CLI Tools

Modules powering the command-line interfaces.

ensemble_analyzer.cli.check_setup.check_gaussian() → None[source]: Check for Gaussian availability (Optional). Looks for ‘g16’ or ‘g09’ in PATH.

ensemble_analyzer.cli.check_setup.check_ml_potentials() → None[source]: Check optional ML potential dependencies (TBLite, AIMNet).

ensemble_analyzer.cli.check_setup.check_models_dir() → None[source]: Check ENAN_MODELS_DIR environment variable.

ensemble_analyzer.cli.check_setup.check_orca() → bool[source]

Verify ORCA installation and environment configuration.

Checks: 1. ‘orca’ executable in PATH. 2. ‘ORCAVERSION’ environment variable.

Returns:: True if ORCA is correctly configured.
Return type:: bool

ensemble_analyzer.cli.check_setup.check_python_dependencies() → bool[source]

Verify that all required Python libraries are installed and importable.

Returns:: True if all critical dependencies are found.
Return type:: bool

ensemble_analyzer.cli.check_setup.log_fail(msg) → None[source]: Print a failure message in red.

ensemble_analyzer.cli.check_setup.log_pass(msg) → None[source]: Print a success message in green.

ensemble_analyzer.cli.check_setup.log_warn(msg) → None[source]: Print a warning message in yellow.

ensemble_analyzer.cli.check_setup.main() → None[source]: Run the complete installation check suite.

Interactive Protocol Wizard for Ensemble Analyser Requires: Python >= 3.10, InquirerPy

ensemble_analyzer.cli.protocol_wizard.clean_protocol_dict(step: dict[str, Any]) → dict[str, Any][source]: Remove None, empty values, and defaults from protocol dictionary.

ensemble_analyzer.cli.protocol_wizard.get_constrains() → list[list[int]][source]: Prompt for geometric constraints.

ensemble_analyzer.cli.protocol_wizard.get_float_input(message: str, default: str = '', allow_empty: bool = True) → float | None[source]: Safe float input with optional empty value.

ensemble_analyzer.cli.protocol_wizard.get_int_input(message: str, default: str = '1') → int[source]: Safe integer input with validation and retry.

ensemble_analyzer.cli.protocol_wizard.get_internal_coordinates() → list[list[int]][source]: Prompt for internal coordinates to monitor (bond/angle/dihedral).

ensemble_analyzer.cli.protocol_wizard.load_basis_sets() → dict[str, Any][source]

Interactively configure a single protocol step.

Prompts the user for parameters (calculator, method, settings) based on the selected complexity level.

Parameters:

step_num (int) – The index of the step being configured.
level (str, optional) – Configuration depth (‘Basic’, ‘Intermediate’, ‘Advanced’). Defaults to “Basic”.

Returns:

Dictionary of parameters for this protocol step.

Return type:

dict[str, Any]

ensemble_analyzer.cli.protocol_wizard.load_functionals() → list[str][source]

Load available DFT functionals from the package database.

Returns:: List of functional names.
Return type:: list[str]

ensemble_analyzer.cli.protocol_wizard.load_grouped(path: str) → list[str][source]

Load grouped choices (functionals/basis sets) from a parameter file.

Parses files with ‘#!’ category markers to group options for the UI.

Parameters:: path (str) – Path to the parameters file.
Returns:: List of formatted choices for the fuzzy search prompt.
Return type:: list[str]

ensemble_analyzer.cli.protocol_wizard.main() → int[source]

Main entry point for the Protocol Wizard CLI.

Orchestrates the creation of the protocol.json file through an interactive terminal session.

Returns:: Exit code (0 for success, 1 for error).
Return type:: int

ensemble_analyzer.cli.protocol_wizard.parse_choice(choice: str) → str[source]: Extract clean value from formatted choice string.

ensemble_analyzer.cli.protocol_wizard.print_step_summary(idx: int, step: dict[str, Any]) → None[source]: Print formatted summary of protocol step.

ensemble_analyzer.cli.protocol_wizard.protocol_step(step_num: int, level: str = 'Basic') → dict[str, Any][source]

Create a single protocol step with level-dependent options.

Parameters:

step_num – Step number in the protocol
level – Configuration level (Basic/Intermediate/Advanced)

Returns:

Dictionary containing all protocol parameters

Graph Editor

Core module for MatplotlibPickleEditor.

Handles loading, modifying and saving serialized matplotlib figures.

class ensemble_analyzer.cli.pickle_editor.core.MatplotlibPickleEditor(pickle_path: Path, strict_validation: bool = True)[source]

Core editor to modify colors, labels, and styles in serialized matplotlib figures.

COMMON_COLORS

List of common predefined colors for quick selection.

Type:: List[str]

change_line_alpha(alpha_map: Dict[str, float]) → int[source]

Change line transparency and legend transparency.

Parameters:: alpha_map – Dictionary {label: alpha} (0-1)
Returns:: Number of alpha values changed
Raises:: RuntimeError – If load() has not been called

change_line_colors(label_color_map: Dict[str, str]) → int[source]

Update the color of lines associated with specific legend labels.

Parameters:: label_color_map (Dict[str, str]) – Map of {label: hex_color/name}.
Returns:: Number of lines updated.
Return type:: int

change_line_linestyle(style_map: Dict[str, str]) → int[source]

Update the line style (e.g., solid, dashed) for specific labels.

Parameters:: style_map (Dict[str, str]) – Map of {label: style_string} (e.g. ‘–‘).
Returns:: Number of lines updated.
Return type:: int

change_line_linewidth(width_map: Dict[str, float]) → int[source]

Change line widths and legend widths.

Parameters:: width_map – Dictionary {label: width}
Returns:: Number of widths changed
Raises:: RuntimeError – If load() has not been called

change_line_visibility(visibility_map: Dict[str, bool]) → int[source]

Change line visibility (show/hide).

Parameters:: visibility_map – Dictionary {label: bool} (True=visible, False=hidden)
Returns:: Number of lines changed
Raises:: RuntimeError – If load() has not been called

get_legend_labels() → Dict[int, str][source]

Retrieve current legend labels mapped by index.

Returns:: Dictionary {index: label_text}.
Return type:: Dict[int, str]

get_line_colors() → Dict[str, str][source]

Get current line colors.

Returns:: hex_color}
Return type:: Dictionary {label
Raises:: RuntimeError – If load() has not been called

has_modifications() → bool[source]

Check if there are unsaved modifications.

Returns:: True if there are unsaved modifications

load() → None[source]

Load and deserialize the pickle file.

Raises:: PickleSecurityError – If the file is corrupted or not a valid Figure.

preview() → None[source]

Display a copy of the current figure for preview.

Raises:: RuntimeError – If load() has not been called

rename_legend_labels(mapping: Dict[str, str]) → int[source]

Rename specific legend labels.

Parameters:: mapping (Dict[str, str]) – Map of {old_name: new_name}.
Returns:: Number of labels successfully renamed.
Return type:: int

save(output_path: Path | None = None, format: str = 'pickle') → Path[source]

Serialize the modified figure to disk.

Parameters:

output_path (Optional[Path]) – Destination file. If None, overwrites original.
format (str) – Output format (‘pickle’, ‘png’, ‘pdf’, ‘svg’).

Returns:

The actual path of the saved file.

Return type:

Path

exception ensemble_analyzer.cli.pickle_editor.core.PickleSecurityError[source]: Exception for security issues in pickle loading.

CLI entry point for Matplotlib Pickle Editor.

Supports interactive (TUI) and batch modes.

ensemble_analyzer.cli.pickle_editor.cli.batch_mode(args: Namespace) → int[source]

Execute edits in non-interactive (batch) mode.

Parameters:: args – Parsed command-line arguments.
Returns:: Exit code (0 for success, 1 for error).
Return type:: int

ensemble_analyzer.cli.pickle_editor.cli.main() → int[source]

Main entry point for the Graph Editor CLI.

Dispatches control to either the TUI or Batch mode.

Returns:: Exit code.
Return type:: int

ensemble_analyzer.cli.pickle_editor.cli.parse_mapping_file(filepath: Path) → Dict[str, str][source]

Parse a text file containing ‘OLD=NEW’ mappings.

Parameters:: filepath (Path) – Path to the mapping file.
Returns:: Dictionary of mappings.
Return type:: Dict[str, str]

Interactive Terminal User Interface for MatplotlibPickleEditor.

Interactive interface based on InquirerPy and Rich.

class ensemble_analyzer.cli.pickle_editor.tui.InteractiveTUI(editor: MatplotlibPickleEditor)[source]

Terminal User Interface for the graph editor using InquirerPy.

change_alpha_flow() → None[source]: Interactive flow to change transparency (alpha).

change_colors_flow() → None[source]: Interactive flow to change colors.

change_linestyle_flow() → None[source]: Interactive flow to change line style.

change_linewidth_flow() → None[source]: Interactive flow to change line width.

change_visibility_flow() → None[source]: Interactive flow to change visibility.

print_panel(message: str, title: str = 'Info', style: str = 'cyan') → None[source]

Print a formatted panel.

Parameters:

message – Message to display
title – Panel title
style – Border color style

rename_labels_flow() → None[source]: Interactive flow to rename labels.

run() → None[source]: Start the main interactive event loop. Displays menus and handles user input until exit.

save_flow() → None[source]: Interactive flow to save.

show_current_state() → None[source]: Display a formatted table of the current figure state (Labels, Colors).