documentation prepared for filling

README.rst

@@ -1,5 +1,5 @@
-spectrum_fundamentals
-===========================
+Spectrum Fundamentals
+=====================
 
 |PyPI| |Python Version| |License| |Read the Docs| |Build| |Tests| |Codecov| |pre-commit| |Black|
 
@@ -21,7 +21,7 @@ spectrum_fundamentals
 .. |Tests| image:: https://github.com/wilhelm-lab/spectrum_fundamentals/workflows/Run%20spectrum_fundamentals%20Tests/badge.svg
    :target: https://github.com/wilhelm-lab/spectrum_fundamentals/actions?workflow=Tests
    :alt: Run Tests Status
-.. |Codecov| image:: https://codecov.io/gh/wilhelm-lab/spectrum_fundamentals/branch/master/graph/badge.svg
+.. |Codecov| image:: https://codecov.io/gh/wilhelm-lab/spectrum_fundamentals/branch/main/graph/badge.svg
    :target: https://codecov.io/gh/wilhelm-lab/spectrum_fundamentals
    :alt: Codecov
 .. |pre-commit| image:: https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white
@@ -31,43 +31,10 @@ spectrum_fundamentals
    :target: https://github.com/psf/black
    :alt: Black
 
-Spectrum Fundamentals
-=====================
-
-Spectrum Fundamentals is a package we use in our rescoring pipeline. It was created to be able to handle spectra from different files.
-
-Features
---------
-
-- Annotate Spectra.
-- Modify peptide sequence to follow one of the recommended notations of ProForma.
-- Generate features than can be used by percoltor for rescoring (spectral angle, cosine similarity, Pearson's correlation, Spearman's correlation, etc.).
-
-
-Installation
-------------
-
-You can install *spectrum_fundamentals* via pip_ from PyPI_:
-
-.. code:: console
-
-   $ pip install spectrum_fundamentals
-
-
-Usage
------
-
-Please see the `Command-line Reference <Usage_>`_ for details.
-
-
-Credits
--------
-
-This package was created with cookietemple_ using Cookiecutter_ based on Hypermodern_Python_Cookiecutter_.
+spectrum_fundamentals is a package primarily developed for usage within the rescoring and spectral library generation pipeline oktoberfest (https://github.com/wilhelm-lab/oktoberfest).
 
-.. _cookietemple: https://cookietemple.com
-.. _Cookiecutter: https://github.com/audreyr/cookiecutter
-.. _PyPI: https://pypi.org/
-.. _Hypermodern_Python_Cookiecutter: https://github.com/cjolowicz/cookiecutter-hypermodern-python
-.. _pip: https://pip.pypa.io/
-.. _Usage: https://spectrum_fundamentals.readthedocs.io/en/latest/usage.html
+It provides the following functionalities:
+ -  conversion between search engine-specific modstrings and the ProForma standard
+ -  calculation of theoretical peptide / ion masses
+ -  annotation of spectra
+ -  spectral similarity calculation with various metrics

ReadMe.md

@@ -1,35 +1,30 @@
-# Spectrum Fundamentals
-
-Spectrum Fundamentals is a package we use in our rescoring pipeline. It was created to be able to handle spectra from different files.
-
-## Features
+[![PyPI](https://img.shields.io/pypi/v/spectrum_fundamentals.svg)](https://pypi.org/project/spectrum_fundamentals/)
+[![Python Version](https://img.shields.io/pypi/pyversions/spectrum_fundamentals)](https://pypi.org/project/spectrum_fundamentals)
+[![License](https://img.shields.io/github/license/wilhelm-lab/spectrum_fundamentals)](https://opensource.org/licenses/MIT)
+[![Read the Docs](https://img.shields.io/readthedocs/spectrum_fundamentals/latest.svg?label=Read%20the%20Docs)](https://spectrum_fundamentals.readthedocs.io/)
+[![Build](https://github.com/wilhelm-lab/spectrum_fundamentals/workflows/Build%20oktoberfest%20Package/badge.svg)](https://github.com/wilhelm-lab/spectrum_fundamentals/actions?workflow=Package)
+[![Tests](https://github.com/wilhelm-lab/spectrum_fundamentals/workflows/Run%20oktoberfest%20Tests/badge.svg)](https://github.com/wilhelm-lab/spectrum_fundamentals/actions?workflow=Tests)
+[![Codecov](https://codecov.io/gh/wilhelm-lab/spectrum_fundamentals/branch/main/graph/badge.svg)](https://codecov.io/gh/wilhelm-lab/spectrum_fundamentals)
+[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
+[![Black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
--   Annotate Spectra.
--   Modify peptide sequence to follow one of the recommended notations of ProForma.
--   Generate features than can be used by percoltor for rescoring (spectral angle, cosine similarity, Pearson's correlation, Spearman's correlation, etc.).
-
-## Installation
-
-Install with:
+# Spectrum Fundamentals
 
-```
-pip install git+https://github.com/wilhelm-lab/spectrum_fundamentals
-```
+spectrum_fundamentals is a package primarily developed for usage within the rescoring and spectral library generation pipeline oktoberfest (https://github.com/wilhelm-lab/oktoberfest).
 
-## Usage
+It provides the following functionalities:
 
-### Annotation Pipeline
+-   conversion between search engine-specific modstrings and the ProForma standard
+-   calculation of theoretical peptide / ion masses
+-   annotation of spectra
+-   spectral similarity calculation with various metrics
 
-The annotation script can be found in the package in annotation/annotation.py.
+## Documentation
 
--   Install and import the function:
+The official documentation can be found at https://spectrum_fundamentals.readthedocs.io
 
-```
-from spectrum_fundamentals.annotation.annotation import annotate_spectra
-```
+## How to cite
 
--   Apply the function on any given dataframe with peptides meta data, raw intensities and mz:
+Please always cite the main publication:
 
-```
-annotate_spectra(dataframe)
-```
+[Oktoberfest] Picciani M, Gabriel W, Giurcoiu VG et al. (2023), _Oktoberfest: Open-source spectral library generation and rescoring pipeline based on Prosit_, [Proteomics](https://doi.org/10.1002/pmic.202300112)

docs/API.rst

@@ -1,41 +1,33 @@
-.. module:: spectrum_io
+.. module:: spectrum_fundamentals
 
-.. automodule:: spectrum_io
+.. automodule:: spectrum_fundamentals
    :noindex:
 
 API
 ===
 
-Import SpectrumIO using
+Import spectrum_fundamentals using
 
 .. code-block:: python
 
-   import spectrum_io as specio
+   import spectrum_fundamentals as specfun
 
-File conversions
-----------------
 
-.. module:: spectrum_io.d
+Modstring conversions: :code:`convert`
+--------------------------------------
 
-.. currentmodule:: spectrum_io
 
-Todo: add functions for bruker d conversions here
+Peptide and ion mass / mz calculations: :code:`peptide`
+-------------------------------------------------------
 
-.. autosummary::
-   :toctree: api/d
 
-.. module:: spectrum_io.raw
+Annotation of spectra: :code:`annot`
+------------------------------------
 
-.. currentmodule:: spectrum_io
 
-Todo: add functions for thermoraw here
-
-Modstring conversions
----------------------
-
-Todo
-----
-
-other modules
+Spectral similarity calculation: :code:`similarity`
+---------------------------------------------------
 
 
+Further utility functions: :code:`utils`
+----------------------------------------

docs/_key_contributors.rst

@@ -5,11 +5,11 @@
    * `Mario Picciani <https://github.com/picciama>`_: lead developer since 2022, maintainer
    * `Mostafa Kalhor <https://github.com/mostafakalhor>`_: developer, crosslinking
    * `Wassim Gabriel <https://github.com/WassimG>`_: developer, PTMs, neutral losses, GUI
-   * Arne van den Berg: developer, diverse contributions
+   * `Arne van den Berg <https://github.com/arne-vdb>`_: developer, diverse contributions
    * `Victor-George Giurcoiu <https://github.com/victorgiurcoiu>`_: developer, diverse contributions
    * `Ludwig Lautenbacher <https://github.com/LLautenbacher>`_: developer, Koina, GUI
    * `Armin Soleymaniniya <https://github.com/arminsl>`_: developer, GUI
-   * Ayla Schröder: developer, pickedGroupFDR
+   * `Ayla Schröder <https://github.com/ayla-s>`_: developer, pickedGroupFDR
    * Zixuan Xiao: developer, GUI
 
    Previous developers

docs/contributing.rst

@@ -32,7 +32,7 @@ Request features on the `Issue Tracker`_.
 How to set up your development environment
 ------------------------------------------
 
-You need Python 3.8+ and the following tools:
+You need Python 3.9+ and the following tools:
 
 - Poetry_
 - Nox_

docs/index.rst

@@ -22,3 +22,4 @@
    reference
 
 .. _github: https://github.com/wilhelm-lab/spectrum_fundamentals
+

docs/installation.rst

@@ -1,9 +1,12 @@
 .. highlight:: shell
 
-============
 Installation
 ============
 
-.. include:: ../README.rst
-   :start-line: 40
-   :end-line: 47
+spectrum_fundamentals is listed on the Python Package Index (PyPI) and can be installed with pip.
+
+.. code-block:: bash
+
+   pip install spectrum_fundamentals
+
+

docs/quickstart.rst

@@ -3,4 +3,5 @@ Quickstart
 
 -  Discuss usage, development and issues on `GitHub <https://github.com/wilhelm-lab/spectrum_fundamentals>`_.
 -  Check the `usage principles <./usage.html>`_ or the `API <./API.html>`_.
--  Check the `Contributor Guide <./contributing.html>`_ if you want to participate in developing.
+-  Check the `Contributor Guide <./contributing.html>`_ if you want to participate in developing.
+-  Consider citing the main publication, `Oktoberfest <https://doi.org/10.1002/pmic.202300112>`_.

docs/reference.rst

@@ -1,2 +1,8 @@
-References
-==========
+How to cite
+===========
+
+If you want to cite spectrum_fundamentals in your work, please cite the main Oktoberfest publication following:
+
+.. [1] Picciani M, Gabriel W, Giurcoiu VG et al. (2023),
+    *Oktoberfest: Open-source spectral library generation and rescoring pipeline based on Prosit*,
+    `Proteomics <https://doi.org/10.1002/pmic.202300112>`__.