bigraph-schema 0.0.56__tar.gz → 0.0.58__tar.gz

bigraph-schema-0.0.58/.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-0.0.58/.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-0.0.58/.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-0.0.58/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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+   Contributions.
+
+6. You are not expected to provide support for Your Contributions,
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+
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+
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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-0.0.58/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-0.0.58/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-0.0.56/bigraph_schema.egg-info → bigraph-schema-0.0.58}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bigraph-schema
-Version: 0.0.56
+Version: 0.0.58
 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-0.0.56 → bigraph-schema-0.0.58}/bigraph_schema/registry.py

@@ -151,6 +151,52 @@ def set_path(tree, path, value, top=None, cursor=None):
     return tree
 
 
+def set_star_path(tree, path, value, top=None, cursor=()):
+    if tree is None:
+        tree = {}
+    if top is None:
+        top = tree
+    if path is None or len(path) == 0:
+        return tree
+    else:
+        if isinstance(path, str):
+            path = (path,)
+
+        head = path[0]
+        tail = path[1:]
+
+        if head == '..':
+            if len(cursor) == 0:
+                raise Exception(
+                    f'trying to travel above the top of the tree: {path}')
+            else:
+                return set_star_path(
+                    top,
+                    cursor[:-1],
+                    value)
+        elif head == '*':
+            for key in value:
+                tree[key] = set_star_path(
+                    {},
+                    tail,
+                    value[key],
+                    cursor=(key,))
+            return top
+        else:
+            if len(tail) == 0:
+                tree[head] = value
+                return top
+            else:
+                if head not in tree:
+                    tree[head] = {}
+                return set_star_path(
+                    tree[head],
+                    tail,
+                    value,
+                    top=top,
+                    cursor=tuple(cursor) + (head,))
+
+
 def transform_path(tree, path, transform):
     """
     Given a tree, a path, and a transform (function), mutate the tree by replacing the subtree at the path by whatever 

bigraph-schema-0.0.56/bigraph_schema/type_system_tests.py → bigraph-schema-0.0.58/bigraph_schema/tests.py

@@ -838,7 +838,7 @@ def test_inherits_from(core):
 
     assert core.inherits_from(
         'tree[path]',
-        'tree[list[string]]')
+        'tree[list[string~integer]]')
 
     assert not core.inherits_from(
         'tree[path]',
@@ -1861,6 +1861,7 @@ def test_star_path(core):
                 'green': 9999.4,
                 'yellow': 11,
                 'blue': 'umbrella'}}}
+
     # TODO: can you do everything the * is doing here with _path instead?
     nested_path = ['aaa', '*', 'green']
 
@@ -1873,6 +1874,51 @@ def test_star_path(core):
     assert state['ccc'] == 9999.4
 
 
+def test_star_view_project(core):
+    schema = {
+        'edges': 'map[edge[view:map[float],project:map[string]]]',
+        'stores': 'map[map[green:float|yellow:integer|blue:string]]'}
+
+    state = {
+        'edges': {
+            'edge': {
+                'inputs': {
+                    'view': ['..', 'stores', 'aaa', '*', 'green']},
+                'outputs': {
+                    'project': ['..', 'stores', 'aaa', '*', 'blue']}}},
+        'stores': {
+            'aaa': {
+                'bbb': {
+                    'green': 1.1,
+                    'yellow': 55,
+                    'blue': 'what'},
+                'ccc': {
+                    'green': 9999.4,
+                    'yellow': 11,
+                    'blue': 'umbrella'}}}}
+
+    edge_path = ['edges', 'edge']
+
+    view = core.view_edge(
+        schema,
+        state,
+        edge_path)
+
+    internal = {
+        'project': {
+            'bbb': 'everything',
+            'ccc': 'inside out'}}
+
+    project = core.project_edge(
+        schema,
+        state,
+        edge_path,
+        internal)
+
+    assert view['view']['bbb'] == state['stores']['aaa']['bbb']['green']
+    assert project['stores']['aaa']['ccc']['blue'] == internal['project']['ccc']
+
+
 def test_set_slice(core):
     float_schema, float_state = core.set_slice(
         'map[float]',
@@ -2342,8 +2388,6 @@ def fix_test_slice_edge(core):
 
     schema, state = core.generate(initial_schema, initial_state)
 
-    import ipdb; ipdb.set_trace()
-
     inner_schema, inner_state = core.slice(
         schema,
         state,
@@ -2381,6 +2425,58 @@ def fix_test_complex_wiring(core):
     assert state['AAAA']['AAAAA']['d'] == 0.0
 
 
+def test_tree_equivalence(core):
+    initial_state = {
+        'store1': {
+            'store1.1': '1.0'}}
+
+    # create a nested store type and register it
+    store11 = {
+        'store1.1': {
+            '_type': 'float',
+            '_default': '1.0'}}
+
+    core.register('store1.1', store11)
+
+    # create a tree schema that uses this type
+    store_tree = {
+        '_type': 'tree',
+        '_leaf': 'store1.1'}
+
+    # interpret the state as a simple tree of float
+    store_schema, store_state = core.generate(
+        'tree[float]',
+        initial_state)
+
+    # use the nested type to fill in the state
+    tree_schema, tree_state = core.generate(
+        store_tree,
+        {'store1': None})
+
+    # use the nested type but with an empty dict instead
+    fill_schema, fill_state = core.generate(
+        store_tree,
+        {'store1': {}})
+
+    # supply the whole schema at once instead of registering
+    inline_schema, inline_state = core.generate({
+        '_type': 'tree',
+        '_leaf': {
+            'store1.1': {
+                '_type': 'float',
+                '_default': '1.0'}}},
+        {'store1': {}})
+
+    # here is the state we expect from each of these calls
+    # to generate
+    target_state = {
+        'store1': {
+            'store1.1': 1.0}}
+
+    # all of the resulting generated states are the same
+    assert store_state == tree_state == fill_state == inline_state == target_state
+
+
 if __name__ == '__main__':
     core = TypeSystem()
     core = register_test_types(core)
@@ -2432,5 +2528,8 @@ if __name__ == '__main__':
     test_merge(core)
     test_remove_omitted(core)
     test_union_key_error(core)
+    test_tree_equivalence(core)
+    test_star_view_project(core)
+
     # test_slice_edge(core)
     # test_complex_wiring(core)