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1.0.0 - #5

Merged

peterrrock2 merged 222 commits into

mainfrom

1.0.0

Jun 16, 2026

Merged

1.0.0#5
peterrrock2 merged 222 commits into
mainfrom
1.0.0

Commits on Mar 12, 2026
- reorganize the repo to acutally make it maintainable
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  committed
  43d6b38
- improve testing in ben
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  8da732f
- reorg the clis
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  committed
  a85511e
- add cli tests
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  committed
  af2586b
- modernize the logging structure in ben
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  c46d18c
- small reorg and cleanup of pathologic cases in pyben
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  6fdaa1c
Commits on Mar 13, 2026
- migrate to taskfile
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  committed
  8c11fc9
- add tests and coverage for whole package
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  48bcd73
- rename internals so imports are use/import binary_ensemble
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  aaf413e
Commits on Mar 16, 2026
- More doc strings
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  committed
  80ef93b
- Try to make relabeling faster
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  72fcaf1
- fix pben counting logic
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  34c3907
- speed up pben conversoin logic
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  committed
  475c607
- Add in spectral and Cuthill-McKee ordering to just see how well it does
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  34ead30
- swap spectral for nested dissection
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  f737f33
- swap nested for mla
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  07750f0
- swap mla for mlc
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  a1862b9
- optimize mlc a bit
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  82ca34b
Commits on Mar 17, 2026
- Start of twodelta
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  bffa8df
- more tests
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  57e3cd9
- Opitimize the checks for eqality to improve write speed
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  committed
  80f5eb6
- add twodelta to reben
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  a19fb26
- add twodelta to xben
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  e0054a1
- move banners to their own section
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  b023278
- add way to convert between ben versions
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  98b8541
- format
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  5ca5e65
- fix read-all bug
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  befb641
- update docs
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  ed71980
- fix labelling issue
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  8dc1ce9
- Speed up conversion
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  3967b9a
- optimize the twodelta case
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  committed
  d1a85d0
- fix header double-check bug
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  committed
  f2dd39b
- small opt for xben encoder
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  9cc8efc
- opt decode
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  392cf9c
- get rid of extreneous copy
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  4a06e29
- possible xz compression improvement for twodelta
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  69fabd9
- remove mla
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  c6bcfaf
Commits on Mar 18, 2026
- Cleanup of twodelta method
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  762c8f6
Commits on Mar 19, 2026
- Start stubbing out bigger reorg
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  713d303
Commits on Mar 20, 2026
- More reorg
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  7dd91fe
- Make a better error system
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  committed
  a0e8f73
- Fix up twodelta so that the tests all work again
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  2ce7fbf
- More org
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  a911ff6
- Modify responsibilities of the encoder
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  1199d50
- Remove redundant code in io/writer/ben
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  committed
  d352036
- Reorg (I will figure out the design I like eventually)
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  committed
  0f009b2
- Centralized constructor impl for Ben-type frames
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  committed
  6078ab2
- Change BenEncoder -> AssignmentWriter
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  cd0233a
- Change XBenEncoder -> XZAssignmentWriter
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  8321f3e
Commits on Mar 23, 2026
- Change writer/ben.rs -> write/assignment_writer and make better use of encoders
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  committed
  03da065
- Update XZAssignment writer to be more parallel with the AssigmentWriter
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  committed
  f8735dc
- Rename twodelta.rs -> twodelta_encode.rs
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  committed
  b126117
- Update decoder and readers
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  c8e2348
Commits on Mar 31, 2026
- Update some tests
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  committed
  2433fa9
Commits on Apr 7, 2026
- Add twodelta into cli
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  committed
  9e8fa32
Commits on Apr 8, 2026
- add twodelta to python side
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  committed
  edc9647
- improve docs for things that should not use twodelta
  peterrrock2
  committed
  f53715e
- Improve test suite
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  committed
  b1c0813
- add edge-case tests
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  committed
  0f8d0ff
- change format spec for bendl
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  committed
  cc53e8a
Commits on Apr 10, 2026
- move over to using petgraph internals
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  committed
  f9224ae
- try louvain
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  027ba0d
Commits on Apr 11, 2026
- revert louvain
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  266f11e
- add bendl
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  committed
  612512e
- better stess testing
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  committed
  5b5ba8b
- update pyben decoder
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  committed
  f933629
- fix warnings
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  committed
  cdfd7d8
- allow multiple iterator passes
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  42e191a
Commits on Apr 13, 2026
- Lots more tests and remove PyBundleReader
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  committed
  cbcad0d
Commits on Apr 20, 2026
- More testing
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  committed
  9ae12c2
Commits on Apr 30, 2026
- Get coverage to 98% on rust side
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  committed
  a43cf51
Commits on May 1, 2026
- better json reader
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  committed
  d58276c
- we will continue testing until moral improves
  peterrrock2
  committed
  75049bf
- move writer tests
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  committed
  70912ca
- reorganize bundle module
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  committed
  5b35451
- reorg cli module
  peterrrock2
  committed
  092bdac
- reog pyben side to parallel ben side
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  committed
  ae44ce5
- reorg to make cli easier to test
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  committed
  aa8ad81
Commits on May 4, 2026
- fix twodelta inconsistency
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  committed
  3c86805
Commits on May 5, 2026
- fix up some ambiguous / clashing terminology
  peterrrock2
  committed
  288045d
- tweaks to cli behavior
  peterrrock2
  committed
  1c5255a
- change pyben -> ben-py
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  committed
  e6a98ee
- change progress to spinner
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  d9b5a3b
Commits on May 6, 2026
- get rid of frame duplicates
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  committed
  12aabce
- Fix python tests
  peterrrock2
  committed
  6c1318d
- Increase size of xz block to improve ability to parallelize
  peterrrock2
  committed
  143bf91
- Allow --n-cpus -1 to mean all cores
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  e71975b
Commits on May 7, 2026
- Unify stream readers
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  860012f
- small writer extraction
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  74d0dd5
Commits on May 9, 2026
- consolodate relabel module
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  c712179
- small dedupe in graph module
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  46655eb
Commits on May 10, 2026
- Unify stream writers
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  committed
  ecc39df
- add known asset kind enum for bendl
  peterrrock2
  committed
  6c2a904
- add in an XBEN variant
  peterrrock2
  committed
  92f2b3e
- update pcompress translation to be more consistent
  peterrrock2
  committed
  aa185d8
- Update bundle protocol
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  committed
  2263240
- clean up bendl stream api
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  899e270
Commits on May 18, 2026
- add in checksum logic
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  7a7ef6c
Commits on May 21, 2026
- formatting pass
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  1ce870c
- checksum for the assignment streams
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  b76de04
- Add in some edge-case tests
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  f4d95e3
Commits on May 22, 2026
- add strict payload length enforcement
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  committed
  c2aac6e
- add some fixtures and stability tests
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  committed
  18ad3ec
- enforce bit width consistency and add size guard
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  committed
  c04cee7
- add adversarial tests
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  committed
  7acb805
- add more edge-case stress tests
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  committed
  f4a93f9
- check twodelta boundary test
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  committed
  3cfee66
- more boundary tests
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  committed
  f8986c8
- check label value 0 makes the round trip
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  committed
  24f8672
- add property tests for bendl
  peterrrock2
  committed
  f146f52
- add property-based equivalence tests
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  committed
  5d84063
- add some forward-compatibility tests
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  committed
  da50034
- add tests for multi-step decode
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  committed
  8797434
- test parallel reads
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  committed
  aa00f83
- test zero and one sample edge cases
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  committed
  4187b8c
- add cli tests
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  committed
  d6aef70
- better testing of the bendl write path
  peterrrock2
  committed
  107d880
- more cli path tests for bendl
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  committed
  d0c5b71
- remove redundant tests
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  7b58410
Commits on May 25, 2026
- formatting
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  abac92d
Commits on May 30, 2026
- split bundle reader up
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  4f8c064
- create asset registry
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  committed
  ff2d3ec
- Improve crash safety of BENDL and tighten verified stream APIs
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  4de8883
Commits on May 31, 2026
- Fix maximum number of directory entries
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  committed
  39a6ee8
- remove repetition in verify
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  e343f1f
- More consistent progress bar semantics
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  committed
  841d16b
- clean up fast path in relabel
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  committed
  d78b271
- improve readability
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  committed
  189b2d6
- make clippy happy
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  committed
  c53baf0
- better recovery for dropped stream
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  912e526
Commits on Jun 1, 2026
- finish benpy rename
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  committed
  696038d
Commits on Jun 2, 2026
- make two-delta work better on things like SB or arbitrary ensembles
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  committed
  b2a0a37
- fix clippy
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  committed
  b13b0ed
Commits on Jun 4, 2026
- reorg python side and add bundle bindings
  peterrrock2
  committed
  6475871
- add relabel bundle helper and reformat
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  committed
  2d32712
- api change to add_graph on the python side
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  committed
  3ca70d0
Commits on Jun 5, 2026
- update cli to use dualgraph rather than shapefile
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  committed
  70caba8
Commits on Jun 8, 2026
- major docs overhaul
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  committed
  1712c3b
Commits on Jun 9, 2026
- update docs
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  committed
  0ae330c
- a different color theme
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  committed
  aa038e4
- better contrast in color theme
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  committed
  c4b616f
- better doc strings for the api section
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  committed
  9dcaee7
- more docs!!
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  committed
  ec3c1f7
Commits on Jun 10, 2026
- reroute old methods through the ben stream reader
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  committed
  3d20a76
- format
  peterrrock2
  committed
  6b8adde
- harden against oversized assets
  peterrrock2
  committed
  a4f5b39
- harden against malicious assignment lengths and middle zero-byte corruption
  peterrrock2
  committed
  add9fc3
- better reader errors (propagate)
  peterrrock2
  committed
  1fb97c2
- fix some edge case issues in the pcompress translation
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  committed
  4123e9a
- handle duplicate index in remap and failed final flush edge cases
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  committed
  7f7e998
- better coverage harnass
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  cb41eec
Commits on Jun 11, 2026
- get rid of the try_from_parts symantics and fix potential zero drop
  peterrrock2
  committed
  c557b11
- fix issue with twodelta silently failing on a pathological 2 distrcit TX
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  committed
  87cf6e6
- Add in cross architecture tests
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  committed
  5593e37
- remove the from_parts from twodelta
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  committed
  7f6b0f8
- convert panics into errors for better handling
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  committed
  38f9f43
- add rust linter into workflow
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  committed
  a33b35c
- make sure interop with Pcompress still lives
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  committed
  5e76363
- better ci
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  committed
  0fe0e4c
- more fuzzing
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  committed
  b83148a
- add soak test
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  committed
  929ecc4
- better ci / cd with a smoke test on wheels
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  committed
  0611dc4
Commits on Jun 12, 2026
- autocompress larger assets in bundle
  peterrrock2
  committed
  cedd613
- Note compression bomb risk (consequence of format and nothing to do here)
  peterrrock2
  committed
  72d0018
- tuning for fuzz tests
  peterrrock2
  committed
  a3b3400
- better api for asset payloads
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  committed
  1361ace
- make sure python assets verify
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  committed
  bf4179c
- enabling remove asset
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  committed
  14304b8
- Docs.....
  peterrrock2
  committed
  99c568e
- naming fixes
  peterrrock2
  committed
  f26b2b1
- make sure payload lengths do not overrun file size
  peterrrock2
  committed
  44dbe9b
- fix mid-write crash bug
  peterrrock2
  committed
  60f6bce
- unify remove and compact
  peterrrock2
  committed
  3e2fac4
- remove large memory buffering of tail payloads
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  committed
  3ff79c2
- power loss safety because I'm paranoid
  peterrrock2
  committed
  33ce37c
- better file swap dicipline
  peterrrock2
  committed
  39c91d8
- poison the encoder on failed stream finalize
  peterrrock2
  committed
  2020092
- guard against mutations to underlying bendl (b/c jupyter)
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  committed
  dc8d0ad
- prevent custom assets from claiming known names
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  committed
  82dfbba
Commits on Jun 13, 2026
- deal with GIL
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  committed
  a698eaa
- validate content type before writing
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  committed
  1eebdf4
- dedup pass
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  committed
  23b8761
- docs
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  committed
  35975b6
- put fuzzing back in
  peterrrock2
  committed
  a70ac38
- give control over asset compression
  peterrrock2
  committed
  741bee9
- cleanup comments
  peterrrock2
  committed
  6c04ef4
- more docs for me
  peterrrock2
  committed
  0648dd8
- better visited link color
  peterrrock2
  committed
  6e1faf5
- phrasing sweep on docs
  peterrrock2
  committed
  c17f410
- docs org
  peterrrock2
  committed
  0fb781e
- rename stream -> ben_stream
  peterrrock2
  committed
  db2e62c
- prettify docs
  peterrrock2
  committed
  e56ac50
- fix links
  peterrrock2
  committed
  5a4a1b1
- fix links again
  peterrrock2
  committed
  bf211ba
- increase timout for link check
  peterrrock2
  committed
  75d42cc
- prettier
  peterrrock2
  committed
  23f45b1
- more link fixing
  peterrrock2
  committed
  5b7c23a
- you're killin me smalls
  peterrrock2
  committed
  979bb2d
- link
  peterrrock2
  committed
  967c2e3
- fix link ignore regex
  peterrrock2
  committed
  a2f378c
- remove landing page buttons
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  committed
  6c20a7c
- update log levels
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  committed
  4d94ef4
Commits on Jun 14, 2026
- change the way that reben does suffixes
  peterrrock2
  committed
  798efd2
- make canonicalize start at 0 rather than 1. lock in ability for arbitrary dists
  peterrrock2
  committed
  a22c62d
- change cli shape
  peterrrock2
  committed
  cdac4cc
- fix up transcode to/from pcompress
  peterrrock2
  committed
  e14d5f2
- better banner error
  peterrrock2
  committed
  f791ef0
- small cosmetic changes to cli
  peterrrock2
  committed
  d063994
- go back to fast lookup on standard and mkv ben files
  peterrrock2
  committed
  35e6a0c
- faster twodelta lookup
  peterrrock2
  committed
  c72ecee
Commits on Jun 15, 2026
- better spinner behavior on xz and lookup
  peterrrock2
  committed
  0959ed0
- update ci suite to run fast tests on PRs
  peterrrock2
  committed
  27789fe
- more corrupt header protection on the ben side
  peterrrock2
  committed
  004672e
- protect against overlong stream len on python side
  peterrrock2
  committed
  29a77ad
- fix unchecked total runs and relabel bundle
  peterrrock2
  committed
  d965df6
- errors / docs cleanliness
  peterrrock2
  committed
  f3fe085
- change main CO example
  peterrrock2
  committed
  a76f418
- add checksum for the header
  peterrrock2
  committed
  951abc8
- some reorg / cleanup
  peterrrock2
  committed
  2d27f0f
- centralize stamp header (tests) and remove ability to write w/o header checksum
  peterrrock2
  committed
  cf955d2
- fix fuzz workflow
  peterrrock2
  committed
  d57d79a
Commits on Jun 16, 2026
- Merge branch 'main' into 1.0.0
  peterrrock2
  authored
  91eda43

Commits

Commits on Mar 12, 2026

Commits on Mar 13, 2026

Commits on Mar 16, 2026

Commits on Mar 17, 2026

Commits on Mar 18, 2026

Commits on Mar 19, 2026

Commits on Mar 20, 2026

Commits on Mar 23, 2026

Commits on Mar 31, 2026

Commits on Apr 7, 2026

Commits on Apr 8, 2026

Commits on Apr 10, 2026

Commits on Apr 11, 2026

Commits on Apr 13, 2026

Commits on Apr 20, 2026

Commits on Apr 30, 2026

Commits on May 1, 2026

Commits on May 4, 2026

Commits on May 5, 2026

Commits on May 6, 2026

Commits on May 7, 2026

Commits on May 9, 2026

Commits on May 10, 2026

Commits on May 18, 2026

Commits on May 21, 2026

Commits on May 22, 2026