If the input is a string, then ensure that it is a valid +name for a subnode in a zarr group
+ +src/pydantic_zarr/core.pyA similarity check for a pair pydantic.BaseModel, parametrized over included or excluded fields.
+ +src/pydantic_zarr/core.py
+ Bases: StrictBase
The base class for V2 ArraySpec and GroupSpec.
Attributes:
+| Name | +Type | +Description | +
|---|---|---|
zarr_format |
+
+ Literal[2]
+ |
+
+
+
+ The Zarr version represented by this node. Must be 2. + |
+
+ Bases: NodeSpec, Generic[TAttr]
A model of a Zarr Version 2 Array. The specification for the data structure being modeled by +this class can be found in the +Zarr specification.
+ + + +Attributes:
+| Name | +Type | +Description | +
|---|---|---|
attributes |
+
+ TAttr, default = {}
+ |
+
+
+
+ User-defined metadata associated with this array. Should be JSON-serializable. + |
+
shape |
+
+ tuple[int, ...]
+ |
+
+
+
+ The shape of this array. + |
+
dtype |
+
+ str
+ |
+
+
+
+ The data type of this array. + |
+
chunks |
+
+ Tuple[int, ...]
+ |
+
+
+
+ The chunk size for this array. + |
+
order |
+
+ "C" | "F", default = "C"
+ |
+
+
+
+ The memory order of this array. Must be either "C", which designates "C order", +AKA lexicographic ordering or "F", which designates "F order", AKA colexicographic ordering. +The default is "C". + |
+
fill_value |
+
+ FillValue, default = 0
+ |
+
+
+
+ The fill value for this array. The default is 0. + |
+
compressor |
+
+ CodecDict | None
+ |
+
+
+
+ A JSON-serializable representation of a compression codec, or None. The default is None. + |
+
filters |
+
+ List[CodecDict] | None, default = None
+ |
+
+
+
+ A list of JSON-serializable representations of compression codec, or None. +The default is None. + |
+
dimension_separator |
+
+ "." | "/", default = "/"
+ |
+
+
+
+ The character used for partitioning the different dimensions of a chunk key. +Must be either "/" or ".", or absent, in which case it is interpreted as ".". +The default is "/". + |
+
Check that the shape and chunks and attributes have the same length.
src/pydantic_zarr/v2.pyclassmethod
+
+
+#from_array(
+ array,
+ chunks="auto",
+ attributes="auto",
+ fill_value="auto",
+ order="auto",
+ filters="auto",
+ dimension_separator="auto",
+ compressor="auto",
+)
+Create an ArraySpec from an array-like object. This is a convenience method for when Zarr array will be modelled from an existing array.
+This method takes nearly the same arguments as the ArraySpec constructor, minus shape and dtype, which will be inferred from the array argument.
+Additionally, this method accepts the string "auto" as a parameter for all other ArraySpec attributes, in which case these attributes will be
+inferred from the array argument, with a fallback value equal to the default ArraySpec parameters.
Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
array |
+
+ an array-like object.
+ |
+
+
+
+ Must have |
+ + required + | +
attributes |
+
+ Literal['auto'] | TAttr
+ |
+
+
+
+ User-defined metadata associated with this array. Should be JSON-serializable. The default is "auto", which means that |
+
+ 'auto'
+ |
+
chunks |
+
+ Literal['auto'] | tuple[int, ...]
+ |
+
+
+
+ The chunks for this |
+
+ 'auto'
+ |
+
order |
+
+ Literal['auto', 'C', 'F']
+ |
+
+
+
+ The memory order of the |
+
+ 'auto'
+ |
+
fill_value |
+
+ Literal['auto'] | int | float | None
+ |
+
+
+
+ The fill value for this array. Either "auto" or FillValue. The default is "auto", which means that |
+
+ 'auto'
+ |
+
compressor |
+
+ Literal['auto'] | CodecDict | None
+ |
+
+
+
+ The compressor for this |
+
+ 'auto'
+ |
+
filters |
+
+ Literal['auto'] | list[CodecDict] | None
+ |
+
+
+
+ The filters for this |
+
+ 'auto'
+ |
+
dimension_separator |
+
+ Literal['auto', '/', '.']
+ |
+
+
+
+ Sets the character used for partitioning the different dimensions of a chunk key.
+Must be one of "auto", "/" or ".". The default is "auto", which means that |
+
+ 'auto'
+ |
+
Returns:
+| Type | +Description | +
|---|---|
+ ArraySpec
+ |
+
+
+
+ An instance of |
+
Examples:
+>>> from pydantic_zarr.v2 import ArraySpec
+>>> import numpy as np
+>>> x = ArraySpec.from_array(np.arange(10))
+>>> x
+ArraySpec(zarr_version=2, attributes={}, shape=(10,), chunks=(10,), dtype='<i8', fill_value=0, order='C', filters=None, dimension_separator='/', compressor=None)
+src/pydantic_zarr/v2.py181 +182 +183 +184 +185 +186 +187 +188 +189 +190 +191 +192 +193 +194 +195 +196 +197 +198 +199 +200 +201 +202 +203 +204 +205 +206 +207 +208 +209 +210 +211 +212 +213 +214 +215 +216 +217 +218 +219 +220 +221 +222 +223 +224 +225 +226 +227 +228 +229 +230 +231 +232 +233 +234 +235 +236 +237 +238 +239 +240 +241 +242 +243 +244 +245 +246 +247 +248 +249 +250 +251 +252 +253 +254 +255 +256 +257 +258 +259 +260 +261 +262 +263 +264 +265 +266 +267 +268 +269 +270 +271 +272 +273 +274 +275 +276 +277 +278 +279 +280 +281 +282 +283 +284 +285 +286 +287 | |
classmethod
+
+
+#Create an ArraySpec from an instance of zarr.Array.
Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
array |
+
+ Array
+ |
+
+
+
+
+ |
+ + required + | +
Returns:
+| Type | +Description | +
|---|---|
+ ArraySpec
+ |
+
+
+
+ An instance of |
+
Examples:
+>>> import zarr
+>>> from pydantic_zarr.v2 import ArraySpec
+>>> x = zarr.create((10,10))
+>>> ArraySpec.from_zarr(x)
+ArraySpec(zarr_version=2, attributes={}, shape=(10, 10), chunks=(10, 10), dtype='<f8', fill_value=0.0, order='C', filters=None, dimension_separator='.', compressor={'id': 'blosc', 'cname': 'lz4', 'clevel': 5, 'shuffle': 1, 'blocksize': 0})
+src/pydantic_zarr/v2.pySerialize an ArraySpec to a Zarr array at a specific path in a Zarr store. This operation
+will create metadata documents in the store, but will not write any chunks.
Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
store |
+
+ instance of zarr.BaseStore
+ |
+
+
+
+ The storage backend that will manifest the array. + |
+ + required + | +
path |
+
+ str
+ |
+
+
+
+ The location of the array inside the store. + |
+ + required + | +
overwrite |
+
+ bool
+ |
+
+
+
+ Whether to overwrite existing objects in storage to create the Zarr array. + |
+
+ False
+ |
+
**kwargs |
+
+ Any
+ |
+
+
+
+ Additional keyword arguments are passed to |
+
+ {}
+ |
+
Returns:
+| Type | +Description | +
|---|---|
+ Array
+ |
+
+
+
+ A Zarr array that is structurally identical to |
+
src/pydantic_zarr/v2.pyCompare am ArraySpec to another ArraySpec or a zarr.Array, parameterized over the
+fields to exclude or include in the comparison. Models are first converted to dict via the
+model_dump method of pydantic.BaseModel, then compared with the == operator.
Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
other |
+
+ ArraySpec | Array
+ |
+
+
+
+ The array (model or actual) to compare with. If other is a |
+ + required + | +
include |
+
+ IncEx
+ |
+
+
+
+ A specification of fields to include in the comparison. The default value is |
+
+ None
+ |
+
exclude |
+
+ IncEx
+ |
+
+
+
+ A specification of fields to exclude from the comparison. The default value is |
+
+ None
+ |
+
Returns:
+| Type | +Description | +
|---|---|
+ bool
+ |
+
+
+
+
|
+
Examples:
+>>> import zarr
+>>> from pydantic_zarr.v2 import ArraySpec
+>>> x = zarr.create((10,10))
+>>> x.attrs.put({'foo': 10})
+>>> x_model = ArraySpec.from_zarr(x)
+>>> print(x_model.like(x_model)) # it is like itself.
+True
+>>> print(x_model.like(x))
+True
+>>> y = zarr.create((10,10))
+>>> y.attrs.put({'foo': 11}) # x and y are the same, other than their attrs
+>>> print(x_model.like(y))
+False
+>>> print(x_model.like(y, exclude={'attributes'}))
+True
+src/pydantic_zarr/v2.py
+ Bases: NodeSpec, Generic[TAttr, TItem]
A model of a Zarr Version 2 Group. +The specification for the data structure being modeled by this +class can be found in the +Zarr specification.
+ + + +Attributes:
+| Name | +Type | +Description | +
|---|---|---|
attributes |
+
+ TAttr, default = {}
+ |
+
+
+
+ The user-defined attributes of this group. Should be JSON-serializable. + |
+
members |
+
+ dict[str, TItem] | None, default = {}
+ |
+
+
+
+ The members of this group. |
+
classmethod
+
+
+#Create a GroupSpec from an instance of zarr.Group. Subgroups and arrays contained in the
+Zarr group will be converted to instances of GroupSpec and ArraySpec, respectively,
+and these spec instances will be stored in the members attribute of the parent
+GroupSpec.
This is a recursive function, and the depth of recursion can be controlled by the depth
+keyword argument. The default value for depth is -1, which directs this function to
+traverse the entirety of a zarr.Group. This may be slow for large hierarchies, in which
+case setting depth to a positive integer can limit how deep into the hierarchy the
+recursion goes.
Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
group |
+
+ Group
+ |
+
+
+
+ The Zarr group to model. + |
+ + required + | +
depth |
+
+ int
+ |
+
+
+
+ An integer which may be no lower than -1. Determines how far into the tree to parse. + |
+
+ -1
+ |
+
Returns:
+| Type | +Description | +
|---|---|
+ An instance of GroupSpec that represents the structure of the Zarr hierarchy.
+ |
+
+
+
+
+ |
+
src/pydantic_zarr/v2.pySerialize this GroupSpec to a Zarr group at a specific path in a zarr.BaseStore.
+This operation will create metadata documents in the store.
Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
store |
+
+ BaseStore
+ |
+
+
+
+ The storage backend that will manifest the group and its contents. + |
+ + required + | +
path |
+
+ str
+ |
+
+
+
+ The location of the group inside the store. + |
+ + required + | +
overwrite |
+
+ bool
+ |
+
+
+
+ Whether to overwrite existing objects in storage to create the Zarr group. + |
+
+ False
+ |
+
**kwargs |
+
+ Any
+ |
+
+
+
+ Additional keyword arguments that will be passed to |
+
+ {}
+ |
+
Returns:
+| Type | +Description | +
|---|---|
+ Group
+ |
+
+
+
+ A zarr group that is structurally identical to |
+
src/pydantic_zarr/v2.pyCompare a GroupSpec to another GroupSpec or a zarr.Group, parameterized over the
+fields to exclude or include in the comparison. Models are first converted to dict via the
+model_dump method of pydantic.BaseModel, then compared with the == operator.
Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
other |
+
+ GroupSpec | Group
+ |
+
+
+
+ The group (model or actual) to compare with. If other is a |
+ + required + | +
include |
+
+ IncEx
+ |
+
+
+
+ A specification of fields to include in the comparison. The default is |
+
+ None
+ |
+
exclude |
+
+ IncEx
+ |
+
+
+
+ A specification of fields to exclude from the comparison. The default is |
+
+ None
+ |
+
Returns:
+| Type | +Description | +
|---|---|
+ bool
+ |
+
+
+
+
|
+
Examples:
+>>> import zarr
+>>> from pydantic_zarr.v2 import GroupSpec
+>>> import numpy as np
+>>> z1 = zarr.group(path='z1')
+>>> z1a = z1.array(name='foo', data=np.arange(10))
+>>> z1_model = GroupSpec.from_zarr(z1)
+>>> print(z1_model.like(z1_model)) # it is like itself
+True
+>>> print(z1_model.like(z1))
+True
+>>> z2 = zarr.group(path='z2')
+>>> z2a = z2.array(name='foo', data=np.arange(10))
+>>> print(z1_model.like(z2))
+True
+>>> z2.attrs.put({'foo' : 100}) # now they have different attributes
+>>> print(z1_model.like(z2))
+False
+>>> print(z1_model.like(z2, exclude={'attributes'}))
+True
+src/pydantic_zarr/v2.py586 +587 +588 +589 +590 +591 +592 +593 +594 +595 +596 +597 +598 +599 +600 +601 +602 +603 +604 +605 +606 +607 +608 +609 +610 +611 +612 +613 +614 +615 +616 +617 +618 +619 +620 +621 +622 +623 +624 +625 +626 +627 +628 +629 +630 +631 +632 +633 +634 +635 +636 +637 +638 +639 +640 +641 +642 +643 +644 +645 +646 | |
Flatten this GroupSpec.
+This method returns a dict with string keys and values that are GroupSpec or
+ArraySpec.
Then the resulting dict will contain a copy of the input with a null members attribute
+under the key root_path, as well as copies of the result of calling node.to_flat on each
+element of node.members, each under a key created by joining root_path with a '/`
+character to the name of each member, and so on recursively for each sub-member.
Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
root_path |
+
+ str
+ |
+
+
+
+ The root path. The keys in |
+
+ ''
+ |
+
Returns:
+| Type | +Description | +
|---|---|
+ Dict[str, ArraySpec | GroupSpec]
+ |
+
+
+
+ A flattened representation of the hierarchy. + |
+
Examples:
+>>> from pydantic_zarr.v2 import to_flat, GroupSpec
+>>> g1 = GroupSpec(members=None, attributes={'foo': 'bar'})
+>>> to_flat(g1)
+{'': GroupSpec(zarr_version=2, attributes={'foo': 'bar'}, members=None)}
+>>> to_flat(g1 root_path='baz')
+{'baz': GroupSpec(zarr_version=2, attributes={'foo': 'bar'}, members=None)}
+>>> to_flat(GroupSpec(members={'g1': g1}, attributes={'foo': 'bar'}))
+{'/g1': GroupSpec(zarr_version=2, attributes={'foo': 'bar'}, members=None), '': GroupSpec(zarr_version=2, attributes={'foo': 'bar'}, members=None)}
+src/pydantic_zarr/v2.pyclassmethod
+
+
+#Create a GroupSpec from a flat hierarchy representation. The flattened hierarchy is a
+dict with the following constraints: keys must be valid paths; values must
+be ArraySpec or GroupSpec instances.
Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
data |
+
+ Dict[str, ArraySpec | GroupSpec]
+ |
+
+
+
+ A flattened representation of a Zarr hierarchy. + |
+ + required + | +
Returns:
+| Type | +Description | +
|---|---|
+ GroupSpec
+ |
+
+
+
+ A |
+
Examples:
+>>> from pydantic_zarr.v2 import GroupSpec, ArraySpec
+>>> import numpy as np
+>>> flat = {'': GroupSpec(attributes={'foo': 10}, members=None)}
+>>> GroupSpec.from_flat(flat)
+GroupSpec(zarr_version=2, attributes={'foo': 10}, members={})
+>>> flat = {
+ '': GroupSpec(attributes={'foo': 10}, members=None),
+ '/a': ArraySpec.from_array(np.arange(10))}
+>>> GroupSpec.from_flat(flat)
+GroupSpec(zarr_version=2, attributes={'foo': 10}, members={'a': ArraySpec(zarr_version=2, attributes={}, shape=(10,), chunks=(10,), dtype='<i8', fill_value=0, order='C', filters=None, dimension_separator='/', compressor=None)})
+src/pydantic_zarr/v2.pyConvert a numpy.dtype object into a str.
Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
value |
+
+ DTypeLike
+ |
+
+
+
+ Some object that can be coerced to a numpy dtype + |
+ + required + | +
Returns:
+| Type | +Description | +
|---|---|
+ A numpy dtype string representation of `value`.
+ |
+
+
+
+
+ |
+
src/pydantic_zarr/v2.pyEnsure that a numcodecs.abc.Codec is converted to a dict. If the input is not an
+insance of numcodecs.abc.Codec, then it is assumed to be a dict with string keys
+and it is returned unaltered.
Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
value |
+
+ dict[str, Any] | Codec
+ |
+
+
+
+ The value to be dictified if it is not already a dict. + |
+ + required + | +
Returns:
+| Type | +Description | +
|---|---|
+ dict[str, Any]
+ |
+
+
+
+ If the input was a |
+
src/pydantic_zarr/v2.pyParse the dimension_separator metadata as per the Zarr version 2 specification.
+If the input is None, this returns ".".
+If the input is either "." or "/", this returns it.
+Otherwise, raises a ValueError.
Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
data |
+
+ Any
+ |
+
+
+
+ The input data to parse. + |
+ + required + | +
Returns:
+| Type | +Description | +
|---|---|
+ Literal['/', '.']
+ |
+
+
+
+
+ |
+
src/pydantic_zarr/v2.pyRecursively parse a zarr.Group or zarr.Array into an ArraySpec or GroupSpec.
Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
element |
+
+ Array | Group
+ |
+
+
+
+ The |
+ + required + | +
depth |
+
+ int
+ |
+
+
+
+ An integer which may be no lower than -1. If |
+
+ -1
+ |
+
Returns:
+| Type | +Description | +
|---|---|
+ ArraySpec | GroupSpec
+ |
+
+
+
+ An instance of |
+
src/pydantic_zarr/v2.pySerialize a GroupSpec or ArraySpec to a Zarr group or array at a specific path in
+a Zarr store.
Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
spec |
+
+ ArraySpec | GroupSpec
+ |
+
+
+
+ The |
+ + required + | +
store |
+
+ BaseStore
+ |
+
+
+
+ The storage backend that will manifest the Zarr group or array modeled by |
+ + required + | +
path |
+
+ str
+ |
+
+
+
+ The location of the Zarr group or array inside the store. + |
+ + required + | +
overwrite |
+
+ bool
+ |
+
+
+
+ Whether to overwrite existing objects in storage to create the Zarr group or array. + |
+
+ = False
+ |
+
**kwargs |
+ + | +
+
+
+ Additional keyword arguments will be + |
+
+ {}
+ |
+
Returns:
+| Type | +Description | +
|---|---|
+ Array | Group
+ |
+
+
+
+ A |
+
src/pydantic_zarr/v2.pyFlatten a GroupSpec or ArraySpec.
+Converts a GroupSpec or ArraySpec and a string, into a dict with string keys and
+values that are GroupSpec or ArraySpec.
If the input is an ArraySpec, then this function just returns the dict {root_path: node}.
If the input is a GroupSpec, then the resulting dict will contain a copy of the input
+with a null members attribute under the key root_path, as well as copies of the result of
+calling flatten_node on each element of node.members, each under a key created by joining
+root_path with a '/` character to the name of each member, and so on recursively for each
+sub-member.
Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
node |
+
+ ArraySpec | GroupSpec
+ |
+
+
+
+ The node to flatten. + |
+ + required + | +
root_path |
+
+ str
+ |
+
+
+
+ The root path. If |
+
+ ''
+ |
+
Returns:
+| Type | +Description | +
|---|---|
+ Dict[str, ArraySpec | GroupSpec]
+ |
+
+
+
+ A flattened representation of the hierarchy. + |
+
Examples:
+>>> from pydantic_zarr.v2 import flatten, GroupSpec
+>>> g1 = GroupSpec(members=None, attributes={'foo': 'bar'})
+>>> to_flat(g1)
+{'': GroupSpec(zarr_version=2, attributes={'foo': 'bar'}, members=None)}
+>>> to_flat(g1 root_path='baz')
+{'baz': GroupSpec(zarr_version=2, attributes={'foo': 'bar'}, members=None)}
+>>> to_flat(GroupSpec(members={'g1': g1}, attributes={'foo': 'bar'}))
+{'/g1': GroupSpec(zarr_version=2, attributes={'foo': 'bar'}, members=None), '': GroupSpec(zarr_version=2, attributes={'foo': 'bar'}, members=None)}
+src/pydantic_zarr/v2.pyWraps from_flat_group, handling the special case where a Zarr array is defined at the root of
+a hierarchy and thus is not contained by a Zarr group.
Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
data |
+
+ Dict[str, ArraySpec | GroupSpec]
+ |
+
+
+
+ A flat representation of a Zarr hierarchy. This is a |
+ + required + | +
Returns:
+| Type | +Description | +
|---|---|
+ ArraySpec | GroupSpec
+ |
+
+
+
+ The |
+
Examples:
+>>> from pydantic_zarr.v2 import from_flat, GroupSpec, ArraySpec
+>>> import numpy as np
+>>> tree = {'': ArraySpec.from_array(np.arange(10))}
+>>> from_flat(tree) # special case of a Zarr array at the root of the hierarchy
+ArraySpec(zarr_version=2, attributes={}, shape=(10,), chunks=(10,), dtype='<i8', fill_value=0, order='C', filters=None, dimension_separator='/', compressor=None)
+>>> tree = {'/foo': ArraySpec.from_array(np.arange(10))}
+>>> from_flat(tree) # note that an implicit Group is created
+GroupSpec(zarr_version=2, attributes={}, members={'foo': ArraySpec(zarr_version=2, attributes={}, shape=(10,), chunks=(10,), dtype='<i8', fill_value=0, order='C', filters=None, dimension_separator='/', compressor=None)})
+src/pydantic_zarr/v2.pyGenerate a GroupSpec from a flat representation of a hierarchy, i.e. a dict with
+string keys (paths) and ArraySpec / GroupSpec values (nodes).
Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
data |
+
+ Dict[str, ArraySpec | GroupSpec]
+ |
+
+
+
+ A flat representation of a Zarr hierarchy rooted at a Zarr group. + |
+ + required + | +
Returns:
+| Type | +Description | +
|---|---|
+ GroupSpec
+ |
+
+
+
+ A |
+
Examples:
+>>> from pydantic_zarr.v2 import from_flat_group, GroupSpec, ArraySpec
+>>> import numpy as np
+>>> tree = {'/foo': ArraySpec.from_array(np.arange(10))}
+>>> from_flat_group(tree) # note that an implicit Group is created
+GroupSpec(zarr_version=2, attributes={}, members={'foo': ArraySpec(zarr_version=2, attributes={}, shape=(10,), chunks=(10,), dtype='<i8', fill_value=0, order='C', filters=None, dimension_separator='/', compressor=None)})
+src/pydantic_zarr/v2.py912 +913 +914 +915 +916 +917 +918 +919 +920 +921 +922 +923 +924 +925 +926 +927 +928 +929 +930 +931 +932 +933 +934 +935 +936 +937 +938 +939 +940 +941 +942 +943 +944 +945 +946 +947 +948 +949 +950 +951 +952 +953 +954 +955 +956 +957 +958 +959 +960 +961 +962 +963 +964 +965 +966 +967 +968 +969 +970 +971 +972 +973 +974 +975 +976 +977 +978 +979 +980 +981 +982 +983 +984 +985 +986 +987 +988 +989 +990 | |
Guess chunks from:
+ input with a chunksize attribute, or
+ input with a chunks attribute, or,
+ input with shape and dtype attributes
src/pydantic_zarr/v2.pyGuess attributes from:
+ input with an attrs attribute, or
+ input with an attributes attribute,
+ or anything (returning {})
src/pydantic_zarr/v2.pyGuess fill value from an input with a fill_value attribute, returning 0 otherwise.
Guess compressor from an input with a compressor attribute, returning None otherwise.
src/pydantic_zarr/v2.pyGuess filters from an input with a filters attribute, returning None otherwise.
src/pydantic_zarr/v2.pyGuess array order from an input with an order attribute, returning "C" otherwise.
Guess dimension separator from an input with a dimension_separator attribute, returning "/" otherwise.
src/pydantic_zarr/v2.py
+ Bases: StrictBase
The base class for V3 ArraySpec and GroupSpec.
+ + + +Attributes:
+| Name | +Type | +Description | +
|---|---|---|
zarr_format |
+
+ Literal[3]
+ |
+
+
+
+ The Zarr version represented by this node. Must be 3. + |
+
+ Bases: NodeSpec, Generic[TAttr]
A model of a Zarr Version 3 Array.
+ + + +Attributes:
+| Name | +Type | +Description | +
|---|---|---|
node_type |
+
+ Literal['array']
+ |
+
+
+
+ The node type. Must be the string 'array'. + |
+
attributes |
+
+ TAttr
+ |
+
+
+
+ User-defined metadata associated with this array. + |
+
shape |
+
+ Sequence[int]
+ |
+
+
+
+ The shape of this array. + |
+
data_type |
+
+ str
+ |
+
+
+
+ The data type of this array. + |
+
chunk_grid |
+
+ NamedConfig
+ |
+
+
+
+ A |
+
chunk_key_encoding |
+
+ NamedConfig
+ |
+
+
+
+ A |
+
fill_value |
+
+ FillValue
+ |
+
+
+
+ The fill value for this array. + |
+
codecs |
+
+ Sequence[NamedConfig]
+ |
+
+
+
+ The sequence of codices for this array. + |
+
storage_transformers |
+
+ Optional[Sequence[NamedConfig]]
+ |
+
+
+
+ An optional sequence of |
+
dimension_names |
+
+ Optional[Sequence[str]]
+ |
+
+
+
+ An optional sequence of strings that gives names to each axis of the array. + |
+
classmethod
+
+
+#Create an ArraySpec from a numpy array-like object.
+ + + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
array |
+
+ object that conforms to the numpy array API.
+ |
+
+
+
+ The shape and dtype of this object will be used to construct an ArraySpec.
+If the |
+ + required + | +
**kwargs |
+
+ keyword arguments to the ArraySpec class constructor.
+ |
+
+
+
+
+ |
+
+ {}
+ |
+
Returns:
+| Type | +Description | +
|---|---|
+ An instance of ArraySpec with properties derived from the provided array.
+ |
+
+
+
+
+ |
+
src/pydantic_zarr/v3.pyclassmethod
+
+
+#Create an ArraySpec from a zarr array.
+ + + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
zarray |
+
+ zarr array
+ |
+
+
+
+
+ |
+ + required + | +
Returns:
+| Type | +Description | +
|---|---|
+ An instance of ArraySpec with properties derived from the provided zarr
+ |
+
+
+
+
+ |
+
+ array.
+ |
+
+
+
+
+ |
+
src/pydantic_zarr/v3.pySerialize an ArraySpec to a zarr array at a specific path in a zarr store.
+ + + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
store |
+
+ instance of zarr.BaseStore
+ |
+
+
+
+ The storage backend that will manifest the array. + |
+ + required + | +
path |
+
+ str
+ |
+
+
+
+ The location of the array inside the store. + |
+ + required + | +
overwrite |
+
+ bool
+ |
+
+
+
+ Whether to overwrite an existing array or group at the path. If overwrite is +False and an array or group already exists at the path, an exception will be +raised. Defaults to False. + |
+
+ False
+ |
+
Returns:
+| Type | +Description | +
|---|---|
+ A zarr array that is structurally identical to the ArraySpec.
+ |
+
+
+
+
+ |
+
+ This operation will create metadata documents in the store.
+ |
+
+
+
+
+ |
+
src/pydantic_zarr/v3.py
+ Bases: NodeSpec, Generic[TAttr, TItem]
A model of a Zarr Version 3 Group.
+ + + +Attributes:
+| Name | +Type | +Description | +
|---|---|---|
node_type |
+
+ Literal['group']
+ |
+
+
+
+ The type of this node. Must be the string "group". + |
+
attributes |
+
+ TAttr
+ |
+
+
+
+ The user-defined attributes of this group. + |
+
members |
+
+ dict[str, TItem]
+ |
+
+
+
+ The members of this group. |
+
classmethod
+
+
+#Create a GroupSpec from a zarr group. Subgroups and arrays contained in the zarr +group will be converted to instances of GroupSpec and ArraySpec, respectively, +and these spec instances will be stored in the .members attribute of the parent +GroupSpec. This occurs recursively, so the entire zarr hierarchy below a given +group can be represented as a GroupSpec.
+ + + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
group |
+
+ zarr group
+ |
+
+
+
+
+ |
+ + required + | +
Returns:
+| Type | +Description | +
|---|---|
+ An instance of GroupSpec that represents the structure of the zarr hierarchy.
+ |
+
+
+
+
+ |
+
src/pydantic_zarr/v3.pySerialize a GroupSpec to a zarr group at a specific path in a zarr store.
+ + + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
store |
+
+ instance of zarr.BaseStore
+ |
+
+
+
+ The storage backend that will manifest the group and its contents. + |
+ + required + | +
path |
+
+ str
+ |
+
+
+
+ The location of the group inside the store. + |
+ + required + | +
overwrite |
+
+ bool
+ |
+
+
+
+ Whether to overwrite an existing array or group at the path. If overwrite is +False and an array or group already exists at the path, an exception will be +raised. Defaults to False. + |
+
+ False
+ |
+
Returns:
+| Type | +Description | +
|---|---|
+ A zarr group that is structurally identical to the GroupSpec.
+ |
+
+
+
+
+ |
+
+ This operation will create metadata documents in the store.
+ |
+
+
+
+
+ |
+
src/pydantic_zarr/v3.pyRecursively parse a Zarr group or Zarr array into an ArraySpec or GroupSpec.
+ + + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
element |
+
+ a zarr Array or zarr Group
+ |
+
+
+
+
+ |
+ + required + | +
Returns:
+| Type | +Description | +
|---|---|
+ An instance of GroupSpec or ArraySpec that represents the
+ |
+
+
+
+
+ |
+
+ structure of the zarr group or array.
+ |
+
+
+
+
+ |
+
src/pydantic_zarr/v3.pySerialize a GroupSpec or ArraySpec to a zarr group or array at a specific path in +a zarr store.
+ + + +Parameters:
+| Name | +Type | +Description | +Default | +
|---|---|---|---|
spec |
+
+ GroupSpec or ArraySpec
+ |
+
+
+
+ The GroupSpec or ArraySpec that will be serialized to storage. + |
+ + required + | +
store |
+
+ instance of zarr.BaseStore
+ |
+
+
+
+ The storage backend that will manifest the group or array. + |
+ + required + | +
path |
+
+ str
+ |
+
+
+
+ The location of the group or array inside the store. + |
+ + required + | +
overwrite |
+
+ bool
+ |
+
+
+
+ Whether to overwrite an existing array or group at the path. If overwrite is +False and an array or group already exists at the path, an exception will be +raised. Defaults to False. + |
+
+ False
+ |
+
Returns:
+| Type | +Description | +
|---|---|
+ A zarr Group or Array that is structurally equivalent to the spec object.
+ |
+
+
+
+
+ |
+
+ This operation will create metadata documents in the store.
+ |
+
+
+
+
+ |
+
src/pydantic_zarr/v3.py