OpenMS · tapaswenipathak · May 29, 2022 · May 27, 2022 · May 27, 2022 · May 27, 2022
diff --git a/conf.py b/conf.py
@@ -37,6 +37,7 @@
   'myst_parser',
   'notfound.extension',
   'sphinxcontrib.images',
+  'sphinx_inline_tabs',
 ]
 
 autosummary_generate = True

diff --git a/docs/additional-resources/openms-git-workflow.md b/docs/additional-resources/openms-git-workflow.md
@@ -14,8 +14,8 @@ Naming conventions for the following apply:
 * A **local repository** is the repository that lies on your hard drive after cloning.
 * A **remote repository** is a repository on a git server such as GitHub.
 * A **fork** is a copy of a repository. Forking a repository allows you to freely experiment with changes without affecting the original project.
-* **Origin** refers to a remote repository that you have forked. Call this repository https://github.com/_YOURUSERNAME_/OpenMS.
-* **Upstream** refers to the original remote OpenMS repository. Call this repository https://github.com/OpenMS/OpenMS.
+* **Origin** refers to a remote repository that you have forked. Call this repository `https://github.com/_YOURUSERNAME_/OpenMS`.
+* **Upstream** refers to the original remote OpenMS repository. Call this repository `https://github.com/OpenMS/OpenMS`.
 
 ## Create fork
 

diff --git a/docs/contact-us.md b/docs/contact-us.md
@@ -1,9 +1,11 @@
 Contact Us
 =========
 
-Contact us:
+Join us on [Discord](https://discord.com/invite/swkxs72CHB)!
 
-1. Using the user and contributor real time [Gitter chat](https://gitter.im/OpenMS/OpenMS).
+You can also contact us:
+
+1. On the user and contributor real time [Gitter chat](https://gitter.im/OpenMS/OpenMS).
 2. Drop us an email at user support [open-ms-general](https://sourceforge.net/projects/open-ms/lists/open-ms-general)
    mailing list.
 3. To stay updated of new versions of OpenMS and releases, subscribe to [openms-announcements mailing list](https://sourceforge.net/projects/open-ms/lists/open-ms-announcements).

diff --git a/docs/downloads.md b/docs/downloads.md
@@ -1,9 +1,4 @@
-Downloads
-========
-
-Download OpenMS installers, workflows, and other resources.
-
-# OpenMS installers
+# OpenMS Installers
 
 | Platform | Name | SHA256 Hash |
 |----------|------|-------------|
@@ -17,27 +12,27 @@ Download OpenMS installers, workflows, and other resources.
 
 | Workflow | Description | Download Link |
 |----------|-------------|---------------|
-|ProteomicsLFQ_tool_and_MSstats_postprocessing | Label-free identification and quantification using the comet search engine, the ProteomicsLFQ tool and statistical down-stream processing using MSstats. Compared to the other proteomics LFQ workflows, it is less complex as it combines quantification and inference steps in a single ProtemicLFQ tool. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/ProteomicsLFQ_tool_and_MSstats_postprocessing.knwf?raw=true) |
-| basic_peptide_identification | Label-free identification using the omssa search engine. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/basic_peptide_identification.knwf?raw=true) |
-| DIAMetAlyzer | Metabolomics assay library construction with decoy generation from DDA data and targeted DIA analysis using OpenSWATH and pyprophet for statistical validation. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/DIAMetAlyzer.knwf?raw=true) |
-| Identification_quantification_with_inference_isobaric_epifany_MSstatsTMT | Identification and quantification for isobaric experiments using MSGFPlus as search engine, epifany for inference and MSstatsTMT for statistical down-stream analysis. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/Identification_quantification_with_inference_isobaric_epifany_MSstatsTMT.knwf?raw=true) |
-| labelfree_with_protein_quantification | Label-free with protein quantification steps implemented using individual OpenMS tools | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/labelfree_with_protein_quantification.knwf?raw=true) |
-| Metabolite_Adduct_Grouping | Quantification and identification via accurate mass based on multiple adduct grouping steps (adducts, neutral losses). | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/Metabolite_Adduct_Grouping.knwf?raw=true) |
-| Metabolite_DeNovoID | Quantification and identification via adduct grouping and de-novo identification using SIRIUS/CSI:FingerID. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/Metabolite_DeNovoID.knwf?raw=true) |
-| Metabolite_ID | Quantification and identification via accurate mass based with downstream processing and visualisation. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/Metabolite_ID.knwf?raw=true) |
-| Metabolite_SpectralID | Identification via spectral library search for small molecules. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/Metabolite_SpectralID.knwf?raw=true) |
-| MSstats_statPostProcessing_iPRG2015 | Post processing workflow for using MSstats based on "Example_OneTool_ProteomicsLFQ_MSstats.knwf" | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/MSstats_statPostProcessing_iPRG2015.knwf?raw=true) |
-| MSstatsTMT | Post processing workflow for using MSstatsTMT based on "Identification_quantification_with_inference_isobaric_epifany_MSstatsTMT". | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/MSstatsTMT.knwf?raw=true) |
-| OpenSWATH | Targeted extraction and scoring of transitions in DIA data based on an (iRT) assay library. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/OpenSWATH.knwf?raw=true) |
-| Phosphoproteomics_ID | Identification of Phosphorilation sites. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/Phosphoproteomics_ID.knwf?raw=true) |
+|`ProteomicsLFQ_tool_and_MSstats_postprocessing` | Label-free identification and quantification using the comet search engine, the ProteomicsLFQ tool and statistical down-stream processing using MSstats. Compared to the other proteomics LFQ workflows, it is less complex as it combines quantification and inference steps in a single ProtemicLFQ tool. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/ProteomicsLFQ_tool_and_MSstats_postprocessing.knwf?raw=true) |
+|`basic_peptide_identification` | Label-free identification using the omssa search engine. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/basic_peptide_identification.knwf?raw=true) |
+|`DIAMetAlyzer` | Metabolomics assay library construction with decoy generation from DDA data and targeted DIA analysis using OpenSWATH and pyprophet for statistical validation. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/DIAMetAlyzer.knwf?raw=true) |
+|`Identification_quantification_with_inference_isobaric_epifany_MSstatsTMT` | Identification and quantification for isobaric experiments using MSGFPlus as search engine, epifany for inference and MSstatsTMT for statistical down-stream analysis. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/Identification_quantification_with_inference_isobaric_epifany_MSstatsTMT.knwf?raw=true) |
+|`labelfree_with_protein_quantification` | Label-free with protein quantification steps implemented using individual OpenMS tools | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/labelfree_with_protein_quantification.knwf?raw=true) |
+|`Metabolite_Adduct_Grouping` | Quantification and identification via accurate mass based on multiple adduct grouping steps (adducts, neutral losses). | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/Metabolite_Adduct_Grouping.knwf?raw=true) |
+|`Metabolite_DeNovoID` | Quantification and identification via adduct grouping and de-novo identification using SIRIUS/CSI:FingerID. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/Metabolite_DeNovoID.knwf?raw=true) |
+|`Metabolite_ID` | Quantification and identification via accurate mass based with downstream processing and visualisation. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/Metabolite_ID.knwf?raw=true) |
+|`Metabolite_SpectralID` | Identification via spectral library search for small molecules. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/Metabolite_SpectralID.knwf?raw=true) |
+|`MSstats_statPostProcessing_iPRG2015` | Post processing workflow for using MSstats based on "Example_OneTool_ProteomicsLFQ_MSstats.knwf" | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/MSstats_statPostProcessing_iPRG2015.knwf?raw=true) |
+|`MSstatsTMT` | Post processing workflow for using MSstatsTMT based on "Identification_quantification_with_inference_isobaric_epifany_MSstatsTMT". | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/MSstatsTMT.knwf?raw=true) |
+|`OpenSWATH` | Targeted extraction and scoring of transitions in DIA data based on an (iRT) assay library. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/OpenSWATH.knwf?raw=true) |
+|`Phosphoproteomics_ID` | Identification of Phosphorilation sites. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/Phosphoproteomics_ID.knwf?raw=true) |
 
 # OpenMS Releases
 
-| Release |  Installers |
-|---------|-------------|
-| Stable release | [Archive Link](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/) |
-| RC release | [Archive Link](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/RC/) |
-| Nightly release | [Archive Link](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/nightly/) |
+| Release                                                |  Installers |
+|--------------------------------------------------------|-------------|
+| Stable release    | [Archive Link](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/) |
+| RC release        | [Archive Link](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/RC/) |
+| Nightly release   | [Archive Link](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/nightly/) |
 
 # Other Resources
 

diff --git a/docs/guides/user-guides/user-quickstart-guide.md b/docs/guides/user-guides/user-quickstart-guide.md
@@ -2,14 +2,14 @@ User Quickstart Guide
 ====================
 
 Read the User Quickstart guide to gain a brief understanding of key concepts and how to use the tools. For more in-depth
-information, consult [OpenMS documentation]().
+information, consult [OpenMS API Reference](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/index.html).
 
 ## What is OpenMS
 
-[OpenMS.org](https://www.openms.de/) is a free, open-source C++ library with Python bindings. It is commonly used for liquid
+[OpenMS](https://www.openms.de/) is a free, open-source C++ library with Python bindings. It is commonly used for liquid
 chromatography-mass spectrometry (LC-MS) data management and analyses. OpenMS provides an infrastructure for the rapid
 development of mass spectrometry related software as well as a rich toolset built on top of it. OpenMS is available
-under the three clause BSD licence and runs under Windows, macOS, and Linux operating systems.
+under the [three clause BSD licence](https://github.com/OpenMS/OpenMS/blob/develop/LICENSE) and runs under Windows, macOS, and Linux operating systems.
 
 ## Background
 

diff --git a/docs/index.rst b/docs/index.rst
@@ -42,6 +42,7 @@ Contents
    installations/installation-on-gnu-linux
    installations/installation-on-windows
    installations/installation-on-macos
+   installations/build-openms-from-source
 
 .. toctree::
    :maxdepth: 2

diff --git a/docs/installations/installation-on-macos.md b/docs/installations/installation-on-macos.md
@@ -8,25 +8,25 @@ To install OpenMS on macOS, run the following steps:
 1. Download and install the macOS drag-and-drop installer from the [archive](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/latest/).
 2. Double click on the dowloaded file. It will start to open the download `openms-<version>-macos.dmg` file
 
-<img src="https://raw.githubusercontent.com/OpenMS/OpenMS-docs/main/docs/images/installations/macos/opening-openms%3Cversion%3E-macos.png" alt="Verifying OpenMS-<version>-macOS.dmg" width="500" float: left/>
+<img src="https://raw.githubusercontent.com/OpenMS/OpenMS-docs/staging/docs/images/installations/macos/opening-openms%3Cversion%3E-macos.png" alt="Verifying OpenMS-<version>-macOS.dmg" width="500" float: left/>
 
 3. Verify the download.
 
-<img src="https://raw.githubusercontent.com/OpenMS/OpenMS-docs/main/docs/images/installations/macos/verifying-OpenMS%3Cversion%3E.png" alt="Verifying OpenMS-<version>-macOS.dmg" width="500" float: left/>
+<img src="https://raw.githubusercontent.com/OpenMS/OpenMS-docs/staging/docs/images/installations/macos/verifying-OpenMS%3Cversion%3E.png" alt="Verifying OpenMS-<version>-macOS.dmg" width="500" float: left/>
 
 4. Agree the license agreements.
 
-<img src="https://raw.githubusercontent.com/OpenMS/OpenMS-docs/main/docs/images/installations/macos/license-agreements.png" alt="License Agreement" width="500" float: left/>
+<img src="https://raw.githubusercontent.com/OpenMS/OpenMS-docs/staging/docs/images/installations/macos/license-agreements.png" alt="License Agreement" width="500" float: left/>
 
 5. Drag openms to applications.
 
-<img src="https://raw.githubusercontent.com/OpenMS/OpenMS-docs/main/docs/images/installations/macos/move-openms-to-applications.png" alt="License Agreement" width="500" float: left/>
+<img src="https://raw.githubusercontent.com/OpenMS/OpenMS-docs/staging/docs/images/installations/macos/move-openms-to-applications.png" alt="License Agreement" width="500" float: left/>
 
 6. It will start copying to applications.
 
-<img src="https://raw.githubusercontent.com/OpenMS/OpenMS-docs/main/docs/images/installations/macos/preparing-to-copy-to-applications.png" alt="Preparing to Copy to Applications" width="500" float: left/>
+<img src="https://raw.githubusercontent.com/OpenMS/OpenMS-docs/staging/docs/images/installations/macos/preparing-to-copy-to-applications.png" alt="Preparing to Copy to Applications" width="500" float: left/>
 
-<img src="https://raw.githubusercontent.com/OpenMS/OpenMS-docs/main/docs/images/installations/macos/copying-to-applications.png" alt="Copying to Applications" width="500" float: left/>
+<img src="https://raw.githubusercontent.com/OpenMS/OpenMS-docs/staging/docs/images/installations/macos/copying-to-applications.png" alt="Copying to Applications" width="500" float: left/>
 
 To use TOPP as regular app in the shell, add the following lines to the `~/.profile` file.
 

diff --git a/docs/introduction.md b/docs/introduction.md
@@ -26,7 +26,7 @@ of ions are stored in mass spectra and used to identify and quantify the analyte
 methods. The quantity and identity of analytes can then be used, for instance, in biomarker discovery, medical diagnostics,
 or basic research.
 
-# Liquid Chromatography(LC)
+## Liquid Chromatography(LC)
 
 LC aims to reduce the complexity of the measured sample by separating analytes based on their physicochemical properties.
 Separating analytes in time ensures that a manageable amount of analytes elute at the same time. In mass
@@ -45,7 +45,7 @@ spectrometer.
 
 ![](images/introduction/introduction_LC.png)
 
-# Mass Spectrometry
+## Mass Spectrometry
 
 MS is an analytical technique used to determine the mass of molecules. In order to achieve highly accurate and sensitive
 mass measurements at the atomic scale, mass spectrometers manipulate charged particles using magnetic and electrostatic
@@ -87,3 +87,19 @@ spectrometry (MS/MS) can be applied to assess the analyte substructure. To this
 kinetically fragmented using an inert gas (e.g., Argon). Fragments produced by collision-induced fragmentation (CID) are
 stored in an MS2 (or MS/MS) spectrum and provide information that helps to resolve the ambiguities in identification.
 Alternatively, MS/MS spectra can be used for quantification.
+
+Get started with installing OpenMS using the installers available for different operating systems!
+
+## Installation on different platforms
+
+```{tab} GNU/Linux
+wget https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/latest/OpenMS-2.8.0-Debian-Linux-x86_64.deb
+```
+
+```{tab} Windows
+wget https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/latest/OpenMS-2.8.0-Win64.exe
+```
+
+```{tab} MacOS
+wget https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/latest/OpenMS-2.8.0-macOS.dmg
+```
diff --git a/docs/topp/topp.md b/docs/topp/topp.md
@@ -10,7 +10,13 @@ experiments and OpenSWATH, peptide property prediction, cross-linking, quality-c
 
 Few of the graphical tools are explained below:
 
-- [TOPPView](toppview.md): A viewer for mass spectrometry data.
-- [TOPPAS](toppas.md): An assistant for GUI-driven TOPP workflow design.
-- [INIFileEditor](ini-file-editor.md): An editor for OpenMS configuration files.
-- [SwathWizard](swathwizard.md): A user-friendly step-by-step wizard for SWATH data analysis.
+```{toctree}
+:maxdepth: 1
+
+toppview: A viewer for mass spectrometry data.
+toppas: An assistant for GUI-driven TOPP workflow design.
+ini-file-editor: An editor for OpenMS configuration files.
+swathwizard: A user-friendly step-by-step wizard for SWATH data analysis.
+```
+
+For advanced documentation on every TOPP tool, see the [OpenMS TOPP API Reference](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_documentation.html).
diff --git a/docs/tutorials/TOPP/TOPP-tutorial.md b/docs/tutorials/TOPP/TOPP-tutorial.md
@@ -6,48 +6,72 @@ compared to OpenMS. Later, we will move to the handling of TOPPView which is our
 TOPPView can also be used to analyze it using selected TOPP tools; how-to is explained in the third part of the tutorial.
 Finally, the tutorial lists the command line interfaces for all TOPP tools contained in the release.
 
-## Concepts
+# Concepts
 
 Let's understand the intent of [TOPP and OpenMS](topp-and-openms-introduction.md) in this part.
 
-## TOPPView Main Interface
+```{toctree}
+:maxdepth: 1
+
+topp-and-openms-introduction
+```
+
+# TOPPView Main Interface
 
 In this part of the tutorial, we will learn about the main features of TOPPView and its basic uses.
 
-- [TOPPView introduction](toppview-introduction.md)
-- [Views in TOPPView](views-in-toppview.md)
-- [Display modes and view options](display-modes-and-view-options.md)
-- [Data analysis in TOPPView](data-analysis-in-toppview.md)
-- [Data editing](data-editing-in-toppview.md)
-- [Hotkeys](hotkeys-table.md)
+```{toctree}
+:maxdepth: 1
 
-## Calling TOPP tools from TOPPView
+toppview-introduction
+views-in-toppview
+display-modes-and-view-options
+data-analysis-in-toppview
+data-editing-in-toppview
+hotkeys-table
+```
+
+# Calling TOPP tools from TOPPView
 
 This part of the tutorial illustrates how to interactively analyse proteomics data using TOPP tools from within TOPPView.
 
-- [Smoothing raw data](smoothing-raw-data.md)
-- [Subtracting a baseline from a spectrum](subtracting-a-baseline-from-a-spectrum.md)
-- [Picking peaks](picking-peaks.md)
-- [Feature detection on centroided data](feature-detection-on-centroided-data.md)
+```{toctree}
+:maxdepth: 1
+
+smoothing-raw-data
+subtracting-a-baseline-from-a-spectrum
+picking-peaks
+feature-detection-on-centroided-data
+```
 
-## Advanced Users: Tips & Tricks
+# Advanced Users: Tips & Tricks
 
 Read [TOPP for Advanced Users](topp-for-advanced-users.md) to know more about how to use advanced functionalities,
 increasing productivity.
 
-## Scripting with TOPP
+```{toctree}
+:maxdepth: 1
+
+topp-for-advanced-users
+```
+
+# Scripting with TOPP
 
 This part of the tutorial gives a detailed overview of the most important TOPP tools. First, some basics needed for
 every TOPP tool are explained, then several example pipelines are shown.
 
-- [General introduction](general-introduction.md)
-- [File Handling](file-handling.md)
-- [Profile data processing](profile-data-processing.md)
-- [Calibration](calibration.md)
-- [Map alignment](map-alignment.md)
-- [Feature detection](feature-detection.md)
-- [Feature grouping](feature-grouping.md)
-- [Consensus peptide identification](consensus-peptide-identification.md)
-- [Peptide property prediction](peptide-property-prediction.md)
-- [Quality control](quality-control.md)
-- [Conversion between OpenMS XML formats and text formats](conversion-between-openms-xml-formats-and-text-formats.md)
+```{toctree}
+:maxdepth: 1
+
+general-introduction
+file-handling
+profile-data-processing
+calibration
+map-alignment
+feature-detection
+feature-grouping
+consensus-peptide-identification
+peptide-property-prediction
+quality-control
+conversion-between-openms-xml-formats-and-text-formats
+```