├── .github ├── dependabot.yml └── workflows │ ├── black.yml │ └── python-app.yml ├── .gitignore ├── .pyup.yml ├── .travis.yml ├── AUTHORS.rst ├── CONTRIBUTING.rst ├── HISTORY.rst ├── LICENSE ├── MANIFEST.in ├── Makefile ├── README.rst ├── check_and_fix_style.sh ├── codecov.yml ├── docs ├── Makefile ├── authors.rst ├── conf.py ├── contributing.rst ├── history.rst ├── index.rst ├── installation.rst ├── make.bat ├── readme.rst └── usage.rst ├── example_data └── example_molecules.csv ├── example_scripts ├── complex_mix_simulation.py ├── inspect_simulated_peak.py ├── plot_simulated_chromatogram.py ├── simulate_fasta.py ├── write_filtered_mzml.py ├── write_peptides.py ├── write_simulated_mzML.py └── write_simulated_peaks_adenosine_inosine.py ├── pyproject.toml ├── requirements.txt ├── requirements_dev.txt ├── setup.cfg ├── setup.py ├── smiter ├── .pyre_configuration ├── __init__.py ├── cli.py ├── ext │ ├── __init__.py │ ├── get_modomics_csv.sh │ ├── modomics.csv │ ├── nucleoside_fragment_kb.py │ ├── test.csv │ └── trim_lines.py ├── fragmentation_functions.py ├── lib.py ├── noise_functions.py ├── params │ ├── default_params.py │ └── header_param.py ├── peak_distribution.py ├── synthetic_mzml.py ├── synthetic_mzml.py.bck └── todos.md ├── tests ├── __init__.py ├── data │ └── molecules_test.csv ├── test_fragmentation.py ├── test_lib.py ├── test_noise_injection.py ├── test_peak_distribution.py ├── test_smiter_cli.py └── test_synthetic_mzml.py └── tox.ini /.github/dependabot.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LeidelLab/SMITER/HEAD/.github/dependabot.yml -------------------------------------------------------------------------------- /.github/workflows/black.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LeidelLab/SMITER/HEAD/.github/workflows/black.yml 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