From cf8c74ff532be1d36690eeb53ea6a88379fbd900 Mon Sep 17 00:00:00 2001 From: greengypsy Date: Fri, 27 May 2022 19:05:23 +0930 Subject: [PATCH 1/2] modified conf.py and requirements.txt to include pygments code --- conf.py | 4 ++++ requirements.txt | 1 + 2 files changed, 5 insertions(+) diff --git a/conf.py b/conf.py index cc62819e..eddbdf24 100644 --- 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/requirements.txt b/requirements.txt index 5e20b3ed..862245ba 100644 --- a/requirements.txt +++ b/requirements.txt @@ -5,3 +5,4 @@ sphinx-copybutton myst-parser sphinx-notfound-page sphinxcontrib-images +pygments From 4e1090a9c8a9ac2f0d1925620893542767283572 Mon Sep 17 00:00:00 2001 From: greengypsy Date: Fri, 27 May 2022 19:13:05 +0930 Subject: [PATCH 2/2] added lexers to code in several files --- docs/installations/installation-on-gnu-linux.md | 2 +- docs/installations/installation-on-macos.md | 4 ++-- docs/topp/toppas.md | 2 +- docs/topp/toppview.md | 2 +- docs/tutorials/TOPP/calibration.md | 2 +- ...onversion-between-openms-xml-formats-and-text-formats.md | 4 ++-- docs/tutorials/TOPP/general-introduction.md | 2 +- docs/tutorials/TOPP/peptide-property-prediction.md | 6 +++--- 8 files changed, 12 insertions(+), 12 deletions(-) diff --git a/docs/installations/installation-on-gnu-linux.md b/docs/installations/installation-on-gnu-linux.md index b9fcc984..1ef7e249 100644 --- 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 index 2cad2a25..c0c88a38 100644 --- 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= source ${OPENMS_TOPP_PATH}/.TOPP_bash_profile ``` @@ -51,7 +51,7 @@ Make sure `` 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- sudo xattr -r -d com.apple.quarantine * ``` diff --git a/docs/topp/toppas.md b/docs/topp/toppas.md index cd2e7e7c..cd496144 100644 --- 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 index ecf1cf6f..0b001e51 100644 --- 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 index 4262049b..c570e6cc 100644 --- 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 index a11491a0..57d2af30 100644 --- 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 index 8878dd5e..12266c7d 100644 --- 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 diff --git a/docs/tutorials/TOPP/peptide-property-prediction.md b/docs/tutorials/TOPP/peptide-property-prediction.md index fcb7a998..1406e81f 100644 --- 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