API changes before 1.0

[sroet]

This is the list of new API changes that we want to implement before cutting a 1.0 release

https://github.com/SBC-Utrecht/pytom-match-pick/blob/main/src/pytom_tm/angles.py:

• Change load_angle_list and angle_to_angle_list to private

https://github.com/SBC-Utrecht/pytom-match-pick/blob/main/src/pytom_tm/correlation.py

• make normalise and normalised_cross_correlation private (maybe even split out to test only utils)

https://github.com/SBC-Utrecht/pytom-match-pick/blob/main/src/pytom_tm/extract.py

• pull out plotting_available to the main init of the package

• pytom-match-pick/src/pytom_tm/extract.py

  Line 29 in 9f1e4e7

  def predict_tophat_mask(

  to (make private as well)

def _predict_tophat_mask(
    score_volume: npt.NDArray[float],
    n_false_positives: float = 1.0,
    tophat_connectivity: int = 1,
    bins: int = 50,
    create_plot: bool = True,
    output_path_plot: Optional[pathlib.Path] = None,
)

• split gauss and log_gauss into a utils and also use these inside plotting
• alter extract_particles to

def extract_particles(
    job: TMJob,
    particle_radius_px: int,
    n_particles: int,
    cut_off: Optional[float] = None,
    n_false_positives: float = 1.0,
    relion5_compat: bool = False,
    tophat_filter: bool = False,
    tophat_connectivity: int = 1,
    tophat_bins: int = 50,
    tomogram_mask_path: Optional[pathlib.Path] = None,
    ignore_tomogram_mask: bool = False,
    create_plot: bool = True,
    plot_bins: int = 20,
) -> tuple[pd.DataFrame, list[float, ...]]:

https://github.com/SBC-Utrecht/pytom-match-pick/blob/main/src/pytom_tm/io.py

• pull out all argparse checkers to a seperate file
• move UnequalSpacingError to utils
• remove write_angle_list
• make read_txt_file private
• make read_imod_defocus_file private

https://github.com/SBC-Utrecht/pytom-match-pick/blob/main/src/pytom_tm/matching.py

• make std_under_mask_convolution private

https://github.com/SBC-Utrecht/pytom-match-pick/blob/main/src/pytom_tm/parallel.py

• make gpu_runner private

https://github.com/SBC-Utrecht/pytom-match-pick/blob/main/src/pytom_tm/plotting.py

• remove check_square_fdr
• remove distance_to_diag
• remove calculate_histogram
• remove evaluate_estimates
• remove fdr_recall
• remove distance_to_random
• remove get_distance
• move gauss, gauss_integral and bimodal to utils
• add typing and docstring to plist_quality_gaussian_fit (@McHaillet )

https://github.com/SBC-Utrecht/pytom-match-pick/blob/main/src/pytom_tm/tmjob.py

• make get_defocus_offsets private
• [ ]
• change order of https://github.com/SBC-Utrecht/pytom-match-pick/blob/main/src/pytom_tm/tmjob.py#L259

    def __init__(
        self,
        job_key: str,
        log_level: int,
        tomogram: pathlib.Path,
        template: pathlib.Path,
        mask: pathlib.Path,
        output_dir: pathlib.Path,
        angle_increment: Optional[Union[str, float]] = None,
        particle_diameter: Optional[float] = None,
        rotational_symmetry: int = 1,
        mask_is_spherical: bool = True,
        voxel_size: Optional[float] = None,
        low_pass: Optional[float] = None,
        high_pass: Optional[float] = None,
	tilt_angles: Optional[list[float, ...]] = None,
        tilt_weighting: bool = False,
        dose_accumulation: Optional[list[float, ...]] = None,
        ctf_data: Optional[list[dict, ...]] = None,
        defocus_handedness: int = 0,
        search_x: Optional[list[int, int]] = None,
        search_y: Optional[list[int, int]] = None,
        search_z: Optional[list[int, int]] = None,
        tomogram_mask: Optional[pathlib.Path] = None,
        whiten_spectrum: bool = False,
        random_phase_correction: bool = False,
        rng_seed: int = 321,
        output_dtype: np.dtype = np.float32,
        job_loaded_for_extraction: bool = False,
        pytom_tm_version_number: str = PYTOM_TM_VERSION,
    ):

https://github.com/SBC-Utrecht/pytom-match-pick/blob/main/src/pytom_tm/weights.py

• make hwhm_to_sigma private

• remove sigma_to_hwhm

• make wavelength_ev2m private

• think about restructuring ‎create_gaussian_high_pass and ‎create_gaussian_low_pass (lot of code duplication)

• make sure create_gaussian_band_pass is the only public gaussian_*_pass function, rewrite other files to use this instead

• make create_ctf private and update docstring in

  pytom-match-pick/src/pytom_tm/tmjob.py

  Line 336 in 9f1e4e7

  pytom_tm.weight.create_ctf() for parameter definition

• make radial_average private

• update version number

• up test coverage to 100%

• make release

• drop packages following SPEC0/NEP29