bigraph-schema 0.0.58__tar.gz → 0.0.60__tar.gz

{bigraph-schema-0.0.58/bigraph_schema.egg-info → bigraph-schema-0.0.60}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bigraph-schema
-Version: 0.0.58
+Version: 0.0.60
 Summary: A serializable type schema for compositional systems biology
 Home-page: https://github.com/vivarium-collective/bigraph-schema
 Author: Eran Agmon, Ryan Spangler

{bigraph-schema-0.0.58 → bigraph-schema-0.0.60}/bigraph_schema/__init__.py

@@ -4,3 +4,5 @@ from bigraph_schema.registry import (
 from bigraph_schema.utilities import get_path, visit_method
 from bigraph_schema.edge import Edge
 from bigraph_schema.type_system import TypeSystem, type_schema_keys, resolve_path
+from bigraph_schema.protocols import local_lookup_module
+from bigraph_schema.type_functions import FUNCTION_TYPE, METHOD_TYPE

{bigraph-schema-0.0.58 → bigraph-schema-0.0.60}/bigraph_schema/parse.py

@@ -37,7 +37,7 @@ parameter_grammar = Grammar(
     nest = symbol colon tree
     type_name = symbol parameter_list?
     parameter_list = square_left expression (comma expression)* square_right
-    symbol = ~r"[\w\d-_/*&^%$#@!`+ ]+"
+    symbol = ~r"[\\w\\d-_/*&^%$#@!`+ ]+"
     dot = "."
     colon = ":"
     bar = "|"
@@ -49,7 +49,7 @@ parameter_grammar = Grammar(
     tilde = "~"
     not_newline = ~r"[^\\n\\r]"*
     newline = ~"[\\n\\r]+"
-    ws = ~"\s*"
+    ws = ~r"\\s*"
     nothing = ""
     """)
 

{bigraph-schema-0.0.58 → bigraph-schema-0.0.60}/bigraph_schema/tests.py

@@ -7,10 +7,10 @@ import pprint
 import numpy as np
 from dataclasses import asdict
 
+from bigraph_schema import TypeSystem, local_lookup_module
 from bigraph_schema.type_functions import (
     divide_longest, base_types, accumulate, to_string, deserialize_integer, apply_schema, data_module)
 from bigraph_schema.utilities import compare_dicts, NONE_SYMBOL
-from bigraph_schema import TypeSystem
 from bigraph_schema.units import units
 from bigraph_schema.registry import establish_path, remove_omitted
 
@@ -1229,6 +1229,29 @@ def test_reaction(core):
                     {'id': 'daughter2', 'ratio': 0.7}]}}}
 
 
+def A(a):
+    return a * 5
+
+def B(b):
+    return b + 11
+
+def test_function_type(core):
+    A_serialized = core.serialize(
+        'function',
+        A)
+
+    A_deserialized = core.deserialize(
+        'function',
+        A_serialized)
+
+    C = core.apply(
+        'function',
+        A_deserialized,
+        B)
+
+    assert C(6) == 41
+
+
 def test_map_type(core):
     schema = 'map[integer]'
 
@@ -2508,6 +2531,7 @@ if __name__ == '__main__':
     test_maybe_type(core)
     test_tuple_type(core)
     test_array_type(core)
+    test_function_type(core)
     test_union_type(core)
     test_union_values(core)
     test_infer_edge(core)

{bigraph-schema-0.0.58 → bigraph-schema-0.0.60}/bigraph_schema/type_functions.py

@@ -68,6 +68,7 @@ import types
 import copy
 import numbers
 import numpy as np
+from abc import ABCMeta
 from pint import Quantity
 from pprint import pformat as pf
 
@@ -76,6 +77,7 @@ from typing import NewType, Union, Mapping, List, Dict, Optional, Callable
 from dataclasses import field, make_dataclass
 
 from bigraph_schema import get_path, set_path
+from bigraph_schema.protocols import local_lookup_module
 from bigraph_schema.units import units, render_units_type
 from bigraph_schema.registry import (
     is_schema_key, non_schema_keys, type_parameter_key, deep_merge, hierarchy_depth, establish_path
@@ -421,6 +423,16 @@ def apply_array(schema, current, update, top_schema, top_state, path, core):
     else:
         return current + update
 
+def apply_function(schema, current, update, top_schema, top_state, path, core):
+    def compose(a):
+        return update(
+            current(
+                a))
+
+    return compose
+
+def apply_meta(schema, current, update, top_schema, top_state, path, core):
+    return update
 
 # =========================
 # Check Functions Overview
@@ -484,6 +496,22 @@ def check_float(schema, state, core=None):
 def check_string(schema, state, core=None):
     return isinstance(state, str)
 
+class Empty():
+    def method(self):
+        pass
+
+FUNCTION_TYPE = type(check_string)
+METHOD_TYPE = type(Empty().method)
+
+def check_function(schema, state, core=None):
+    return isinstance(state, FUNCTION_TYPE)
+
+def check_method(schema, state, core=None):
+    return isinstance(state, METHOD_TYPE)
+
+def check_meta(schema, state, core=None):
+    return isinstance(state, ABCMeta)
+
 def check_list(schema, state, core):
     element_type = core.find_parameter(
         schema,
@@ -1070,6 +1098,9 @@ def serialize_maybe(schema, value, core):
             value_type,
             value)
 
+def serialize_function(schema, value, core=None):
+    return f'{value.__module__}.{value.__name__}'
+
 def serialize_map(schema, value, core=None):
     value_type = core.find_parameter(
         schema,
@@ -1315,6 +1346,9 @@ def deserialize_units(schema, encoded, core):
     else:
         return units(encoded)
 
+def deserialize_function(schema, value, core=None):
+    return local_lookup_module(value)
+
 def deserialize_map(schema, encoded, core=None):
     if isinstance(encoded, dict):
         value_type = core.find_parameter(
@@ -2189,6 +2223,33 @@ def generate_any(core, schema, state, top_schema=None, top_state=None, path=None
 
     return generated_schema, generated_state, top_schema, top_state
 
+
+def generate_list(core, schema, state, top_schema=None, top_state=None, path=None):
+    schema = schema or {}
+    state = state or core.default(schema)
+    top_schema = top_schema or schema
+    top_state = top_state or state
+    path = path or []
+
+    element_type = core.find_parameter(
+        schema,
+        'element')
+
+    generated_state = []
+
+    for index, element in enumerate(state):
+        subschema, substate, top_schema, top_state = core.generate_recur(
+                element_type,
+                element,
+                top_schema=top_schema,
+                top_state=top_state,
+                path=path + [index])
+
+        generated_state.append(substate)
+
+    return schema, generated_state, top_schema, top_state
+    
+
 def generate_quote(core, schema, state, top_schema=None, top_state=None, path=None):
     return schema, state, top_schema, top_state
 
@@ -2764,6 +2825,7 @@ base_types = {
     'list': {
         '_type': 'list',
         '_default': [],
+        # '_generate': generate_list,
         '_check': check_list,
         '_slice': slice_list,
         '_apply': apply_list,
@@ -2838,6 +2900,25 @@ base_types = {
         '_type_parameters': ['value'],
         '_description': 'type to represent values that could be empty'},
 
+    'function': {
+        '_type': 'function',
+        '_apply': apply_function,
+        '_serialize': serialize_function,
+        '_deserialize': deserialize_function,
+        '_check': check_function},
+
+    'method': {
+        '_type': 'function',
+        '_apply': apply_meta,
+        '_serialize': serialize_function,
+        '_deserialize': deserialize_function,
+        '_check': check_method},
+
+    'meta': {
+        '_inherit': 'function',
+        '_apply': apply_meta,
+        '_check': check_meta},
+
     'path': {
         '_type': 'path',
         '_inherit': 'list[string~integer]',

{bigraph-schema-0.0.58 → bigraph-schema-0.0.60/bigraph_schema.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bigraph-schema
-Version: 0.0.58
+Version: 0.0.60
 Summary: A serializable type schema for compositional systems biology
 Home-page: https://github.com/vivarium-collective/bigraph-schema
 Author: Eran Agmon, Ryan Spangler

{bigraph-schema-0.0.58 → bigraph-schema-0.0.60}/setup.py

@@ -1,7 +1,7 @@
 from setuptools import setup, find_packages
 
 
-VERSION = '0.0.58'
+VERSION = '0.0.60'
 
 
 with open("README.md", "r") as readme: