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Merge pull request #442 from cbielow/tutorial_enhancements
Tutorial enhancements
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‎.github/workflows/test-pr.yaml

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name: Build and Test code in notebooks
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on:
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pull_request:
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branches:
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- master
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jobs:
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build-test:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/setup-python@v4
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with:
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python-version: '3.10' # Version range or exact version of a Python version to use, using SemVer's version range syntax
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- name: Get changed files
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id: changed-files
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uses: tj-actions/changed-files@v41
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with:
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dir_names_max_depth: 0
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files: |
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docs/source/*.rst
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docs/source/**/*.rst
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!docs/source/**/_templates
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- uses: r-lib/actions/setup-pandoc@v2
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with:
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pandoc-version: '3.1.2'
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# - uses: actions/setup-python@v4
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# with:
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# python-version: '3.7' # Version range or exact version of a Python version to use, using SemVer's version range syntax
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- name: Installing Dependencies
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run: |
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python3 -m pip install --upgrade pip
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python3 -m pip install --upgrade pandocfilters jupyter
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python3 -m pip install --upgrade -r requirements.txt
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- name: Generating notebooks
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run: |
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pushd docs/source
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./generate_ipynb.sh
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popd
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- name: Execute all notebooks generated from modified files
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run: |
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for file in ${{ steps.changed-files.outputs.all_modified_files }}; do
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jupyter nbconvert --to notebook --inplace --execute ${file%.rst}.ipynb || (echo "${file%.rst}" >> failed_nbs.txt)
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done
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if [ -f "failed_nbs.txt" ]; then
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echo "Some notebooks failed to run. Please check logs."
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cat failed_nbs.txt
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exit 1
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fi
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name: Build and Test code in notebooks
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on:
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pull_request:
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branches:
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- master
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jobs:
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build-test:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/setup-python@v4
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with:
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python-version: '3.10' # Version range or exact version of a Python version to use, using SemVer's version range syntax
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- name: Get changed files
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id: changed-files
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uses: tj-actions/changed-files@v45
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with:
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dir_names_max_depth: 0
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files: |
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docs/source/*.rst
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docs/source/**/*.rst
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!docs/source/**/_templates
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- uses: r-lib/actions/setup-pandoc@v2
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with:
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pandoc-version: '3.1.2'
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# - uses: actions/setup-python@v4
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# with:
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# python-version: '3.7' # Version range or exact version of a Python version to use, using SemVer's version range syntax
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- name: Installing Dependencies
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run: |
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python3 -m pip install --upgrade pip
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python3 -m pip install --upgrade pandocfilters jupyter
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python3 -m pip install --upgrade -r requirements.txt
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- name: Generating notebooks
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run: |
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pushd docs/source
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./generate_ipynb.sh
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popd
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- name: Execute all notebooks generated from modified files
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run: |
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for file in ${{ steps.changed-files.outputs.all_changed_files }}; do
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jupyter nbconvert --to notebook --inplace --execute ${file%.rst}.ipynb || (echo "${file%.rst}" >> failed_nbs.txt)
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done
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if [ -f "failed_nbs.txt" ]; then
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echo "Some notebooks failed to run. Please check logs."
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cat failed_nbs.txt
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exit 1
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fi

‎.gitignore

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@@ -5,4 +5,5 @@ docs/source/_autosummary/*
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docs/source/apidocs/_autosummary/*
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docs/source/_build/
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docs/build/
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venv
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venv
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build/

‎docs/README.md

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pyOpenMS Documentation
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======================
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The source code for the pyOpenMS documentation lies here. We use sphinx to
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build documentation and to build you can run
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build documentation.
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Preparation
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Install Sphinx (which is a Python package) and some of its modules/plugins.
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We recommend doing this in a [python venv](https://docs.python.org/3/library/venv.html).
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python -m venv /path/to/myenv
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# activate it, e.g.
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source <venv>/bin/activate
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sphinx-build source/ build/
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Once the environment is active, you can install all required python packages using
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On a linux system, you can also use the provided Makefile and run
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cd <pyOpenMS_dir>/docs
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pip install -r requirements.txt
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To build the docs run the line below (works on all operating systems), but make sure that your working dir is `<pyOpenMS_dir>/docs` (see above):
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make html
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and check validity of links using
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make linkcheck
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‎docs/make.bat

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@ECHO OFF
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pushd %~dp0
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REM Command file for Sphinx documentation
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if "%SPHINXBUILD%" == "" (
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set SPHINXBUILD=sphinx-build
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)
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set SOURCEDIR=source
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set BUILDDIR=build
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if "%SPHINXOPTS%" == "" (
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set SPHINXOPTS=-j auto
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)
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%SPHINXBUILD% >NUL 2>NUL
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if errorlevel 9009 (
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echo.
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echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
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echo.installed, then set the SPHINXBUILD environment variable to point
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echo.to the full path of the 'sphinx-build' executable. Alternatively you
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echo.may add the Sphinx directory to PATH.
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echo.
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echo.If you don't have Sphinx installed, grab it from
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echo.https://www.sphinx-doc.org/
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exit /b 1
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)
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if "%1" == "" goto help
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%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
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goto end
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:help
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%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
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:end
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popd

‎docs/requirements.txt

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sphinx-copybutton==0.5.1
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sphinx-hoverxref
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sphinx-remove-toctrees
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## for pygment coloring of code snippets using ipython syntax
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ipython
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pygments-lexer-pseudocode
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--extra-index-url https://pypi.cs.uni-tuebingen.de/simple/
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pyopenms

‎docs/source/community/index.rst

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All edits need to happen through the .rst files in the OpenMS/pyopenms-docs repository.)
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If you are unsure how to do that or want to discuss questions
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(e.g. your example workflow can be included on this webpage) contact us via the
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`OpenMS Gitter chat channel <https://gitter.im/OpenMS/OpenMS/>`_.
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(e.g. your example workflow can be included on this webpage) contact the
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`contact the OpenMS team <https://openms.de/communication/>`_ today.
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pyopenms sources
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----------------

‎docs/source/community/wrapping_workflows_new_classes.rst

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- Note: The space between the hash and wrap-doc (# wrap-doc) is not necessary, but used for consistency.
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- Note: Please start the comment with a capital letter.
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See the next section for a `simple example <#A-Simple-Example>`_ and a more `advanced example <#A-Further-Example>`_ of a wrapped class with several functions.
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See the next section for a `simple example <#a-simple-example>`_ and a more `advanced example <#a-further-example>`_ of a wrapped class with several functions.
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How to Wrap New Classes
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^^^^^^^^^^^^^^^^^^^^^^^

‎docs/source/hyperscore.rst

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This file was deleted.

‎docs/source/index.rst

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Summary
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=======
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pyOpenMS is an open-source Python library for :term:`mass spectrometry<Mass spectrometry>`, specifically for the analysis of proteomics
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pyOpenMS is an open-source Python library for :term:`mass spectrometry<Mass Spectrometry>`, specifically for the analysis of proteomics
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and metabolomics data in Python. pyOpenMS implements a set of Python bindings to the OpenMS library for computational
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:term:`mass spectrometry<Mass spectrometry>` and is available for Windows, Linux and macOS.
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:term:`mass spectrometry<Mass Spectrometry>` and is available for Windows, Linux and macOS.
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pyOpenMS provides functionality that is commonly used in computational mass
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spectrometry. The pyOpenMS package contains Python bindings for a large part of the `OpenMS <openms.de>`_
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library for :term:`mass spectrometry<Mass spectrometry>` based proteomics. It thus provides easy access to
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spectrometry. The pyOpenMS package contains Python bindings for a large part of the `OpenMS <https://openms.de>`_
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library for :term:`mass spectrometry<Mass Spectrometry>` based proteomics. It thus provides easy access to
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a feature-rich, open-source algorithm library for mass-spectrometry based proteomics analysis.
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pyOpenMS facilitates the execution of common tasks in proteomics (and other fields of mass spectrometry) such as
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- Chromatogram analysis (chromatographic peak picking, smoothing, elution profiles and peak scoring for :term:`SRM`/MRM/PRM/:term:`SWATH`/DIA data)
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- Interaction with common tools in proteomics and metabolomics:
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- Search engines such as Comet, Mascot, MSGF+, MSFragger, SpectraST, XTandem
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- Post-processing tools such as Percolator, MSstats, Fido
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- Search engines such as Comet, Mascot, MSGF+, MSFragger, SpectraST, Sage
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- Post-processing tools such as Percolator, MSstats, Epiphany
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- Metabolomics tools such as SIRIUS, CSI:FingerId
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‎docs/source/user_guide/adduct_detection.rst

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| **Suggested follow up step:**
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| The resulting feature map can be exported to a pandas DataFrame with adduct information from the *dc_charge_adducts* feature meta values.
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| Multiple feature maps can be `combined using the feature linking algorithms <feature_linking.html>`_. Each consensus feature will get a new meta value *best ion* based on the most common annotated adduct within the consensus feature group.
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| Multiple :term:`feature maps` can be `combined using the feature linking algorithms <feature_linking.html>`_. Each consensus feature will get a new meta value *best ion* based on the most common annotated adduct within the consensus feature group.
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.. code-block:: python
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‎docs/source/user_guide/background.rst

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Why use OpenMS
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==============
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OpenMS is an open-source, C++ framework for analyzing large volumes of mass spectrometry data.
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OpenMS is an open-source, C++ framework hosted on `Github <https://github.com/OpenMS/OpenMS>` for analyzing large volumes of mass spectrometry data.
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It has been specially designed for analyzing high performance :term:`LC-MS` data but over recent times,
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has been extended to analyze data generated by other techniques.
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.. note::
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OpenMS in recent times has been expanded to support a wide variety of mass spectrometry experiments.
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To design your analysis solution, `contact the OpenMS team <https://openms.github.io/community/>`_ today.
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To design your analysis solution, `contact the OpenMS team <https://openms.de/communication/>`_ today.
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To use OpenMS effectively, an understanding of :term:`liquid chromatography` (:term:`LC`) and
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mass spectrometry (MS) is required as many of the algorithms are based on these techniques. This

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