ChangeLog

CHANGES
=======

0.50.0
------

* Version 0.50.0
* feat: delete black uploads flag (#212)
* docs: add link to public dataset examples
* docs: update README
* docs: add description of CloudVolume to \_\_init\_\_.py
* chore: update ChangeLog AUTHORS

0.49.3
------

* Version 0.49.3
* perf: omit a network request when creating a GCS connection (#223)
* perf: improve initialization performance of CV

0.49.2
------

* Version 0.49.2
* fix: http(s) should handle 404 like gs and s3

0.49.1
------

* Version 0.49.1
* feat: Support for GCS Batch Delete (#219)
* docs: fix typo on autocrop (should be False, not True)
* chore: update Trove classifiers, add markdown description classification
* Add allow\_cropped flag to CloudVolume.download\_point (#215)
* docs: replace npm server with vol.view() in documentation

0.49.0
------

* Version 0.49.0
* docs: added neuroglancer view server invocation to examples
* feat: neuroglancer compatible link with vol.view() (#214)
* docs: remove obsolete downsample parameter
* docs: underlying -> chunk\_size, download\_point
* fix: upgrade urllib3 (#213)

0.48.0
------

* Version 0.48.0
* feat: download\_point lets you download a cutout from just a coordinate
* refactor: remove deprecated "output\_to\_shared\_memory" parameter
* feat: export Vec class for use in other applications
* misc enhancements (#209)
* fix: missing protocol in error message

0.47.5
------

* Version 0.47.5
* feat: create\_new\_info accepts numpy datatypes for 'data\_type'
* fix: color jpeg encoding support (#210)
* fix: FutureWarning on type coercion
* chore: prophylactic to avoid accidently uploading secrets
* fix: more robust dtype detection
* fix: select single channel in save\_images (#207)

0.47.4
------

* Version 0.47.4
* feat: more robust provenance refreshes (#205)
* changing to an os independant character (#204)

0.47.3
------

* Version 0.47.3
* fix: add exp backoff to connection creation in connection pool

0.47.2
------

* Version 0.47.2
* perf: 1.5-2x faster CloudVolume on Google Cloud Storage (#202)

0.47.1
------

* Version 0.47.1
* chore: make sure intern is bumped to the latest version 0.9.13
* chore: drop python 3.4 testing
* chore: remove old python builds deployment
* fix: Bbox.volume() would easily overflow
* fix(from\_numpy): add boolean and use floating abstract dtype (#200)

0.47.0
------

* Version 0.47.0
* docs: Updated CloudVolume docstring
* fix: from\_numpy error when using multiple mip levels (#197)
* docs: Python 2.7 EOL statement + pretty up "Spinoff Projects"

0.46.0
------

* Version 0.46.0
* feat: Bbox.from\_delta
* chore: fpzip 1.1.3 compatibility (#196)
* fix: more robust SWC importer

0.45.0
------

* Version 0.45.0
* feat: from\_numpy function to create a Precomputed Volume (#188)
* add support for default region (#195)
* docs: update ChangeLog

0.44.2
------

* Version 0.44.2
* docs: add bool as a supported uViewer data type
* docs: fix display of segmentation in uViewer
* feat(uViewer): convert 64-bit int data to float64 for display w/ warning
* refactor(uViewer): remove redundant branch logic
* fix(uViewer): infinite and nan value handling
* feat: support boolean arrays in microviewer
* docs: update AUTHORS and ChangeLog

0.44.1
------

* Version 0.44.1
* feat: retry for Storage.list\_files
* fix(save\_images): typo (#193)

0.44.0
------

* Version 0.44.0
* feat: Bbox serialize, deserialize, to\_dict, from\_dict
* add a little bit comments; add support for environment variables (#185)
* adding a chunk based duplicate vertex removal function (#182)

0.43.1
------

* Version 0.43.1
* fix: numpy 1.16.0 disallows write=True on string buffers
* fix: remove uniqueItems from layer provenance schema

0.43.0
------

* Version 0.43.0
* feat(skeletonservice): joint preserving downsample (#177)

0.42.3
------

* Version 0.42.3
* fix: single mesh id save adds file suffix if filepath is None
* fix: ensure fused mesh construction order stability
* fix: make mesh vertices a uniform float32 array

0.42.2
------

* Version 0.42.2
* fix: https get\_files
* chore: tab size 2 for test\_storage.py
* docs: upload ChangeLog

0.42.1
------

* Version 0.42.1
* perf(meshservice): multithreaded mesh manifests (#176)

0.42.0
------

* Version 0.42.0
* fix: close requests streams  (#173)
* feat: support ellipsis operator
* fix: allow numpy scalar types for cloudvolume access
* feat(uviewer): cast 2D and 4D images to 3D automatically
* refactor(lib): remove unused list\_shape function
* fix: accomodate python2.7 in Bbox division
* test: bbox.subvoxel() vs pathological behavior of bbox.volume()
* feat: support dtype on Bbox
* fix: tests for subvoxel bounding box size were faulty
* feat: vol.skeleton.get now accepts multiple segids

0.41.0
------

* Version 0.41.0
* allow reestablishing viewer server in the same python session (#169)
* feat(skeletonservice): upload takes PrecomputedSkeleton as input

0.40.4
------

* Version 0.40.4
* perf(skeletonservice): faster component search ~3x
* perf(skeletonservice): faster cable\_length operator

0.40.3
------

* Version 0.40.3
* fix: multiprocess upload crashes on thin non-aligned images (#168)
* Bbox Upgrades (#167)

0.40.2
------

* Version 0.40.2
* feat(storage): Batch requests for GCS files\_exist() (#165)
* docs: formatting
* docs: info on serving local files
* fix(skeletonservice): downsample was blowing stack

0.40.1
------

* Version 0.40.1
* perf(skeletonservice): made rendering components much faster
* perf(skeletonservice): faster rendering of components
* fix(skeletonservice): \_compute\_components wasn't treating loops correctly
* refactor: moved skeleton exceptions into exceptions.py
* feat: add chunk size info to non\_aligned\_write error message

0.40.0
------

* Version 0.40.0
* fix: transfer\_to retains Content-Type and respects existing info. (#157)
* feat: cable\_length, downsample, improved Consolidation, SWC file support, connected components (#152)
* vol.mesh.save() refactor path code (#158)
* docs: update ChangeLog

0.39.0
------

* Version 0.39.0
* fix: uViewer hotkeys work for lower and upper case
* feat: floating point images handle infinity and NaN in uViewer

0.38.0
------

* Version 0.38.0
* feat: add encoding parameter to "add\_scale"
* feat: Storage works for any path, not just Neuroglancer paths (#154)
* fix: ./, stepping 2 at a time in uViewer
* feat: add offset to view in uViewer
* test: s3 parallel read
* docs: added reference to Google Storage setup
* Update README.md
* fix: uViewer automatically uses image resolution
* Update README.md
* docs: updated pip installation instructions
* docs: link to SfN 2018 poster
* Revert "fix: VolumeCutout slices generate real VolumeCutouts"
* fix: VolumeCutout slices generate real VolumeCutouts
* fix: to\_volumecutout deals with slices cutouts gracefully

0.37.4
------

* Version 0.37.4
* docs: fixed spelling error
* fix: support floating point images in hyperview

0.37.3
------

* Version 0.37.3
* docs: links to fpzip and compressed\_segmentation repos
* refactor: use new compressed-segmentation pypi package

0.37.2
------

* Version 0.37.2
* fix: microviewer was not installed correctly on anaconda
* feat: added UI updates and resolution option to viewer invocation
* Update README.md

0.37.1
------

* Version 0.37.1
* feat: added "selected segments" to microviewer
* feat: change title of microviewer depending on layer and mode
* Update README.md

0.37.0
------

* Version 0.37.0
* Specifying mip level by voxel resolution (#151)
* chore: rename volumeviewer to microviewer
* chore: add MANIFEST.in to ensure microviewer inclusion
* feat: MicroViewer (#150)
* Update README.md

0.36.2
------

* Version 0.36.2
* fix: last update broke VolumeCutout.save\_images()

0.36.1
------

* Version 0.36.1
* fix: forgot to import lib.Bbox in skeletonservice.py

0.36.0
------

* Version 0.36.0
* feat: add merge, crop, and from\_path to PrecomputedSkeleton

0.35.0
------

* Version 0.35.0
* feat: skeleton consolidation, equivalence, and equality operators (#147)
* Update README.md

0.34.4
------

* Version 0.34.4
* chore: bump fpzip to 1.1.1
* fix: skeleton upload supports vertex types

0.34.3
------

* Version 0.34.3
* chore: comply with updated fpzip treatment of memory order
* chore: bump version of python-jsonschema-objects
* docs: update changelog

0.34.2
------

* Version 0.34.2
* fix: only reset connection pool when unpicking on a new PID (#145)
* feat: add setter for scales and scale property. vol.cloudpath alias of vol.layer\_cloudpath

0.34.1
------

* Version 0.34.1
* Easy External Multiprocessing (#142)

0.34.0
------

* Version 0.34.0
* feat: chunk\_size argument for add\_scale

0.33.4
------

* Version 0.33.4
* chore: bump intern to 0.9.10

0.33.3
------

* Version 0.33.3
* feat: added "chunk\_size" attribute as synonym for "underlying"
* chore: bump intern to no\_cache fixed version

0.33.2
------

* Version 0.33.2
* fix: didn't handle vertices=None correctly in PrecomputedSkeleton

0.33.1
------

* Version 0.33.1
* fix: allow for empty skeleton creation

0.33.0
------

* Version 0.33.0
* feat: PrecomputedSkeleton.empty()
* docs: added http and matrix to documentation
* Update README.md

0.32.0
------

* Version 0.32.0
* feat(meshservice): Faster mesh processing + PLY support (#138)

0.31.3
------

* Version 0.31.3
* feat: use new no\_cache argument for BOSS
* chore: upgrade intern
* feat: bump zfill to 3 in save\_images

0.31.2
------

* Version 0.31.2
* feat(meshservice): Remove duplicate vertices (#137)

0.31.1
------

* Version 0.31.1
* fix: failing test for transfer\_to (the test was wrong)
* docs: updated changelog
* feat: upgrade 'matrix' protocol to encrypted (https)

0.31.0
------

* Version 0.31.0
* feat: skeletonservice upload\_multiple
* feat: add compress argument to transfer\_to
* docs: updated changelog

0.30.2
------

* Version 0.30.2
* chore: bump tenacity to be python3.7 compliant
* docs: updated installation instructions for Anaconda

0.30.1
------

* Version 0.30.1
* fix: skeleton upload respects cdn\_cache setting
* feat: add mip information to non-aligned writes

0.30.0
------

* Version 0.30.0
* feat: transfer\_to implementation (#135)
* fix: create\_new\_info supports skeletons correctly

0.29.0
------

* Version 0.29.0
* docs: documented the save\_images function
* feat: add global normalization option to save\_images
* feat: handle 3d arrays in save\_images
* feat: support boolean images in save\_images

0.28.3
------

* Version 0.28.3
* chore: upgrade fpzip to 1.0.4

0.28.2
------

* Version 0.28.2
* Wms fix fpzip install (#134)

0.28.1
------

* Version 0.28.1
* fix: memory leak in compressed\_segmentation.pyx decompression
* Update README.md

0.28.0
------

* Version 0.28.0
* refactor: Use fpzip PyPI package (#133)
* feat: independent control of cache compression (#132)
* feat: initialization of the "matrix" protocol. (#128)

0.27.1
------

* Version 0.27.1
* chore(requirements.txt): replace deprecated google-cloud (#131)

0.27.0
------

* Version 0.27.0
* feat: bbox\_to\_mip (#127)

0.26.3
------

* Version 0.26.3
* fix: add compressed\_segmentation\_block\_size support to create\_new\_info

0.26.2
------

* Version 0.26.2
* feat: added radii and swc vertex attrs to skeleton binary format (#123)

0.26.1
------

* Version 0.26.1
* fix: support compressed\_segmentation\_block\_size in add\_scale
* docs: thank C++ compressed\_segmentation authors
* Version 0.26.0
* feat: compressed segmentation C extension (#121)
* docs: changelog

0.25.1
------

* Version 0.25.1
* chore: upgrade tenacity to 4.10.0 for python 3.7 compatibility (#125)
* Update README.md
* Update README.md
* Update README.md
* Update README.md
* docs: added install info for fpzip and more acknowledgements
* Update README.md
* Update README.md

0.25.0
------

* Version 0.25.0
* feat: add fpzip encoding C extension (+ "kempression") (#117)
* docs: added flush\_info and flush\_provenance to examples
* feat: added vol.cache.flush\_info() and vol.cache.flush\_provenance()
* fix: add intelligible error when skeletons don't exist

0.24.0
------

* Version 0.24.0
* feat: vol.skeleton for accessing Neuroglancer skeletons (#120)
* Update README.md
* feat: cleanup shared memory on SIGTERM or SIGINT (#115)
* Update README.md
* Version 0.23.0
* feat: specify C or Fortran order in upload\_from\_shared\_memory (#113)

0.22.0
------

* Version 0.22.0
* docs: updated README with new download\_to\_shared\_memory method
* perf: 1x memory usage for parallel downloads (#112)
* refactor: output\_to\_shared\_memory -> download\_to\_shared\_memory() (#111)

0.21.2
------

* Version 0.21.2
* fix: make futures conditional on python 2 (#110)
* docs: made the roles of Igneous and CloudVolume more clear
* docs: reorganized new dataset creation
* docs: added information on bucket-specific credentials
* docs: updated README.md narrative

0.21.1
------

* Version 0.21.1
* fix: use concurrent.futures.ProcessPoolExecutor vs mp.Pool (#108)

0.21.0
------

* Version 0.21.0
* feat: Http(s) Storage interface

0.20.2
------

* Version 0.20.2
* fix: add legacy support for \*\_credentials\_path

0.20.1
------

* Version 0.20.1
* feat: supporting bucket specific secrets for aws and google
* fix: add save\_images visualization support for float32 and float64

0.20.0
------

* Version 0.20.0
* feat: Storage now has put\_json and get\_json

0.19.1
------

* Version 0.19.1
* fix: tqdm race condition "AttributeError: 'tqdm' object has no attribute 'pos'" (#104)
* docs: updated benchmarks for test\_v0, mip 0, parallel 1
* docs: fixed misspelling in comment

0.19.0
------

* Version 0.19.0
* feat: upload from shared memory (#101)
* perf: change BOSS calls to fortran order as well

0.18.0
------

* Version 0.18.0
* perf: use fortran order internally in numpy arrays (#99)
* docs: added some acknowledgements for important code and intellectual contributions by third parties

0.17.0
------

* Version 0.17.0
* feat: parallel uploads (#98)

0.16.0
------

* fix: updated setversion.py to not clobber
* Python Compressed Segmentation Codec (#95)
* feat: shared memory emulation using the filesystem for OSX (#97)
* feat: script to help set versions and tags
* fix: errors closing mmap handle (\_\_del\_\_ not existing as a superclass method?)
* fix: errors closing mmap handle (\_\_del\_\_ not existing as a superclass method?)
* feat: added \_\_version\_\_ to cloudvolume
* Update README.md
* docs: updated README to discuss parallel, shared memory, non\_aligned\_writes

0.15.0
------

* feat: parallel download + shared memory output (#94)
* refactor: use txrx.shade instead of reinventing the wheel + BOSS tests

0.14.0
------

* feat: Added non-aligned chunk uploads. (#92)
* Update README.md
* Update README.md
* Update README.md
* Update README.md

0.13.0
------

* feat: preserve option for fush\_cache + flush\_cache\_region (#86)
* Update README.md
* Changing the docs a bit (#91)

0.12.3
------

* fix: added reset\_connection\_pools to storage.py (#90)

0.12.2
------

* fix: s3 listing was limited to 1000 files (#89)
* Update README.md

0.12.1
------

* fix: bounds check for short end chunks
* Update README.md
* Update README.md
* docs: updated README for autocrop

0.12.0
------

* Autocrop (#81)

0.11.0
------

* Reduce Memory Usage for Non-Aligned Downloads (#79)

0.10.4
------

* feat: more informative error message for non-compliant cloudpaths

0.10.3
------

* fix: slices\_from\_global\_coords was not computing maxsize properly
* feat: added support for downloading different MIPs from BOSS (#73)

0.10.1
------

* feat: exported ConnectionPools

0.10.0
------

* feat: removed requirement for project\_name file

0.9.0
-----

* Concurrent painting w/ Download & Upload (Save image size worth of memory) (#69)
* docs: memory usage graphs for image and segmentation download
* docs: example memory profile of running pytest
* feat: more memorable colors for plots
* feat: sorted plots for benchmark
* docs: benchmark data and plotting for gcloud
* Performance Benchmark (#67)
* Update README.md
* feat: added compress option to CloudVolume (#66)
* fix: force chunk sizes to be integers
* test+perf: make boss download 1/20th the size
* test: Changed travis API keys to environment variables
* chore: liberalized requirements for boto3
* chore: liberalize Pillow version requirements
* test: added BOSS test
* fix: boss bounds were off by one at border + cast cutout to correct type
* refactor: added vol.mesh interface (#64)
* refactor: seperate file location computation from fetching
* fix: Vec.rectVolume was broken in python3
* feat: slices\_to\_global\_coords + tests
* chore: expand protobuf dependency qualifications
* fix: remove unnecessary dependency
* chore: removed old depencency for google-resumable-media
* chore: remove unnecessary independent jsonschema dependency
* chore: fork intern and install from github to resolve dependency issue (#63)
* fix: make commit\_info more resilent to numpy arrays
* chore: additional flexibility in requirements
* fix: added python3 division to Bbox
* fix: add\_scale in Python3 rendered np.int64
* fix: python3 xrange compatibility
* fix: python3 incompatible unicode call in lib.py
* fix: better error message for missing info file
* feat: manual control over cache-control headers for uploaded files (#62)
* fix: file read errors were crashing incorrectly
* chore: bump google-cloud-python to 0.30.0
* feat: file:// protocol now supports the ~ prefix for your home dir (#60)
* feat: better error message for missing mesh manifests (#61)
* feat: reveal secrets (#58)
* feat: backwards compatible secrets (#57)
* feat: pretty print info and provenance files (#56)
* fix: pool on buckets instead of clients for gcloud (#53)
* chore: downgrade google-cloud from 0.27 to 0.26.1
* fix: cache + fill\_missing interaction crash (#52)
* feat: added cache-control options to Storage (#51)
* fix: layer\_cloudpath was not handling intermediate paths correctly
* Optimize Sleep Patterns (#50)
* fix: save\_mesh supports progress bar
* Fix gcloud Access in 0.5.0 (#46)
* feat: negative index downloads (#45)
* feat: CloudVolume supports intermediate paths (#38)
* Optionally pass provenance to CloudVolume constructor (#41)
* Wms test metadata (#44)
* Fix Double Upload (#43)
* feat: provenance files are now decoded with the json5 module (#40)
* Update README.md
* fix: missing support for progress and caching for delete and exists
* docs: Added exists, delete, cache, and progress to README.md
* feat: delete bounding boxes on a given mip level (#35)
* feat: backwards compatibility with ~/.neuroglancer (#33)
* feat: added cache flag to CloudVolume (#12)
* feat: progress flag for CloudVolume, Storage (#21)
* feat: add support for intermediate paths in URIs (#30)
* feat: CloudVolume.exists (#14)
* fix: python3 compatibility (#25)
* test: deconflict parallel storage tests (#19)
* docs: CloudVolume methods, mip\_ functions, and VolumeCutout in README.md
* docs: added additional CloudVolume init examples
* docs: added boss-secret.json to docs
* docs: added property list to README.md
* feat: exported several useful libraries
* feat(Provenance): added support for data layer provenance (#6)
* feat: added exponential window random retry to Storage (#5)
* feat: python3 support (#4)
* Update README.md
* fix: removed scipy from requirmements list
* docs: formatting README.md
* docs: added BOSS and virtualenvwrapper to README
* docs: added save\_mesh to the README
* fix: compress for raw and compressed\_encoding
* fix: added chardet to requirements.txt
* fix: added missing items to requirements.txt
* feat(BOSS): added reading and writing capability to BOSS MIP 0
* fix: upgraded urllib3 to urllib3[secure]
* feat: added connection pools
* fix: google secrets is only read from disk once
* feat: support saving equivalences as a single obj
* feat: added get\_mesh, save\_mesh to CloudVolume
* chore: bumped google-cloud to 0.27 from 0.26
* test: chunks.py now has some tests
* docs: added more detailed insallation instructions to README.md
* test(secrets): added API keys for Storage
* fix(ThreadedQueue): ensure processed matches task\_done
* test: added travis config file
* docs: updated setup.cfg info
* feat(VolumeCutout): prepend 0 to single digit numbers
* chore: added saved\_images to .gitignore
* fix: missing PIL import
* refactor(CloudVolume): clean up package import namespace
* feat(CloudVolume): created minimal implementation
* Initial commit