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Add N5 Support - #309

Merged

jakirkham merged 76 commits into

zarr-developers:masterfrom

funkey:master

Feb 26, 2019

Merged

Add N5 Support#309
jakirkham merged 76 commits into
zarr-developers:masterfrom
funkey:master

Commits on Oct 13, 2018
- Add N5Store for paths ending in '.n5'
  funkey
  committed
  92eab8c
Commits on Oct 14, 2018
- Add N5 chunk headers via N5ChunkWrapper as a codec
  funkey
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  8f1d721
- Add compressor support to N5ChunkWrapper
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  f21ae8e
- Invert axis order for dimensions and blockSize N5 attributes
  funkey
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  c74c79f
- Convert raw chunks to big endian in N5ChunkWrapper
  funkey
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  38675fe
- Consolidate compressor conversion according to N5 spec 1.0.0
  funkey
  committed
  89b95dd
- Always change byte-order to big endian in N5ChunkWrapper
  funkey
  committed
  89ca5c9
- Cleanup unused code fragments in n5.py
  funkey
  committed
  deb8c2d
- Transparently inject N5ChunkWrapper in array meta data
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  1e84925
Commits on Oct 16, 2018
- Map array attributes fill_value, order, and filters
  funkey
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  e12e32b
- Use numpy's tobytes for raw encoding in N5ChunkWrapper
  funkey
  committed
  0e416f4
- Add gzip compressor support to N5Storage
  funkey
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  cba3e56
- Support N5's partial chunks at dataset boundaries
  funkey
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  719bf5b
- Add unit test stub for N5Store
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  59cb72e
Commits on Oct 18, 2018
- Comply with zarr meta key names in N5Store
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  1534e0c
- Overwrite __delitem__ and listdir in N5Store
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  a4939e7
- Allow fill_value==None in N5Store
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  ae95a38
- Allow compressor_config to be None in N5Store
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  a6a6c15
- Support older np.byteswap API
  funkey
  committed
  cdffeb7
- Expose N5Store in zarr top-level package
  funkey
  committed
  2557661
- Refactor attribute conversion between zarr and N5
  funkey
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  f04eaf7
- Delegate __getitem__ to parent class for unrecognized keys
  funkey
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  f471e7d
- Fix runtime errors in N5Store
  funkey
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  3abf68c
- Invert coords only for chunk keys in N5Store
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  committed
  d22aabb
- Add no cover pragmas to N5Store
  funkey
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  dd07cc2
- Use _load_n5_attrs where possible in N5Store
  funkey
  committed
  2a17ae2
- Remove conditional that is always true in N5Store
  funkey
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  08b11a7
- Add tests for N5Store
  funkey
  committed
  ca4c516
- Add N5Store entry to release notes
  funkey
  committed
  82c7bc3
Commits on Oct 20, 2018
- Ensure str type for json.loads in N5Store
  funkey
  committed
  eb5c17c
Commits on Oct 21, 2018
- Fix reading of partial N5 chunks
  funkey
  committed
  9ddf849
Commits on Nov 30, 2018
- Merge 'zarr-developers/master' into 'funkey/master'
  jakirkham
  committed
  50b6555
- Bump the Numcodecs requirement to 0.6.1
  jakirkham
  committed
  9fe09ce
- Enable testing of GZip as well
  jakirkham
  committed
  b8c40b8
- Change `_ensure_str` to `ensure_str`
  jakirkham
  committed
  1b04af4
- Switch from `buffer_copy` to `ndarray_copy`
  jakirkham
  committed
  a6ca2e7
Commits on Dec 17, 2018
- Merge 'zarr-developers/master' into 'funkey/master'
  jakirkham
  committed
  fb662af
Commits on Dec 19, 2018
- Raise more informative TypeError for unsupported dtypes in N5
  funkey
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  d0a1c93
- Skip test_structured_array_* for N5
  funkey
  committed
  e3546e0
- Fix flake8 errors for N5 store and related tests
  funkey
  committed
  4510da5
Commits on Dec 20, 2018
- Use `struct.pack` to convert integers to `bytes`
  jakirkham
  committed
  28761ce
- Use `struct.unpack` to convert `bytes` to integers
  jakirkham
  committed
  7a7b83c
- Optionally use LZMA if it is available
  jakirkham
  committed
  fa71958
- Ensure `str` before using `json.loads`
  jakirkham
  committed
  325a3db
- Ensure JSON output is the same for Python 2/3
  jakirkham
  committed
  dd2100a
Commits on Jan 14, 2019
- Fix remaining coveralls tests
  funkey
  committed
  cef6ea5
Commits on Jan 16, 2019
- Merge 'zarr-developers/master' into 'funkey/master'
  jakirkham
  committed
  6ccde35
Commits on Feb 4, 2019
- Add N5 paragraph to tutorial
  funkey
  committed
  7aa2a5d
- Fix typo in zarr/tests/test_storage.py
  
  alimanfoo
  and
  funkey
  authored
  11104e5
Commits on Feb 12, 2019
- Merge 'zarr-developers/master' into 'funkey/master'
  jakirkham
  committed
  e8db9b8
- Move N5 containers entry to 2.3.0
  jakirkham
  committed
  1586481
- Add author info to release entry
  jakirkham
  committed
  4bb046f
- Add experimental notes to N5 support
  jakirkham
  committed
  3bb9c24
Commits on Feb 13, 2019
- Drop `mode` from `N5Store`
  jakirkham
  committed
  8bac1db
- Test N5 without filters and with
  jakirkham
  committed
  6abc758
- Test that using Fortran order with N5 errors
  jakirkham
  committed
  8b213c4
Commits on Feb 14, 2019
- Test structured array cases raise TypeError on N5
  jakirkham
  committed
  a6d6480
- Test object arrays raise with N5
  jakirkham
  committed
  6bb94d0
- Add API docs for N5
  jakirkham
  committed
  6aaf2eb
- Drop unneeded call to `close`
  jakirkham
  committed
  7713d70
Commits on Feb 16, 2019
- Merge 'zarr-developers/master' into 'funkey/master'
  jakirkham
  committed
  09d5351
- Drop storage tests integrated into array tests
  jakirkham
  committed
  a4eaba4
- Drop unused imports (reported by flake8)
  jakirkham
  committed
  0efe4bd
Commits on Feb 23, 2019
- Convert user-facing assertions to errors
  jakirkham
  committed
  c537eef
- Use non-deprecated `.warning(...)` instead
  jakirkham
  committed
  5168d47
- Use warnings instead of logging
  jakirkham
  committed
  9f45993
- Drop unused `logging` import
  jakirkham
  committed
  86f5f82
- Check N5Store RuntimeWarnings for some compressors
  jakirkham
  committed
  8548f30
- Limit `RuntimeWarning` check to array creation
  jakirkham
  committed
  ca17069
- Test that N5Store raises for certain attributes
  jakirkham
  committed
  87c9864
- Test `fill_values` with N5Store-backed arrays
  jakirkham
  committed
  c711246
- Convert Blosc blocksize check back to an assert
  jakirkham
  committed
  b908b72
Commits on Feb 24, 2019
- Handle loading and storing XZ data for N5
  jakirkham
  committed
  149f3a4
- Test XZ support and update LZMA for N5Store arrays
  jakirkham
  committed
  ba1298b
- Remove LZ4 support for N5
  jakirkham
  committed
  ed467e8
- Merge 'zarr-developers/master' into 'funkey/master'
  jakirkham
  committed
  08009f5

Commits

Commits on Oct 13, 2018

Commits on Oct 14, 2018

Commits on Oct 16, 2018

Commits on Oct 18, 2018

Commits on Oct 20, 2018

Commits on Oct 21, 2018

Commits on Nov 30, 2018

Commits on Dec 17, 2018

Commits on Dec 19, 2018

Commits on Dec 20, 2018

Commits on Jan 14, 2019

Commits on Jan 16, 2019

Commits on Feb 4, 2019

Commits on Feb 12, 2019

Commits on Feb 13, 2019

Commits on Feb 14, 2019

Commits on Feb 16, 2019

Commits on Feb 23, 2019

Commits on Feb 24, 2019