Ms2rescore

Improvements 🚀

- MS²Rescore now runs on Windows!
- Graphical user interface (GUI) added, built with [Gooey](https://github.com/chriskiehl/Gooey)
Install with `pip install ms2rescore[gui]` and run `python -m ms2rescore.gui`
- Install, upgrade, and run scripts added for Windows users without an existing Python installation who simply want to use the new GUI
- MS²Rescore can now output a PDF with useful plots displaying the results.

Refactoring and minor changes 🔧
- ⚠️Breaking change: MS²Rescore is now written with a lowercase S (instead of "MS²ReScore). This means that some class names and exceptions have been renamed accordingly, breaking the Python API with previous versions.
- ⚠️Breaking change: The `feature_sets` option now expects instead of a string with a predefined feature set, such as `ms2pip_rt`, a list of strings including one of the following: `searchengine`, `rt`, or `ms2pip`. By default, MS²Rescore uses all features: `['searchengine', 'rt', 'ms2pip']`.
- MS²PIP is now imported and called through the Python API instead of the CLI

Includes PRs 34 and 37.

Improvements 🚀

- PSMs with invalid amino acids (B, J, O, U, X, and Z), which are unsupported by MS²PIP, are now removed in all pipelines (Fixes 31).


Bugfixes 🐛

- Case-insensitive matching of msms.txt column names (e.g. both `Mass Deviations [Da]` and `Mass deviations [Da]` will now both be accepted)
- Fix MGF title parsing in MaxQuant pipeline


Refactoring and minor changes 🔧

- Replaced assertions with specific exceptions
- Removed empty module `runner.py`
- Dropped support for Python 3.6 (did not work with subprocess capture_output)

Fixed:
- Prevent duplicate columns in pin output

New:
- X!Tandem pipeline outputs flanking amino acids to PIN file (24, 27)

Fixed:
- Temporary fix for Tensorflow NUMEXPR_MAX_THREADS (25, compomics/DeepLC19)
- `tandem_id` column was erroneously written to X!Tandem PIN files
- Use logger instead of logging

New and fixed:
- Rescore with DeepLC retention time prediction
- New pipeline for X!Tandem search results
- Support for C-terminal modifications
- Simplified configuration (see README.md and configuration.md)
- By default, the pipeline is inferred from the identification file extension
- Major code refactoring
- Many bugfixes
- Installable from PyPI

Before DeepLC integration and refactoring.