TypeError: mokapot.read_pin() missing 1 required positional argument: 'max_workers' when rescoring with mokapot

[ab-omicscouts]

Describe the bug

When running oktoberfest (version 0.10.0) with mokapot for rescoring (mokapot version 0.10.1.dev5+g2b1f13a) on Ubuntu 22.04.5 LTS (Python 3.11, oktoberfest conda environment), an error occurs during rescoring:

File: .../python3.11/site-packages/oktoberfest/rescore/rescore.py, line 328
psms = mokapot.read_pin(input_file)
TypeError: read_pin() missing 1 required positional argument: 'max_workers'

To Reproduce

Steps to reproduce the behavior:

1. Use the following configuration file:

   {
       "type": "Rescoring",
       "tag": "tmtpro",
       "inputs": {
           "search_results": "path/to/input",
           "search_results_type": "Maxquant",
           "spectra": "/spectra/dir",
           "spectra_type": "raw"
       },
       "var_mods": {
           "K(Lys8_Mod)": [259, 8.0141]
       },
       "output": "/path/to/output",
       "models": {
           "intensity": "Prosit_2020_intensity_TMT",
           "irt": "Prosit_2020_irt_TMT"
       },
       "massTolerance": 20,
       "unitMassTolerance": "ppm",
       "prediction_server": "koina.wilhelmlab.org:443",
       "ssl": true,
       "thermoExe": "/opt/compomics/ThermoRawFileParser.exe",
       "numThreads": 4,
       "fdr_estimation_method": "mokapot",
       "regressionMethod": "spline",
       "allFeatures": false
   }

2. Run the command:

   python -m oktoberfest --config_path ./issue_config.json

Expected behavior

Oktoberfest completes rescoring using mokapot without errors.

System [please complete the following information]:

• OS: Ubuntu 22.04.5 LTS
• Language Version: Python 3.11
• Virtual environment: Conda
• Oktoberfest version: 0.10.0
• Mokapot version: 0.10.1.dev5+g2b1f13a

Additional context

• The configuration file and full command used are provided above.
• Please advise if further logs or a sample input file are needed for diagnosis.

[picciama]

Oktoberfest 0.10.0 requires numpy 2.0 for which mokapot seems to have no stable version for yet. Mokapot has a newer version though, that is not yet released on pypi (0.11.0 RC1) and @WassimG apparently tested this successfully. Please install that version from mokapot for now directly from github: https://github.com/wfondrie/mokapot We will update the dependency accordingly, once the pypi version becomes available.