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https://github.com/altaris/turbo-broccoli
JSON (de)serialization extensions
https://github.com/altaris/turbo-broccoli
bokeh json keras numpy pandas pytorch serialization sklearn tensorflow
Last synced: 2 months ago
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JSON (de)serialization extensions
- Host: GitHub
- URL: https://github.com/altaris/turbo-broccoli
- Owner: altaris
- License: mit
- Created: 2022-06-06T09:48:24.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2024-09-21T03:17:47.000Z (3 months ago)
- Last Synced: 2024-09-29T09:21:17.479Z (3 months ago)
- Topics: bokeh, json, keras, numpy, pandas, pytorch, serialization, sklearn, tensorflow
- Language: Python
- Homepage: http://altaris.github.io/turbo-broccoli/
- Size: 2.19 MB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
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README
# TurboBroccoli 🥦
[](https://github.com/altaris/turbo-broccoli)
[](https://pypi.org/project/turbo-broccoli/)
[](https://pypi.org/project/black)
[](https://altaris.github.io/turbo-broccoli/turbo_broccoli.html)
JSON (de)serialization extensions, originally aimed at `numpy` and `tensorflow`
objects, but now supporting a wide range of objects.
## Installation
```sh
pip install turbo-broccoli
```
## Usage
### To/from string
```py
import numpy as np
import turbo_broccoli as tb
obj = {"an_array": np.array([[1, 2], [3, 4]], dtype="float32")}
tb.to_json(obj)
```
produces the following string (modulo indentation and the value of
`$.an_array.data.data`):
```json
{
"an_array": {
"__type__": "numpy.ndarray",
"__version__": 5,
"data": {
"__type__": "bytes",
"__version__": 3,
"data": "QAAAAAAAAAB7ImRhd..."
}
}
}
```
For deserialization, simply use
```py
tb.from_json(json_string)
```
### To/from file
Simply replace
[`turbo_broccoli.to_json`](https://altaris.github.io/turbo-broccoli/turbo_broccoli/turbo_broccoli.html#to_json)
and
[`turbo_broccoli.from_json`](https://altaris.github.io/turbo-broccoli/turbo_broccoli/turbo_broccoli.html#from_json)
with
[`turbo_broccoli.save_json`](https://altaris.github.io/turbo-broccoli/turbo_broccoli/turbo_broccoli.html#save_json)
and
[`turbo_broccoli.load_json`](https://altaris.github.io/turbo-broccoli/turbo_broccoli/turbo_broccoli.html#load_json):
```py
import numpy as np
import turbo_broccoli as tb
obj = {"an_array": np.array([[1, 2], [3, 4]], dtype="float32")}
tb.save_json(obj, "foo/bar/foobar.json")
...
obj = tb.load_json("foo/bar/foobar.json")
```
It is also possible to read/write compressed (with
[zlib](https://www.zlib.net/)) JSON files:
```py
tb.save_json(obj, "foo/bar/foobar.json.gz")
...
obj = tb.load_json("foo/bar/foobar.json.gz")
```
### [Contexts](https://altaris.github.io/turbo-broccoli/turbo_broccoli/context.html#Context)
The behaviour of
[`turbo_broccoli.to_json`](https://altaris.github.io/turbo-broccoli/turbo_broccoli/turbo_broccoli.html#to_json)
and
[`turbo_broccoli.from_json`](https://altaris.github.io/turbo-broccoli/turbo_broccoli/turbo_broccoli.html#from_json)
can be tweaked by using
[contexts](https://altaris.github.io/turbo-broccoli/turbo_broccoli/context.html#Context).
For example, to set a encryption/decryption key for [secret
types](https://altaris.github.io/turbo-broccoli/turbo_broccoli/custom/secret.html):
```py
import nacl.secret
import nacl.utils
import turbo_broccoli as tb
key = nacl.utils.random(nacl.secret.SecretBox.KEY_SIZE)
ctx = tb.Context(nacl_shared_key=key)
obj = {"user": "alice", "password": tb.SecretStr("dolphin")}
doc = tb.to_json(obj, ctx)
...
obj = tb.from_json(doc, ctx)
```
The behaviour of
[`turbo_broccoli.save_json`](https://altaris.github.io/turbo-broccoli/turbo_broccoli/turbo_broccoli.html#save_json)
and
[`turbo_broccoli.load_json`](https://altaris.github.io/turbo-broccoli/turbo_broccoli/turbo_broccoli.html#load_json)
can be tweaked in a similar manner. For convenience, the argument of the
context can be passed directly to the method instead of creating a context
object manually:
```py
import nacl.secret
import nacl.utils
import turbo_broccoli as tb
key = nacl.utils.random(nacl.secret.SecretBox.KEY_SIZE)
obj = {"user": "alice", "password": tb.SecretStr("dolphin")}
tb.save_json(obj, "foo/bar/foobar.json", nacl_shared_key=key)
```
See [the
documentation](https://altaris.github.io/turbo_broccoli/context.html#Context).
### [Guarded blocks](https://altaris.github.io/turbo-broccoli/turbo_broccoli/guard.html)
A
[`turbo_broccoli.GuardedBlockHandler`](https://altaris.github.io/turbo-broccoli/turbo_broccoli/guard.html#GuardedBlockHandler)
"guards" a block of code, meaning it prevents it from being executed if it has
been in the past. Check out [the
documentation](https://altaris.github.io/turbo-broccoli/turbo_broccoli/guard.html)
for some examples.
### [Guarded-parallel executors](https://altaris.github.io/turbo-broccoli/turbo_broccoli/parallel.html)
A mix of
[`joblib.Parallel`](https://joblib.readthedocs.io/en/latest/generated/joblib.Parallel.html)
and
[`turbo_broccoli.GuardedBlockHandler`](https://altaris.github.io/turbo-broccoli/turbo_broccoli/guard.html#GuardedBlockHandler):
a
[`turbo_broccoli.Parallel`](https://altaris.github.io/turbo-broccoli/turbo_broccoli/parallel.html#Parallel)
object can be used to execute jobs in parallel, but those whose results have
already been obtained in the past are skipped. See [the
documentation](https://altaris.github.io/turbo-broccoli/turbo_broccoli/parallel.html)
for some examples.
### Custom encoders/decoders
You can register you own custom encoders and decoders using
[`turbo_broccoli.register_encoder`](https://altaris.github.io/turbo-broccoli/turbo_broccoli/user.html#register_encoder)
and
[`turbo_broccoli.register_decoder`](https://altaris.github.io/turbo-broccoli/turbo_broccoli/user.html#register_decoder):
```py
import turbo_broccoli as tb
class MyClass:
a: int
b: np.ndarray
c: np.ndarray
def __init__(self, a: int, b: np.ndarray):
self.a, self.b = a, b
self.c = a + b
def encoder_c(obj: MyClass, ctx: tb.Context) -> dict:
# If you register a decoder, you must include the key "__type__" and it
# must have value "user."
# ↓
return {"__type__": "user.MyClass", "a": obj.a, "b": obj.b}
def decoder_c(obj: dict, ctx: tb.Context) -> MyClass:
return MyClass(obj["a"], obj["b"])
tb.register_encoder(encoder_c, "MyClass")
tb.register_decoder(decoder_c, "MyClass")
```
An encoder (for `MyClass`) is a function that takes two arguments: an object of
type `MyClass` and a
[`turbo_broccoli.Context`](https://altaris.github.io/turbo-broccoli/turbo_broccoli/context.html#Context),
and returns a `dict`. That dict must contain objects that can be further
serialized using TurboBroccoli (which includes all [supported
types](https://altaris.github.io/turbo-broccoli/turbo_broccoli.html#supported-types)
and any other type for which you registered an encoder). The return dict needs
not be flat.
If you register a decoder for `MyClass` (as in the example above), the dict
must contain the key/value `"__type__": "user.MyClass"`.
A decoder (for `MyClass`) is a function that takes two arguments: a dict and a
[`turbo_broccoli.Context`](https://altaris.github.io/turbo-broccoli/turbo_broccoli/context.html#Context),
and returns an object of type `MyClass`. The dict's values have already been
deserialized.
### Artifacts
If an object inside `obj` is too large to be embedded inside the JSON file
(e.g. a large numpy array), then an *artifact* file is created:
```py
import numpy as np
import turbo_broccoli as tb
obj = {"an_array": np.random.rand(1000, 1000)}
tb.save_json(obj, "foo/bar/foobar.json")
```
produces the JSON file
```json
{
"an_array": {
"__type__": "numpy.ndarray",
"__version__": 5,
"data": {
"__type__": "bytes",
"__version__": 3,
"id": "1e6dff28-5e26-44df-9e7a-75bc726ce9aa"
}
}
}
```
and a file `foo/bar/foobar.1e6dff28-5e26-44df-9e7a-75bc726ce9aa.tb` containing
the array data. The artifact directory can be explicitely specified by setting
it in the [serialization
context](https://altaris.github.io/turbo-broccoli/turbo_broccoli/context.html#Context)
or by setting the `TB_ARTIFACT_PATH` environment variable (see below.). The
code for loading the JSON file does not change:
```py
obj = tb.load_json("foo/bar/foobar.json")
```
If using
[`turbo_broccoli.to_json`](https://altaris.github.io/turbo-broccoli/turbo_broccoli/turbo_broccoli.html#to_json),
since there is no output file path specified, the artifacts are storied in a
temporary directory instead:
```py
import numpy as np
import turbo_broccoli as tb
obj = {"an_array": np.random.rand(1000, 1000)}
doc = tb.to_json(obj)
# An artifact has been created somewhere in e.g. /tmp
```
Since no information about this directory is stored in the output JSON string,
it is not possible to load `doc` using
[`turbo_broccoli.from_json`](https://altaris.github.io/turbo-broccoli/turbo_broccoli/turbo_broccoli.html#load_json).
If deserialization is necessary, instantiate a [context](https://altaris.github.io/turbo-broccoli/turbo_broccoli/context.html#Context):
```py
import numpy as np
import turbo_broccoli as tb
ctx = tb.Context()
obj = {"an_array": np.random.rand(1000, 1000)}
doc = tb.to_json(obj, ctx)
# An artifact has been created in ctx.artifact_path
...
obj = tb.from_json(doc, ctx)
```
## Supported types
### Basic types
- [`bytes`](https://altaris.github.io/turbo-broccoli/turbo_broccoli/custom/bytes.html#to_json)
- [Collections](https://altaris.github.io/turbo-broccoli/turbo_broccoli/custom/collections.html#to_json):
`collections.deque`, `collections.namedtuple`
- [Dataclasses](https://altaris.github.io/turbo-broccoli/turbo_broccoli/custom/dataclass.html#to_json):
serialization is straightforward:
```py
@dataclass
class C:
a: int
b: str
doc = tb.to_json({"c": C(a=1, b="Hello")})
```
For deserialization, first register the class:
```py
ctx = tb.Context(dataclass_types=[C])
tb.from_json(doc, ctx)
```
- [`datetime.datetime`, `datetime.time`,
`datetime.timedelta`](https://altaris.github.io/turbo-broccoli/turbo_broccoli/custom/datetime.html#to_json)
- Non JSON-able dicts, i.e. dicts whose keys are not all `str`, `int`, `float`,
`bool` or `None`
- [UUID objects](https://docs.python.org/3/library/uuid.html)
- [`pathlib.Path`](https://docs.python.org/3/library/pathlib.html#pathlib.Path)
### Generic objects
**Serialization only**. A generic object is an object that
has the `__turbo_broccoli__` attribute. This attribute is expected to be a list
of attributes whose values will be serialized. For example,
```py
class C:
__turbo_broccoli__ = ["a", "b"]
a: int
b: int
c: int
x = C()
x.a, x.b, x.c = 42, 43, 44
tb.to_json(x)
```
produces the following string:
```json
{"a": 42,"b": 43}
```
Registered attributes can of course have any type supported by TurboBroccoli,
such as numpy arrays. Registered attributes can be `@property` methods.
### [Keras](https://altaris.github.io/turbo-broccoli/turbo_broccoli/custom/keras.html#to_json)
- [`keras.Model`](https://keras.io/api/models/model/);
- standard subclasses of [`keras.layers.Layer`](https://keras.io/api/layers/),
[`keras.losses.Loss`](https://keras.io/api/losses/),
[`keras.metrics.Metric`](https://keras.io/api/metrics/), and
[`keras.optimizers.Optimizer`](https://keras.io/api/optimizers/).
### [Numpy](https://altaris.github.io/turbo-broccoli/turbo_broccoli/custom/numpy.html#to_json)
`numpy.number`, `numpy.ndarray` with numerical dtype, and `numpy.dtype`.
### [Pandas](https://altaris.github.io/turbo-broccoli/turbo_broccoli/custom/pandas.html#to_json)
`pandas.DataFrame` and `pandas.Series`, but with the following limitations:
- the following dtypes are not supported: `complex`, `object`, `timedelta`;
- the column / series names cannot be ints or int-strings: the following are
not acceptable
```py
df = pd.DataFrame([[1, 2], [3, 4]])
df = pd.DataFrame([[1, 2], [3, 4]], columns=["0", "1"])
```
### [Tensorflow](https://altaris.github.io/turbo-broccoli/turbo_broccoli/custom/tensorflow.html#to_json)
`tensorflow.Tensor` with numerical dtype, but not `tensorflow.RaggedTensor`.
### [Pytorch](https://altaris.github.io/turbo-broccoli/turbo_broccoli/custom/pytorch.html#to_json)
- `torch.Tensor`, **Warning**: loaded tensors are automatically placed on the
CPU and gradients are lost;
- `torch.nn.Module`, don't forget to register your module type using a
[`turbo_broccoli.Context`](https://altaris.github.io/turbo-broccoli/turbo_broccoli/context.html#Context):
```py
# Serialization
class MyModule(torch.nn.Module):
...
module = MyModule() # Must be instantiable without arguments
doc = tb.to_json({"module": module})
# Deserialization
ctx = tb.Context(pytorch_module_types=[MyModule])
module = tb.from_json(doc, ctx)
```
**Warning**: It is not possible to register and deserialize [standard pytorch
module containers](https://pytorch.org/docs/stable/nn.html#containers)
directly. Wrap them in your own custom module class. For following is not
acceptable
```py
import turbo_broccoli as tb
import torch
module = torch.nn.Sequential(
torch.nn.Linear(4, 2),
torch.nn.ReLU(),
torch.nn.Linear(2, 1),
torch.nn.ReLU(),
)
obj = {"module": module}
doc = tb.to_json(obj) # works, but...
tb.from_json(a, ctx) # does't work
```
but the following works:
```py
class MyModule(torch.nn.Module):
module: torch.nn.Sequential # Wrapped sequential
def __init__(self):
super().__init__()
self.module = torch.nn.Sequential(
torch.nn.Linear(4, 2),
torch.nn.ReLU(),
torch.nn.Linear(2, 1),
torch.nn.ReLU(),
)
...
module = MyModule() # Must be instantiable without arguments
doc = tb.to_json({"module": module})
ctx = tb.Context(pytorch_module_types=[MyModule])
module = tb.from_json(doc, ctx)
```
To circumvent all these limitations, use custom encoders / decoders.
- `torch.utils.data.ConcatDataset`, `torch.utils.data.StackDataset`,
`torch.utils.data.Subset`, `torch.utils.data.TensorDataset`, as long as the
nested structure of datasets ultimately lead to
`torch.utils.data.TensorDataset`s (e.g. a subset of a stack of subsets of
tensor datasets is supported)
### [Scipy](https://altaris.github.io/turbo-broccoli/turbo_broccoli/custom/scipy.html#to_json)
Just `scipy.sparse.csr_matrix`. ^^"
### [Scikit-learn](https://altaris.github.io/turbo-broccoli/turbo_broccoli/custom/sklearn.html#to_json)
`sklearn` estimators (i.e. that inherit from
[`sklean.base.BaseEstimator`](https://scikit-learn.org/stable/modules/generated/sklearn.base.BaseEstimator.html)).
Supported estimators are: `AdaBoostClassifier`, `AdaBoostRegressor`,
`AdditiveChi2Sampler`, `AffinityPropagation`, `AgglomerativeClustering`,
`ARDRegression`, `BayesianGaussianMixture`, `BayesianRidge`, `BernoulliNB`,
`BernoulliRBM`, `Binarizer`, `CategoricalNB`, `CCA`, `ClassifierChain`,
`ComplementNB`, `DBSCAN`, `DecisionTreeClassifier`, `DecisionTreeRegressor`,
`DictionaryLearning`, `ElasticNet`, `EllipticEnvelope`, `EmpiricalCovariance`,
`ExtraTreeClassifier`, `ExtraTreeRegressor`, `ExtraTreesClassifier`,
`ExtraTreesRegressor`, `FactorAnalysis`, `FeatureUnion`, `GaussianMixture`,
`GaussianNB`, `GaussianRandomProjection`, `GraphicalLasso`, `HuberRegressor`,
`IncrementalPCA`, `IsolationForest`, `Isomap`, `KernelCenterer`,
`KernelDensity`, `KernelPCA`, `KernelRidge`, `KMeans`, `KNeighborsClassifier`,
`KNeighborsRegressor`, `KNNImputer`, `LabelBinarizer`, `LabelEncoder`,
`LabelPropagation`, `LabelSpreading`, `Lars`, `Lasso`, `LassoLars`,
`LassoLarsIC`, `LatentDirichletAllocation`, `LedoitWolf`,
`LinearDiscriminantAnalysis`, `LinearRegression`, `LinearSVC`, `LinearSVR`,
`LocallyLinearEmbedding`, `LocalOutlierFactor`, `LogisticRegression`,
`MaxAbsScaler`, `MDS`, `MeanShift`, `MinCovDet`, `MiniBatchDictionaryLearning`,
`MiniBatchKMeans`, `MiniBatchSparsePCA`, `MinMaxScaler`, `MissingIndicator`,
`MLPClassifier`, `MLPRegressor`, `MultiLabelBinarizer`, `MultinomialNB`,
`MultiOutputClassifier`, `MultiOutputRegressor`, `MultiTaskElasticNet`,
`MultiTaskLasso`, `NearestCentroid`, `NearestNeighbors`,
`NeighborhoodComponentsAnalysis`, `NMF`, `Normalizer`, `NuSVC`, `NuSVR`,
`Nystroem`, `OAS`, `OneClassSVM`, `OneVsOneClassifier`, `OneVsRestClassifier`,
`OPTICS`, `OrthogonalMatchingPursuit`, `PassiveAggressiveRegressor`, `PCA`,
`Pipeline`, `PLSCanonical`, `PLSRegression`, `PLSSVD`, `PolynomialCountSketch`,
`PolynomialFeatures`, `PowerTransformer`, `QuadraticDiscriminantAnalysis`,
`QuantileRegressor`, `QuantileTransformer`, `RadiusNeighborsClassifier`,
`RadiusNeighborsRegressor`, `RandomForestClassifier`, `RandomForestRegressor`,
`RANSACRegressor`, `RBFSampler`, `RegressorChain`, `RFE`, `RFECV`, `Ridge`,
`RidgeClassifier`, `RobustScaler`, `SelectFromModel`, `SelfTrainingClassifier`,
`SGDRegressor`, `ShrunkCovariance`, `SimpleImputer`, `SkewedChi2Sampler`,
`SparsePCA`, `SparseRandomProjection`, `SpectralBiclustering`,
`SpectralClustering`, `SpectralCoclustering`, `SpectralEmbedding`,
`StackingClassifier`, `StackingRegressor`, `StandardScaler`, `SVC`, `SVC`,
`SVR`, `SVR`, `TheilSenRegressor`, `TruncatedSVD`, `TSNE`, `VarianceThreshold`,
`VotingClassifier`, `VotingRegressor`.
Doesn't work with:
- All CV classes because the `score_` attribute is a dict indexed with
`np.int64`, which `json.JSONEncoder._iterencode_dict` rejects.
- Everything that is parametrized by an arbitrary object/callable/estimator:
`FunctionTransformer`, `TransformedTargetRegressor`.
- Other classes that have non JSON-serializable attributes:
| Class | Non-serializable attr. |
| --------------------------- | ------------------------- |
| `Birch` | `_CFNode` |
| `BisectingKMeans` | `function` |
| `ColumnTransformer` | `slice` |
| `GammaRegressor` | `HalfGammaLoss` |
| `GaussianProcessClassifier` | `Product` |
| `GaussianProcessRegressor` | `Sum` |
| `IsotonicRegression` | `interp1d` |
| `OutputCodeClassifier` | `_ConstantPredictor` |
| `Perceptron` | `Hinge` |
| `PoissonRegressor` | `HalfPoissonLoss` |
| `SGDClassifier` | `Hinge` |
| `SGDOneClassSVM` | `Hinge` |
| `SplineTransformer` | `BSpline` |
| `TweedieRegressor` | `HalfTweedieLossIdentity` |
- Other errors:
- `FastICA`: I'm not sure why...
- `BaggingClassifier`: `IndexError: only integers, slices (:), ellipsis
(...), numpy.newaxis (None) and integer or boolean arrays are valid
indices`.
- `GradientBoostingClassifier`, `GradientBoostingRegressor`,
`RandomTreesEmbedding`, `KBinsDiscretizer`: `Exception:
dtype object is not covered`.
- `HistGradientBoostingClassifier`: Problems with deserialization of
`_BinMapper` object?
- `PassiveAggressiveClassifier`: some unknown label type error...
- `SequentialFeatureSelector`: Problem with the unit test itself ^^"
- `KNeighborsTransformer`: A serialized-deserialized instance seems to
`fit_transform` an array to a sparse matrix whereas the original object
returns an array?
- `RadiusNeighborsTransformer`: Inverse problem from `KNeighborsTransformer`.
### [Bokeh](https://altaris.github.io/turbo-broccoli/turbo_broccoli/custom/bokeh.html#to_json)
Bokeh [figures](https://docs.bokeh.org/en/latest) and
[models](https://docs.bokeh.org/en/latest/docs/reference/models.html).
### [NetworkX](https://altaris.github.io/turbo-broccoli/turbo_broccoli/custom/networkx.html#to_json)
All NetworkX [graph
objects](https://networkx.org/documentation/stable/reference/classes/index.html#which-graph-class-should-i-use).
### [Secrets](https://altaris.github.io/turbo-broccoli/turbo_broccoli/custom/secret.html#to_json)
Basic Python types can be wrapped in their corresponding secret type according
to the following table
| Python type | Secret type |
| ----------- | ---------------------------- |
| `dict` | `turbo_broccoli.SecretDict` |
| `float` | `turbo_broccoli.SecretFloat` |
| `int` | `turbo_broccoli.SecretInt` |
| `list` | `turbo_broccoli.SecretList` |
| `str` | `turbo_broccoli.SecretStr` |
The secret value can be recovered with the `get_secret_value` method. At
serialization, the this value will be encrypted. For example,
```py
## See https://pynacl.readthedocs.io/en/latest/secret/#key
import nacl.secret
import nacl.utils
import turbo_broccoli as tb
key = nacl.utils.random(nacl.secret.SecretBox.KEY_SIZE)
ctx = tb.Context(nacl_shared_key=key)
obj = {"user": "alice", "password": tb.SecretStr("dolphin")}
tb.to_json(obj, ctx)
```
produces the following string (modulo indentation and modulo the encrypted
content):
```json
{
"user": "alice",
"password": {
"__type__": "secret",
"__version__": 2,
"data": {
"__type__": "bytes",
"__version__": 3,
"data": "gbRXF3hq9Q9hIQ9Xz+WdGKYP5meJ4eTmlFt0r0Ov3PV64065plk6RqsFUcynSOqHzA=="
}
}
}
```
Deserialization decrypts the secrets, but they stay wrapped inside the secret
types above. If the wrong key is provided, an exception is raised. If no key is
provided, the secret values are replaced by a
`turbo_broccoli.LockedSecret`. Internally, TurboBroccoli uses
[`pynacl`](https://pynacl.readthedocs.io/en/latest/)'s
[`SecretBox`](https://pynacl.readthedocs.io/en/latest/secret/#nacl.secret.SecretBox).
**Warning**: In the case of `SecretDict` and `SecretList`, the values contained
within must be JSON-serializable **without** TurboBroccoli. The following is
not acceptable:
```py
import nacl.secret
import nacl.utils
import numpy as np
import turbo_broccoli as tb
key = nacl.utils.random(nacl.secret.SecretBox.KEY_SIZE)
ctx = tb.Context(nacl_shared_key=key)
obj = {"data": tb.SecretList([np.array([1, 2, 3])])}
tb.to_json(obj, ctx)
```
See also the `TB_SHARED_KEY` environment variable below.
### Embedded dict/lists
Sometimes, it may be useful to store part of a document in its own file and
have referrenced in the main file. This is possible using
[`EmbeddedDict`](https://altaris.github.io/turbo-broccoli/turbo_broccoli/custom/embedded.html)
and
[`EmbeddedList`](https://altaris.github.io/turbo-broccoli/turbo_broccoli/custom/embedded.html).
For example,
```py
from turbo_broccoli import save_json, EmbeddedDict
data = {"a": 1, "b": EmbeddedDict({"c": 2, "d": 3})}
save_json(data, "data.json")
```
will result in a `data.json` file containing
```json
{
"a": 1,
"b": {
"__type__": "embedded.dict",
"__version__": 1,
"id": "4ea0b3f3-f3e4-42bd-9db9-1e4e0b9f4fae"
}
}
```
(modulo indentation and the id), and an artefact file
`data.4ea0b3f3-f3e4-42bd-9db9-1e4e0b9f4fae.json` containing
```json
{"c": 2, "d": 3}
```
### Â External data
If you are serializing/deserializing from a file, you can use
[`turbo_broccoli.ExternalData`](https://altaris.github.io/turbo-broccoli/turbo_broccoli/custom/external.html)
to point to data contained in another file without integrating it to the
current document.
For example, let's say you want to create `foo/bar.json` where the `a` key
points to the data contained in `foo/foooooo/data.np`:
```py
import turbo_broccoli as tb
document = {
"a": tb.ExternalData("foooooo/data.np"),
...
}
# data.np is loaded when creating the ExternalData object
print(document["a"].data)
# Saving
tb.save_json(document, "foo/bar.json")
# Loading
document2 = tb.load_json("foo/bar.json")
from numpy.testing import assert_array_equal
assert_array_equal(document["a"].data, document2["a"].data)
```
Warnings:
- `document["a"].data` is read only, the following will have no effect on
`foo/foooooo/data.np`:
```py
document["a"].data += 1
tb.save_json(document, "foo/bar.json")
```
- When serializing/deserializing a `ExternalData` object, an actual JSON
document must be involved. In particular, using `tb.to_json` or
`tb.from_json` is not possible.
- The external data file's path must be a subpath of the output/intput JSON
file, and provided either relative to the output/intput JSON file, or in
absolute form:
```py
# OK, relative
document = {"a": tb.ExternalData("foooooo/data.np")}
tb.save_json(document, "foo/bar.json")
# OK, absolute
document = {"a": tb.ExternalData("/home/alice/foo/foooooo/data.np")}
tb.save_json(document, "foo/bar.json")
# ERROR, not subpath
document = {"a": tb.ExternalData("/home/alice/data.np")}
tb.save_json(document, "/home/alice/foo/bar.json")
```
## Environment variables
Some behaviors of TurboBroccoli can be tweaked by setting specific environment
variables. If you want to modify these parameters programatically, do not do so
by modifying `os.environ`. Rather, use a
[`turbo_broccoli.Context`](https://altaris.github.io/turbo-broccoli/turbo_broccoli/context.html#Context).
- `TB_ARTIFACT_PATH` (default: output JSON file's parent directory): During
serialization, TurboBroccoli may create artifacts to which the JSON object
will point to. The artifacts will be stored in `TB_ARTIFACT_PATH` if
specified.
- `TB_KERAS_FORMAT` (default: `tf`, valid values are `keras`, `tf`, and `h5`):
The serialization format for keras models. If `h5` or `tf` is used, an
artifact following said format will be created in `TB_ARTIFACT_PATH`. If
`json` is used, the model will be contained in the JSON document (anthough
the weights may be in artifacts if they are too large).
- `TB_MAX_NBYTES` (default: `8000`):
The maximum byte size of a python object beyond which serialization will
produce an artifact instead of storing it in the JSON document. This does not
limit the size of the overall JSON document though. 8000 bytes should be
enough for a numpy array of 1000 `float64`s to be stored in-document.
- `TB_NODECODE` (default: empty):
Comma-separated list of types to not deserialize, for example
`bytes,numpy.ndarray`. Excludable types are:
- `bokeh`, `bokeh.buffer`, `bokeh.generic`,
- `bytes`, **Warning** excluding `bytes` will also exclude `bokeh`,
`numpy.ndarray`, `pytorch.module`, `pytorch.tensor`, `secret`,
`tensorflow.tensor`,
- `collections`, `collections.deque`, `collections.namedtuple`,
`collections.set`,
- `dataclass`, `dataclass.` (case sensitive),
- `datetime`, `datetime.datetime`, `datetime.time`, `datetime.timedelta`,
- `dict` (this only prevents decoding dicts with non-string keys),
- `embedded`, `embedded.dict`, `embedded.list`,
- `external`,
- `generic`,
- `keras`, `keras.model`, `keras.layer`, `keras.loss`, `keras.metric`,
`keras.optimizer`,
- `networkx`, `networkx.graph`,
- `numpy`, `numpy.ndarray`, `numpy.number`, `numpy.dtype`,
`numpy.random_state`,
- `pandas`, `pandas.dataframe`, `pandas.series`, **Warning**: excluding
`pandas.dataframe` will also exclude `pandas.series`,
- `pathlib`, `pathlib.path`, **Warning**: excluding `pathlib.path` will also
exclude `external`,
- `pytorch`, `pytorch.tensor`, `pytorch.module`, `pytorch.concatdataset`,
`pytorch.stackdataset`, `pytorch.subset`, `pytorch.tensordataset`
- `scipy`, `scipy.csr_matrix`,
- `secret`,
- `sklearn`, `sklearn.estimator`, `sklearn.estimator.` (case
sensitive, see the list of supported sklearn estimators below),
- `tensorflow`, `tensorflow.sparse_tensor`, `tensorflow.tensor`,
`tensorflow.variable`.
- `uuid`
- `external`
- `TB_SHARED_KEY` (default: empty):
Secret key used to encrypt/decrypt secrets. The encryption uses [`pynacl`'s
`SecretBox`](https://pynacl.readthedocs.io/en/latest/secret/#nacl.secret.SecretBox).
An exception is raised when attempting to serialize a secret type while no
key is set.
## Contributing
### Dependencies
- `python3.10` or newer;
- `requirements.txt` for runtime dependencies;
- `requirements.dev.txt` for development dependencies.
- `make` (optional);
Simply run
```sh
virtualenv venv -p python3.10
. ./venv/bin/activate
pip install --upgrade pip
pip install -r requirements.txt
pip install -r requirements.dev.txt
```
### Documentation
Simply run
```sh
make docs
```
This will generate the HTML doc of the project, and the index file should be at
`docs/index.html`. To have it directly in your browser, run
```sh
make docs-browser
```
### Code quality
Don't forget to run
```sh
make
```
to format the code following [black](https://pypi.org/project/black/),
typecheck it using [mypy](http://mypy-lang.org/), and check it against coding
standards using [pylint](https://pylint.org/).
### Unit tests
Run
```sh
make test
```
to have [pytest](https://docs.pytest.org/) run the unit tests in `tests/`.
## Credits
This project takes inspiration from
[Crimson-Crow/json-numpy](https://github.com/Crimson-Crow/json-numpy).