OpenMS · Copilot · Oct 30, 2025 · Oct 30, 2025 · Oct 30, 2025 · Oct 30, 2025
diff --git a/docs/about/installation/installation-on-macos.md b/docs/about/installation/installation-on-macos.md
@@ -13,8 +13,8 @@ To install OpenMS on macOS, run the following steps:
 2.Double click on the downloaded file. It will start to open the `OpenMS-<version>-macOS.pkg` installer file.
 
 ```{image} /_images/installations/macos/Warning-openMS-3.3.0-macOS-Silicon.pkg-Not-Opened.png
-:alt: macOS warning message when opening OpenMS-<version>-macOS.pkg  
-:width: 500px  
+:alt: macOS warning message when opening OpenMS-<version>-macOS.pkg
+:width: 500px
 ```
 **Why This Warning Appears:**
 
@@ -24,39 +24,39 @@ The warning indicates that the OpenMS installer hasn't been notarized or recogni
 
 Bypassing Gatekeeper to Install OpenMS on macOS
 
-A. Bypassing Gatekeeper Using System Settings 
+A. Bypassing Gatekeeper Using System Settings
 
-1. Open **System Settings**.  
-2. Navigate to **Privacy & Security**.  
-3. Under the **Security** section, locate the message about the blocked application.  
-4. Click the **Open Anyway** button .  
+1. Open **System Settings**.
+2. Navigate to **Privacy & Security**.
+3. Under the **Security** section, locate the message about the blocked application.
+4. Click the **Open Anyway** button .
 
 ```{image} /_images/installations/macos/Bypassing-Gatekeeper-to-Install-OpenMS-on-macOS.png
-:alt: Bypassing Gatekeeper on macOS  
-:width: 500px  
+:alt: Bypassing Gatekeeper on macOS
+:width: 500px
 ```
-B. Bypassing Gatekeeper Using Command-Line    
+B. Bypassing Gatekeeper Using Command-Line
 
-For users comfortable with the command line, you can bypass the security warning using Terminal:  
+For users comfortable with the command line, you can bypass the security warning using Terminal:
 
-1. Open **Terminal**.  
-2. Navigate to the directory containing the installer using the `cd` command:  
+1. Open **Terminal**.
+2. Navigate to the directory containing the installer using the `cd` command:
 
    ```bash
    cd /path/to/installer
    ```
-3. Run the following command to remove the quarantine attribute:   
+3. Run the following command to remove the quarantine attribute:
 
    ```bash
    xattr -d com.apple.quarantine OpenMS-<version>-macOS.pkg
    ```
-By following these steps, you’re instructing macOS to trust the OpenMS installer and allow its execution. Ensure that you’ve downloaded the installer from a **trusted source** (i.e., build archive of the Unversity of Tübingen or OpenMS' GitHub artifacts) before proceeding.     
+By following these steps, you’re instructing macOS to trust the OpenMS installer and allow its execution. Ensure that you’ve downloaded the installer from a **trusted source** (i.e., build archive of the Unversity of Tübingen or OpenMS' GitHub artifacts) before proceeding.
 
-4. Install OpenMS 
+4. Install OpenMS
 
 ```{image} /_images/installations/macos/Installation-successful-message.png
-:alt: OpenMS installation started on macOS  
-:width: 500px  
+:alt: OpenMS installation started on macOS
+:width: 500px
 ```
 
 5. Agree to the license agreements.
@@ -69,16 +69,16 @@ By following these steps, you’re instructing macOS to trust the OpenMS install
 6. Installation Confirmation
 
 ```{image} /_images/installations/macos/Installation-successful-message.png
-:alt: OpenMS installation successful  
-:width: 500px  
+:alt: OpenMS installation successful
+:width: 500px
 ```
 
 To use {term}`TOPP` as regular app in the shell, add the following lines to the `~/.profile` file.
 
 :::{warning} Known Installer Issues
 
 1. Nothing happens when you click OpenMS apps or the validity of the developer could not be confirmed.
-   
+
    This usually means the OpenMS software lands in quarantine even after installation of the `.pkg`. This was more common with our older `.dmg` image but may still happen.
    Since macOS Catalina (maybe also Mojave) all apps and executables have to be officially notarized by Apple but we
    currently do not have the resources for a streamlined notarization workflow.
@@ -91,7 +91,7 @@ To use {term}`TOPP` as regular app in the shell, add the following lines to the
    cd /Applications/OpenMS-<version>
    sudo xattr -r -d com.apple.quarantine *
    ```
-   
+
 2. Bug with running Java based thirdparty tools like {term}`MSGFPlusAdapter` and {term}`LuciphorAdapter` from within **TOPPAS.app**
 
    If you face issues while running Java based thirdparty tools from within {term}`TOPPAS.app <TOPPAS>`, run the {term}`TOPPAS.app <TOPPAS>`

diff --git a/docs/about/installation/installation-on-windows.md b/docs/about/installation/installation-on-windows.md
@@ -5,13 +5,13 @@ Windows
 
 To Install the binary package of OpenMS & {term}`TOPP`:
 
-1. Download the installer `OpenMS-<version>-Win64.exe` from the [archive](https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/latest/) 
+1. Download the installer `OpenMS-<version>-Win64.exe` from the [archive](https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/latest/)
 2. Execute the installer under the user account that later runs OpenMS and follow its instructions.
-   
+
    You may see a Windows Defender Warning, since our installer is not digitally signed.
-   
+
    Click on "More Info", and then "Run anyways".
-   
+
    ![](/_images/installations/win/smartscreen.gif)
 
    When asked for an admin authentication, please enter the credentials (it is not advised to directly invoke the installer using an admin account).
@@ -47,4 +47,4 @@ The windows installer works with Windows 10 and 11 (older versions might still w
 4. For Win8 or later, Windows will report an error while installing `.net4` as it's mostly included. But it might occur
    that `.net3.5` does not get properly installed during the process.
 
-   Fix is to enable the .NET Framework 3.5 yourself through Control Panel. See this [Microsoft help page](https://docs.microsoft.com/en-us/dotnet/framework/install/dotnet-35-windows).aspx#ControlPanel) for detailed information. Even if this step fails, this does not affect the functionality of OpenMS, except for the executability of included third party tools (ProteoWizard).
+   Fix is to enable the .NET Framework 3.5 yourself through Control Panel. See this [Microsoft help page](https://docs.microsoft.com/en-us/dotnet/framework/install/dotnet-35-windows#enable-the-net-framework-35-in-control-panel) for detailed information. Even if this step fails, this does not affect the functionality of OpenMS, except for the executability of included third party tools (ProteoWizard).
diff --git a/docs/about/installation/installation-with-conda.md b/docs/about/installation/installation-with-conda.md
@@ -81,7 +81,7 @@ obtain release versions (`bioconda` channel) and nightly versions (`openms` chan
    :::{tab-item} openms
    :sync: openms
 
-   ```{code-block} bash 
+   ```{code-block} bash
    conda install openms
    ```
    :::
@@ -119,7 +119,7 @@ obtain release versions (`bioconda` channel) and nightly versions (`openms` chan
    :::{tab-item} openms
    :sync: openms
 
-   ```{code-block} bash 
+   ```{code-block} bash
    conda install -c openms openms
    ```
    :::

diff --git a/docs/about/learning/background.md b/docs/about/learning/background.md
@@ -1,9 +1,9 @@
 Learning
 ========
 
-Proteomics and metabolomics focus on complex interactions within biological systems; the former is centered on proteins while the latter is based on metabolites. To understand these interactions, we need to accurately identify the different biological components involved. 
+Proteomics and metabolomics focus on complex interactions within biological systems; the former is centered on proteins while the latter is based on metabolites. To understand these interactions, we need to accurately identify the different biological components involved.
 
-{term}`Liquid chromatography` (LC) and {term}`mass spectrometry` (MS) are the analytical techniques used to isolate and identify biological components in proteomics and metabolomics. LC-MS data can be difficult to analyze manually given its amount and complexity. Therefore, we need specialized software that can analyze high-throughput LC-MS data quickly and accurately. 
+{term}`Liquid chromatography` (LC) and {term}`mass spectrometry` (MS) are the analytical techniques used to isolate and identify biological components in proteomics and metabolomics. LC-MS data can be difficult to analyze manually given its amount and complexity. Therefore, we need specialized software that can analyze high-throughput LC-MS data quickly and accurately.
 
 <ins>**Why use OpenMS**</ins>
 
@@ -13,7 +13,7 @@ OpenMS is an open-source, C++ framework for analyzing large volumes of mass spec
 OpenMS in recent times has been expanded to support a wide variety of mass spectrometry experiments. To design your analysis solution, [contact the OpenMS team](https://openms.de/communication/) today.
 ```
 
-To use OpenMS effectively, an understanding of chromatography and mass spectrometry is required as many of the algorithms are based on these techniques. 
+To use OpenMS effectively, an understanding of chromatography and mass spectrometry is required as many of the algorithms are based on these techniques.
 This section provides a detailed explanation on LC and MS, and how they are combined to identify and quantify substances.
 
 

diff --git a/docs/about/learning/lc-chromatography.md b/docs/about/learning/lc-chromatography.md
@@ -1,33 +1,33 @@
 Liquid chromatography (LC)
 ==========================
 
-Chromatography is a technique used by life scientists to separate molecules based on a specific physical or chemical property. 
+Chromatography is a technique used by life scientists to separate molecules based on a specific physical or chemical property.
 
 <div class="admonition video">
 <p class="admonition-title">**Video**</p>
 For more information on chromatography, [view this video](https://timms.uni-tuebingen.de:/tp/UT_20141028_001_cpm_0001?t=210.00).
 </div>
 
-There are many types of chromatography, but this section focuses on LC as it is widely used in proteomics and metabolomics. 
+There are many types of chromatography, but this section focuses on LC as it is widely used in proteomics and metabolomics.
 
 LC separates molecules based on a specific physical or chemical property by mixing a sample containing the molecules of interest (otherwise known as **analytes**) in a liquid solution.
 
 ## Key components of LC
 
 An LC setup is made up of the following components:
-- **A liquid solution**, known as the **mobile phase**, containing the analytes. 
+- **A liquid solution**, known as the **mobile phase**, containing the analytes.
 - **A pump** which transports the liquid solution.
 - **A stationary phase** which is a solid, homogeneous substance.
-- **A column** that contains the stationary phase. 
+- **A column** that contains the stationary phase.
 - **A detector** that plots the time it takes for the analyte to escape the column (retention time) against the analyte's concentration. This plot is called a **chromatogram**.
 
-Refer to the image below for a diagrammatic representation of an LC setup. 
+Refer to the image below for a diagrammatic representation of an LC setup.
 
 ![schematic illustration of an LC setup](/_images/introduction/lc-components.png)
 
 ## How does LC work?
 
-The liquid solution containing the analytes is pumped through a column that is attached to the stationary phase. Analytes are separated based on how strongly they interact with each phase. Some analytes will interact strongly with the mobile phase while others will be strongly attracted to the stationary phase, depending on their physical or chemical properties. The stronger an analyte's attraction is to the mobile phase, the faster it will leave the column. The time it takes for an analyte to escape from the column is called the analyte's {term}`retention time`. As a result of their differing attractions to the mobile and stationary phases, different analytes will have different retention times, which is how separation occurs. 
+The liquid solution containing the analytes is pumped through a column that is attached to the stationary phase. Analytes are separated based on how strongly they interact with each phase. Some analytes will interact strongly with the mobile phase while others will be strongly attracted to the stationary phase, depending on their physical or chemical properties. The stronger an analyte's attraction is to the mobile phase, the faster it will leave the column. The time it takes for an analyte to escape from the column is called the analyte's {term}`retention time`. As a result of their differing attractions to the mobile and stationary phases, different analytes will have different retention times, which is how separation occurs.
 
 The retention times for each analyte are recorded by a detector. The most common detector used is the mass spectrometer, which we discuss later. However, other detection methods exist, such as:
 - Light absorption (photometric detector)
@@ -36,7 +36,7 @@ The retention times for each analyte are recorded by a detector. The most common
 
 ## High performance liquid chromatography (HPLC)
 
-HPLC is the most commonly used technique for separating proteins and metabolites. In HPLC, a high-pressured pump is used to transport a liquid (solvent) containing the molecules of interest through a thin capillary column. The stationary phase is ‘packed’ into the column. 
+HPLC is the most commonly used technique for separating proteins and metabolites. In HPLC, a high-pressured pump is used to transport a liquid (solvent) containing the molecules of interest through a thin capillary column. The stationary phase is ‘packed’ into the column.
 
 <div class="admonition video">
 <p class="admonition-title">**Video**</p>

diff --git a/docs/getting-started/nextflow-get-started.md b/docs/getting-started/nextflow-get-started.md
@@ -1,15 +1,15 @@
 NextFlow
 ========
 
-Nextflow is a workflow system for creating scalable, portable, and reproducible workflows. 
-It is based on the dataflow programming model, which greatly simplifies the writing of parallel and distributed pipelines, 
-allowing you to focus on the flow of data and computation. 
-Nextflow can deploy workflows on a variety of execution platforms, including your local machine, HPC schedulers, 
-AWS Batch, Azure Batch, Google Cloud Batch, and Kubernetes. 
+Nextflow is a workflow system for creating scalable, portable, and reproducible workflows.
+It is based on the dataflow programming model, which greatly simplifies the writing of parallel and distributed pipelines,
+allowing you to focus on the flow of data and computation.
+Nextflow can deploy workflows on a variety of execution platforms, including your local machine, HPC schedulers,
+AWS Batch, Azure Batch, Google Cloud Batch, and Kubernetes.
 Additionally, it supports many ways to manage your software dependencies, including Conda, Spack, Docker, Podman, Singularity, and more.[^1]
 
 ## Installation
-Click [here](https://www.nextflow.io/docs/latest/getstarted.html#installation) to install Nextflow only. 
+Click [here](https://www.nextflow.io/docs/latest/getstarted.html#installation) to install Nextflow only.
 Alternatively click [here](https://nf-co.re/docs/usage/installation) to follow the instructions for using nf-core curated pipelines in Nextflow.
 
 ## Ready-made OpenMS nextflow workflows

diff --git a/docs/getting-started/visualize-with-openms.md b/docs/getting-started/visualize-with-openms.md
@@ -91,7 +91,7 @@ To filter your data:
 
 1. Select a layer from the **Layers window**.
 
-  ![display selected layer](/_images/tutorials/toppview/layers-window.png)  
+  ![display selected layer](/_images/tutorials/toppview/layers-window.png)
 
 2. Open the **Data filters window** by clicking the tab at the bottom of the screen.
 

diff --git a/docs/manual/contribute.md b/docs/manual/contribute.md
@@ -3,7 +3,7 @@ Contribute
 
 ## Reporting Bugs and Issues
 
-A list of known issues in the current OpenMS release can be found [here](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/known_dev_bugs.html). 
+A list of known issues in the current OpenMS release can be found [here](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/known_dev_bugs.html).
 Please check if your OpenMS version matches the current version and if the bug has already been reported.
 
 In order to report a new bug, please create a [GitHub issue](manual/contribute.md#Write and Label GitHub Issues) or [contact us](/about/communication.md).

diff --git a/docs/manual/contribute/openms-git-workflow.md b/docs/manual/contribute/openms-git-workflow.md
@@ -13,7 +13,7 @@ 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 
+* 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`.
@@ -66,7 +66,7 @@ $ git remote -v
 
 ```
 
-Fetch changes and new branches from your fork (`origin`) as well as from the central, upstream OpenMS repository by 
+Fetch changes and new branches from your fork (`origin`) as well as from the central, upstream OpenMS repository by
 executing:
 
 ```bash
@@ -161,7 +161,7 @@ The above commands:
 2. Applies all commits that have been integrated into `develop`.
 3. Reapplies your commits on top of the commits integrated into `develop`.
 
-For more information, refer to a [visual explanation of rebasing](http://git-scm.com/book/en/v2/Git-Branching-Rebasing).
+For more information, refer to a [visual explanation of rebasing](https://git-scm.com/book/en/v2/Git-Branching-Rebasing).
 
 ```{tip}
 Do not rebase published branches (e.g. branches that are part of a pull request). If you created a pull request, you

diff --git a/docs/manual/contribute/pull-request-checklist.md b/docs/manual/contribute/pull-request-checklist.md
@@ -4,7 +4,7 @@ Pull Request Checklist
 Before opening a pull request, check the following:
 
 1. **Does the code build?**
-  Execute `make` (or your build system's equivalent, e.g., `cmake --build . --target ALL_BUILD --config Release` on 
+  Execute `make` (or your build system's equivalent, e.g., `cmake --build . --target ALL_BUILD --config Release` on
   Windows).
 2. **Do all tests pass?**
    To check if all tests have passed, execute `ctest`.
@@ -15,7 +15,7 @@ Before opening a pull request, check the following:
    It is also recommended to document non-public members and methods.
 4. **Does the code introduce changes to the API?**
    If the code introduces changes to the API, make sure that the documentation is up-to-date and that the Python bindings
-   (pyOpenMS) still work. For each change in the C++ API, make a change in the Python API wrapper via 
+   (pyOpenMS) still work. For each change in the C++ API, make a change in the Python API wrapper via
    the `pyOpenMS/pxds/` files.
 5. **Have you completed regression testing?**
    Make sure that you include a test in the test suite for:
@@ -43,5 +43,5 @@ Make sure to:
 
 * **Describe what you have changed in your pull request.**
   When opening the pull request, give a detailed overview of what has changed and why. Include a clear rationale for the
-  changes and add benchmark data if available. See [this request](https://github.com/bitly/dablooms/pull/19) for 
+  changes and add benchmark data if available. See [this request](https://github.com/bitly/dablooms/pull/19) for
   an example.
diff --git a/docs/manual/develop.md b/docs/manual/develop.md
@@ -27,7 +27,7 @@ code base.
 
 ### Development model
 
-OpenMS follows the [Gitflow development workflow](http://nvie.com/posts/a-successful-git-branching-model/).
+OpenMS follows the [Gitflow development workflow](https://nvie.com/posts/a-successful-git-branching-model/).
 
 Every contributor is encouraged to create their own fork (even if they are eligible to push directly to OpenMS).
 To create a fork:

diff --git a/docs/manual/develop/adding-new-tool-to-topp.md b/docs/manual/develop/adding-new-tool-to-topp.md
@@ -70,7 +70,7 @@ otherwise.
 
 - Create a resource file: Create a text file named `.rc` (e.g. TOPPView.rc) Insert the following line: 101 ICON
   "TOPPView.ico" , replacing TOPPView with your binary name. Put both files in `OpenMS/source/APPLICATIONS/TOPP/`
-  (similar files for other TOPP tools already present). Re-run cmake and re-link your TOPP tool. 
+  (similar files for other TOPP tools already present). Re-run cmake and re-link your TOPP tool.
 
 Voila. You should have an iconized TOPP tool.