CodeEntropy 2.5.0__py3-none-any.whl → 2.6.0__py3-none-any.whl

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Files changed (11) hide show
  1. CodeEntropy/__init__.py +1 -1
  2. CodeEntropy/cli.py +12 -4
  3. CodeEntropy/config/argparse.py +6 -0
  4. CodeEntropy/config/runtime.py +9 -7
  5. CodeEntropy/levels/dihedrals/conformational_state_builder.py +15 -5
  6. CodeEntropy/levels/dihedrals/state_assignment.py +9 -6
  7. {codeentropy-2.5.0.dist-info → codeentropy-2.6.0.dist-info}/METADATA +7 -7
  8. {codeentropy-2.5.0.dist-info → codeentropy-2.6.0.dist-info}/RECORD +11 -11
  9. {codeentropy-2.5.0.dist-info → codeentropy-2.6.0.dist-info}/WHEEL +0 -0
  10. {codeentropy-2.5.0.dist-info → codeentropy-2.6.0.dist-info}/entry_points.txt +0 -0
  11. {codeentropy-2.5.0.dist-info → codeentropy-2.6.0.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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9
  """
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10
 
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- __version__ = "2.5.0"
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+ __version__ = "2.6.0"
CodeEntropy/cli.py CHANGED
@@ -4,16 +4,18 @@ This module provides the CLI entry point used to run the multiscale cell
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4
  correlation entropy workflow.
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5
 
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6
  The entry point is intentionally small and only responsible for:
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- 1) Creating a job folder.
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- 2) Constructing a CodeEntropyRunner.
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- 3) Executing the entropy workflow.
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- 4) Handling fatal errors with a non-zero exit code.
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+ 1) Handling informational flags such as ``--version``.
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+ 2) Creating a job folder.
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+ 3) Constructing a CodeEntropyRunner.
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+ 4) Executing the entropy workflow.
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+ 5) Handling fatal errors with a non-zero exit code.
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  """
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13
 
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  from __future__ import annotations
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  import logging
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17
 
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+ from CodeEntropy.config.argparse import ConfigResolver
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  from CodeEntropy.config.runtime import CodeEntropyRunner
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20
 
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  logger = logging.getLogger(__name__)
@@ -22,9 +24,15 @@ logger = logging.getLogger(__name__)
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  def main() -> None:
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  """Run the entropy workflow.
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+ Arguments are parsed before any side effects so that informational flags such
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+ as ``--version`` and ``--help`` exit without creating a job folder or
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+ rendering the splash screen.
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+
25
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  Raises:
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  SystemExit: Exits with status code 1 on any unhandled exception.
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  """
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+ ConfigResolver().build_parser().parse_known_args()
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+
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  folder = CodeEntropyRunner.create_job_folder()
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37
 
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  try:
CodeEntropy/config/argparse.py CHANGED
@@ -31,6 +31,7 @@ from typing import Any
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  import yaml
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+ from CodeEntropy import __version__
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  from CodeEntropy.core.dask_clusters import HPCDaskManager
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  logger = logging.getLogger(__name__)
@@ -318,6 +319,11 @@ class ConfigResolver:
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  parser = argparse.ArgumentParser(
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  description="CodeEntropy: entropy calculation with the MCC method."
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  )
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+ parser.add_argument(
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+ "--version",
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+ action="version",
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+ version=f"CodeEntropy {__version__}",
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+ )
321
327
 
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  for name, spec in self._arg_specs.items():
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  arg_name = f"--{name}"
CodeEntropy/config/runtime.py CHANGED
@@ -32,6 +32,7 @@ from rich.rule import Rule
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  from rich.table import Table
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  from rich.text import Text
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+ from CodeEntropy import __version__
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  from CodeEntropy.config.argparse import ConfigResolver
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  from CodeEntropy.core.dask_clusters import HPCDaskManager
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  from CodeEntropy.core.logging import LoggingConfig
@@ -135,20 +136,21 @@ class CodeEntropyRunner:
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  return None
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  def show_splash(self) -> None:
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- """Render a Rich splash screen with optional citation metadata."""
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+ """Render a Rich splash screen.
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+
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+ The version shown is that of the locally installed package. Remaining
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+ metadata (authors, description, URL) comes from the online citation file
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+ when it is reachable.
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+ """
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  citation = self.load_citation_data()
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+ version_text = Align.center(Text(f"Version {__version__}", style="green"))
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  if citation:
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  ascii_title = text2art(citation.get("title", "CodeEntropy"))
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  ascii_render = Align.center(Text(ascii_title, style="bold white"))
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151
 
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- version = citation.get("version", "?")
146
- release_date = citation.get("date-released", "?")
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152
  url = citation.get("url", citation.get("repository-code", ""))
148
153
 
149
- version_text = Align.center(
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- Text(f"Version {version} | Released {release_date}", style="green")
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- )
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  url_text = Align.center(Text(url, style="blue underline"))
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155
 
154
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  abstract = citation.get("abstract", "No description available.")
@@ -193,7 +195,7 @@ class CodeEntropyRunner:
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  else:
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  ascii_title = text2art("CodeEntropy")
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  ascii_render = Align.center(Text(ascii_title, style="bold white"))
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- splash_content = Group(ascii_render)
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+ splash_content = Group(ascii_render, Rule(style="cyan"), version_text)
197
199
 
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  splash_panel = Panel(
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  splash_content,
CodeEntropy/levels/dihedrals/conformational_state_builder.py CHANGED
@@ -46,7 +46,12 @@ class ConformationStateBuilder(ConformationPeakDetector, ConformationStateAssign
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  frame_selection: FrameSelection,
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  progress: _RichProgressSink | None = None,
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  chunk_size: int | None = None,
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- ) -> tuple[dict[UAKey, list[str]], list[list[str]], dict[UAKey, int], list[int]]:
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+ ) -> tuple[
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+ dict[UAKey, list[str]],
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+ dict[int, list[str]],
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+ dict[UAKey, int],
53
+ dict[int, int],
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+ ]:
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  """Build conformational state labels from selected trajectory frames.
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56
 
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  Args:
@@ -87,7 +92,12 @@ class ConformationStateBuilder(ConformationPeakDetector, ConformationStateAssign
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  frame_selection: FrameSelection,
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  chunk_size: int,
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  progress: _RichProgressSink | None = None,
90
- ) -> tuple[dict[UAKey, list[str]], list[list[str]], dict[UAKey, int], list[int]]:
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+ ) -> tuple[
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+ dict[UAKey, list[str]],
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+ dict[int, list[str]],
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+ dict[UAKey, int],
99
+ dict[int, int],
100
+ ]:
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  """Build conformational states with serial frame-chunk map-reduce.
92
102
 
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  Args:
@@ -108,11 +118,10 @@ class ConformationStateBuilder(ConformationPeakDetector, ConformationStateAssign
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118
  if chunk_size < 1:
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  raise ValueError("chunk_size must be >= 1")
110
120
 
111
- number_groups = len(groups)
112
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  states_ua: dict[UAKey, list[str]] = {}
113
- states_res: list[list[str]] = [[] for _ in range(number_groups)]
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+ states_res: dict[int, list[str]] = {}
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123
  flexible_ua: dict[UAKey, int] = {}
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- flexible_res: list[int] = []
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+ flexible_res: dict[int, int] = {}
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125
 
117
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  task: TaskID | None = None
118
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  if progress is not None:
@@ -186,6 +195,7 @@ class ConformationStateBuilder(ConformationPeakDetector, ConformationStateAssign
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195
  state_data = self._reduce_state_partials(state_partials)
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196
 
188
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  self._merge_group_state_data(
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+ group_id=group_id,
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199
  state_data=state_data,
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  states_ua=states_ua,
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  states_res=states_res,
CodeEntropy/levels/dihedrals/state_assignment.py CHANGED
@@ -170,20 +170,23 @@ class ConformationStateAssigner:
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170
 
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  @staticmethod
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  def _merge_group_state_data(
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+ group_id: int,
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  state_data: ConformationStateData,
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  states_ua: dict[UAKey, list[str]],
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- states_res: list[list[str]],
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+ states_res: dict[int, list[str]],
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  flexible_ua: dict[UAKey, int],
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- flexible_res: list[int],
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+ flexible_res: dict[int, int],
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  ) -> None:
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  """Merge one group's state data into final output accumulators.
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181
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  Args:
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+ group_id: Id of the group the state data belongs to.
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  state_data: Serial conformational state data for one group.
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  states_ua: UA state accumulator to mutate.
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- states_res: Residue state accumulator to mutate.
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+ states_res: Residue state accumulator, keyed by group id, to mutate.
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  flexible_ua: UA flexible-dihedral accumulator to mutate.
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- flexible_res: Residue flexible-dihedral accumulator to mutate.
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+ flexible_res: Residue flexible-dihedral accumulator, keyed by group id,
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+ to mutate.
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188
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  Returns:
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  None. Mutates the provided accumulators.
@@ -199,8 +202,8 @@ class ConformationStateAssigner:
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  state_data.flexible_ua_updates[key],
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  )
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204
 
202
- states_res.append(state_data.state_res)
203
- flexible_res.append(state_data.flex_res)
205
+ states_res[group_id] = state_data.state_res
206
+ flexible_res[group_id] = state_data.flex_res
204
207
 
205
208
  def _process_conformations_from_angles(
206
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  self,
{codeentropy-2.5.0.dist-info → codeentropy-2.6.0.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
1
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  Metadata-Version: 2.5
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  Name: CodeEntropy
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- Version: 2.5.0
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+ Version: 2.6.0
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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.
5
5
  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>
@@ -16,21 +16,21 @@ Classifier: License :: OSI Approved :: MIT License
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  Classifier: Natural Language :: English
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  Classifier: Development Status :: 5 - Production/Stable
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  License-File: LICENSE
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- Requires-Dist: numpy>=2.3.2,<2.5.0
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+ Requires-Dist: numpy>=2.3.5,<2.6.0
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  Requires-Dist: mdanalysis>=2.10,<3.0
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  Requires-Dist: pandas>=2.3.3,<4.0
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- Requires-Dist: psutil>=5.9.4,<8.0
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+ Requires-Dist: psutil>=7.1.3,<8.0
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  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: requests>=2.32.2,<3.0
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- Requires-Dist: rdkit>=2025.3.4,<2026
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+ Requires-Dist: rdkit>=2025.3.4,<2027
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  Requires-Dist: numba>=0.63.0,<0.70
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- Requires-Dist: dask>=2025.4.0,<2027.1.0
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+ 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>=2025.4.0,<2027.1.0
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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"
@@ -56,7 +56,7 @@ 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) |
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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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  | **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) |
{codeentropy-2.5.0.dist-info → codeentropy-2.6.0.dist-info}/RECORD RENAMED
@@ -1,9 +1,9 @@
1
- CodeEntropy/__init__.py,sha256=QM8PCDQ0OM8HKjPNiIHHpPFtqLhnyTcGo8Tc6-_Nh-s,404
1
+ CodeEntropy/__init__.py,sha256=hAmtMNRexWP67gOAWLWAag9bka7HMDFyE3BMl7IRJHw,404
2
2
  CodeEntropy/__main__.py,sha256=5i_ZrxQaq0q2aPllbB4SZ6BApV6oUFCgx0cGyjfMPrU,108
3
- CodeEntropy/cli.py,sha256=xgSgagCV6HQ3CoXUpG7p7Ef5hCExgxp7orz6dZZWA6c,960
3
+ CodeEntropy/cli.py,sha256=nSshc8P7F7n3jAW36vzwXsFdffLfFdCpkfLvA-tJb3c,1318
4
4
  CodeEntropy/config/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
5
- CodeEntropy/config/argparse.py,sha256=Yjb2SWNdfKhHmfznU439cZPtdPM_QjhUD4uug2fnsek,19515
6
- CodeEntropy/config/runtime.py,sha256=iyeUrSAmz3eGpkAslAGsDzEzu7s4T8npy_Di3d8tnaU,14846
5
+ CodeEntropy/config/argparse.py,sha256=SBDTrFpEStgKeremqhpHA8ZWTJGH6IirthLFFcTitFY,19695
6
+ CodeEntropy/config/runtime.py,sha256=1lfLy57vv6nF6ND0cspGpIWQdfwj_ZiZpU9GohfvkwI,14914
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7
  CodeEntropy/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  CodeEntropy/core/dask_clusters.py,sha256=FsvLyYQPImTWRf9J4x7wUILqf3syS0Ji5JUsJN-Qp1A,8992
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  CodeEntropy/core/logging.py,sha256=XLr2lSSC5kGPq7rQDhWCi7Vcvh3DGO9e5TDbI4l2Bvc,7775
@@ -28,10 +28,10 @@ CodeEntropy/levels/neighbors.py,sha256=vswveQCIVBlDPQBFGc0e3whzmTJD01GjEJTpJ2UMn
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  CodeEntropy/levels/search.py,sha256=p4aqyj6GV7YGLDnlmZqi12cDbjfajSIB8IIcBAoUmaQ,8769
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  CodeEntropy/levels/dihedrals/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  CodeEntropy/levels/dihedrals/angle_observations.py,sha256=ZsIaXRvNRzZQjBxafiWD2_3zn_GnKjc9EkN8GjrVh6Q,9861
31
- CodeEntropy/levels/dihedrals/conformational_state_builder.py,sha256=3ajT_v1Cga1JocIvuJtHPx2JZwGUtleemuF45S31iAQ,7598
31
+ CodeEntropy/levels/dihedrals/conformational_state_builder.py,sha256=OU1Tzi3bGWADReVbFh4N4P2mS-nOH0XlIPR3ddhjUMg,7673
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  CodeEntropy/levels/dihedrals/kernels.py,sha256=gX75jgDDs-dv-IdI0V-u7NM-M4RVmpVppDAADFkHWxc,3594
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  CodeEntropy/levels/dihedrals/peak_detection.py,sha256=h8j78gczkf9tlYFTMqITDc51K9l9NxS5Y-ul1gHytzw,9486
34
- CodeEntropy/levels/dihedrals/state_assignment.py,sha256=QtfYjXEBbW95lomT9linK1_5uU0nsHh1P6PyMT_VR1g,9672
34
+ CodeEntropy/levels/dihedrals/state_assignment.py,sha256=d4en88oTSH37vGNavoRZ4xWrxSLxjCJ-LX_8xahBKJE,9834
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  CodeEntropy/levels/dihedrals/topology.py,sha256=LJ_u6cY-N91A5CuNBYzk_I0xHEpvqYSC30u9T4aku7c,8825
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  CodeEntropy/levels/execution/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  CodeEntropy/levels/execution/chunks.py,sha256=VD1LQA-thRaJZKVR_5qIQk5VZQWHGE2e2JzF5JspDe0,754
@@ -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-2.5.0.dist-info/entry_points.txt,sha256=8Oa3H9ErsrGtx5Hc6hIHOw73wK3Ylkvfgtl_4cBb_GU,52
62
- codeentropy-2.5.0.dist-info/licenses/LICENSE,sha256=hgMaAAVW1Q6dL586OHoz8vFO-6BYn-d2aAFBpVQylFc,1072
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- codeentropy-2.5.0.dist-info/WHEEL,sha256=lqN8jXt_QloFOGcx9kStvWbryhfEXoI2F2z-YURm350,81
64
- codeentropy-2.5.0.dist-info/METADATA,sha256=OAUfGJ1rsObNQ9ftW76e4CZr3m6PFxG1ycdM6B5HdsI,6348
65
- codeentropy-2.5.0.dist-info/RECORD,,
61
+ codeentropy-2.6.0.dist-info/entry_points.txt,sha256=8Oa3H9ErsrGtx5Hc6hIHOw73wK3Ylkvfgtl_4cBb_GU,52
62
+ codeentropy-2.6.0.dist-info/licenses/LICENSE,sha256=hgMaAAVW1Q6dL586OHoz8vFO-6BYn-d2aAFBpVQylFc,1072
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+ codeentropy-2.6.0.dist-info/WHEEL,sha256=lqN8jXt_QloFOGcx9kStvWbryhfEXoI2F2z-YURm350,81
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+ codeentropy-2.6.0.dist-info/METADATA,sha256=dDomybrlzZoHk5m116Ap4v8TI9QtKclsW6XIJhSkQ5E,6547
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+ codeentropy-2.6.0.dist-info/RECORD,,