├── .github └── workflows │ └── actions.yml ├── .gitignore ├── .readthedocs.yml ├── LICENSE ├── README.md ├── conda.recipe └── recipe.yaml ├── deimos ├── __init__.py ├── alignment.py ├── calibration.py ├── cli.py ├── deconvolution.py ├── filters.py ├── grid.py ├── io.py ├── isotopes.py ├── peakpick.py ├── plot.py ├── subset.py └── utils.py ├── docs ├── Makefile ├── make.bat └── source │ ├── api_reference │ ├── alignment.rst │ ├── calibration.rst │ ├── cli.rst │ ├── deconvolution.rst │ ├── deimos.rst │ ├── filters.rst │ ├── grid.rst │ ├── io.rst │ ├── isotopes.rst │ ├── peakpick.rst │ ├── plot.rst │ ├── subset.rst │ └── utils.rst │ ├── assets │ ├── icon.png │ ├── logo.png │ └── overview.png │ ├── conf.py │ ├── generate_skeleton.py │ ├── getting_started │ ├── cli.rst │ ├── example_data.rst │ └── installation.rst │ ├── index.rst │ ├── project_info │ ├── acknowledgements.rst │ ├── citing_and_citations.rst │ ├── contributing.rst │ ├── disclaimer.rst │ └── license.rst │ ├── requirements.txt │ └── user_guide │ ├── alignment.ipynb │ ├── ccs_calibration.ipynb │ ├── extracted_ion.ipynb │ ├── isotope_detection.ipynb │ ├── loading_saving.ipynb │ ├── ms2_extraction.ipynb │ └── peak_detection.ipynb ├── environment.yml ├── examples ├── alignment.ipynb ├── ccs_calibration.ipynb ├── extracted_ion.ipynb ├── isotope_detection.ipynb ├── loading_saving.ipynb ├── ms2_extraction.ipynb └── peak_detection.ipynb ├── requirements.txt ├── setup.py ├── tests ├── __init__.py ├── resources │ ├── example_data.h5 │ └── isotope_example_data.h5 ├── test_alignment.py ├── test_calibration.py ├── test_deconvolution.py ├── test_deimos.py ├── test_filters.py ├── test_grid.py ├── test_io.py ├── test_isotopes.py ├── test_peakpick.py ├── test_subset.py └── test_utils.py └── workflows ├── __init__.py ├── default.smk └── default_config.yaml /.github/workflows/actions.yml: -------------------------------------------------------------------------------- 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