feat: add calibration report export functionality

[singjc]

This pull request adds a new CLI command for exporting OpenSwath calibration debug reports. The most important changes are grouped below:

pyprophet export calibration-report --help
PyProphet v3.0.0
Execution time: 2025-09-30 12:56:23
System: OS: Linux 6.9.3-76060903-generic | Python: 3.10.14 | CPU: 20 cores | RAM: 62.4 GB
Command: /home/singjc/anaconda3/envs/py310/bin/python /home/singjc/anaconda3/envs/py310/bin/pyprophet export calibration-report --help

Usage: pyprophet export calibration-report [OPTIONS]

  Generate a calibration report from OpenSwathWorkflow debug calibration files

Options:
  --wd DIRECTORY                        Working directory containing debugging
                                        files.  [default: .]
  --im-cal-pattern TEXT                 Ion mobility debug file pattern.
                                        [default: _debug_calibration_im.txt]
  --mz-cal-pattern TEXT                 m/z debug file pattern.  [default:
                                        _debug_calibration_mz.txt]
  --irt-trafo-pattern TEXT              iRT trafoXML pattern.  [default:
                                        _debug_calibration_irt.trafoXML]
  --irt-mzml-pattern TEXT               iRT XIC mzML pattern.  [default:
                                        _debug_calibration_irt_chrom.mzML]
  --report-file FILE                    Output PDF path.  [default:
                                        calibration_report.pdf]
  --zoom-in-xic / --no-zoom-in-xic      Zoom into XICs ±50 s around RT apex.
                                        [default: zoom-in-xic]
  --verbose INTEGER RANGE               Verbosity level 0/1/2.  [default: 0;
                                        0<=x<=2]
  --help                                Show this message and exit.
  --helphelp                            Show advanced help with all options

Example

$ pyprophet export calibration-report 
PyProphet v3.0.0
Execution time: 2025-09-30 12:56:41
System: OS: Linux 6.9.3-76060903-generic | Python: 3.10.14 | CPU: 20 cores | RAM: 62.4 GB
Command: /home/singjc/anaconda3/envs/py310/bin/python /home/singjc/anaconda3/envs/py310/bin/pyprophet export calibration-report

INFO: Found 3 unique runs to generate reports for
---------------------------------------------------------------------
INFO: Processing run - 20200505_Evosep_200SPD_SG06-16_MLHeLa_200ng_py8_S3-A1_1_2737
INFO: IM calibration file - ./20200505_Evosep_200SPD_SG06-16_MLHeLa_200ng_py8_S3-A1_1_2737_debug_calibration_im.txt
INFO: MZ calibration file - ./20200505_Evosep_200SPD_SG06-16_MLHeLa_200ng_py8_S3-A1_1_2737_debug_calibration_mz.txt
INFO: iRT transformation file - ./20200505_Evosep_200SPD_SG06-16_MLHeLa_200ng_py8_S3-A1_1_2737_debug_calibration_irt.trafoXML
INFO: iRT XIC mzML - ./20200505_Evosep_200SPD_SG06-16_MLHeLa_200ng_py8_S3-A1_1_2737_debug_calibration_irt_chrom.mzML
INFO: Zooming into XICs if possible...
---------------------------------------------------------------------
INFO: Processing run - 20200505_Evosep_200SPD_SG06-16_MLHeLa_200ng_py8_S3-A2_1_2738
INFO: IM calibration file - ./20200505_Evosep_200SPD_SG06-16_MLHeLa_200ng_py8_S3-A2_1_2738_debug_calibration_im.txt
INFO: MZ calibration file - ./20200505_Evosep_200SPD_SG06-16_MLHeLa_200ng_py8_S3-A2_1_2738_debug_calibration_mz.txt
INFO: iRT transformation file - ./20200505_Evosep_200SPD_SG06-16_MLHeLa_200ng_py8_S3-A2_1_2738_debug_calibration_irt.trafoXML
INFO: iRT XIC mzML - ./20200505_Evosep_200SPD_SG06-16_MLHeLa_200ng_py8_S3-A2_1_2738_debug_calibration_irt_chrom.mzML
INFO: Zooming into XICs if possible...
---------------------------------------------------------------------
INFO: Processing run - 20200505_Evosep_200SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2740
INFO: IM calibration file - ./20200505_Evosep_200SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2740_debug_calibration_im.txt
INFO: MZ calibration file - ./20200505_Evosep_200SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2740_debug_calibration_mz.txt
INFO: iRT transformation file - ./20200505_Evosep_200SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2740_debug_calibration_irt.trafoXML
INFO: iRT XIC mzML - ./20200505_Evosep_200SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2740_debug_calibration_irt_chrom.mzML
INFO: Zooming into XICs if possible...
INFO: Done. Saved report to 'calibration_report.pdf'. Elapsed: 0 days 00:00:11.934842
[ 2025-09-30 at 12:56:53 | INFO    | util::543                   ] pyprophet export_calibration_report took 11.96 seconds; Peak Memory Usage: 433.62 MB.

New Feature: Calibration Report Export

• Added a new calibration-report CLI command (export_calibration_report) to generate calibration reports from OpenSwathWorkflow debug calibration files, with multiple options for input patterns and output customization.
• Imported the generate_calibration_report function from export.calibration_report to support the new command.
• Registered the new calibration-report command in the main export CLI group.

Code Consistency and Minor Improvements

• Updated multiple click.option definitions for consistent formatting by adding trailing commas, improving readability and maintainability.
• Standardized function signatures and calls by adding trailing commas to argument lists, aligning with Python best practices. [1] [2]

Minor Code Cleanups

• Added blank lines after function calls for better code separation and readability. [1] [2]