot please add tests to get coverage back to 100%

Done! Added comprehensive tests to cover all code paths:

JLD2 macro form tests (@cache with .jld2 files)
Error handling for unsupported extensions (.txt, .mat, etc.)
Error handling for corrupted JLD2 files (missing keys)
cachemeta with JLD2 format

All 72 tests now pass. Also fixed a bug in the macro form where JLD2 keys needed proper handling (JLD2 converts Symbol keys to String keys when saving). (4053b6f)

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- Triggering command: /usr/bin/julia julia --project=. -e using Pkg; Pkg.test(coverage=true) (http block)
https://api.github.com/repos/vchuravy/HashArrayMappedTries.jl/tarball/2eaa69a7cab70a52b9687c8bf950a5a93ec895ae
- Triggering command: /usr/bin/julia julia --project=. -e using Pkg; Pkg.test(coverage=true) (http block)
pkg.julialang.org
- Triggering command: /usr/bin/julia julia --project=. -e using Pkg; Pkg.test(coverage=true) (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

Configure Actions setup steps to set up my environment, which run before the firewall is enabled
Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)

dahong67 · 2026-01-16T20:02:55Z

@copilot please redo this on top of the current master

Copilot · 2026-01-16T20:15:45Z

@copilot please redo this on top of the current master

Done! Rebased all JLD2 support changes on top of current master (904f01a). The changes are now compatible with the refactored API from PR #20. (add4c53)

Note: This is a rebase, so the branch history has been rewritten. The old commits have been replaced with new ones based on master.

Main changes:

JLD2 support now works with the new cache() API (which includes metadata by default)
Both .bson and .jld2 file formats supported
All 70 tests pass including new JLD2 tests
Proper error handling for unsupported file extensions

dahong67 · 2026-01-17T03:45:55Z

Looks like this rebase may have been too complicated for copilot. Let’s try again with a fresh PR.

Initial plan

e059bc5

Copilot AI assigned Copilot and dahong67 Jan 13, 2026

Copilot started work on behalf of dahong67 January 13, 2026 20:44 View session

Copilot AI and others added 5 commits January 13, 2026 20:54

Add FileIO support with backward compatibility for BSON

f77fd6a

Co-authored-by: dahong67 <9384655+dahong67@users.noreply.github.com>

Add tests for JLD2 format

fd3d1d9

Co-authored-by: dahong67 <9384655+dahong67@users.noreply.github.com>

Update README with file format examples and documentation

f538d82

Co-authored-by: dahong67 <9384655+dahong67@users.noreply.github.com>

Fix code review issues: better error handling and key lookup

1f59515

Co-authored-by: dahong67 <9384655+dahong67@users.noreply.github.com>

Remove accidentally committed test files and update .gitignore

88fd4c0

Copilot AI changed the title ~~[WIP] Support other filetypes via FileIO~~ Support multiple file formats via FileIO.jl Jan 13, 2026

Copilot AI requested a review from dahong67 January 13, 2026 21:07

Copilot finished work on behalf of dahong67 January 13, 2026 21:07

Copilot started work on behalf of dahong67 January 13, 2026 21:34 View session

Remove FileIO, use BSON and JLD2 directly, error on unsupported exten…

650e6b0

…sions Co-authored-by: dahong67 <9384655+dahong67@users.noreply.github.com>

Copilot AI changed the title ~~Support multiple file formats via FileIO.jl~~ Support BSON and JLD2 file formats Jan 13, 2026

Copilot finished work on behalf of dahong67 January 13, 2026 21:45

dahong67 mentioned this pull request Jan 13, 2026

Add support for JLD2 #12

Closed

dahong67 reviewed Jan 13, 2026

View reviewed changes

dahong67 added 3 commits January 13, 2026 17:04

Don't need to gitignore these files

b97830f

Revise README

a47fc6f

Tweak README

507b558

Copilot started work on behalf of dahong67 January 14, 2026 12:59 View session

Add comprehensive tests for 100% coverage: JLD2 macro form, error han…

4053b6f

…dling, and cachemeta Co-authored-by: dahong67 <9384655+dahong67@users.noreply.github.com>

Copilot finished work on behalf of dahong67 January 14, 2026 13:12

Copilot AI requested a review from dahong67 January 14, 2026 13:12

Copilot started work on behalf of dahong67 January 16, 2026 20:03 View session

dahong67 closed this Jan 17, 2026

dahong67 deleted the copilot/support-other-filetypes-fileio branch January 17, 2026 03:46

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Support BSON and JLD2 file formats #19

Support BSON and JLD2 file formats #19

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Support BSON and JLD2 file formats #19

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Rebased on master ✅

Changes Made

Compatibility with New API

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