bigraph-schema 0.0.57__tar.gz → 0.0.59__tar.gz

bigraph-schema-0.0.59/.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-0.0.59/.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-0.0.59/.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-0.0.59/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
+   the Authors. For legal entities, the entity making a Contribution and
+   all other entities that control, are controlled by, or are under
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+   of fifty percent (50%) or more of the outstanding shares, or (iii)
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+
+   "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
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+   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
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+   or counterclaim in a lawsuit) alleging that your Contribution, or the
+   Work to which you have contributed, constitutes direct or
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+   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
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+   you create that includes your Contributions, you represent that you
+   have received permission to make Contributions on behalf of that
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+   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-0.0.59/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-0.0.59/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-0.0.57/bigraph_schema.egg-info → bigraph-schema-0.0.59}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bigraph-schema
-Version: 0.0.57
+Version: 0.0.59
 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-0.0.57 → bigraph-schema-0.0.59}/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-0.0.57 → bigraph-schema-0.0.59}/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-0.0.57 → bigraph-schema-0.0.59}/bigraph_schema/tests.py

@@ -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]',
@@ -2483,5 +2529,7 @@ if __name__ == '__main__':
     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)

{bigraph-schema-0.0.57 → bigraph-schema-0.0.59}/bigraph_schema/type_functions.py

@@ -292,6 +292,9 @@ def apply_list(schema, current, update, top_schema, top_state, path, core):
         raise Exception(f'trying to apply an update to an existing list, but the update is not a list or of element type:\n  update: {update}\n  element type: {pf(element_type)}')
 
 def apply_map(schema, current, update, top_schema, top_state, path, core=None):
+    if update is None:
+        return current
+
     if not isinstance(current, dict):
         raise Exception(f'trying to apply an update to a value that is not a map:\n  value: {current}\n  update: {update}')
     if not isinstance(update, dict):

{bigraph-schema-0.0.57 → bigraph-schema-0.0.59}/bigraph_schema/type_system.py

@@ -14,7 +14,7 @@ from pprint import pformat as pf
 from bigraph_schema import Registry, non_schema_keys, is_schema_key, deep_merge, type_parameter_key
 from bigraph_schema.parse import parse_expression
 from bigraph_schema.utilities import union_keys
-from bigraph_schema.registry import remove_omitted, set_path, transform_path
+from bigraph_schema.registry import remove_omitted, set_path, transform_path, set_star_path
 
 from bigraph_schema.type_functions import (
     registry_types, base_types, unit_types, register_base_reactions, is_empty, apply_schema, set_apply)
@@ -1366,23 +1366,55 @@ class TypeSystem(Registry):
                 state,
                 head)
 
-            try:
-                result_schema, result_state = self.set_slice(
-                    down_schema,
-                    down_state,
-                    tail,
-                    target_schema,
-                    target_state,
-                    defer=defer)
-            except Exception as e:
-                raise Exception(f'failed to set_slice at path {path}\n{str(e)}')
+            if head == '*':
+                result_schema, result_state = down_schema, down_state
+                for key in down_state:
+                    if key in target_state:
+                        subtarget_schema, subtarget_state = self.slice(
+                            target_schema,
+                            target_state,
+                            key)
+
+                        try:
+                            result_schema, result_state = self.set_slice(
+                                result_schema,
+                                result_state,
+                                tail,
+                                subtarget_schema,
+                                subtarget_state,
+                                defer=defer)
+
+                        except Exception as e:
+                            raise Exception(
+                                f'failed to set_slice at path {path}\n{str(e)}')
 
-            return self.bind(
-                schema,
-                state,
-                head,
-                result_schema,
-                result_state)
+                        schema, state = self.bind(
+                            schema,
+                            state,
+                            key,
+                            result_schema,
+                            result_state)
+
+                return schema, state
+
+            else:
+                try:
+                    result_schema, result_state = self.set_slice(
+                        down_schema,
+                        down_state,
+                        tail,
+                        target_schema,
+                        target_state,
+                        defer=defer)
+                except Exception as e:
+                    raise Exception(f'failed to set_slice at path {path}\n{str(e)}')
+
+                return self.bind(
+                    schema,
+                    state,
+                    head,
+                    result_schema,
+                    result_state)
 
 
     def serialize(self, schema, state):
@@ -1634,7 +1666,7 @@ class TypeSystem(Registry):
 
         if isinstance(wires, (list, tuple)):
             destination = resolve_path(list(path) + list(wires))
-            result = set_path(
+            result = set_star_path(
                 result,
                 destination,
                 states)

{bigraph-schema-0.0.57 → bigraph-schema-0.0.59/bigraph_schema.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bigraph-schema
-Version: 0.0.57
+Version: 0.0.59
 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-0.0.57 → bigraph-schema-0.0.59}/bigraph_schema.egg-info/SOURCES.txt

@@ -1,7 +1,15 @@
+.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
@@ -16,4 +24,10 @@ 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
+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