OpenMS · trickyck · May 27, 2022 · May 27, 2022 · May 27, 2022
diff --git a/conf.py b/conf.py
@@ -72,6 +72,10 @@
 html_theme = 'furo'
 html_logo = 'assets/OpenMS_transparent_background.png'
 
+pygments_style = 'sas'
+
+pygments_dark_style = 'rrt'
+
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

diff --git a/docs/installations/installation-on-gnu-linux.md b/docs/installations/installation-on-gnu-linux.md
@@ -16,7 +16,7 @@ If you encounter errors with unavailable packages, troubleshoot using the follow
    It might be because your Debian is too old to have a recent enough version in its official repositories. It is
    suggested to use the same packages that are used while building (make sure to adapt the Qt version and your
    Debian/Ubuntu version, here Xenial):
-   ```
+   ```bash
    sudo add-apt-repository ppa:beineri/opt-qt59-xenial
    sudo apt-get update
    ```

diff --git a/docs/installations/installation-on-macos.md b/docs/installations/installation-on-macos.md
@@ -28,7 +28,7 @@ To install OpenMS on macOS, run the following steps:
 
 To use TOPP as regular app in the shell, add the following lines to the `~/.profile` file.
 
-```
+```bash
 export OPENMS_TOPP_PATH=<OpenMS-PATH>
 source ${OPENMS_TOPP_PATH}/.TOPP_bash_profile
 ```
@@ -51,7 +51,7 @@ Make sure `<OpenMS-PATH>` points to the folder where OpenMS is installed locally
    using the following steps:
 
    Open the Terminal.app and type the following (replace the first line with the actual installation directory):
-   ```
+   ```bash
    cd /Applications/OpenMS-<version>
    sudo xattr -r -d com.apple.quarantine *
    ```

diff --git a/docs/topp/toppas.md b/docs/topp/toppas.md
@@ -17,7 +17,7 @@ More information about TOPPAS can be found in the [TOPPAS tutorial](../tutorials
 
 **The command line parameters of this tool are**:
 
-```
+```bash
 TOPPAS -- An assistant for GUI-driven TOPP workflow design.
 
 Usage:

diff --git a/docs/topp/toppview.md b/docs/topp/toppview.md
@@ -11,7 +11,7 @@ More information about TOPPView can be found in the [TOPP tutorial](../tutorials
 
 **The command line parameters of this tool are**:
 
-```
+```bash
 TOPPView -- A viewer for mass spectrometry data.
 
 Usage:

diff --git a/docs/tutorials/TOPP/calibration.md b/docs/tutorials/TOPP/calibration.md
@@ -15,7 +15,7 @@ using a linear function.
 
 In a typical setting one would first pick the TOF-data, then perform the TOFCalibration and then the InternalCalibration:
 
-```
+```bash
 PeakPickerWavelet -in raw_tof.mzML -out picked_tof.mzML -ini pp.ini
 TOFCalibration -in picked_tof.mzML -out picked.mzML -ext_calibrants ext_cal.mzML
                -ref_masses ext_cal_masses

diff --git a/docs/tutorials/TOPP/conversion-between-openms-xml-formats-and-text-formats.md b/docs/tutorials/TOPP/conversion-between-openms-xml-formats-and-text-formats.md
@@ -24,14 +24,14 @@ Feature data in text format, e.g. from other analysis tools, can be imported usi
 mode accepts comma separated values containing the following columns: RT, m/z, intensity. Additionally meta data
 columns may follow. If meta data is used, meta data column names have to be specified in a header line. Without headers:
 
-```
+```bash
 1201	503.123	1435000
 1201	1006.246	1235200
 ```
 
 Or with headers:
 
-```
+```bash
 RT	m/z	Int	isHeavy	myMeta
 1201	503.123	1435000	true	2
 1201	1006.246	1235200	maybe	1

diff --git a/docs/tutorials/TOPP/general-introduction.md b/docs/tutorials/TOPP/general-introduction.md
@@ -117,7 +117,7 @@ specified in this section, thus the `common` **FileFilter** section is checked f
 When looking up the `debug` parameter, the tool would search the instance section and tool-specific common section
 without finding a value. Finally, the *general common section* would be checked, where the debug level is specified.
 
-```
+```xml
 <PARAMETERS>
 
   <NODE name="FileFilter">

diff --git a/docs/tutorials/TOPP/peptide-property-prediction.md b/docs/tutorials/TOPP/peptide-property-prediction.md
@@ -22,7 +22,7 @@ identification runs:
 
 A typical sequence of TOPP tools would look like this:
 
-```
+```bash
 MapAligner -in Run1.mzML,...,Run4.mzML -out Run1_aligned.mzML,...,Run4_aligned.mzML
 MascotAdapter -in Run1_aligned.mzML -out Run1_aligned.idXML -ini Mascot.ini
 MascotAdapter -in Run2_aligned.mzML -out Run2_aligned.idXML -ini Mascot.ini
@@ -42,7 +42,7 @@ For a file with certainly identified peptides used to train a model for RT predi
 has to have one peptide sequence together with the RT per line (separated by one tab or space). This can then be loaded
 by `RTModel` using the `-textfile_input` flag:
 
-```
+```bash
 RTModel -in IDs_with_RTs.txt -out IDs_with_RTs.model -ini RT.ini -textfile_input
 ```
 
@@ -53,7 +53,7 @@ a fasta file containing the amino acid sequences of these proteins called `mixtu
 negative peptides (peptides, which are not proteotypic) are required. Therefore, one can use the Digestor, which is
 located in the `APPLICATIONS/UTILS/` folder together with the `IDFilter`:
 
-```
+```bash
 Digestor -in mixture.fasta -out all.idXML
 IDFilter -in all.idXML -out NonPT.idXML -exclusion_peptides_file PT.idXML
 

diff --git a/requirements.txt b/requirements.txt
@@ -5,3 +5,4 @@ sphinx-copybutton
 myst-parser
 sphinx-notfound-page
 sphinxcontrib-images
+pygments
-Original file line number
+Diff line change
@@ Expand Up @@
     **The command line parameters of this tool are**:
-    ```
+    ```bash
     TOPPAS -- An assistant for GUI-driven TOPP workflow design.
     Usage:
@@ Expand Down @@