Ms2pip

New:
- Command to predict and plot a single spectrum (PR 136)

Improved:
- fasta2speclib improvements (135)
- Pass through options from config file to DeepLC (fixes 138)
- Pass `num_cpu` to DeepLC, either from the `deeplc` section in the configuration, or from the `num_cpu` option in the fasta2speclib configuration

Fixed:
- Parse modifications on L (144, PR 145)

New:
- Python 3.9 support (PR 122)

Fixed in this release:
- Fixes in logging formatting (64, 65)
- Use float formatting in CSV output
- Retention time predictions can also be added without writing output to file
- When MS²PIP is running in a daemon process, it will not attempt to use multiprocessing
- Various improvments in match_spectra functionality (e.g. sqldb-backend, output, ...)
- General cleanup of repository (e.g. unused models)

New in this release:
- Small fix in fasta2speclib parameter handing
- New option `save_peprec` in fasta2speclib to save peprec files (including DeepLC predictions, if present)

New since previous release:
- [DeepLC integration](https://github.com/compomics/DeepLC)! Predict spectral libraries with accurate LC retention time prediction, even for modified peptides. Enable DeepLC with the `-r` flag in MS²PIP or by adding `"add_retention_time":true` to the [`fasta2speclib`](http://compomics.github.io/projects/ms2pip_c/wiki/fasta2speclib.html) configuration.
- Additional support for TOML-based configuration files: see [config.toml example](https://github.com/compomics/ms2pip_c/blob/releases/config.toml)
- New Skyline `.blib` to PEPREC and MGF converter script in [conversion_tools](https://github.com/compomics/ms2pip_c/tree/releases/conversion_tools)
- Various under-the-hood improvements


Includes the following models:

Model | Current version | Train-test dataset (unique peptides) | Evaluation dataset (unique peptides) | Median Pearson correlation on evaluation dataset
-|-|-|-|-
HCD | v20190107 | [MassIVE-KB](https://doi.org/10.1016/j.cels.2018.08.004) (1 623 712) | [PXD008034](https://doi.org/10.1016/j.jprot.2017.12.006) (35 269) | 0.903786
CID | v20190107 | [NIST CID Human](https://chemdata.nist.gov/) (340 356) | [NIST CID Yeast](https://chemdata.nist.gov/) (92 609) | 0.904947
iTRAQ | v20190107 | [NIST iTRAQ](https://chemdata.nist.gov/) (704 041) | [PXD001189](https://doi.org/10.1182/blood-2016-05-714048) (41 502) | 0.905870
iTRAQphospho | v20190107 | [NIST iTRAQ phospho](https://chemdata.nist.gov/) (183 383) | [PXD001189](https://doi.org/10.1182/blood-2016-05-714048) (9 088) | 0.843898
TMT | v20190107 | [Peng Lab TMT Spectral Library](https://doi.org/10.1021/acs.jproteome.8b00594) (1 185 547) | [PXD009495](https://doi.org/10.15252/msb.20188242) (36 137) | 0.950460
TTOF5600 | v20190107 | [PXD000954](https://doi.org/10.1038/sdata.2014.31) (215 713) | [PXD001587](https://doi.org/10.1038/nmeth.3255) (15 111) | 0.746823
HCDch2 | v20190107 | [MassIVE-KB](https://doi.org/10.1016/j.cels.2018.08.004) (1 623 712) | [PXD008034](https://doi.org/10.1016/j.jprot.2017.12.006) (35 269) | 0.903786 (+) and 0.644162 (++)
CIDch2 | v20190107 | [NIST CID Human](https://chemdata.nist.gov/) (340 356) | [NIST CID Yeast](https://chemdata.nist.gov/) (92 609) | 0.904947 (+) and 0.813342 (++)

New since previous release:
- Hotfix: add header files to manifest