process-bigraph 0.0.42__tar.gz → 0.0.44__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (38) hide show
  1. {process-bigraph-0.0.42 → process_bigraph-0.0.44}/.gitignore +3 -1
  2. {process-bigraph-0.0.42/process_bigraph.egg-info → process_bigraph-0.0.44}/PKG-INFO +11 -18
  3. {process-bigraph-0.0.42 → process_bigraph-0.0.44}/process_bigraph/__init__.py +3 -2
  4. {process-bigraph-0.0.42 → process_bigraph-0.0.44}/process_bigraph/composite.py +241 -384
  5. {process-bigraph-0.0.42 → process_bigraph-0.0.44}/process_bigraph/emitter.py +2 -3
  6. process_bigraph-0.0.44/process_bigraph/process_types.py +473 -0
  7. {process-bigraph-0.0.42 → process_bigraph-0.0.44}/process_bigraph/processes/growth_division.py +5 -3
  8. {process-bigraph-0.0.42 → process_bigraph-0.0.44}/process_bigraph/tests.py +274 -16
  9. process_bigraph-0.0.44/process_bigraph/units.py +25 -0
  10. {process-bigraph-0.0.42 → process_bigraph-0.0.44/process_bigraph.egg-info}/PKG-INFO +11 -18
  11. {process-bigraph-0.0.42 → process_bigraph-0.0.44}/process_bigraph.egg-info/SOURCES.txt +1 -1
  12. process_bigraph-0.0.44/process_bigraph.egg-info/requires.txt +6 -0
  13. {process-bigraph-0.0.42 → process_bigraph-0.0.44}/pyproject.toml +7 -4
  14. {process-bigraph-0.0.42 → process_bigraph-0.0.44}/release.sh +18 -20
  15. process_bigraph-0.0.44/setup.py +10 -0
  16. process-bigraph-0.0.42/process_bigraph/process_types.py +0 -382
  17. process-bigraph-0.0.42/process_bigraph/protocols.py +0 -27
  18. process-bigraph-0.0.42/process_bigraph.egg-info/requires.txt +0 -3
  19. process-bigraph-0.0.42/setup.py +0 -57
  20. {process-bigraph-0.0.42 → process_bigraph-0.0.44}/.github/workflows/notebook_to_html.yml +0 -0
  21. {process-bigraph-0.0.42 → process_bigraph-0.0.44}/.github/workflows/pytest.yml +0 -0
  22. {process-bigraph-0.0.42 → process_bigraph-0.0.44}/AUTHORS.md +0 -0
  23. {process-bigraph-0.0.42 → process_bigraph-0.0.44}/CLA.md +0 -0
  24. {process-bigraph-0.0.42 → process_bigraph-0.0.44}/CODE_OF_CONDUCT.md +0 -0
  25. {process-bigraph-0.0.42 → process_bigraph-0.0.44}/CONTRIBUTING.md +0 -0
  26. {process-bigraph-0.0.42 → process_bigraph-0.0.44}/LICENSE +0 -0
  27. {process-bigraph-0.0.42 → process_bigraph-0.0.44}/README.md +0 -0
  28. {process-bigraph-0.0.42 → process_bigraph-0.0.44}/doc/_static/process-bigraph.png +0 -0
  29. {process-bigraph-0.0.42 → process_bigraph-0.0.44}/notebooks/process-bigraphs.ipynb +0 -0
  30. {process-bigraph-0.0.42 → process_bigraph-0.0.44}/notebooks/visualize_processes.ipynb +0 -0
  31. {process-bigraph-0.0.42 → process_bigraph-0.0.44}/process_bigraph/experiments/__init__.py +0 -0
  32. {process-bigraph-0.0.42 → process_bigraph-0.0.44}/process_bigraph/experiments/minimal_gillespie.py +0 -0
  33. {process-bigraph-0.0.42 → process_bigraph-0.0.44}/process_bigraph/processes/__init__.py +0 -0
  34. {process-bigraph-0.0.42 → process_bigraph-0.0.44}/process_bigraph/processes/parameter_scan.py +0 -0
  35. {process-bigraph-0.0.42 → process_bigraph-0.0.44}/process_bigraph.egg-info/dependency_links.txt +0 -0
  36. {process-bigraph-0.0.42 → process_bigraph-0.0.44}/process_bigraph.egg-info/top_level.txt +0 -0
  37. {process-bigraph-0.0.42 → process_bigraph-0.0.44}/pytest.ini +0 -0
  38. {process-bigraph-0.0.42 → process_bigraph-0.0.44}/setup.cfg +0 -0
{process-bigraph-0.0.42 → process_bigraph-0.0.44}/.gitignore RENAMED
@@ -12,4 +12,6 @@ venv/
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  process_bigraph.egg-info/
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  out/
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  .devenv*
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- devenv.lock
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+ devenv.lock
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+ containers/
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+ uv.lock
{process-bigraph-0.0.42/process_bigraph.egg-info → process_bigraph-0.0.44}/PKG-INFO RENAMED
@@ -1,25 +1,18 @@
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- Metadata-Version: 2.1
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+ Metadata-Version: 2.4
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  Name: process-bigraph
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- Version: 0.0.42
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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
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- Classifier: Development Status :: 3 - Alpha
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- Classifier: Intended Audience :: Developers
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- Classifier: License :: OSI Approved :: MIT License
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- Classifier: Operating System :: OS Independent
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- Classifier: Programming Language :: Python
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- Classifier: Programming Language :: Python :: 3
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- Classifier: Programming Language :: Python :: 3.6
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- Classifier: Programming Language :: Python :: 3.7
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- Classifier: Programming Language :: Python :: 3.8
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- Classifier: Programming Language :: Python :: 3.9
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- Classifier: Programming Language :: Python :: 3.10
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- Classifier: Programming Language :: Python :: 3.11
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- Requires-Python: >=3.6
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+ Version: 0.0.44
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+ Summary: protocol and execution for compositional systems biology
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+ Requires-Python: >=3.11
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  Description-Content-Type: text/markdown
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  License-File: LICENSE
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  License-File: AUTHORS.md
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+ Requires-Dist: bigraph-schema
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+ Requires-Dist: docker>=7.1.0
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+ Requires-Dist: ipdb>=0.13.13
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+ Requires-Dist: matplotlib
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+ Requires-Dist: pint>=0.24.4
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+ Requires-Dist: pytest
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+ Dynamic: license-file
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  # Process-Bigraph
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{process-bigraph-0.0.42 → process_bigraph-0.0.44}/process_bigraph/__init__.py RENAMED
@@ -1,9 +1,10 @@
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  import pprint
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  from bigraph_schema.registry import deep_merge, default
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  from process_bigraph.processes import register_processes
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- from process_bigraph.composite import Process, Step, Composite, interval_time_precision, ProcessTypes
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+ from process_bigraph.composite import Process, Step, Composite, interval_time_precision
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  from process_bigraph.emitter import Emitter, gather_emitter_results, generate_emitter_state, BASE_EMITTERS
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-
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+ from process_bigraph.process_types import ProcessTypes
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+ from process_bigraph.package.discover import discover_packages
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  pretty = pprint.PrettyPrinter(indent=2)
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