bigraph-schema 0.0.35__tar.gz → 0.0.38__tar.gz

bigraph-schema-0.0.38/.github/workflows/notebook_to_html.yml

@@ -0,0 +1,48 @@
+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-0.0.38/.github/workflows/pytest.yml

@@ -0,0 +1,29 @@
+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-0.0.38/.gitignore

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

bigraph-schema-0.0.38/CLA.md

@@ -0,0 +1,113 @@
+# 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
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+
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+
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+   this Agreement, You hereby grant to the Authors and to recipients
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+
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+   in this section) patent license to make, have made, use, offer to
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+   are necessarily infringed by Your Contribution(s) alone or by
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+
+4. You represent that you are legally entitled to grant the above
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+
+5. You represent that each of Your Contributions is Your original
+   creation (see section 7 for submissions on behalf of others). You
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+   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
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+
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+   other restriction (including, but not limited to, related patents,
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+
+8. You agree to notify the Authors of any facts or circumstances of
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+
+-----------------------------------------------------------------------
+
+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-0.0.38/CODE_OF_CONDUCT.md

@@ -0,0 +1,137 @@
+# 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

bigraph-schema-0.0.38/CONTRIBUTING.md

@@ -0,0 +1,44 @@
+# Contributing to Bigraph-Schema
+
+## Making a Contribution
+
+Thank you for your interest in contributing to Vivarium Core! Here's how
+you can get started:
+
+1. Review the [Contributor License Agreement](CLA.md) (CLA). Whenever
+   you submit a contribution to Vivarium Core, you are agreeing to the
+   CLA, which grants us rights to use your contribution. You don't need
+   to do anything special to "sign" the CLA. Instead, opening a pull
+   request indicates your agreement to the CLA.
+2. [Optional] If you want to make a contribution that isn't covered by
+   an existing issue, go ahead an open a new one!
+3. Once you have found or created an issue that describes the
+   contribution you want to make, wait to get feedback from the project
+   maintainers.
+4. If the project maintainers agree that your proposal makes sense, you
+   can fork the repository, make your changes, and open a pull request.
+   If you haven't done this before, check out [GitHub's guide to open
+   source
+   contributions](https://docs.github.com/en/get-started/quickstart/contributing-to-projects).
+5. Wait to get feedback from the project maintainers and then address
+   any review comments they leave. Once your pull request is approved,
+   the project maintainers will merge it.
+
+## Contacting Us
+
+* To request features or report bugs, please open an
+  [issue](https://github.com/vivarium-collective/bigraph-schema/issues).
+* To ask questions or request help, please open a [discussion
+  thread](https://github.com/vivarium-collective/bigraph-schema/discussions).
+* To contact the maintainers privately, for example to report a
+  violation of our [code of conduct](CODE_OF_CONDUCT.md) or to notify us
+  of a security issue, you can use the contact information in the
+  [`AUTHORS.md` file](AUTHORS.md).
+
+## Code of Conduct
+
+We expect kindness and respect in all interactions with the Vivarium
+Collective community. Harassing or insulting behavior is not welcome and will
+result in enforcement actions. Please review our [code of
+conduct](CODE_OF_CONDUCT.md), which describes our expectations and
+enforcement actions in more detail.

{bigraph-schema-0.0.35/bigraph_schema.egg-info → bigraph-schema-0.0.38}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bigraph-schema
-Version: 0.0.35
+Version: 0.0.38
 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-0.0.38/bigraph_schema/data.py

@@ -0,0 +1 @@
+

{bigraph-schema-0.0.35 → bigraph-schema-0.0.38}/bigraph_schema/registry.py

@@ -13,9 +13,12 @@ import traceback
 import numpy as np
 
 from pprint import pformat as pf
+from typing import Any, Tuple, Union, Optional, Mapping
+from dataclasses import field, make_dataclass
 
 from bigraph_schema.parse import parse_expression
 from bigraph_schema.protocols import local_lookup_module, function_module
+import bigraph_schema.data
 
 
 NONE_SYMBOL = '!nil'
@@ -525,6 +528,34 @@ def fold_union(schema, state, method, values, core):
     return result
 
 
+def type_parameters_for(schema):
+    parameters = []
+    for key in schema['_type_parameters']:
+        subschema = schema.get(f'_{key}', 'any')
+        parameters.append(subschema)
+
+    return parameters
+
+
+def dataclass_union(schema, path, core):
+    parameters = type_parameters_for(schema)
+    subtypes = []
+    for parameter in parameters:
+        dataclass = core.dataclass(
+            parameter,
+            path)
+
+        if isinstance(dataclass, str):
+            subtypes.append(dataclass)
+        elif isinstance(dataclass, type):
+            subtypes.append(dataclass.__name__)
+        else:
+            subtypes.append(str(dataclass))
+
+    parameter_block = ', '.join(subtypes)
+    return eval(f'Union[{parameter_block}]')
+
+
 def divide_any(schema, state, values, core):
     divisions = values.get('divisions', 2)
 
@@ -551,6 +582,92 @@ def divide_any(schema, state, values, core):
             for _ in range(divisions)]
 
 
+def is_schema_key(schema, key):
+    return key.strip('_') not in schema.get('_type_parameters', []) and key.startswith('_')
+
+
+def resolve_any(schema, update, core):
+    outcome = schema.copy()
+
+    for key, subschema in update.items():
+        if key == '_type' and key in outcome:
+            if outcome[key] != subschema:
+                if core.inherits_from(outcome[key], subschema):
+                    continue
+                elif core.inherits_from(subschema, outcome[key]):
+                    outcome[key] = subschema
+                else:
+                    raise Exception(f'cannot resolve types when updating\ncurrent type: {schema}\nupdate type: {update}')
+
+        elif not key in outcome or is_schema_key(update, key):
+            if subschema:
+                outcome[key] = subschema
+        else:
+            outcome[key] = core.resolve_schemas(
+                outcome.get(key),
+                subschema)
+
+    return outcome
+
+
+def dataclass_any(schema, path, core):
+    parts = path
+    if not parts:
+        parts = ['top']
+    dataclass_name = '_'.join(parts)
+
+    if isinstance(schema, dict):
+        type_name = schema.get('_type', 'any')
+
+        branches = {}
+        for key, subschema in schema.items():
+            if not key.startswith('_'):
+                branch = core.dataclass(
+                    subschema,
+                    path + [key])
+
+                def default(subschema=subschema):
+                    return core.default(subschema)
+
+                branches[key] = (
+                    key,
+                    branch,
+                    field(default_factory=default))
+
+        dataclass = make_dataclass(
+            dataclass_name,
+            branches.values(),
+            namespace={
+                '__module__': 'bigraph_schema.data'})
+
+        setattr(
+            bigraph_schema.data,
+            dataclass_name,
+            dataclass)
+
+    else:
+        schema = core.access(schema)
+        dataclass = core.dataclass(schema, path)
+
+    return dataclass
+
+
+def dataclass_tuple(schema, path, core):
+    parameters = type_parameters_for(schema)
+    subtypes = []
+
+    for index, key in enumerate(schema['type_parameters']):
+        subschema = schema.get(key, 'any')
+        subtype = core.dataclass(
+            subschema,
+            path + [index])
+
+        subtypes.append(subtype)
+
+    parameter_block = ', '.join(subtypes)
+    return eval(f'tuple[{parameter_block}]')
+
+
 def divide_tuple(schema, state, values, core):
     divisions = values.get('divisions', 2)
 
@@ -740,10 +857,13 @@ def merge_any(schema, current_state, new_state, core):
     elif isinstance(new_state, dict):
         if isinstance(current_state, dict):
             for key, value in new_state.items():
-                current_state[key] = core.merge(
-                    schema.get(key),
-                    current_state.get(key),
-                    value)
+                if key.startswith('_'):
+                    current_state[key] = value
+                else:
+                    current_state[key] = core.merge(
+                        schema.get(key),
+                        current_state.get(key),
+                        value)
             return current_state
         else:
             return new_state
@@ -954,6 +1074,8 @@ registry_types = {
         '_check': check_any,
         '_serialize': serialize_any,
         '_deserialize': deserialize_any,
+        '_dataclass': dataclass_any,
+        '_resolve': resolve_any,
         '_fold': fold_any,
         '_merge': merge_any,
         '_bind': bind_any,
@@ -967,6 +1089,7 @@ registry_types = {
         '_slice': slice_tuple,
         '_serialize': serialize_tuple,
         '_deserialize': deserialize_tuple,
+        '_dataclass': dataclass_tuple,
         '_fold': fold_tuple,
         '_divide': divide_tuple,
         '_bind': bind_tuple,
@@ -980,6 +1103,7 @@ registry_types = {
         '_slice': slice_union,
         '_serialize': serialize_union,
         '_deserialize': deserialize_union,
+        '_dataclass': dataclass_union,
         '_fold': fold_union,
         '_description': 'union of a set of possible types'}}