Programs deprecated

Deprecating programs

We have a “legacy” folder with programs and code that is outdated. Some of the reasons we did this are uninteresting code, programs that do not have a protocol and are not used, and programs that are not used and are difficult to maintain. You can visit the issue with more information and the list of deprecated programs and protocols can be found here.

We managed to speed up the installation time by 25%, and we were also able to reduce the lines of code to maintain and the number of code smells that were reported by SonarCloud.

However, it is possible to recover a program if anyone needs it. If you are an external user, please contact us (opening an issue is a good way, see here). If you are part of the Xmipp team: Each deprecated program has an associated commit. Visit it and review all the changes the program needs to be recovered. Here are some clues:

• Go to the legacy folder and

• Search in the applications/programs folder for the folder of your program.

• Search in the libraries folder for the script of your program.

• Most of the deprecated programs had a test; go to the commit and search in tests_programs_xmipp.py for the test of your program.

• The last step is to remove the program that has been recovered from this list (see listDeprecatedFiles() in utils.py).

List of deprecated programs

• angular_distribution_show

• apropos

• classify_significant

• ctf_correct_idr

• ctf_create_ctfdat

• ctf_show

• DeepAlign

• idr_xray_tomo

• image_common_lines

• metadata_convert_to_spider

• metadata_selfile_create

• mlf_refine_3d, ml_refine_3d, ml_tomo

• mrc_create_metadata

• pdb_construct_dictionary, pdb_restore_with_dictionary

• reconstruct_admn

• reconstruct_art_pseudo

• resolution_ibw

• resolution_ssnr

• score_micrograph

• reconstruct_fourier_starpu

• tomo_align_tilt_series, tomo_align_dual_tilt_series, tomo_align_refinement, tomo_align_refinement, tomo_extract_subvolume, tomo_project_main, tomo_remove_fluctuations

• tomo_align_tilt

• deep_denoissing

List of deprecated protocols

• mltomo

• movie_average

• subtract_projection

• deep_align

• reconstruct_heterogeneous

• metaprotocol_create_output

• metaprotocol_discrete_heterogeneity_scheduler

• apply_deformation_zernike3d

• classify_kmeans2d

• kmeans_clustering

• rotational_spectra

• particle_boxSize

• protocol_split_volume_hierarchical_cluster

• deep_denoissing

• metaprotocol_create_subset

• metaprotocol_golden_highres

• solid_angle

• split_volume