chore: deprecate apps method

[stevenhua0320]

@sbillinge ready to review. Note that these are not functionality based code, so it does not have test for these functions. Therefore I only deprecate them without creating tests.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 99.16%. Comparing base (5f64982) to head (279d29d).
⚠️ Report is 5 commits behind head on v3.4.0.

Additional details and impacted files

@@           Coverage Diff           @@
##           v3.4.0     #179   +/-   ##
=======================================
  Coverage   99.16%   99.16%           
=======================================
  Files          15       15           
  Lines        2400     2400           
=======================================
  Hits         2380     2380           
  Misses         20       20           

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[sbillinge]

great! How close are we to being finished with this task now? I hope there is not too much more to go!

[stevenhua0320]

great! How close are we to being finished with this task now? I hope there is not too much more to go!

I think we are very close now. I think we are left with Atom and Spacegroupclass, which I would start on deprecating it tomorrow.(It would be 10-12 methods which would take about four PRs). Also I would open a PR shortly for one parser method that I forgot to deprecate. After all these done I would do a comprehensive check for all the methods and if all methods are deprecated we can merge to main and release it. One question then is whether we need to care about the code that is not in the package distribution? Since I noticed that we have a script created by Pavol for Spacegroup for cctbx, I wonder whether we need to do it for that. The code description for that code is shown below.

"""Quick and extremely dirty script for generating code for SpaceGroup
that are defined in cctbx, but not in mmLib.  It was used to generate
module sgtbxspacegroups.

This is a utility script that should not be included with code
distribution.

Not to be included with code distributions.
"""

[sbillinge]

for the utility script we should probably change the name of the function but not bother fully deprecating it as noone outside is presumably using it.