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‎.github/workflows/gpu_test.yml

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@@ -55,7 +55,7 @@ jobs:
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cache: 'pip'
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- name: Install Hatch and CuPy
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run: |
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python -m pip install --upgrade pip
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python -m pip install --upgrade pip
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pip install hatch
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- name: Set Up Hatch Env
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run: |

‎.github/workflows/releases.yml

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- name: Install PyBuild
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run: |
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python -m pip install --upgrade pip
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python -m pip install --upgrade pip
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pip install hatch
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- name: Build wheel and sdist
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run: hatch build

‎.github/workflows/test.yml

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cache: 'pip'
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- name: Install Hatch
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run: |
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python -m pip install --upgrade pip
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python -m pip install --upgrade pip
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pip install hatch
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- name: Set Up Hatch Env
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run: |
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cache: 'pip'
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- name: Install Hatch
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run: |
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python -m pip install --upgrade pip
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python -m pip install --upgrade pip
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pip install hatch
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- name: Set Up Hatch Env
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run: |

‎.pre-commit-config.yaml

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rev: v5.0.0
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hooks:
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- id: check-yaml
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- id: trailing-whitespace
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- repo: https://github.com/pre-commit/mirrors-mypy
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rev: v1.13.0
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hooks:

‎README-v3.md

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@@ -38,7 +38,7 @@ hatch env create test
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## Run the Tests
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```
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hatch run test:run
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hatch run test:run
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```
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or

‎bench/compress_normal.txt

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@@ -19,7 +19,7 @@ Line # Hits Time Per Hit % Time Line Contents
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==============================================================
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137 def compress(source, char* cname, int clevel, int shuffle):
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138 """Compress data in a numpy array.
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139
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140 Parameters
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141 ----------
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142 source : array-like
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147 Compression level.
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148 shuffle : int
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149 Shuffle filter.
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150
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151 Returns
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152 -------
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153 dest : bytes-like
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154 Compressed data.
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156 """
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158 cdef:
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159 char *source_ptr
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160 char *dest_ptr
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161 Py_buffer source_buffer
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162 size_t nbytes, cbytes, itemsize
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163 200 506 2.5 0.2 array.array char_array_template = array.array('b', [])
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164 array.array dest
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166 # setup source buffer
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167 200 458 2.3 0.2 PyObject_GetBuffer(source, &source_buffer, PyBUF_ANY_CONTIGUOUS)
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168 200 119 0.6 0.0 source_ptr = <char *> source_buffer.buf
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169
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170 # setup destination
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171 200 239 1.2 0.1 nbytes = source_buffer.len
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172 200 103 0.5 0.0 itemsize = source_buffer.itemsize
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173 200 2286 11.4 0.8 dest = array.clone(char_array_template, nbytes + BLOSC_MAX_OVERHEAD,
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174 zero=False)
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175 200 129 0.6 0.0 dest_ptr = <char *> dest.data.as_voidptr
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177 # perform compression
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178 200 1734 8.7 0.6 if _get_use_threads():
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179 # allow blosc to use threads internally
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184 cbytes = blosc_compress(clevel, shuffle, itemsize, nbytes,
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185 source_ptr, dest_ptr,
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186 nbytes + BLOSC_MAX_OVERHEAD)
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188 else:
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189 with nogil:
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190 cbytes = blosc_compress_ctx(clevel, shuffle, itemsize, nbytes,
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191 source_ptr, dest_ptr,
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192 nbytes + BLOSC_MAX_OVERHEAD, cname,
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193 0, 1)
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195 # release source buffer
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196 200 616 3.1 0.2 PyBuffer_Release(&source_buffer)
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198 # check compression was successful
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199 200 120 0.6 0.0 if cbytes <= 0:
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200 raise RuntimeError('error during blosc compression: %d' % cbytes)
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202 # resize after compression
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203 200 1896 9.5 0.6 array.resize(dest, cbytes)
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205 200 186 0.9 0.1 return dest
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*******************************************************************************
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==============================================================
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75 def decompress(source, dest):
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76 """Decompress data.
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78 Parameters
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79 ----------
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80 source : bytes-like
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81 Compressed data, including blosc header.
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82 dest : array-like
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83 Object to decompress into.
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85 Notes
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86 -----
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87 Assumes that the size of the destination buffer is correct for the size of
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88 the uncompressed data.
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90 """
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91 cdef:
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92 int ret
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96 array.array source_array
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97 Py_buffer dest_buffer
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98 size_t nbytes
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100 # setup source buffer
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102 # workaround fact that array.array does not support new-style buffer
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108 200 112 0.6 0.0 release_source_buffer = True
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109 200 144 0.7 0.1 PyObject_GetBuffer(source, &source_buffer, PyBUF_ANY_CONTIGUOUS)
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112 # setup destination buffer
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113 200 552 2.8 0.2 PyObject_GetBuffer(dest, &dest_buffer,
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114 PyBUF_ANY_CONTIGUOUS | PyBUF_WRITEABLE)
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115 200 100 0.5 0.0 dest_ptr = <char *> dest_buffer.buf
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116 200 84 0.4 0.0 nbytes = dest_buffer.len
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118 # perform decompression
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119 200 1856 9.3 0.8 if _get_use_threads():
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120 # allow blosc to use threads internally
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123 else:
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124 with nogil:
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125 ret = blosc_decompress_ctx(source_ptr, dest_ptr, nbytes, 1)
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127 # release buffers
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128 200 754 3.8 0.3 if release_source_buffer:
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129 200 326 1.6 0.1 PyBuffer_Release(&source_buffer)
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130 200 165 0.8 0.1 PyBuffer_Release(&dest_buffer)
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132 # handle errors
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133 200 128 0.6 0.1 if ret <= 0:
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134 raise RuntimeError('error during blosc decompression: %d' % ret)

‎docs/guide/storage.rst

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Zarr-Python supports multiple storage backends, including: local file systems,
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Zip files, remote stores via ``fsspec`` (S3, HTTP, etc.), and in-memory stores. In
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Zarr-Python 3, stores must implement the abstract store API from
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:class:`zarr.abc.store.Store`.
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:class:`zarr.abc.store.Store`.
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.. note::
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Unlike Zarr-Python 2 where the store interface was built around a generic ``MutableMapping``
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Zip Store
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~~~~~~~~~
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The :class:`zarr.storage.ZipStore` stores the contents of a Zarr hierarchy in a single
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Zip file. The `Zip Store specification_` is currently in draft form.
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The :class:`zarr.storage.ZipStore` stores the contents of a Zarr hierarchy in a single
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Zip file. The `Zip Store specification_` is currently in draft form.
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The :class:`zarr.storage.RemoteStore` stores the contents of a Zarr hierarchy in following the same
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logical layout as the ``LocalStore``, except the store is assumed to be on a remote storage system
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such as cloud object storage (e.g. AWS S3, Google Cloud Storage, Azure Blob Store). The
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such as cloud object storage (e.g. AWS S3, Google Cloud Storage, Azure Blob Store). The
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:class:`zarr.storage.RemoteStore` is backed by `Fsspec_` and can support any Fsspec backend
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~~~~~~~~~~~~
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The :class:`zarr.storage.RemoteStore` a in-memory store that allows for serialization of
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Zarr data (metadata and chunks) to a dictionary.
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Zarr data (metadata and chunks) to a dictionary.
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.. code-block:: python
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‎docs/roadmap.rst

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- Martin Durrant / @martindurant
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.. note::
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This document was written in the early stages of the 3.0 refactor. Some
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aspects of the design have changed since this was originally written.
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Questions and discussion about the contents of this document should be directed to
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async def get_partial_values(self, key_ranges: List[Tuple[str, int, int]) -> bytes:
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...
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async def set(self, key: str, value: Union[bytes, bytearray, memoryview]) -> None:
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... # required for writable stores
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# additional (optional methods)
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async def getsize(self, prefix: str) -> int:
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async def rename(self, src: str, dest: str) -> None
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...
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Recognizing that there are many Zarr applications today that rely on the
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``MutableMapping`` interface supported by Zarr-Python 2, a wrapper store

‎docs/tutorial.rst

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a ZIP-archived Zarr group on s3 using `s3fs <https://s3fs.readthedocs.io/en/latest/>`_ and ``ZipFileSystem``:
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>>> s3 = s3fs.S3FileSystem()
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>>> f = s3.open(s3_path)
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>>> fs = ZipFileSystem(f, mode="r")
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>>> store = FSMap("", fs, check=False)
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>>>
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>>> # caching may improve performance when repeatedly reading the same data
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>>> cache = zarr.storage.LRUStoreCache(store, max_size=2**28)
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>>> z = zarr.group(store=cache)

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