Use correct admonitions

docs/installations/installation-on-gnu-linux.md

@@ -4,7 +4,7 @@ Installation on GNU/Linux
 ## Install via Debian Package
 
 For Debian-based Linux users, it is suggested to  use the [deb-package](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/latest/) provided. It is most easily installed with **[gdebi](https://launchpad.net/gdebi)**
-which automatically resolves the dependencies available in the PPA Respositories.
+which automatically resolves the dependencies available in the PPA Repositories.
 
 ```bash
 sudo apt-get install gdebi
@@ -41,16 +41,21 @@ Packaged versions of **OpenMS** are provided for Fedora, OpenSUSE, Debian, and U
 [here](https://pkgs.org/download/openms). For other GNU/Linux distributions or to obtain the most recent version of the
 library, installation should be done via building from the source code.
 
-> **_NOTE:_**  Please note that these packages are not directly maintained by OpenMS and they  can not be guaranteed the
+```{important}
+These packages are not directly maintained by OpenMS and they  can not be guaranteed the
 same behaviour as when building it on from source code. Also, their availability and version is subject to change and
 support might be limited (due to unforeseen or untested behaviour). It is suggested not to install them parallel to our
 Debian package.
 
+```
+
 ## Installation via Building From Source Code
 
 The source code of OpenMS is available on GitHub. Follow [Building OpenMS on GNU/Linux](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/install_linux.html) instructions on how to build OpenMS from source.
 
-> **_NOTE:_** Some thirdparty software used via adapter tools in OpenMS might also require an installed JavaVM.
+```{note}
+Some thirdparty software used via adapter tools in OpenMS might also require an installed JavaVM.
+```
 
 ## Run via a (Bio)Docker Image
 

docs/installations/installation-on-macos.md

@@ -41,9 +41,11 @@ Make sure `<OpenMS-PATH>` points to the folder where OpenMS is installed locally
 
    Since macOS Catalina (maybe also Mojave) notarized apps and executables are mandatory.
 
-   > **_NOTE:_** Although there is a lot of effort in signing and notarizing everything, it seems like openms software
+   ```{important}
+   Although there is a lot of effort in signing and notarizing everything, it seems like openms software
    still lands in quarantine on the above mentioned systems, after installation of the DMG (when downloading it from a
    browser).
+   ```
 
    To have a streamlined experience without blocking popups, it is recommended to remove the quarantine flag manually,
    using the following steps:

docs/installations/installation-on-windows.md

@@ -7,8 +7,10 @@ To Install the binary package of OpenMS & TOPP:
 2. Run the installer under the user account that later runs OpenMS. It is not advised to use admin account for
    installation. When asked for an admin authentication, please enter the credentials.
 
-> **_NOTE:_** The windows binary version works with most versions of windows from Win7 to Win10 (older versions might
+```{tip}
+The windows binary version works with most versions of windows from Win7 to Win10 (older versions might
   still work but are untested).
+```
 
  ## Known Issues
 

docs/tutorials/TOPP/data-analysis-in-toppview.md

@@ -27,8 +27,10 @@ and sample description.
 
 ![Meta Data Browser](../../images/tutorials/topp/MetaDataBrowser.png)
 
-> **_NOTE:_** Identification data, e.g. from a Mascot run, can be annotated to the spectra or features, too. After
+```{tip}
+Identification data, e.g. from a Mascot run, can be annotated to the spectra or features, too. After
 annotation, this data is listed in the metadata.
+```
 
 ## Statistics
 

docs/tutorials/TOPP/feature-detection.md

@@ -14,14 +14,16 @@ wavelet**, which has been tailored to the detection of isotopic patterns followi
 information about the theory behind this technique, please refer to Hussong et al.: "Efficient Analysis of Mass
 Spectrometry Data Using the Isotope Wavelet" (2007).
 
-Please note that this algorithm features no "modelling stage", since the structure of the isotopic pattern is explicitly
+```{attention}
+This algorithm features no "modelling stage", since the structure of the isotopic pattern is explicitly
 coded by the wavelet itself. The algorithm also works for 2D maps (in combination with the so-called *sweep-line*
 technique (Schulz-Trieglaff et al.: "A Fast and Accurate Algorithm for the Quantification of Peptides from Mass
 Spectrometry Data" (2007))). The algorithm could originally be executed on (several) high-speed CUDA graphics cards.
 Tests on real-world data sets revealed potential speedups beyond factors of 200 (using 2 NVIDIA Tesla cards in parallel).
 Support for CUDA was removed in [OpenMS]() due to maintenance overhead. Please refer to Hussong et al.: "Highly
 accelerated feature detection in proteomics data sets using modern graphics processing units" (2009) for more details on
 the implementation.
+```
 
 ### Seeding
 

docs/tutorials/TOPP/feature-grouping.md

@@ -29,5 +29,7 @@ To differentially quantify the features of two or more label-free HPLC-MS map.
 
 ![TOPP labelfree quant](../../images/tutorials/topp/TOPP_labelfree_quant.png)
 
-> **_NOTE:_** This algorithm assumes that the retention time axes of all input maps are very similar. To correct for
+```{tip}
+This algorithm assumes that the retention time axes of all input maps are very similar. To correct for
 retention time distortions, please have a look at [Map alignment](map-alignment.md).
+```

docs/tutorials/TOPP/general-introduction.md

@@ -61,10 +61,11 @@ can contain the configuration of one or several TOPP tools.
 The following examples will give an overview of how TOPP tools can be chained in order to create analysis pipelines. INI
 files are the recommended way to store all settings of such a pipeline in a single place.
 
-Note that the issue of finding suitable parameters for the tools is not addressed here. For problems during the
+```{attention}
+The issue of finding suitable parameters for the tools is not addressed here. For problems during the
 execution of the example pipelines on the data, adapt the parameters. Have a look at the documentation of the
 corresponding TOPP tool in that case.
-
+```
 
 ### Parameter documentation
 

docs/tutorials/TOPP/hotkeys-table.md

@@ -41,7 +41,9 @@ TOPPView Hotkeys
 | <kbd>CTRL</kbd> + <kbd>ALT</kbd> + <kbd>+</kbd>     | 2D draw mode: increase maximum point size (for raw peak scaling)                |
 | <kbd>CTRL</kbd> + <kbd>ALT</kbd> + <kbd>-</kbd>     | 2D draw mode: decrease maximum point size (for raw peak scaling)                |
 
-> **_NOTE:_**  <kbd>Home</kbd> on macOS keyboards is also <kbd>Fn</kbd> + <kbd>ArrowLeft</kbd>. <kbd>End</kbd> on macOSX keyboards is also <kbd>Fn</kbd> + <kbd>ArrowRight</kbd>.
+```{tip}
+kbd>Home</kbd> on macOS keyboards is also <kbd>Fn</kbd> + <kbd>ArrowLeft</kbd>. <kbd>End</kbd> on macOSX keyboards is also <kbd>Fn</kbd> + <kbd>ArrowRight</kbd>.
+```
 
 ## Annotations in 1D view
 

docs/tutorials/TOPP/topp-for-advanced-users.md

@@ -12,14 +12,18 @@ specify one or more directories where FASTA files (or related, e.g., `.psq` file
 directories specified in `id_db_dir` will be searched. This allows to build scripts and/or TOPPAS pipelines which are
 portable across several computers, just adapt the OpenMS.ini once on each machine.
 
-> **_NOTE:_** When using TOPPAS: Use an "input file" node to specify the FASTA file for several engines simultaneously.
+```{tip}
+When using TOPPAS: Use an "input file" node to specify the FASTA file for several engines simultaneously.
 However, when selecting the file, TOPPAS will use the absolute pathname and the dialog will not allow to name a
 non-existing file. After selecting the file you can however edit the filename and remove the path (this will issue a
 warning which can be ignored).
+```
 
-> **_NOTE:_** This approach does not work for OpenMS MascotAdapters, as each Mascot instance has its own database
+```{note}
+This approach does not work for OpenMS MascotAdapters, as each Mascot instance has its own database
 managed internally. Make sure that the database is present on all mascot servers you're going to use, thus making the
 INI settings portable.
+```
 
 ## Using external tools in workflows
 

docs/tutorials/TOPPAS/examples.md

@@ -52,8 +52,10 @@ text based format using the TextExporter for further processing (e.g., in Micros
 The results can be opened in TOPPView. The next figures show the results in 2D and 3D view, together with the feature
 intermediate results.
 
-> **_NOTE:_** The intensities and retention times are slightly different between the runs. To correct for retention
+```{tip}
+The intensities and retention times are slightly different between the runs. To correct for retention
 times shift, a map alignment could be done, either on the spectral data or on the feature data.
+```
 
 ![TOPPAS BSA Results 2D](../../images/tutorials/toppas/TOPPAS_BSA_results_2d.png)
 

docs/tutorials/TOPPAS/user-interface.md

@@ -54,13 +54,15 @@ selected, TOPPAS will parallelize the pipeline execution in the following scenar
 - The pipeline contains multiple branches that are independent of each other. In this case, multiple tools can run in
   parallel.
 
+```{caution}
 Be careful with this setting, however, as some of the TOPP tools require large amounts of RAM (depending on the size of
 the dataset). Running too many parallel jobs on a machine with not enough memory will cause problems. Also, do not
 confuse this setting with the `threads` parameter of the individual TOPP tools: every TOPP tool has this parameter
 specifying the maximum number of threads the tool is allowed to use (although only a subset of the TOPP tools make use
 of this parameter, since there are tasks that cannot be computed in parallel). Be especially careful with combinations
 of both parameters! For a pipeline containing the `FeatureFinderCentroided`, as an example, and set its `threads`
 parameter to 8, and additionally set the number of parallel jobs in **TOPPAS** to 8, then you end up using 64 threads.
+```
 
 In addition to `TOPPAS_out`, a `TOPPAS_tmp` directory will be created in the OpenMS temp path (call the `OpenMSInfo`
 tool to see where exactly). It will contain all temporary files that are passed from tool to tool within the pipeline.