Jinjafix

config/templates/hpc.template

@@ -1,6 +1,6 @@
-{%- if site == 'Gent' %}
+{% if site == 'Gent' %}
 site_url: https://docs.hpc.ugent.be/{{ os }}/
-{%- endif %}
+{% endif %}
 site_name: VSC User Documentation - {{ site }} ({{ os }})
 docs_dir: docs/HPC
 repo_url: https://github.com/hpcugent/vsc_user_docs
@@ -14,14 +14,14 @@ nav:
   - Running batch jobs: running_batch_jobs.md
   - Running interactive jobs: running_interactive_jobs.md
   - Running jobs with input/output data: running_jobs_with_input_output_data.md
-{%- if site == 'Gent' %}
+{% if site == 'Gent' %}
   - Available software: ./only/gent/available_software/index.md
-{%- endif %}
+{% endif %}
   - Multi core jobs/Parallel Computing: multi_core_jobs.md
   - Using the HPC-UGent web portal: web_portal.md
-{%- if site == 'Gent' %}
+{% if site == 'Gent' %}
   - Interactive and debug cluster: interactive_debug.md
-{%- endif %}
+{% endif %}
   - XDMoD portal: xdmod.md
   - Troubleshooting: troubleshooting.md
   - HPC Policies: sites/hpc_policies.md
@@ -35,7 +35,7 @@ nav:
       - Best Practices: best_practices.md
       - Graphical applications with VNC: VNC.md
       - Graphical applications with X2Go: x2go.md
-{%- if site == 'Gent' %}
+{% if site == 'Gent' %}
       - GPU clusters: gpu.md
       - Cron scripts: crontab.md
       - Teaching and training: teaching_training.md
@@ -48,7 +48,7 @@ nav:
     - Beyond the basics: linux-tutorial/beyond_the_basics.md 
     - Common pitfalls: linux-tutorial/common_pitfalls.md
     - More on the HPC infrastructure: linux-tutorial/hpc_infrastructure.md
-{%- endif %}
+{% endif %}
   - Software-specific Best Practices:
       - AlphaFold: alphafold.md
       - Apptainer/Singularity: apptainer.md
@@ -78,13 +78,13 @@ plugins:
       site: {{ site }}
       os: {{ os }}
       osneutrallinks: True
-{%- if site == 'Gent' %}
+{% if site == 'Gent' %}
   - redirects:
       redirect_maps:
           gpu_gent.md: gpu.md
           interactive_gent.md: interactive_debug.md
           crontab_gent.md: crontab.md
-{%- endif %}
+{% endif %}
   - macros:
       on_error_fail: true
       include_yaml:
@@ -157,16 +157,16 @@ theme:
         name: Switch to light mode 
 
 extra_javascript:
-{%- if site == 'Gent' %}
+{% if site == 'Gent' %}
     - https://code.jquery.com/jquery-3.7.0.min.js
     - https://cdn.datatables.net/1.13.6/js/jquery.dataTables.min.js
     - available_software/javascripts/populate_overview.js
-{%- endif %}
+{% endif %}
 
 extra_css:
-{%- if site == 'Gent' %}
+{% if site == 'Gent' %}
     - https://cdn.datatables.net/1.13.6/css/jquery.dataTables.min.css
-{%- endif %}
+{% endif %}
 
 extra:
   analytics:

config/templates/os_pick.template

@@ -1,6 +1,6 @@
-{%- if site == 'Gent' %}
+{% if site == 'Gent' %}
 site_url: https://docs.hpc.ugent.be
-{%- endif %}
+{% endif %}
 site_name: VSC User Documentation - {{ site }}
 docs_dir: os_pick/docs
 
@@ -12,13 +12,13 @@ plugins:
         - Linux
         - macOS
         - Windows
-{%- if site == 'Gent' %}
+{% if site == 'Gent' %}
   - redirects:
       redirect_maps:
           gpu_gent.md: gpu.md
           interactive_gent.md: interactive_debug.md
           crontab_gent.md: crontab.md
-{%- endif %}
+{% endif %}
   - macros:
       include_yaml:
         - extra/constants.yml

custom_plugin/constants.py

@@ -10,9 +10,9 @@
 """
 
 OS_PICK_BTN = """
-{{%- if {} %}}
+{{% if {} %}}
 [{}]({}){{ .md-button }}
-{{%- endif %}}
+{{% endif %}}
 """
 
 # This string enables automatic scrolling to section on some page while using OS picking feature.

mkdocs/docs/HPC/linux-tutorial/beyond_the_basics.md

@@ -1,4 +1,3 @@
-{% import './macros/nb.md' as nb %}
 # Beyond the basics
 
 Now that you've seen some of the more basic commands, let's take a look
@@ -123,8 +122,11 @@ The shell will expand certain things, including:
     their value; example: `echo "I am $USER"` or `echo "I am ${USER}"`
 
 4.  square brackets can be used to list a number of options for a
-    particular characters; {{nb.nb("example: `ls *.[oe][0-9]`.")}} This will list all
-    files starting with whatever characters (`*`), then a dot (`.`),
+    particular characters. 
+
+    example: `ls *.[oe][0-9]`
+
+    This will list all files starting with whatever characters (`*`), then a dot (`.`),
     then either an 'o' or an 'e' (`[oe]`), then a character from '0' to
     '9' (so any digit) (`[0-9]`). So this filename will match:
     `anything.o5`, but this one won't: `anything.o52`.
@@ -188,7 +190,7 @@ macOS. `top` will update every second and has a few interesting
 commands.
 
 To see only your processes, type `u` and your username after starting
-`top`, (you can also do this with {{nb.nb("`top -u $USER`")}}). The default is to
+`top`, (you can also do this with `top -u $USER`). The default is to
 sort the display by `%CPU`. To change the sort order, use `<` and `>`
 like arrow keys.
 

mkdocs/docs/HPC/linux-tutorial/common_pitfalls.md

@@ -76,7 +76,7 @@ press enter to put the command in your history so you can come back to
 it later (e.g., while you go check the spelling of your environment
 variables).
 
-{% if OS==windows %}
+{% if OS == windows %}
 
 ### Copying files with WinSCP
 

mkdocs/docs/HPC/linux-tutorial/getting_started.md

@@ -220,7 +220,7 @@ And querying some basic information about the Linux kernel:
 ```
 $ uname -a 
 Linux gligar01.gligar.os 2.6.32-573.8.1.el6.ug.x86_64 #1 SMP Mon Nov 16 15:12:09
-	CET 2015 x86_64 x86_64 x86_64 GNU/Linux 
+    CET 2015 x86_64 x86_64 x86_64 GNU/Linux 
 ```
 
 ## Exercises

mkdocs/docs/HPC/linux-tutorial/hpc_infrastructure.md

@@ -6,7 +6,7 @@ infrastructure, each with their own purpose. See section
 [Where to store your data on the {{ hpc }}](../running_jobs_with_input_output_data.md#where-to-store-your-data-on-the-hpc)
 for a list of available locations.
 
-{% if site==gent %}
+{% if site == gent %}
 ### VO storage
 If you are a member of a (non-default) virtual organisation (VO), see section
 [Virtual Organisations](../running_jobs_with_input_output_data.md#virtual-organisations),

mkdocs/docs/HPC/macros/LinuxManualURL.md

@@ -1,4 +1,6 @@
-{%- macro LinuxManualURL(OS, site) -%}
-<!--- change url once deployed! --->
-[the chapter titled "Uploading/downloading/editing files", section "Symlinks for data/scratch" in the intro to Linux](localhost:8000/{{ site }}/{{ OS }}/intro-Linux/uploading_files/#symlinks-for-datascratch)
-{% endmacro %}
+{% macro LinuxManualURL(OS, site) %}
+<!-- change url once deployed! -->
+[the chapter titled "Uploading/downloading/editing files", section "Symlinks
+for data/scratch" in the intro to Linux](localhost:8000/{{ site }}/{{ OS
+}}/intro-Linux/uploading_files/#symlinks-for-datascratch)
+{% endmacro %}

mkdocs/docs/HPC/macros/nb.md

@@ -1,3 +1,3 @@
-{%- macro nb(content) %}
+{% macro nb(content) %}
 <span style="white-space: nowrap;">{{ content }}</span>
-{% endmacro %}
+{% endmacro %}

mkdocs/docs/HPC/sites/available_modules.md

@@ -1,9 +1,9 @@
 {% if site == leuven %}
 [//]: # (Add include if needed)
 {% elif site == antwerpen %}
-{% include "antwerpen/available-modules.md" %}
+{%     include "antwerpen/available-modules.md" %}
 {% elif site == brussel %}
 [//]: # (Add include if needed)
 {% elif site == gent %}
-{% include "gent/available-modules.md" %}
+{%     include "gent/available-modules.md" %}
 {% endif %}

scripts/available_software/available_software.py

@@ -384,7 +384,10 @@ def generate_software_detail_page(
     md_file.new_paragraph(f"To start using {software_name}, load one of these modules using a `module load` command "
                           f"like:")
     md_file.insert_code(f"module load {newest_version}", language="shell")
-    md_file.new_paragraph("(This data was automatically generated on {{modules_last_updated}})", bold_italics_code="i")
+    md_file.new_paragraph(
+        "(This data was automatically generated on {{ modules_last_updated }})",
+        bold_italics_code="i",
+    )
     md_file.new_line()
 
     md_file.new_table(

scripts/vsc-venv-wrapper/vsc-venv.sh

@@ -132,6 +132,7 @@ activate() {
 
   # === Warn user if they have modules loaded === #
   loaded_modules=($(echo "$LOADEDMODULES" | tr ':' '\n' | grep -v -E '^(env|cluster|vsc-venv)/')) # Remove env, cluster and vsc-venv modules
+  # {# j2lint: disable=S0 #}
   n_loaded_modules="${#loaded_modules[@]}"
   if [ "$n_loaded_modules" -gt 0 ]; then
     echo_warning "You have $n_loaded_modules loaded modules in the current shell. These modules will be purged."

site_pick/index.md

@@ -7,4 +7,4 @@ hide:
 
 {% import 'site_pick.md' as sitepick %}
 
-{{ sitepick.sitepick("Antwerpen", "Gent")}}
+{{ sitepick.sitepick("Antwerpen", "Gent") }}

site_pick/site_pick.md

@@ -1,16 +1,16 @@
 {% macro sitepick(ant_home_url, gent_home_url, brussel_home_url, leuven_home_url) %}
 # Please select your site:
 
-{%- if ant_home_url %}
+{%     if ant_home_url %}
 [Antwerpen]({{ ant_home_url }}){ .md-button }
-{%- endif %}
-{%- if gent_home_url %}
+{%     endif %}
+{%     if gent_home_url %}
 [Gent]({{ gent_home_url }}){ .md-button }
-{%- endif %}
-{%- if brussel_home_url %}
+{%     endif %}
+{%     if brussel_home_url %}
 [Brussel]({{ brussel_home_url }}){ .md-button }
-{%- endif %}
-{%- if leuven_home_url %}
+{%     endif %}
+{%     if leuven_home_url %}
 [Leuven]({{ leuven_home_url }}){ .md-button }
-{%- endif %}
+{%     endif %}
 {% endmacro %}