refactor: New cli for labpdfproc

[cadenmyers13]

I wanted to get this PR in before the weekend, so apologies for the sloppy commits. This PR improves the UX of labpdfproc. It breaks it into 3 subcommands mud, zscan, and sample. These commands do the following

$ labpdfproc -h
usage: labpdfproc [-h] {mud,zscan,sample} ...

Apply absorption corrections to laboratory X-ray diffraction data prior to PDF analysis. Supports manual mu*d, z-scan, or sample-based corrections.

options:
  -h, --help          show this help message and exit

Correction method:
  {mud,zscan,sample}
    mud               Correct diffraction data using known mu*d value
    zscan             Correct diffraction data using a z-scan measurement
    sample            Correct diffraction data using sample composition/density

mud command

$ labpdfproc mud -h
usage: labpdfproc mud [-h] [-w WAVELENGTH] [-x XTYPE] [-m {brute_force,polynomial_interpolation}] [-o OUTPUT_DIRECTORY] [-f] [-c] [-u KEY=VALUE [KEY=VALUE ...]]
                      [--username USERNAME] [--email EMAIL] [--orcid ORCID]
                      input [input ...] mud

positional arguments:
  input                 Input X-ray diffraction data file(s) or directory. Can specify multiple files, directories, or use wildcards.
  mud                   mu*d value

zscan command

$ labpdfproc zscan -h
usage: labpdfproc zscan [-h] [-w WAVELENGTH] [-x XTYPE] [-m {brute_force,polynomial_interpolation}] [-o OUTPUT_DIRECTORY] [-f] [-c] [-u KEY=VALUE [KEY=VALUE ...]]
                        [--username USERNAME] [--email EMAIL] [--orcid ORCID]
                        input [input ...] z_scan_file

positional arguments:
  input                 Input X-ray diffraction data file(s) or directory. Can specify multiple files, directories, or use wildcards.
  z_scan_file           Z-scan measurement file. See diffpy.labpdfproc documentation for more information.

sample command

$ labpdfproc sample -h
usage: labpdfproc sample [-h] [-w WAVELENGTH] [-x XTYPE] [-m {brute_force,polynomial_interpolation}] [-o OUTPUT_DIRECTORY] [-f] [-c] [-u KEY=VALUE [KEY=VALUE ...]]
                       [--username USERNAME] [--email EMAIL] [--orcid ORCID]
                       input [input ...] sample_composition sample_mass_density diameter

positional arguments:
input                 Input X-ray diffraction data file(s) or directory. Can specify multiple files, directories, or use wildcards.
sample_composition    Chemical formula, e.g. Fe2O3
sample_mass_density   Sample mass density in capillary (g/cm^3). If unsure, a good estimate is ~1/3 of the theoretical packing fraction density.
diameter              Outer diameter of the capillary in mm

All commands have the same following options

options:
  -h, --help            show this help message and exit
  -w, --wavelength WAVELENGTH
                        X-ray wavelength in angstroms (numeric) or X-ray source name (allowed: Ag, AgKa1, AgKa1Ka2, Cu, CuKa1, CuKa1Ka2, Mo, MoKa1, MoKa1Ka2). Will be loaded
                        from config files if not specified.
  -x, --xtype XTYPE     X-axis type (default: tth). Allowed values: angle, tth, twotheta, 2theta, d, dspace, q
  -m, --method {brute_force,polynomial_interpolation}
                        Method for cylindrical volume element (CVE) calculation (default: polynomial_interpolation). Allowed methods: brute_force, polynomial_interpolation
  -o, --output-directory OUTPUT_DIRECTORY
                        Directory to save corrected files (created if needed). Defaults to current directory.
  -f, --force           Overwrite existing files
  -c, --output-correction
                        Also output the absorption correction to a separate file
  -u, --user-metadata KEY=VALUE [KEY=VALUE ...]
                        Specify key-value pairs to be loaded into metadata using the format key=value. Separate pairs with whitespace, and ensure no whitespaces before or
                        after the = sign. Avoid using = in keys. If multiple = signs are present, only the first separates the key and value. If a key or value contains
                        whitespace, enclose it in quotes. For example, facility='NSLS II', 'facility=NSLS II', beamline=28ID-2, 'beamline'='28ID-2', 'favorite color'=blue, are
                        all valid key=value items.
  --username USERNAME   Your name (optional, for dataset credit). Will be loaded from config files if not specified.
  --email EMAIL         Your email (optional, for dataset credit). Will be loaded from config files if not specified.
  --orcid ORCID         Your ORCID ID (optional, for dataset credit). Will be loaded from config files if not specified.

Additional changes

• I removed the --anode-type and merged it with --wavelength. If the user wants to specify an anode type, they still can. They just use the --wavelength option (ie --wavelength Mo) and the code recognizes this. I felt as if this made the code smoother.
• I removed the ability to calculate mu*d from packing fraction and just added the help message that density can be approximated with 0.3 x theoretical packing. We can add this back though if we like. I left the function there.

Gooey interface

With this change, the gui now is separated nicely into its three subcommands.

[cadenmyers13]

@sbillinge This is ready for review/discussion if you find some time this weekend. Im marking this as a draft for now so i can come back monday with a clearer head. Also the merge conflict looks to be because of some re-skpkging work. Just wanted to get this to you if you have any comments.

[sbillinge]

I looked through the commands and they look great. I like everything you did here.

[cadenmyers13]

Closing because of merge conflicts. Couldn't figure out how to resolve them and didn't want to lose everything