Linting PR (#179)

* need trailing line

* alt tag in images

* alt tag and spaces before code block

* center figure

* alt tag and lines in admonitions blocks

* trailing line

* empty lines and bullet lists linting

* empty lines

* empty lines

* empty lines

* trailing spaces

* trailing spaces

* fix todo

* empty lines

* define sshutle link

* no kmod special as OP develops it now

* remove from navigation too

* alt text and center figures

* trailing spaces

* multiple empty lines, trailing spaces and eol at eof fixes in all logbook files

* trailing spaces

* eol at eof

* trailing spaces

* eol at eof

* multiple empty lines, trailing spaces and eol at eof fixes

* do not include weirdass AI pictures in the website

* remove assets as well

* alt tag and center figure

* properly close center tag

* html for figure

* specify code fence language

* multiple empty lines, trailing spaces and eol at eof fixes

* multiple empty lines, trailing spaces and eol at eof fixes

* eol at eof

* eol at eof

* explicitely refer to felix carlier

* empty lines

* empty lines

* empty lines, alt tags and 2 spaces for highlighting

* alt tags and centered

* trailing spaces

* eol at eof

* trailing spaces

* fix relative link

* fix relative anchor links

* fix relative anchor links

* remove problematic anchor link

* fix link for new kmod app

* remove another broken anchor link

* fix broken rel link since files move by josch

* fix broken rel link since files move by josch

* fix broken rel link since files move by josch

* and refer to the proper tag

* include alt tag for each image entry and reformat table

* headers consistency and proper pip invocation command

* eol at eof

* spaces around code fences

* empty lines

* headers and list style

* strip end space in code fence

* spaces around code fences

* trailing spaces and empty lines around code fence blocks

* trailing spaces and headers consistency

* proper pip invocation

* and ref

* and from navigation

* eol at eof

* trailing spaces and empty lines around code fence blocks

* trailing spaces

* trailing spaces

* eol at eof and empty space around code block

* eol at eof and empty space around code block

* eol at eof and empty space around code block

* trailing spaces

* eol at eof

* trailing spaces and empty lines around code fence blocks

* empty lines

* trailing spaces, empty lines, deduplicate headers

* no punctuation in headers

* eol at eof

* little arrow last

* use headers as the numbered list would reset anyway

* remove trailing punctuation in header

* empty lines

* remove forgotten html artefact

* imports sorting

* imports sorting, quick formatting

* minor typing, import future annotations

* be explicit in what is replaced, via naming to avoid confusion. Type checker was complaining

* a little type hinting

* linting, formatting, eol at eof

* ruff formatting again

* future annotations

* types and ruff formatting

* escape pip

* proper pip invocation

* proper pip invocation

Author: fsoubelet

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/assets/images/bpm_filtering/badbpm.png

@@ -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/assets/images/bpm_filtering/bpmvsowl.png

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

docs/guis/about.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/ampdet.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/analysis_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/beam_selection.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/bpm_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.