Function check_sixtrack_output_data has a Cognitive Complexity of 68 (exceeds 5 allowed). Consider refactoring.

Open

def check_sixtrack_output_data(jobname: str, basedir: Path):
    """Presence checks for SixDesk tracking output data.

    This checks recursively all directories in `track`.
    Will be busy for a while.

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Function write_bash has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

def write_bash(
    job_df: DataFrame,
    output_dir: Path = None,
    executable: str = "madx",
    cmdline_arguments: dict = None,

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Function convert_paths_in_dict_to_strings has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

def convert_paths_in_dict_to_strings(dict_: dict) -> dict:
    """Converts all Paths in the dict to strings, including those in iterables."""
    dict_ = dict_.copy()
    for key, value in dict_.items():
        if isinstance(value, Path):

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Function _create_stats_df has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

def _create_stats_df(df: pd.DataFrame, parameter: str, global_index: Any = None) -> TfsDataFrame:
    """ Calculates the stats over a given parameter.
    Note: Could be refactored to use `group_by`.

    Args:

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Function remove_twiss_fail_check has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.

Open

def remove_twiss_fail_check(jobname: str, basedir: Path):
    """ Comments out the "Twiss fail" check from mad6t.sh """
    LOG.info("Applying twiss-fail hack.")
    for mad6t_path in (
        get_mad6t_mask_path(jobname, basedir),

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Avoid deeply nested control flow statements.

Open

                    if not len(angle_dirs):
                        raise OSError(f"No angle-dirs present in {str(turn_dir)}.")

Avoid deeply nested control flow statements.

Open

                    for angle_dir in angle_dirs:
                        if not angle_dir.is_dir():
                            continue

                        htcondor_files = list(angle_dir.glob("htcondor.*"))

Avoid deeply nested control flow statements.

Open

                    if not turn_dir.is_dir():
                        continue

Function write_bash has 5 arguments (exceeds 4 allowed). Consider refactoring.

Open

def write_bash(

Function map_kwargs has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

def map_kwargs(add_dict: Dict[str, Any]) -> Dict[str, Any]:
    """
    Maps the kwargs for the job-file. 
    Some arguments have pre-defined choices and defaults, the remaining ones are just passed on.

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Function _plot_seeds has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

def _plot_seeds(ax, df_da: TfsDataFrame, da_col: str, interpolated: bool) -> Tuple[list, list]:
    """Add the Seed lines to the polar plots, if df_da is given.

    Args:
        ax: Axes to plot in

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Function fix_pythonfile_call has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

def fix_pythonfile_call(jobname: str, basedir: Path):
    """ Removes '<' in the `binary file` line in mad6t.sh so __file__ works. """
    LOG.info("Applying python-file call fix.")
    for mad6t_path in (
            get_mad6t_mask_path(jobname, basedir),

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Function submit_sixtrack has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

def submit_sixtrack(jobname: str, basedir: Path, python: Path = None,
                    sixdesk: Path = SIXDESK_UTILS, ssh: str = None, resubmit: bool = False):
    """ Generate simulation files and check if runnable and submit. """
    re_str = "Re-" if resubmit else ""
    LOG.info(f"{re_str}Submitting to sixtrack.")

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