Conversation
Fix critical bugs: dedent QMMM.clone() from inside compute(), replace bare except with specific exceptions, replace asserts with proper errors in AFSSH. Sync version across .bumpversion.cfg and docs/conf.py, update README with accurate models/options/API docs. Add dt validation to AdiabaticMD, default Ehrenfest outcome_type to populations. Unify coupling_energy_threshold as a class attribute in DiabaticModel_ and AdiabaticModel_. Document the needed_gradients/needed_couplings None="all" convention. Standardize all test files from unittest to pytest style. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…naming rules - Remove unused imports across 6 files (Dict, Tuple, sys, math, Union, numpy) - Run yapf formatter with project .style.yapf config - Configure good-names and good-names-rgxs in .pylintrc for scientific variable naming conventions (H, dV, delR, NAC_matrix, etc.) - Disable too-many-positional-arguments (R0917) globally - Disable too-many-instance-attributes for SurfaceHoppingMD - Remove deprecated suggestion-mode option for pylint 4.x compatibility Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Fix genuine bugs: bare-except, dangerous mutable default argument, missing super().__init__(), raise-missing-from, unreachable code, attribute-defined-outside-init, wrong-import-order, and argument names mismatched with base class. Add comprehensive docstrings to turboparse module and remaining undocumented classes/methods. Convert %-formatting and .format() to f-strings, remove superfluous parens, fix simple no-else-return cases, narrow broad exceptions to specific types, disable too-few-public-methods globally, and add augmented_integration to AugmentedFSSH recognized_options. Pylint score: 8.69 -> 9.76/10 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Updated the GitHub Actions workflow to include mypy for type checking alongside pylint. This enhances code quality by ensuring type correctness in the mudslide module.
Introduced a new 'developing.rst' file that outlines the setup of a development environment, instructions for running CI checks locally, and guidelines for code formatting and type checking. Updated the index to include a link to the new developer guide.
- Introduced a new base class `TrajectoryMD` for shared infrastructure across molecular dynamics types, including adiabatic and surface hopping dynamics. - Updated `AdiabaticMD` and `SurfaceHoppingMD` to inherit from `TrajectoryMD`, streamlining initialization and common functionality. - Replaced deprecated `_force` methods with `force` in relevant classes for consistency. - Configured CI to run mypy and pylint, achieving zero mypy errors and improving code quality. - Cleaned up unused imports and ensured compliance with pylint standards across multiple files.
Print step, time, total energy, average temperature, and wall time to stdout and a report file during simulation. SurfaceHoppingMD appends the active state column. Configurable via report_every and report_file options; disabled with report_every=0 or report_file=None. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Also adds mass attribute declaration to ElectronicModel_ base class and uses DiabaticModel_ for surface.py where model.V() is called. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Major effort to clean up code quality through better documentation, and automatically including type checking and linting into the work flow.