bigraph-schema 0.0.54__tar.gz → 0.0.56__tar.gz

{bigraph-schema-0.0.54/bigraph_schema.egg-info → bigraph-schema-0.0.56}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bigraph-schema
-Version: 0.0.54
+Version: 0.0.56
 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-0.0.54 → bigraph-schema-0.0.56}/bigraph_schema/edge.py

@@ -31,6 +31,16 @@ class Edge:
 
 
     def initial_state(self):
+        """The initial state of the edge, which is passed to the core."""
+        return {}
+
+
+    @staticmethod
+    def generate_state(config=None):  # TODO -- config could have a schema
+        """
+        Generate an initial state statically, without any instance-specific config.
+        This could be used to create user-configured initial states based on the Edge's requirements.
+        """
         return {}
 
 

{bigraph-schema-0.0.54 → bigraph-schema-0.0.56}/bigraph_schema/type_functions.py

@@ -75,6 +75,7 @@ import typing
 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.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
@@ -1083,8 +1084,50 @@ def serialize_edge(schema, value, core):
 def serialize_enum(schema, value, core):
     return value
 
+def recur_serialize_schema(schema, core, path=None, parents=None):
+    """ Serialize schema to a string """
+    path = path or []
+    parents = parents or []
+    schema_id = id(schema)
+
+    if schema_id in parents:
+        index = parents.index(schema_id)
+        reference = path[:index]
+        output = '/'.join(reference)
+        return f'/{output}'
+
+    if isinstance(schema, str):
+        return schema
+
+    elif isinstance(schema, tuple):
+        inner = [
+            recur_serialize_schema(
+                schema=element,
+                core=core,
+                path=path+[index],
+                parents=parents+[schema_id])
+            for index, element in enumerate(schema)]
+
+        return inner
+
+    elif isinstance(schema, dict):
+        inner = {}
+        for key in schema:
+            subschema = recur_serialize_schema(
+                schema=schema[key],
+                core=core,
+                path=path+[key],
+                parents=parents+[schema_id])
+            inner[key] = subschema
+
+        return inner
+
+    else:
+        return schema
+
 def serialize_schema(schema, state, core):
-    return state
+    """ Serialize schema to a string """
+    return recur_serialize_schema(schema=state, core=core)
 
 def serialize_array(schema, value, core):
     """ Serialize numpy array to list """
@@ -1229,6 +1272,9 @@ def deserialize_maybe(schema, encoded, core):
 
         return core.deserialize(value_type, encoded)
 
+def deserialize_quote(schema, state, core):
+    return state
+
 def deserialize_boolean(schema, encoded, core) -> bool:
     if encoded == 'true':
         return True
@@ -1313,8 +1359,52 @@ def deserialize_array(schema, encoded, core):
 def deserialize_edge(schema, encoded, core):
     return encoded
 
+def recur_deserialize_schema(schema, core, top_state=None, path=None):
+    top_state = top_state or schema
+    path = path or []
+
+    if isinstance(schema, dict):
+        subschema = {}
+        for key, value in schema.items():
+            subschema[key] = recur_deserialize_schema(
+                value,
+                core,
+                top_state=top_state,
+                path=path+[key])
+
+        return subschema
+
+    elif isinstance(schema, list):
+        subschema = []
+        for index, value in enumerate(schema):
+            subschema.append(
+                recur_deserialize_schema(
+                    value,
+                    core,
+                    top_state=top_state,
+                    path=path+[index]))
+
+        return tuple(subschema)
+
+    elif isinstance(schema, str):
+        if schema.startswith('/'):  # this is a reference to another schema
+            local_path = schema.split('/')[1:]
+            reference = get_path(top_state, local_path)
+
+            set_path(
+                tree=top_state,
+                path=path,
+                value=reference)
+
+            return reference
+        else:
+            return schema
+    else:
+        return schema
+
+
 def deserialize_schema(schema, state, core):
-    return state
+    return recur_deserialize_schema(schema=state, core=core)
 
 
 # =========================
@@ -1366,7 +1456,7 @@ def slice_any(schema, state, path, core):
 
             step = state[head]
 
-        elif hasattr(state, head):
+        elif isinstance(head, str) and hasattr(state, head):
             step = getattr(state, head)
 
         if head in schema:
@@ -1548,6 +1638,8 @@ def slice_array(schema, state, path, core):
     if len(path) > 0:
         head = path[0]
         tail = path[1:]
+        if isinstance(head, str):
+            head = int(head)
         step = state[head]
 
         if isinstance(step, np.ndarray):
@@ -1624,6 +1716,15 @@ def bind_enum(schema, state, key, subschema, substate, core):
 
     return new_schema, tuple(open)
 
+def bind_array(schema, state, key, subschema, substate, core):
+    if state is None:
+        state = core.default(schema)
+    if isinstance(key, str):
+        key = int(key)
+    state[key] = substate
+
+    return schema, state
+
 
 # ==========================
 # Resolve Functions Overview
@@ -2050,6 +2151,8 @@ def generate_any(core, schema, state, top_schema=None, top_state=None, path=None
                 generated_state)
 
     else:
+        if not core.check(schema, state):
+            state = core.deserialize(schema, state)
         generated_schema, generated_state = schema, state
 
     return generated_schema, generated_state, top_schema, top_state
@@ -2065,10 +2168,6 @@ def default_quote(schema, core):
         return None
 
 
-def deserialize_quote(schema, state, core):
-    return state
-
-
 def generate_map(core, schema, state, top_schema=None, top_state=None, path=None):
     schema = schema or {}
     state = state or core.default(schema)
@@ -2311,9 +2410,45 @@ def sort_any(core, schema, state):
 
     return merged_schema, merged_state
 
+
 def sort_quote(core, schema, state):
     return schema, state
 
+
+def sort_map(core, schema, state):
+    if not isinstance(schema, dict):
+        schema = core.find(schema)
+    if not isinstance(state, dict):
+        return schema, state
+
+    merged_schema = {}
+    merged_state = {}
+
+    value_schema = core.find_parameter(
+        schema,
+        'value')
+
+    for key in union_keys(schema, state):
+        if is_schema_key(key):
+            if key in state:
+                merged_schema[key] = core.merge_schemas(
+                    schema.get(key, {}),
+                    state[key])
+            else:
+                merged_schema[key] = schema[key]
+        else:
+            subschema, merged_state[key] = core.sort(
+                schema.get(key, {}),
+                state.get(key, None))
+            if subschema:
+                value_schema = core.merge_schemas(
+                    value_schema,
+                    subschema)
+                # merged_schema[key] = subschema
+
+    return merged_schema, merged_state
+
+
 def find_union_type(core, schema, state):
     parameters = core.parameters_for(schema)
 
@@ -2573,6 +2708,7 @@ base_types = {
         '_slice': slice_map,
         '_fold': fold_map,
         '_divide': divide_map,
+        '_sort': sort_map,
         '_type_parameters': ['value'],
         '_description': 'flat mapping from keys of strings to values of any type'},
 
@@ -2602,6 +2738,7 @@ base_types = {
         '_deserialize': deserialize_array,
         '_dataclass': dataclass_array,
         '_resolve': resolve_array,
+        '_bind': bind_array,
         '_type_parameters': [
             'shape',
             'data'],

{bigraph-schema-0.0.54 → bigraph-schema-0.0.56}/bigraph_schema/type_system.py

@@ -349,20 +349,10 @@ class TypeSystem(Registry):
                 registry_type = self.retrieve(
                     schema['_type'])
 
-                # found = self.resolve(
-                #     registry_type,
-                #     schema)
-
                 found = self.merge_schemas(
                     registry_type,
                     schema)
 
-                # found = schema.copy()
-
-                # for key, value in registry_type.items():
-                #     if  key == '_type' or key not in found:
-                #         found[key] = value
-
             else:
                 found = {
                    key: self.access(
@@ -1610,7 +1600,7 @@ class TypeSystem(Registry):
                 if inner_view is not None:
                     result[port_key] = inner_view
         else:
-            raise Exception(f'trying to project state with these ports:\n{schema}\nbut not sure what these wires are:\n{wires}')
+            raise Exception(f'trying to view state with these ports:\n{schema}\nbut not sure what these wires are:\n{wires}')
 
         return result
 

{bigraph-schema-0.0.54 → bigraph-schema-0.0.56/bigraph_schema.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bigraph-schema
-Version: 0.0.54
+Version: 0.0.56
 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-0.0.54 → bigraph-schema-0.0.56}/bigraph_schema.egg-info/SOURCES.txt

@@ -1,15 +1,7 @@
-.gitignore
 AUTHORS.md
-CLA.md
-CODE_OF_CONDUCT.md
-CONTRIBUTING.md
 LICENSE
 README.md
-pytest.ini
-release.sh
 setup.py
-.github/workflows/notebook_to_html.yml
-.github/workflows/pytest.yml
 bigraph_schema/__init__.py
 bigraph_schema/edge.py
 bigraph_schema/parse.py
@@ -24,10 +16,4 @@ bigraph_schema.egg-info/PKG-INFO
 bigraph_schema.egg-info/SOURCES.txt
 bigraph_schema.egg-info/dependency_links.txt
 bigraph_schema.egg-info/requires.txt
-bigraph_schema.egg-info/top_level.txt
-notebooks/core.ipynb
-notebooks/demo.ipynb
-notebooks/images/place-link.png
-notebooks/images/reaction-after.png
-notebooks/images/reaction-before.png
-notebooks/images/redex-reactum.png
+bigraph_schema.egg-info/top_level.txt

{bigraph-schema-0.0.54 → bigraph-schema-0.0.56}/setup.py

@@ -1,7 +1,7 @@
 from setuptools import setup, find_packages
 
 
-VERSION = '0.0.54'
+VERSION = '0.0.56'
 
 
 with open("README.md", "r") as readme:

bigraph-schema-0.0.54/.github/workflows/notebook_to_html.yml

@@ -1,48 +0,0 @@
-name: Convert Jupyter Notebook to HTML
-
-on:
-  push:
-    paths:
-      - 'notebooks/demo.ipynb'
-      - 'notebooks/core.ipynb'
-
-jobs:
-  convert:
-    runs-on: ubuntu-latest
-    steps:
-    - name: Check out repository
-      uses: actions/checkout@main
-      with:
-        ref: main
-        fetch-depth: 0 # Fetch all history to have access to the gh-pages branch
-
-    - name: Set up Python
-      uses: actions/setup-python@main
-      with:
-        python-version: 3.x
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install nbconvert
-
-    - name: Convert Jupyter Notebook to HTML
-      run: |
-        jupyter nbconvert --to html notebooks/demo.ipynb
-        jupyter nbconvert --to html notebooks/core.ipynb
-
-    - name: Commit and push HTML to gh-pages branch
-      run: |
-        git config --local user.email "eagmon@github.com"
-        git config --local user.name "GitHub Action"
-        git fetch origin
-        mv notebooks/demo.html /tmp/demo.html
-        mv notebooks/core.html /tmp/core.html
-        git checkout gh-pages || git checkout -b gh-pages
-        git pull origin gh-pages
-        mv /tmp/demo.html notebooks/demo.html
-        mv /tmp/core.html notebooks/core.html 
-        git add notebooks/demo.html
-        git add notebooks/core.html
-        git diff-index --quiet HEAD || git commit -m "Update HTML files" 
-        git push origin gh-pages || true

bigraph-schema-0.0.54/.github/workflows/pytest.yml

@@ -1,29 +0,0 @@
-name: Run Pytest
-
-on:
-  pull_request:
-    branches:
-      - main
-
-jobs:
-  test:
-    runs-on: ubuntu-latest
-    steps:
-    - name: Check out repository
-      uses: actions/checkout@v2
-
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.x
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install pytest pytest-cov
-        pip install -e .
-
-    - name: Run pytest
-      run: |
-        pip install pytest
-        pytest --cov=bigraph_schema --cov-report=term

bigraph-schema-0.0.54/.gitignore

@@ -1,14 +0,0 @@
-*.out
-out/
-.idea/
-*-checkpoint.ipynb
-__pycache__
-.DS_Store
-.DS_Store?
-._*
-.python-version
-.pytest_cache
-lib/
-*.ipynb_checkpoints/
-dist/
-bigraph_schema.egg-info/

bigraph-schema-0.0.54/CLA.md

@@ -1,113 +0,0 @@
-# Individual Contributor License Agreement
-
-Thank you for your interest in Vivarium Core. To clarify the
-intellectual property license granted with Contributions from any person
-or entity, each Contribution must indicate each Contributor's agreement
-with the license terms below. This agreement is for your protection as a
-Contributor as well as the protection of the Vivarium Core authors
-(Authors) and Vivarium Core's users. It does not change your rights to
-use your own Contributions for any other purpose.
-
-You accept and agree to the following terms and conditions for Your
-Contributions (present and future) that you submit to the Authors.
-Except for the license granted herein to the Authors and recipients of
-software distributed by the Authors, You reserve all right, title, and
-interest in and to Your Contributions.
-
-1. Definitions
-
-   "You" (or "Your") shall mean the copyright owner or legal entity
-   authorized by the copyright owner that is making this Agreement with
-   the Authors. For legal entities, the entity making a Contribution and
-   all other entities that control, are controlled by, or are under
-   common control with that entity are considered to be a single
-   Contributor. For the purposes of this definition, "control" means (i)
-   the power, direct or indirect, to cause the direction or management
-   of such entity, whether by contract or otherwise, or (ii) ownership
-   of fifty percent (50%) or more of the outstanding shares, or (iii)
-   beneficial ownership of such entity.
-
-   "Contribution" shall mean any original work of authorship, including
-   any modifications or additions to an existing work, that is
-   intentionally submitted by You to the Authors for inclusion in, or
-   documentation of, any of the products owned or managed by the Authors
-   (the "Work"). For the purposes of this definition, "submitted" means
-   any form of electronic, verbal, or written communication sent to the
-   Authors or their representatives, including but not limited to
-   communication on electronic mailing lists, source code control
-   systems, and issue tracking systems that are managed by, or on behalf
-   of, the Authors for the purpose of discussing and improving the Work,
-   but excluding communication that is conspicuously marked or otherwise
-   designated in writing by You as "Not a Contribution."
-
-2. Grant of Copyright License. Subject to the terms and conditions of
-   this Agreement, You hereby grant to the Authors and to recipients
-   of software distributed by the Authors a perpetual, worldwide,
-   non-exclusive, no-charge, royalty-free, irrevocable copyright license
-   to reproduce, prepare derivative works of, publicly display, publicly
-   perform, sublicense, and distribute Your Contributions and such
-   derivative works.
-
-3. Grant of Patent License. Subject to the terms and conditions of this
-   Agreement, You hereby grant to the Authors and to recipients of
-   software distributed by the Authors a perpetual, worldwide,
-   non-exclusive, no-charge, royalty-free, irrevocable (except as stated
-   in this section) patent license to make, have made, use, offer to
-   sell, sell, import, and otherwise transfer the Work, where such
-   license applies only to those patent claims licensable by You that
-   are necessarily infringed by Your Contribution(s) alone or by
-   combination of Your Contribution(s) with the Work to which such
-   Contribution(s) was submitted. If any entity institutes patent
-   litigation against You or any other entity (including a cross-claim
-   or counterclaim in a lawsuit) alleging that your Contribution, or the
-   Work to which you have contributed, constitutes direct or
-   contributory patent infringement, then any patent licenses granted to
-   that entity under this Agreement for that Contribution or Work shall
-   terminate as of the date such litigation is filed.
-
-4. You represent that you are legally entitled to grant the above
-   license. If your employer(s) has rights to intellectual property that
-   you create that includes your Contributions, you represent that you
-   have received permission to make Contributions on behalf of that
-   employer, that your employer has waived such rights for your
-   Contributions to the Authors, or that your employer has executed a
-   separate Corporate CLA with the Authors.
-
-5. You represent that each of Your Contributions is Your original
-   creation (see section 7 for submissions on behalf of others). You
-   represent that Your Contribution submissions include complete details
-   of any third-party license or other restriction (including, but not
-   limited to, related patents and trademarks) of which you are
-   personally aware and which are associated with any part of Your
-   Contributions.
-
-6. You are not expected to provide support for Your Contributions,
-   except to the extent You desire to provide support. You may provide
-   support for free, for a fee, or not at all. Unless required by
-   applicable law or agreed to in writing, You provide Your
-   Contributions on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS
-   OF ANY KIND, either express or implied, including, without
-   limitation, any warranties or conditions of TITLE, NON- INFRINGEMENT,
-   MERCHANTABILITY, or FITNESS FOR A PARTICULAR PURPOSE.
-
-7. Should You wish to submit work that is not Your original creation,
-   You may submit it to the Authors separately from any Contribution,
-   identifying the complete details of its source and of any license or
-   other restriction (including, but not limited to, related patents,
-   trademarks, and license agreements) of which you are personally
-   aware, and conspicuously marking the work as "Submitted on behalf of
-   a third-party: [named here]".
-
-8. You agree to notify the Authors of any facts or circumstances of
-   which you become aware that would make these representations
-   inaccurate in any respect.
-
------------------------------------------------------------------------
-
-End of Contributor License Agreement
-
------------------------------------------------------------------------
-
-The text of this agreement was adapted from the Apache Software
-Foundation's [Individual Contributor License
-Agreement](https://apache.org/licenses/icla.pdf).

bigraph-schema-0.0.54/CODE_OF_CONDUCT.md

@@ -1,137 +0,0 @@
-# Code of Conduct
-
-## Our Pledge
-
-We as members, contributors, and leaders pledge to make participation in
-our community a harassment-free experience for everyone, regardless of
-age, body size, visible or invisible disability, ethnicity, sex
-characteristics, gender identity and expression, level of experience,
-education, socio-economic status, nationality, personal appearance,
-race, caste, color, religion, or sexual identity and orientation.
-
-We pledge to act and interact in ways that contribute to an open,
-welcoming, diverse, inclusive, and healthy community.
-
-## Our Standards
-
-Examples of behavior that contributes to a positive environment for our
-community include:
-
-* Demonstrating empathy and kindness toward other people
-* Being respectful of differing opinions, viewpoints, and experiences
-* Giving and gracefully accepting constructive feedback
-* Accepting responsibility and apologizing to those affected by our
-  mistakes, and learning from the experience
-* Focusing on what is best not just for us as individuals, but for the
-  overall community
-
-Examples of unacceptable behavior include:
-
-* The use of sexualized language or imagery, and sexual attention or
-  advances of any kind
-* Trolling, insulting or derogatory comments, and personal or political
-  attacks
-* Public or private harassment
-* Publishing others' private information, such as a physical or email
-  address, without their explicit permission
-* Other conduct which could reasonably be considered inappropriate in a
-  professional setting
-
-## Enforcement Responsibilities
-
-Community leaders are responsible for clarifying and enforcing our
-standards of acceptable behavior and will take appropriate and fair
-corrective action in response to any behavior that they deem
-inappropriate, threatening, offensive, or harmful.
-
-Community leaders have the right and responsibility to remove, edit, or
-reject comments, commits, code, wiki edits, issues, and other
-contributions that are not aligned to this Code of Conduct, and will
-communicate reasons for moderation decisions when appropriate.
-
-## Scope
-
-This Code of Conduct applies within all community spaces, and also
-applies when an individual is officially representing the community in
-public spaces. Examples of representing our community include using an
-official e-mail address, posting via an official social media account,
-or acting as an appointed representative at an online or offline event.
-
-## Enforcement
-
-Instances of abusive, harassing, or otherwise unacceptable behavior may
-be reported to the Authors at the email addresses in
-[`AUTHORS.md`](AUTHORS.md). All complaints will be reviewed and
-investigated promptly and fairly.
-
-All community leaders are obligated to respect the privacy and security
-of the reporter of any incident.
-
-## Enforcement Guidelines
-
-Community leaders will follow these Community Impact Guidelines in
-determining the consequences for any action they deem in violation of
-this Code of Conduct:
-
-### 1. Correction
-
-**Community Impact**: Use of inappropriate language or other behavior
-deemed unprofessional or unwelcome in the community.
-
-**Consequence**: A private, written warning from community leaders,
-providing clarity around the nature of the violation and an explanation
-of why the behavior was inappropriate. A public apology may be
-requested.
-
-### 2. Warning
-
-**Community Impact**: A violation through a single incident or series of
-actions.
-
-**Consequence**: A warning with consequences for continued behavior. No
-interaction with the people involved, including unsolicited interaction
-with those enforcing the Code of Conduct, for a specified period of
-time. This includes avoiding interactions in community spaces as well as
-external channels like social media. Violating these terms may lead to a
-temporary or permanent ban.
-
-### 3. Temporary Ban
-
-**Community Impact**: A serious violation of community standards,
-including sustained inappropriate behavior.
-
-**Consequence**: A temporary ban from any sort of interaction or public
-communication with the community for a specified period of time. No
-public or private interaction with the people involved, including
-unsolicited interaction with those enforcing the Code of Conduct, is
-allowed during this period. Violating these terms may lead to a
-permanent ban.
-
-### 4. Permanent Ban
-
-**Community Impact**: Demonstrating a pattern of violation of community
-standards, including sustained inappropriate behavior, harassment of an
-individual, or aggression toward or disparagement of classes of
-individuals.
-
-**Consequence**: A permanent ban from any sort of public interaction
-within the community.
-
-## Attribution
-
-This Code of Conduct is adapted from the [Contributor Covenant][homepage],
-version 2.1, available at
-[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
-
-Community Impact Guidelines were inspired by
-[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
-
-For answers to common questions about this code of conduct, see the FAQ at
-[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
-[https://www.contributor-covenant.org/translations][translations].
-
-[homepage]: https://www.contributor-covenant.org
-[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
-[Mozilla CoC]: https://github.com/mozilla/diversity
-[FAQ]: https://www.contributor-covenant.org/faq
-[translations]: https://www.contributor-covenant.org/translations