CodeEntropy 2.7.0__py3-none-any.whl → 2.7.1__py3-none-any.whl

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Files changed (9) hide show
  1. CodeEntropy/__init__.py +1 -1
  2. CodeEntropy/config/argparse.py +9 -1
  3. CodeEntropy/entropy/water.py +11 -5
  4. CodeEntropy/entropy/workflow.py +6 -1
  5. {codeentropy-2.7.0.dist-info → codeentropy-2.7.1.dist-info}/METADATA +7 -8
  6. {codeentropy-2.7.0.dist-info → codeentropy-2.7.1.dist-info}/RECORD +9 -9
  7. {codeentropy-2.7.0.dist-info → codeentropy-2.7.1.dist-info}/WHEEL +1 -1
  8. {codeentropy-2.7.0.dist-info → codeentropy-2.7.1.dist-info}/entry_points.txt +0 -0
  9. {codeentropy-2.7.0.dist-info → codeentropy-2.7.1.dist-info}/licenses/LICENSE +0 -0
CodeEntropy/__init__.py CHANGED
@@ -8,4 +8,4 @@ entropy estimates, supporting a wide range of applications in molecular simulati
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  and statistical mechanics.
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  """
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- __version__ = "2.7.0"
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+ __version__ = "2.7.1"
CodeEntropy/config/argparse.py CHANGED
@@ -129,9 +129,17 @@ ARG_SPECS: dict[str, ArgSpec] = {
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  help="Force partitioning",
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  ),
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  "water_entropy": ArgSpec(
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+ type=bool,
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+ default=False,
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+ help="If set to True, enables the calculation of water entropy",
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+ ),
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+ "water_entropy_parallel": ArgSpec(
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  type=bool,
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  default=True,
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- help="If set to False, disables the calculation of water entropy",
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+ help=(
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+ "If set to False, disables the parallel calculation of "
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+ "water entropy and switches to serial"
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+ ),
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  ),
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  "grouping": ArgSpec(
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  type=str,
CodeEntropy/entropy/water.py CHANGED
@@ -35,6 +35,7 @@ class WaterEntropyInput:
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  end: int
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  step: int
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  temperature: float
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+ parallel: bool
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  group_id: int | None = None
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@@ -53,7 +54,7 @@ class WaterEntropy:
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  self,
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  args: Any,
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  reporter: Any,
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- solver: Callable[..., tuple[dict, Any, Any, Any, Any]] = (
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+ solver: Callable[..., tuple[dict, Any, Any, Any, Any, Any]] = (
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  GetSolvent.get_interfacial_water_orient_entropy
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  ),
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  ) -> None:
@@ -77,6 +78,7 @@ class WaterEntropy:
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  start: int,
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  end: int,
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  step: int,
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+ parallel: bool,
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  group_id: int | None = None,
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  ) -> None:
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  """Compute water entropy and write results to the data logger.
@@ -95,6 +97,7 @@ class WaterEntropy:
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  step=step,
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  temperature=float(self._args.temperature),
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  group_id=group_id,
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+ parallel=parallel,
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  )
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  self._calculate_and_log_from_inputs(inputs)
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@@ -119,10 +122,12 @@ class WaterEntropy:
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  Tuple of solver outputs.
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  """
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  logger.info(
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- "[WaterEntropy] Computing water entropy (start=%s, end=%s, step=%s)",
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+ "[WaterEntropy] Computing water entropy (start=%s, end=%s, step=%s, "
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+ "parallel=%s)",
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  inputs.start,
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  inputs.end,
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  inputs.step,
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+ inputs.parallel,
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  )
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  return self._solver(
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  inputs.universe,
@@ -130,7 +135,7 @@ class WaterEntropy:
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  inputs.end,
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  inputs.step,
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  inputs.temperature,
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- parallel=True,
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+ inputs.parallel,
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  )
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  def _log_orientational_entropy(
@@ -144,8 +149,9 @@ class WaterEntropy:
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  """
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  for _resid, resname_dict in Sorient_dict.items():
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  for resname, values in resname_dict.items():
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- if isinstance(values, list) and len(values) == 2:
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- entropy, count = values
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+ if isinstance(values, dict):
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+ entropy = values["Sorient_Nw_ave"]
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+ count = values["tot_count"]
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  self._reporter.add_residue_data(
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  group_id, resname, "Water", "Orientational", count, entropy
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  )
CodeEntropy/entropy/workflow.py CHANGED
@@ -105,7 +105,11 @@ class EntropyWorkflow:
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  reduced_universe, groups
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  )
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- if self._args.water_entropy and water_groups and nonwater_groups:
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+ if self._args.water_entropy and water_groups:
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+ if not nonwater_groups:
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+ logger.warning(
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+ "You are running waterEntropy on bulk water, this will be slow!"
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+ )
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  self._compute_water_entropy(frame_selection, water_groups)
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  else:
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  nonwater_groups.update(water_groups)
@@ -394,6 +398,7 @@ class EntropyWorkflow:
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  start=start,
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  end=end,
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  step=step,
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+ parallel=self._args.water_entropy_parallel,
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  group_id=group_id,
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  )
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{codeentropy-2.7.0.dist-info → codeentropy-2.7.1.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.5
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  Name: CodeEntropy
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- Version: 2.7.0
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+ Version: 2.7.1
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  Summary: CodeEntropy is a Python package for computing the configurational entropy of macromolecular systems using forces sampled from molecular dynamics (MD) simulations. It implements the multiscale cell correlation method to provide accurate and efficient entropy estimates, supporting a wide range of applications in molecular simulation and statistical mechanics.
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  Keywords: entropy,macromolecular systems,MD simulation
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  Author-email: Arghya 'Argo' Chakravorty <arghyac@umich.edu>, Donald Chung-HK <donald.chung@stfc.ac.uk>, Sarah Fegan <sarah.fegan@stfc.ac.uk>, James Gebbie-Rayet <james.gebbie@stfc.ac.uk>, Sarah Harris <sarah.harris@sheffield.ac.uk>, Richard Henchman <rhen7213@uni.sydney.edu.au>, Jonathan Higham <j.higham4@lancaster.ac.uk>, Jas Kalayan <jas.kalayan@stfc.ac.uk>, Ioana Papa <iapapa1@sheffield.ac.uk>
@@ -24,7 +24,7 @@ Requires-Dist: PyYAML>=6.0.3,<7.0
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  Requires-Dist: rich>=13.0.0,<16.0
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  Requires-Dist: art>=5.0,<7.0
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  Requires-Dist: networkx>=2.8,<4.0
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- Requires-Dist: waterEntropy>=2,<3.0
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+ Requires-Dist: waterEntropy>=2.3.0,<3.0
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  Requires-Dist: requests>=2.32.2,<3.0
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  Requires-Dist: rdkit>=2025.3.4,<2027
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  Requires-Dist: numba>=0.63.0,<0.70
@@ -32,9 +32,8 @@ Requires-Dist: dask>=2025.7.0,<2027.1.0
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  Requires-Dist: dask-jobqueue>=0.9.0,<1.0
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  Requires-Dist: distributed>=2025.7.0,<2027.1.0
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  Requires-Dist: sphinx>=8.0.0,<10.0 ; extra == "docs"
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- Requires-Dist: nbsphinx>=0.9.3,<1.0 ; extra == "docs"
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- Requires-Dist: sphinx_copybutton>=0.5,<1.0 ; extra == "docs"
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- Requires-Dist: furo>=2025.12.19,<2026.0 ; extra == "docs"
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+ Requires-Dist: sphinx-autoapi>=3.8,<4.0 ; extra == "docs"
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+ Requires-Dist: ccpbiosim-sphinx-theme>=1.3.0,<1.4.0 ; extra == "docs"
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  Requires-Dist: markupsafe>=3.0,<4.0 ; extra == "docs"
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  Requires-Dist: pre-commit>=3.5.0,<5.0 ; extra == "pre-commit"
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  Requires-Dist: ruff>=0.15.2,<1.0 ; extra == "pre-commit"
@@ -56,7 +55,7 @@ CodeEntropy
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  | Category | Badges |
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  |----------------|--------|
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- | **Build** | [![PR Checks](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/pr.yaml/badge.svg)](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/pr.yaml) [![Daily Tests](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/daily.yaml/badge.svg)](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/daily.yaml) [![Dependency Floors](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/dependency-floors.yaml/badge.svg)](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/dependency-floors.yaml) |
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+ | **Build** | [![PR Checks](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/pr.yaml/badge.svg)](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/pr.yaml) [![Weekly Tests](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/weekly-tests.yaml/badge.svg)](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/weekly-tests.yaml) |
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  | **Regression** | [![Weekly Regression](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/weekly-regression.yaml/badge.svg)](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/weekly-regression.yaml) |
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  | **Documentation** | [![Weekly Docs](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/weekly-docs.yaml/badge.svg)](https://github.com/CCPBioSim/CodeEntropy/actions/workflows/weekly-docs.yaml) [![Docs - Status](https://app.readthedocs.org/projects/codeentropy/badge/?version=latest)](https://codeentropy.readthedocs.io/en/latest/?badge=latest) |
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  | **Citation** | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17570721.svg)](https://doi.org/10.5281/zenodo.17570721) |
@@ -67,8 +66,8 @@ CodeEntropy
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  CodeEntropy is a Python package for computing the configurational entropy of macromolecular systems using forces sampled from molecular dynamics (MD) simulations. It implements the multiscale cell correlation method to provide accurate and efficient entropy estimates, supporting a wide range of applications in molecular simulation and statistical mechanics.
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  <p align="center">
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- <img src="docs/_static/logos/biosim-codeentropy_logo_light.png#gh-dark-mode-only" alt="CodeEntropy logo" width="300"/>
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- <img src="docs/_static/logos/biosim-codeentropy_logo_dark.png#gh-light-mode-only" alt="CodeEntropy logo" width="300"/>
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+ <img src="docs/source/_static/logos/biosim-codeentropy_logo_light.png#gh-dark-mode-only" alt="CodeEntropy logo" width="300"/>
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+ <img src="docs/source/_static/logos/biosim-codeentropy_logo_dark.png#gh-light-mode-only" alt="CodeEntropy logo" width="300"/>
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  </p>
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  See [CodeEntropy’s documentation](https://codeentropy.readthedocs.io/en/latest/) for more information.
{codeentropy-2.7.0.dist-info → codeentropy-2.7.1.dist-info}/RECORD RENAMED
@@ -1,8 +1,8 @@
1
- CodeEntropy/__init__.py,sha256=6RAN3bQeIAMTRqrJvnQxdaIyZdou_JcpKJo8Ve8-NTM,404
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+ CodeEntropy/__init__.py,sha256=3IcxfleI07bxBR3P5EA6vG13VTtfYGCe1q41Cg4gCSE,404
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  CodeEntropy/__main__.py,sha256=5i_ZrxQaq0q2aPllbB4SZ6BApV6oUFCgx0cGyjfMPrU,108
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  CodeEntropy/cli.py,sha256=nSshc8P7F7n3jAW36vzwXsFdffLfFdCpkfLvA-tJb3c,1318
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  CodeEntropy/config/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- CodeEntropy/config/argparse.py,sha256=SBDTrFpEStgKeremqhpHA8ZWTJGH6IirthLFFcTitFY,19695
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+ CodeEntropy/config/argparse.py,sha256=gCIUlQzMnUAYm7o-Mk2QKOP_HItc7-c1WGCe-YgEvbE,19927
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  CodeEntropy/config/runtime.py,sha256=1lfLy57vv6nF6ND0cspGpIWQdfwj_ZiZpU9GohfvkwI,14914
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  CodeEntropy/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  CodeEntropy/core/dask_clusters.py,sha256=FsvLyYQPImTWRf9J4x7wUILqf3syS0Ji5JUsJN-Qp1A,8992
@@ -12,8 +12,8 @@ CodeEntropy/entropy/configurational.py,sha256=3erd1Ul4sGL5BMBDYq33f27aRTZqiEb6hv
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  CodeEntropy/entropy/graph.py,sha256=LeDF2KxxNVgpetrIE9j0dnW64UhGywDLqoBJEf54vtc,4612
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  CodeEntropy/entropy/orientational.py,sha256=gfpYqCKQjAAx22rrUdbiLvzfEIXy1nwJoub1rgYKCvY,3415
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  CodeEntropy/entropy/vibrational.py,sha256=WeQJ1bKQPSxPrREJ8CDhk9Ph2xeunrWZ0zu76y-H6Ow,9733
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- CodeEntropy/entropy/water.py,sha256=Ob3V08DyQNSWDMqpQ27rqjgHeU5AlKZfjqf9EqUdgqc,8225
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- CodeEntropy/entropy/workflow.py,sha256=bxg8AVXGk7uwlv4u2AZ4kTQ26PMge_Z5ubWghdLtn9U,16100
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+ CodeEntropy/entropy/water.py,sha256=B2VbMYFH8umXO8r2KXHIsq26MpX5Q6w76LjABNg_KDU,8401
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+ CodeEntropy/entropy/workflow.py,sha256=Xypn5Gd7LpVXgoO_sawUBNXehEGv0F8paZ658VnQTF4,16311
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  CodeEntropy/entropy/nodes/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  CodeEntropy/entropy/nodes/aggregate.py,sha256=4SyXP1_bM0IesOuqflRLvPgEfFu0PmKiEm4EFgnNxwg,3062
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  CodeEntropy/entropy/nodes/configurational.py,sha256=-3j2ji_p-twPjZyjQ1T3tgN0pYLSIof9any1w5NI2as,7135
@@ -58,8 +58,8 @@ CodeEntropy/trajectory/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3
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  CodeEntropy/trajectory/frames.py,sha256=MSx_swzFjo4TgkZTR1y6W-1zuKNPg_C36I_uFqvOKpk,4354
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  CodeEntropy/trajectory/mda.py,sha256=epKpAzxkNQi3rE7HJc_tsK_ZY4c575LdXmWewJoP1qE,16954
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  CodeEntropy/trajectory/source.py,sha256=NfYsdm1amr29h2tmJP-RKyCp3phb1SOAtAELJmGm740,1475
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- codeentropy-2.7.0.dist-info/entry_points.txt,sha256=8Oa3H9ErsrGtx5Hc6hIHOw73wK3Ylkvfgtl_4cBb_GU,52
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- codeentropy-2.7.0.dist-info/licenses/LICENSE,sha256=hgMaAAVW1Q6dL586OHoz8vFO-6BYn-d2aAFBpVQylFc,1072
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- codeentropy-2.7.0.dist-info/WHEEL,sha256=lqN8jXt_QloFOGcx9kStvWbryhfEXoI2F2z-YURm350,81
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- codeentropy-2.7.0.dist-info/METADATA,sha256=emvj_HvZSa0vFbaVwumBcY5NoK2Bb_VFW8Ees52sp00,6547
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- codeentropy-2.7.0.dist-info/RECORD,,
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+ codeentropy-2.7.1.dist-info/entry_points.txt,sha256=8Oa3H9ErsrGtx5Hc6hIHOw73wK3Ylkvfgtl_4cBb_GU,52
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+ codeentropy-2.7.1.dist-info/licenses/LICENSE,sha256=hgMaAAVW1Q6dL586OHoz8vFO-6BYn-d2aAFBpVQylFc,1072
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+ codeentropy-2.7.1.dist-info/WHEEL,sha256=rLJE8OLPBZbz7tqxs1yD-wA-ADa1Ec5PuYU-Y_PNWDI,81
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+ codeentropy-2.7.1.dist-info/METADATA,sha256=_vGCZ5Gsa404J5KCRQreC2fmA6LMH1zEwnhO_imSeyw,6336
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+ codeentropy-2.7.1.dist-info/RECORD,,
{codeentropy-2.7.0.dist-info → codeentropy-2.7.1.dist-info}/WHEEL RENAMED
@@ -1,4 +1,4 @@
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  Wheel-Version: 1.0
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- Generator: flit 4.1.0
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+ Generator: flit 4.2.0
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  Root-Is-Purelib: true
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  Tag: py3-none-any