Linting PR

README.md

@@ -18,7 +18,7 @@ Get a local copy of this repository, set up a `Python3.6+` environment and insta
 
 ```bash
 git clone https://github.com/pylhc/pylhc.github.io
-pip install mkdocs mkdocs-material mkdocs-minify-plugin
+python -m pip install mkdocs mkdocs-material mkdocs-minify-plugin
 ```
 
 Create a branch (from master) and make your changes.

docs/guis/about.md

@@ -23,15 +23,15 @@ The GUIs can be started from your development environment or via deployed `.jnlp
     - Latest [Beta-Beating production version][prod_bbgui]{target=_blank}.
     - Latest [Beta-Beating development version][dev_bbgui]{target=_blank}.
     - Complete [list of releases][releases_bbgui]{target=_blank}.
-    
+
 === "Kmod"
 
     The K-modulations GUI is now a Python app published with `acc-py`, and can be run with:
-    
+
     ```bash
     /acc/local/share/python/acc-py/apps/acc-py-cli/pro/bin/acc-py app run pykmodlhc
     ```
-    
+
 === "Multiturn"
 
     - Latest [Multiturn production version][prod_mtgui]{target=_blank}.
@@ -123,14 +123,14 @@ Either fix the permissions on `afs` or ask someone to do so for you.
 [dev_mtgui]: https://bewww.cern.ch/ap/deployments-dev/applications/cern/lhc/lhc-multiturn/PRO/lhc-multiturn-lhc-multiturn.jnlp
 [releases_mtgui]: https://bewww.cern.ch/ap/deployments/applications/cern/lhc/lhc-multiturn/
 
-[prod_kmodgui]: https://bewww.cern.ch/ap/deployments/applications/cern/lhc/lhc-app-kmod/PRO/lhc-app-kmod-lhc-app-kmod.jnlp 
-[dev_kmodgui]: https://bewww.cern.ch/ap/deployments-dev/applications/cern/lhc/lhc-app-kmod/PRO/lhc-app-kmod-lhc-app-kmod.jnlp 
+[prod_kmodgui]: https://bewww.cern.ch/ap/deployments/applications/cern/lhc/lhc-app-kmod/PRO/lhc-app-kmod-lhc-app-kmod.jnlp
+[dev_kmodgui]: https://bewww.cern.ch/ap/deployments-dev/applications/cern/lhc/lhc-app-kmod/PRO/lhc-app-kmod-lhc-app-kmod.jnlp
 [releases_kmodgui]: https://bewww.cern.ch/ap/deployments/applications/cern/lhc/lhc-app-kmod/
 
 [jws_confluence]: https://wikis.cern.ch/display/DVTLS/jws+-+a+replacement+for+javaws
 [jws]: https://wikis.cern.ch/display/DVTLS/jws+-+a+replacement+for+javaws
 
-[mounting_resources]: ../howto/setup/shared_filesystems.md#mounting-tn-resources-on-gn-machines
-[connect_gpn]: ../howto/teleworking/access.md#accessing-cern-internal-websites
-[sshuttle_method]: ../howto/setup/guis.md#running-guis-locally
+[mounting_resources]: ../resources/shared_filesystems.md#mounting-tn-resources-on-gpn-and-other-machines
+[connect_gpn]: ../resources/remote_access.md#accessing-cern-internal-websites
+[sshuttle_method]: usage/remote.md#running-guis-locally
 [jws_calls]: ../resources/links.md#jws-programs

docs/guis/betabeat/ampdet.md

@@ -1 +1 @@
-# Amplitude Detuning Analysis
+# Amplitude Detuning Analysis

docs/guis/betabeat/analysis_panel.md

@@ -23,7 +23,7 @@ It should prevent the appearance of unphysical spikes in the optics functions wh
 Isolation Forest perfroms anomaly detection on the whole set of selected measurements data.
 Clicking on "Detect and remove bad BPMs"-button triggers an external python script which analyses the selected files.
 The output file is written in the TFS format and contains the list of detected bad BPMs is written to the folder of the first selected measurement in the analysis table.
-  
+
 The output can be found in:  `Measurements/.../bad_bpms_iforest_{x,y}`.
 
 During IF-cleaning, the lines corresponding to detected faulty BPMs will be removed from the lin-files.
@@ -33,7 +33,7 @@ After cleaning is finished, the optics function can be computed from the harmoni
 
 <figure>
   <center>
-  <img src="../../assets/images/analysis_panel_cleaning.png" width="65%" />
+  <img src="../../assets/images/analysis_panel_cleaning.png" width="65%" alt="Cleaning before optics analysis" />
   <figcaption> Cleaning before optics analysis </figcaption>
   </center>
 </figure>

docs/guis/betabeat/beam_selection.md

@@ -1,8 +1,10 @@
 # The Beam Selection Window
 
 <figure>
-  <img src="../../assets/images/betabeat_gui/beam_selection.png" width="100%" />
+  <center>
+  <img src="../../assets/images/betabeat_gui/beam_selection.png" width="100%" alt="The beam selection window" />
   <figcaption>The Beam Selection Window.</figcaption>
+  </center>
 </figure>
 
 The Beam Selection Window is your entry point to the GUI.
@@ -21,14 +23,19 @@ The options chosen here will also define the **folder-structure** you will be us
 
 ## Python Executable
 
-In the Beam-Selection Window you need to give it a python-binary (e.g. `venv/bin/python`).
+In the Beam-Selection Window you need to give it a python-binary (e.g. `.venv/bin/python`).
 Best would be if you have a local virtual environment.
 This **needs to have omc3 installed as a package**.
-See [omc3 on github][omc3_github_getting_started]{target=_blank}.
+See [omc3 on github][omc3_github]{target=_blank}.
+
 ```bash
-pip install git+https://github.com/pylhc/omc3.git
+python -m pip install git+https://github.com/pylhc/omc3.git
 ```
+
 This is because python calls are now made by module, i.e.:
+
 ```bash
 python -m omc3.module arg1 arg2 ...
 ```
+
+[omc3_github]: https://github.com/pylhc/omc3

docs/guis/betabeat/bpm_panel.md

@@ -4,6 +4,7 @@ The BPM panel provides a graphical interface to query and visualize information
 It can load data files for all supported beams, mostly binary SDDS files or files in the SDDS ASCII format.
 
 !!! todo
+
     Include a screenshot, possibly of settings when opening files?
 
 ## Opening Files and Applying SVD Cleaning
@@ -36,10 +37,10 @@ when SVD cleaning detects and removes bad BPMs, they will be marked in the BPM n
 
 All the settings mentioned above can be changed in the global settings panel:
 <figure>
-<center>
-  <img src="../../assets/images/cleaning_settings.png" width="95%" />
+  <center>
+  <img src="../../assets/images/cleaning_settings.png" width="95%" alt="Cleaning thresholds in the settings panel"/>
   <figcaption>Settings panel, where cleaning thresholds can be changed.</figcaption>
-</center>
+  </center>
 </figure>
 
 Turn-by-turn data cleaning is summarized in the output file which can be found at:
@@ -48,23 +49,24 @@ Turn-by-turn data cleaning is summarized in the output file which can be found a
 It contains BPM names and corresponding threshold which identified a BPM as faulty.
 
 !!! note
+
     A single BPM can appear twice (for each threshold separately), e.g. in the case of exact zero flat signal.
 
 The content of the loaded files will be displayed in two charts:
 
 - Horizontal BPMs,
 - Vertical BPMs.
 
-
 !!! todo
+
     Include a screenshot with two BPM panels.
 
 The charts are interactive and can be used to zoom in/out, or focus on a given rectangle of the shown data.
 
 The charts can display either the measured amplitude values over turns for every BPM from the list or display the phase space, which is calculated by two consecutive BPMs.
 
-
 !!! todo
+
     Include a screenshot of the bad bpms panel.
 
 ## Removing Turns and Computing an Average
@@ -74,21 +76,25 @@ The buttons on the top left side of the pane provide useful features to handle t
 - `Remove Turns` can be used to cut turns from the start or the end, to focus on a specified range of the data.
 
 !!! todo
+
     Include a screenshot of before-after comparison for `Remove Turns`.
 
 - `Create Average` allows loading several data files too visualize their average repesentations on the same graph, which helps detecting differences or reducing noise.
 
 !!! todo
+
     Include a screenshot of `Create Average` effect.
 
 - `Do Analysis` spawns the configuration dialogue for the external analysis.
   This will call an external program to perform harmonic analysis of the BPM data, in order to compute tunes and similar beam properties.
   The results from the analysis can be seen in the [Analysis Panel](analysis_panel.md).
 
 !!! todo
+
     Include of screenshot of `Do Analysis` dialogue window.
 
 !!! note
+
     The `Create Average` option requires synchronized data from withing the same bounds, otherwise the results will be meaningless.
     The figure below shows three runs from LHC beam one with synchronized peaks for every turn and their corresponding averages.
 

docs/guis/betabeat/correction_panel.md

@@ -30,4 +30,4 @@ By selecting one, the user can examine or visualize the values attributed to eac
     Include a screenshot of the Knob Panel view knobs table
 
 !!! todo
-    Include a screenshot of the Knob Panel view knobs chart
+    Include a screenshot of the Knob Panel view knobs chart

docs/guis/betabeat/optics_panel.md

@@ -3,9 +3,9 @@
 The `Optics Panel` provides graphical interface to compare the computed optics to the nominal model.
 There are in total three main tabs for the optics panel:
 
-- The [Optics](#Optics Tab) tab, where a tree menu (on the left) provides many physical properties to be displayed.
-- The [Segment-by-Segment: Segment](#Segment-by-Segment: Segment Tab) tab, to have a look at properties in a pre-defined segment of the machine.
-- The [Segment-by-Segment: Element](#Segment-by-Segment: Element Tab) tab, to have a look at properties for a pre-defined list of elements in the machine.
+- The [Optics](#optics-tab) tab, where a tree menu (on the left) provides many physical properties to be displayed.
+- The [Segment-by-Segment: Segment](#segment-by-segment-segment-tab) tab, to have a look at properties in a pre-defined segment of the machine.
+- The [Segment-by-Segment: Element](#segment-by-segment-element-tab) tab, to have a look at properties for a pre-defined list of elements in the machine.
 
 ## Optics Tab
 
@@ -37,7 +37,7 @@ Clicking `Go` will call for another python script and take you to the `Segment-b
 ## Segment-by-Segment: Element Tab
 
 Pre-defined lists of elements can be selected to view properties across said elements.
-The working is similar to the one for different [segments](#Segment-by-Segment: Segment).
+The working is similar to the one for different [segments](#segment-by-segment-segment-tab).
 
 !!! todo
     Include a screenshot of the element tab.
@@ -65,9 +65,8 @@ These files store the magnet names and corresponding correction strengths.
 
 They are also displayed in the [Correction Panel](correction_panel.md).
 
-
 ### Optics Plotting
 
-* RDT and CRDT plots are added dynamically depending on the files present in the respective folders.
-* Nicer names and more structure in the tree.
-* Backend was rewritten, so it is now more modular and easier to add new plot-types.
+- RDT and CRDT plots are added dynamically depending on the files present in the respective folders.
+- Nicer names and more structure in the tree.
+- Backend was rewritten, so it is now more modular and easier to add new plot-types.

docs/guis/betabeat/plots.md

@@ -2,7 +2,6 @@
 
 All plots are running with the same backend classes, which allows additional control via mouse and keyboard.
 
-
 ## Keyboard/Mouse Shortcuts
 
 * ++lbutton++ : Draw and zoom into rectangle.
@@ -13,4 +12,3 @@ All plots are running with the same backend classes, which allows additional con
 * ++shift+mousewheel++ : Zoom y-axis relative to mouse position.
 * ++alt+mousewheel++ : Zoom relative to plot center.
 * ++shift+alt+mousewheel++ : Zoom y-axis relative to plot center.
-

docs/guis/betabeat/settings.md

@@ -1,8 +1,7 @@
 # Settings Window
 
-
 * Settings are now all in one place (the settings-button on top).
 * Entries in the settings that are lists (e.g. 'Turns' which will be `STARTTURN ENDTURN`) are given as **space-separated** values, NOT comma separated.
 * Settings can be reverted as long as you do not click apply.
 * Settings are applied automatically on ++okbtn++.
-* Settings are reset to last applied on ++cancelbtn++.
+* Settings are reset to last applied on ++cancelbtn++.

docs/guis/multiturn/gui.md

@@ -1 +1 @@
-# The Multiturn GUI
+# The Multiturn GUI

docs/guis/usage/ide_install.md

@@ -21,17 +21,17 @@ As both IDEs require [CommonBuildNextGeneration (CBNG)][cbng_wiki]{target=_blank
     File -> Settings -> Build, Execution, Deployment -> Build Tools -> Gradle
     ```
     to the specified location `/user/pcrops/devtools/CBNG/PRO/`
-    
+
     A more extensive guide can be found in the [CBNG Wiki for IDEA integration][cbng_idea]{target=_blank}.
-    Alternatively, run CBNG directly [from the commandline](#cbng-from-commandline) instead.
+    Alternatively, run CBNG directly from the commandline instead.
 
 === "CBNG from the Command Line"
-    Another sometimes easier alternative that works with any IDE is to run CBNGs `bob` with the desired command (e.g. `build`, `dependencies`, `eclipse`, `idea`) in the folder of the project from the commandline. 
+    Another sometimes easier alternative that works with any IDE is to run CBNGs `bob` with the desired command (e.g. `build`, `dependencies`, `eclipse`, `idea`) in the folder of the project from the commandline.
     The full path to `bob` is:
     ```
     /user/pcrops/devtools/CBNG/PRO/bin/bob
     ```
-    
+
     !!! info
         See `bob --help` for instructions about its commands.
 
@@ -50,20 +50,20 @@ Firstly, you should clone the desired repository to an adequate location on your
 
 === "Kmod GUI"
     ```bash
-    git clone https://gitlab.cern.ch/acc-co/lhc/lhc-app-kmod
+    git clone https://gitlab.cern.ch/gtrad/pyKmodLHC
     ```
 
 You then simply import the project into your IDE.
 
-??? warning "IntelliJ Specificity" 
-    For IntelliJ, you might have to
-    
-    1. Create an empty `build.gradle` file if you want to trigger a gradle import dialogue where you need to choose **use local gradle distribution** and set the **gradle home** to `/user/pcrops/devtools/CBNG/PRO/bin/bob` ([as above](#gradlehome))
+??? warning "IntelliJ Specificity"
+    For IntelliJ, you might have to:
+
+    1. Create an empty `build.gradle` file if you want to trigger a gradle import dialogue where you need to choose **use local gradle distribution** and set the **gradle home** to `/user/pcrops/devtools/CBNG/PRO/bin/bob` (as above).
     2. Go to `File -> Project Structure ... -> Modules` and set the **Dependencies storage format** to `Eclipse (.classpath)`.
     This one you should check on a regular basis, as it tends to reset itself.
 
 To make it runnable, you will have to use CBNG to **resolve dependencies** and **build** the project first.
-Depending on your IDE you should run CBNGs `eclipse` or `idea` followed by `build`. 
+Depending on your IDE you should run CBNGs `eclipse` or `idea` followed by `build`.
 Running `dependencies` can help.
 
 !!! warning
@@ -79,14 +79,13 @@ If everything worked fine, the Gui should now be runnable via the `void main()`
 * [Accsoft-Eclipse Downloads][accsoft_eclipse]{target=_blank}
 * [Accsoft Eclipse Wiki][accsoft_eclipse_wiki]{target=_blank}
 
-[mounting_tn]: ../../howto/setup/shared_filesystems.md#mounting-tn-resources-on-gn-machines
+[mounting_tn]: ../../resources/shared_filesystems.md#mounting-tn-resources-on-gpn-and-other-machines
 [gui_releases]: releases.md
-
 [idea_download]: https://www.jetbrains.com/idea/download/
 [cbng_wiki]: https://wikis.cern.ch/display/DVTLS/CBNG
 [cbng_eclipse]: https://wikis.cern.ch/display/DVTLS/CBNG+-+Eclipse+Integration
 [cbng_idea]: https://wikis.cern.ch/display/DVTLS/CBNG+-+IntelliJ+IDEA+integration
 [accsoft_eclipse]: http://eclipse.cern.ch/
 [accsoft_eclipse_wiki]: https://wikis.cern.ch/display/DVTLS/Eclipse+IDE
 
-*[DG]: Director General: Currently Fabiola Gianotti
+*[DG]: Director General

docs/guis/usage/releases.md

@@ -2,5 +2,5 @@
 
 ## Releasing the GUIs
 
-
-_TODO: Description how to release the GUIs_
+!!! todo
+    Describe how to release the GUIs

docs/guis/usage/remote.md

@@ -1,7 +1,6 @@
 
 # Running Outside of the TN
 
-
 ## Running GUIs Locally
 
 To use the [KMod GUI][kmod_gui] or the `KnobPanel` in the [Beta-Beat GUI][bb_gui], it is required to be on the TN, as they need to connect to LSA.
@@ -33,15 +32,19 @@ Once logged in with your CERN credentials (Add `CERN.CH\` in front of your usern
 which opens a putty-terminal connected to `lxplus` and starts a `X-Server` in the background.
 
 <figure>
-  <img src="../../assets/images/tricks/putty_and_xserver_cernts.png" width=90%>
+  <center>
+  <img src="../../assets/images/tricks/putty_and_xserver_cernts.png" width="90%" alt="Putty and Xserver on cernts" />
   <figcaption>Putty and XServer on cernts</figcaption>
+  </center>
 </figure>
 
 Executing any graphical software from this terminal will ask for connection authorization, which you need to approve.
 
 <figure>
-  <img src="../../assets/images/tricks/allow_xserver_connection.png" width=60%>
+  <center>
+  <img src="../../assets/images/tricks/allow_xserver_connection.png" width="60%" alt="Approval prompt for a connection to XServer" />
   <figcaption>Approval prompt for a connection to XServer</figcaption>
+  </center>
 </figure>
 
 This way you can run any graphical application smoothly.
@@ -84,5 +87,6 @@ If your internet connection fails, you should still be able to resume your curre
 *[CD]: Continuous Delivery
 *[lxplus]: Linux Public Login User Service
 
+[sshuttle]: https://sshuttle.readthedocs.io/en/stable/
 [kmod_gui]: ../../guis/kmod/gui.md
 [bb_gui]: ../../guis/betabeat/gui.md

docs/logbook/AD/2023_ad.md

@@ -4,4 +4,4 @@
 |:----------------:|:--------:|:------:|:----:|:--------:|:---------------------------------:|:-------------------------------------------------:|
 <!--                                                                       Logbook Links: [LINK_NAME](date, logbook_id, event_id){.logbook-link} -->
 
---8<-- "docs/logbook/footer_shifts"
+--8<-- "docs/logbook/footer_shifts"