bigraph-schema 0.0.71__py3-none-any.whl

bigraph_schema/utilities.py

@@ -0,0 +1,243 @@
+"""
+Utility functions for working with bigraph schemas
+"""
+
+import collections
+import numpy as np
+
+
+NONE_SYMBOL = '!nil'
+
+DTYPE_MAP = {
+    'float': 'float64',
+    'integer': 'int64',
+    'string': 'str'}
+
+overridable_schema_keys = {'_type', '_default', '_check', '_apply', '_serialize', '_deserialize', '_fold', '_divide',
+                           '_slice', '_bind', '_merge', '_type_parameters', '_value', '_description', '_inherit'}
+
+# nonoverridable_schema_keys = type_schema_keys - overridable_schema_keys
+
+merge_schema_keys = (
+    '_ports',
+    '_type_parameters',
+)
+
+
+def type_merge(dct, merge_dct, path=tuple(), merge_supers=False):
+    """
+    Recursively merge type definitions, never overwrite.
+
+    Args:
+    - dct: The dictionary to merge into. This dictionary is mutated and ends up being the merged dictionary.  If you
+        want to keep dct you could call it like ``deep_merge_check(copy.deepcopy(dct), merge_dct)``.
+    - merge_dct: The dictionary to merge into ``dct``.
+    - path: If the ``dct`` is nested within a larger dictionary, the path to ``dct``. This is normally an empty tuple
+        (the default) for the end user but is used for recursive calls.
+    Returns:
+    - dct
+    """
+    for k in merge_dct:
+        if not k in dct or k in overridable_schema_keys:
+            dct[k] = merge_dct[k]
+        elif k in merge_schema_keys or isinstance(
+                dct[k], dict
+        ) and isinstance(
+            merge_dct[k], collections.abc.Mapping
+        ):
+            type_merge(
+                dct[k],
+                merge_dct[k],
+                path + (k,),
+                merge_supers)
+
+        else:
+            raise ValueError(
+                f'cannot merge types at path {path + (k,)}:\n'
+                f'{dct}\noverwrites \'{k}\' from\n{merge_dct}')
+
+    return dct
+
+
+def visit_method(schema, state, method, values, core):
+    """
+    Visit a method for a schema and state and apply it, returning the result
+    """
+    schema = core.access(schema)
+    method_key = f'_{method}'
+
+    # TODO: we should probably cache all this
+    if isinstance(state, dict) and method_key in state:
+        visit = core.find_method(
+            {method_key: state[method_key]},
+            method_key)
+    elif method_key in schema:
+        visit = core.find_method(
+            schema,
+            method_key)
+    else:
+        visit = core.find_method(
+            'any',
+            method_key)
+
+    result = visit(
+        schema,
+        state,
+        values,
+        core)
+
+    return result
+
+
+def is_empty(value):
+    if isinstance(value, np.ndarray):
+        return False
+    elif value is None or value == {}:
+        return True
+    else:
+        return False
+
+
+def union_keys(schema, state):
+    keys = {}
+    for key in schema:
+        keys[key] = True
+    for key in state:
+        keys[key] = True
+
+    return keys
+    # return set(schema.keys()).union(state.keys())
+
+
+def tuple_from_type(tuple_type):
+    if isinstance(tuple_type, tuple):
+        return tuple_type
+
+    elif isinstance(tuple_type, list):
+        return tuple(tuple_type)
+
+    elif isinstance(tuple_type, dict):
+        tuple_list = [
+            tuple_type[f'_{parameter}']
+            for parameter in tuple_type['_type_parameters']]
+
+        return tuple(tuple_list)
+    else:
+        raise Exception(f'do not recognize this type as a tuple: {tuple_type}')
+
+
+def array_shape(core, schema):
+    if '_type_parameters' not in schema:
+        schema = core.access(schema)
+    parameters = schema.get('_type_parameters', [])
+
+    return tuple([
+        int(schema[f'_{parameter}'])
+        for parameter in schema['_type_parameters']])
+
+
+def lookup_dtype(data_name):
+    data_name = data_name or 'string'
+    dtype_name = DTYPE_MAP.get(data_name)
+    if dtype_name is None:
+        raise Exception(f'unknown data type for array: {data_name}')
+
+    return np.dtype(dtype_name)
+
+
+def read_datatype(data_schema):
+    return lookup_dtype(
+        data_schema['_type'])
+
+
+def read_shape(shape):
+    return tuple([
+        int(x)
+        for x in tuple_from_type(
+            shape)])
+
+
+def compare_dicts(a, b):
+    if isinstance(a, dict) and isinstance(b, dict):
+        result = {}
+        for key in union_keys(a, b):
+            if key in a:
+                if key in b:
+                    inner = compare_dicts(a[key], b[key])
+                    if inner:
+                        result[key] = inner
+                else:
+                    result[key] = f'A: {a[key]}\nB: (missing)'
+            else:
+                result[key] = f'A: (missing)\nB: {b[key]}'
+        if result:
+            return result
+    else:
+        if a != b:
+            return f'A: {a}\nB: {b}'
+
+
+def get_path(tree, path):
+    """
+    Given a tree and a path, find the subtree at that path
+
+    Args:
+    - tree: the tree we are looking in (a nested dict)
+    - path: a list/tuple of keys we follow down the tree to find the subtree we are looking for
+
+    Returns:
+    - subtree: the subtree found by following the list of keys down the tree
+    """
+
+    if len(path) == 0:
+        return tree
+    else:
+        head = path[0]
+        if not tree or head not in tree:
+            return None
+        else:
+            return get_path(tree[head], path[1:])
+
+
+def remove_path(tree, path):
+    """
+    Removes whatever subtree lives at the given path
+    """
+
+    if path is None or len(path) == 0:
+        return None
+
+    upon = get_path(tree, path[:-1])
+    if upon is not None:
+        del upon[path[-1]]
+    return tree
+
+
+def type_parameters_for(schema):
+    parameters = []
+    for key in schema['_type_parameters']:
+        subschema = schema.get(f'_{key}', 'any')
+        parameters.append(subschema)
+
+    return parameters
+
+
+def state_instance(dataclass, state):
+    if hasattr(dataclass, '__dataclass_fields__'):
+        fields = dataclass.__dataclass_fields__
+        state = state or {}
+
+        init = {}
+        for key, field in fields.items():
+            substate = state_instance(
+                field.type,
+                state.get(key))
+            init[key] = substate
+        instance = dataclass(**init)
+    # elif get_origin(dataclass) in [typing.Union, typing.Mapping]:
+    #     instance = state
+    else:
+        instance = state
+        # instance = dataclass(state)
+
+    return instance

bigraph_schema-0.0.71.dist-info/METADATA

@@ -0,0 +1,52 @@
+Metadata-Version: 2.4
+Name: bigraph-schema
+Version: 0.0.71
+Summary: A serializable type schema for compositional systems biology
+Author: Eran Agmon, Ryan Spangler
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: AUTHORS.md
+Requires-Dist: fire
+Requires-Dist: numpy
+Requires-Dist: orjson
+Requires-Dist: parsimonious
+Requires-Dist: pint
+Requires-Dist: plum-dispatch
+Requires-Dist: pytest
+Requires-Dist: requests>=2.31.0
+Requires-Dist: setuptools
+Requires-Dist: twine>=4.0.2
+Dynamic: license-file
+
+# Bigraph-schema
+
+[![PyPI version](https://img.shields.io/pypi/v/bigraph-schema.svg)](https://pypi.org/project/bigraph-schema/)
+[![Tutorial](https://img.shields.io/badge/GitHub%20Pages-Tutorial-brightgreen)](https://vivarium-collective.github.io/bigraph-schema/notebooks/demo.html)
+
+Welcome to `bigraph-schema` – a library providing a serializable type schema for composite systems simulations. 
+This library provides the core of the broader Vivarium 2.0 project.
+
+The goal of `bigraph-schema` is to support interoperability and extensibility across composite simulation formats, 
+facilitating integration with existing and future modeling platforms. This is achieved by establishing a 
+standardized and serializable schema for the complex, hierarchical, and multiscale nature of biological systems.
+
+## Installation
+
+To install `bigraph-schema`, you can use pip:
+
+```console
+pip install bigraph-schema
+```
+
+## Getting Started
+
+To get started with bigraph-schema, check out our resources:
+
+* [Type System Overview](https://vivarium-collective.github.io/bigraph-schema/notebooks/core.html): A tutorial demonstrating the functionality of bigraph-schema's type system, "core".
+* [Bigraph Schema Basics Tutorial](https://vivarium-collective.github.io/bigraph-viz/notebooks/basics.html): A  tutorial covering the essential aspects of the bigraph-schema library. 
+This resource will guide you through the core concepts and methods, helping you to master the basic operations.
+
+## License
+
+Bigraph-schema is open-source software released under the [Apache 2 License](https://github.com/vivarium-collective/bigraph-schema/blob/main/LICENSE).

bigraph_schema-0.0.71.dist-info/RECORD

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bigraph_schema-0.0.71.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (80.9.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

bigraph_schema-0.0.71.dist-info/licenses/AUTHORS.md

@@ -0,0 +1,6 @@
+# Authors of Bigraph Schema
+
+The maintainers of the Bigraph-Schema project are:
+
+* Ryan Spangler (@prismofeverything)
+* Eran Agmon  (@eagmon)

bigraph_schema-0.0.71.dist-info/licenses/LICENSE

@@ -0,0 +1,201 @@
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bigraph_schema-0.0.71.dist-info/top_level.txt

@@ -0,0 +1 @@
+bigraph_schema