process-bigraph 0.0.30__tar.gz → 0.0.32__tar.gz

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Files changed (33) hide show
  1. {process-bigraph-0.0.30/process_bigraph.egg-info → process-bigraph-0.0.32}/PKG-INFO +1 -1
  2. {process-bigraph-0.0.30 → process-bigraph-0.0.32}/process_bigraph/composite.py +6 -2
  3. {process-bigraph-0.0.30 → process-bigraph-0.0.32}/process_bigraph/process_types.py +6 -8
  4. {process-bigraph-0.0.30 → process-bigraph-0.0.32/process_bigraph.egg-info}/PKG-INFO +1 -1
  5. {process-bigraph-0.0.30 → process-bigraph-0.0.32}/setup.py +1 -1
  6. {process-bigraph-0.0.30 → process-bigraph-0.0.32}/.github/workflows/notebook_to_html.yml +0 -0
  7. {process-bigraph-0.0.30 → process-bigraph-0.0.32}/.github/workflows/pytest.yml +0 -0
  8. {process-bigraph-0.0.30 → process-bigraph-0.0.32}/.gitignore +0 -0
  9. {process-bigraph-0.0.30 → process-bigraph-0.0.32}/AUTHORS.md +0 -0
  10. {process-bigraph-0.0.30 → process-bigraph-0.0.32}/CLA.md +0 -0
  11. {process-bigraph-0.0.30 → process-bigraph-0.0.32}/CODE_OF_CONDUCT.md +0 -0
  12. {process-bigraph-0.0.30 → process-bigraph-0.0.32}/CONTRIBUTING.md +0 -0
  13. {process-bigraph-0.0.30 → process-bigraph-0.0.32}/LICENSE +0 -0
  14. {process-bigraph-0.0.30 → process-bigraph-0.0.32}/README.md +0 -0
  15. {process-bigraph-0.0.30 → process-bigraph-0.0.32}/doc/_static/process-bigraph.png +0 -0
  16. {process-bigraph-0.0.30 → process-bigraph-0.0.32}/notebooks/process-bigraphs.ipynb +0 -0
  17. {process-bigraph-0.0.30 → process-bigraph-0.0.32}/notebooks/visualize_processes.ipynb +0 -0
  18. {process-bigraph-0.0.30 → process-bigraph-0.0.32}/process_bigraph/__init__.py +0 -0
  19. {process-bigraph-0.0.30 → process-bigraph-0.0.32}/process_bigraph/emitter.py +0 -0
  20. {process-bigraph-0.0.30 → process-bigraph-0.0.32}/process_bigraph/experiments/__init__.py +0 -0
  21. {process-bigraph-0.0.30 → process-bigraph-0.0.32}/process_bigraph/experiments/minimal_gillespie.py +0 -0
  22. {process-bigraph-0.0.30 → process-bigraph-0.0.32}/process_bigraph/processes/__init__.py +0 -0
  23. {process-bigraph-0.0.30 → process-bigraph-0.0.32}/process_bigraph/processes/growth_division.py +0 -0
  24. {process-bigraph-0.0.30 → process-bigraph-0.0.32}/process_bigraph/processes/parameter_scan.py +0 -0
  25. {process-bigraph-0.0.30 → process-bigraph-0.0.32}/process_bigraph/protocols.py +0 -0
  26. {process-bigraph-0.0.30 → process-bigraph-0.0.32}/process_bigraph/tests.py +0 -0
  27. {process-bigraph-0.0.30 → process-bigraph-0.0.32}/process_bigraph.egg-info/SOURCES.txt +0 -0
  28. {process-bigraph-0.0.30 → process-bigraph-0.0.32}/process_bigraph.egg-info/dependency_links.txt +0 -0
  29. {process-bigraph-0.0.30 → process-bigraph-0.0.32}/process_bigraph.egg-info/requires.txt +0 -0
  30. {process-bigraph-0.0.30 → process-bigraph-0.0.32}/process_bigraph.egg-info/top_level.txt +0 -0
  31. {process-bigraph-0.0.30 → process-bigraph-0.0.32}/pytest.ini +0 -0
  32. {process-bigraph-0.0.30 → process-bigraph-0.0.32}/release.sh +0 -0
  33. {process-bigraph-0.0.30 → process-bigraph-0.0.32}/setup.cfg +0 -0
{process-bigraph-0.0.30/process_bigraph.egg-info → process-bigraph-0.0.32}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: process-bigraph
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- Version: 0.0.30
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+ Version: 0.0.32
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  Home-page: https://github.com/vivarium-collective/process-bigraph
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  Author: Ryan Spangler, Eran Agmon
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  Author-email: ryan.spangler@gmail.com, agmon.eran@gmail.com
{process-bigraph-0.0.30 → process-bigraph-0.0.32}/process_bigraph/composite.py RENAMED
@@ -450,10 +450,14 @@ class Composite(Process):
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  raise Exception(
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  f'initial state from edge does not match initial state from other edges:\n{path}\n{edge}\n{edge_state}')
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- self.state = deep_merge(
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- self.state,
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+ self.merge(
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+ self.composition,
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  edge_state)
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+ # self.state = deep_merge(
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+ # self.state,
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+ # edge_state)
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+
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  # TODO: call validate on this composite, not just check
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  # assert self.core.validate(
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  # self.composition,
{process-bigraph-0.0.30 → process-bigraph-0.0.32}/process_bigraph/process_types.py RENAMED
@@ -112,10 +112,8 @@ def deserialize_process(schema, encoded, core):
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  encoded = encoded or {}
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  schema = schema or {}
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- if not encoded:
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- deserialized = core.default(schema)
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- else:
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- deserialized = encoded
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+ default = core.default(schema)
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+ deserialized = deep_merge(default, encoded)
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  if not deserialized.get('address'):
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  return deserialized
@@ -153,6 +151,8 @@ def deserialize_process(schema, encoded, core):
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  core=core)
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  deserialized['instance'] = process
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+ else:
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+ process = deserialized['instance']
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  # TODO: this mutating the original value directly into
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  # the return value is weird (?)
@@ -181,10 +181,8 @@ def deserialize_process(schema, encoded, core):
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  def deserialize_step(schema, encoded, core):
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- if not encoded:
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- deserialized = core.default(schema)
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- else:
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- deserialized = copy.deepcopy(encoded)
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+ default = core.default(schema)
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+ deserialized = deep_merge(default, encoded)
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  if not deserialized['address']:
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  return deserialized
{process-bigraph-0.0.30 → process-bigraph-0.0.32/process_bigraph.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: process-bigraph
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- Version: 0.0.30
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+ Version: 0.0.32
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  Home-page: https://github.com/vivarium-collective/process-bigraph
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  Author: Ryan Spangler, Eran Agmon
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  Author-email: ryan.spangler@gmail.com, agmon.eran@gmail.com
{process-bigraph-0.0.30 → process-bigraph-0.0.32}/setup.py RENAMED
@@ -2,7 +2,7 @@ import re
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  from setuptools import setup, find_packages
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- VERSION = '0.0.30'
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+ VERSION = '0.0.32'
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  with open("README.md", "r") as readme: