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ChangeLog
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CHANGES
=======
3.3.0
-----
* ci: bump cibuildwheel to 2.16.5
* feat: add \_\_contains\_\_ to CompressoArray
3.2.2
-----
* build: rmeove cpp file from version control
* build: switch to dynamically compiling pyx
* build: add pyproject.toml
* fix: add binding for top level functions
* build: update build for py312
3.2.1
-----
* chore: remove versioning property
* build: set version
* chore: update supported python versions
* build: update build system for py311
3.2.0
-----
* fix: small edits to docstrings + update build
* feat: add gzip loading/saving
3.1.0
-----
* docs: fix comment
* feat: add save, load, raw\_labels to cython wrapper
* feat(cli): -i/--info flag prints header info from file
* build: skip musllinux (no numpy binaries, slow compilation)
3.0.0
-----
* build: update build process
* docs: accidently deleted 'z'
* docs: fix outdated format description
* build: ensure windows builds in release mode
* fix: make CompressoArray take more natural slices
* feat: random z access (#8)
* fix(cli): filenotfounderror
2.3.2
-----
* chore: update MANIFEST.in
* test: protect against rle zero overflow
* fix: logic error in RLE window encoder
* fix: calculation for valid stream used bits instead of bytes
* refactor: use templates to shorten the logic for decompress
* chore: tighten up whitespace
2.3.1
-----
* chore: exclude test data files from sdist
2.3.0
-----
* docs: fix whitespace
* perf(remap): substantially faster
* docs: show how to use remap and valid
* docs: add docstring to remap
* feat(remap): adds remap without compression
* refactor: use cython type notation
2.2.0
-----
* feat: if RLE encode error, automatically recompress as 8,8,1
2.1.0
-----
* fix: throw error if unable to RLE encode windows
* fix: catch cpp exceptions in Python
* feat(cli): adds steps and six flags
2.0.0
-----
* chore: update changelog
* docs: note that this implementation is format version 0
* docs: note that a second stage compressor is needed
* docs: make CLI example clearer
* chore: update changelog
* fix: really add CLI
* feat: add compresso cli
* chore: delete obsolete dockerfile
* chore: update dockerfile with oldest-supported-numpy
* chore: rename connectomics.cpso.lzma to connectomics.npy.cpso.lzma
* chore: add sample data to repo
* chore: compresso.hxx to compresso.hpp and add MANIFEST.in
* docs: note that any possible input is possible in header
* docs: name author of modifications
* chore: skip pypy builds
* docs: describe the stream format better
* chore: add github builds
* fix(encode\_boundaries): ensure 1 is correct type
* chore: update all runtime\_errors to start with "compresso"
* fix: ensure that zero locations can never segfault
* feat: allow nonstandard step sizes
* fix: incorrect casting of pointers
* chore(setup.cfg): replace deprecated hyphens
* docs: describe support for 6 connected
* feat: support for both 4 and 6 connectivity (4 is default)
* feat: add connectivity to header
* refactor(cc3d): change name of main fn to connected\_components
* perf(decompress): improve decode\_boundary performance
* docs: change wording slightly
* docs: description of the algorithm
* fix: uint8 windows
* docs: discuss implementation changes
* docs: save edits needed to experiment with 6-way ccl
* docs: update readme
* fix: use new interface to cc3d
* fix(cc3d): add back in optimizations
* chore: update year
* chore: update license for cc3d.hpp to LGPLv3
* docs: compresson performance in docs
* fix: add figure back in to docs
* docs: describe modifications to the protocol
* fix: support window8 in cpp
* test: add tests for steps
* fix: start to support uint32 windows
* test: check black arrays
* test: ensure compresso.labels matches actual unique labels
* chore: update appveyor
* fix: magic should be cpso not cpso\0
* test: make sure maximum values are handled
* feat: add more tests
* fix: handle zero length arrays
* fix(cc3d): can't use optimizations with start\_label
* docs: add comments
* feat: add python methods for inspecting the raw stream
* perf: vectorize decoding of ccids
* chore: whitespace
* fix: prevent amplification of start label
* fix(cc3d): start label was not assigned correctly
* fix: better error messages for decoding locations
* fix: incorrect nx and ny
* fix: add check for zero step size
* fix: more rounding errors for nx,ny,nz
* fix: bug in boundary decoding
* fix: bug with rounding nblocks up
* fix: memory leak
* fix: ensure labels handles 0 properly
* fix(labels): use new decoding protocol for locations
* fix: able to encode last 6 units for indeterminate locations
* docs: fix error in docstring
* feat: add functions for reading labels and dtypes from compressed stream
* docs: add a header
* fix: lots of cleanup
* fix(cc3d): start\_label required some finessing
* fix: make sure output pointer is mapped to right data type
* fix: cc3d needs to offset start label as well in relabel
* fix: bug in rle compression
* fix: skipping first values for uniform arrays
* fix(cc3d): need to have a new offset label for each z level
* perf: specialization for uint16\_t window renumber
* wip: trying to figure out decoding error
* fix: compiles!
* fix: forgot to decode RLE
* feat: add decompression
* feat: support uint16 for 4x4x1
* refactor: cc3d switched to use black as on
* perf: maybe faster unique
* fix: some cleanup
* refactor: move stream writing into a function
* fix: some encoding errors
* feat: read header function
* fix: bounds check was in the wrong direction
* wip: overhauling the code
* fix: wrong order of arguments
* fix: try to match the 2d slice processing of original connected components
* fix: memory errors
* wip: attempting to fix ordering
* test: add order test
* fix: unsigned long -> uint64\_t
* chore: no support for 32-bit windows
* chore: update build system
* docs: place note on unofficialness in a more attractive location
* docs: remove inapplicable section on running experiments
* docs: add example, badge, and update requirements
* chore: a few changes for the 1.0 release
1.0.0
-----
* docs: update docstring for compress/decompress + reference
* test: add size restriction
* test: add reconstitution test
* chore: add Dockerfile for manylinux distribution
* Revert "perf: ~1/3 faster connected components algorithm"
* refactor: remove redundant array inititalizations
* perf: ~1/3 faster connected components algorithm
* fix: used the right implementation of compresso (from experiments)
* chore: update gitignore
* refactor: setup such that it is packageable
* Fixed installation instructions
* Updated requirements.txt to work with conda
* README: fixed formatting
* Removed wrong instructions
* README: added datasets
* Updated README
* Removed old compression location
* requirements.txt: moved to conda environment
* experiments: updated all files to work with new framework
* .gitignore: ignore temp cython files
* .gitignore: ignore the results folder
* compression: removed failed methods
* compression: removed old files
* README: fixed formatting
* README: updated instructions
* \_LEGACY: removed old outdated experiments
* Mention paper explicitly
* Minimize
* Update results
* Update name
* Add link to paper
* Update name
* Update name
* Add plotting script
* Fix failure when using lowercase names
* Add missing no-compression class
* Sanity assertion runs only once
* Added experiment runner. Fixed a bug. Updated README
* Set to root path
* Update to latest banner
* Add logo
* Update references visually
* Update figure composition to save space
* Bockwurst encoding and experiments
* Initial commit