Fix links

Fix all bad links that mkdocs warned about when starting:

INFO    -  Doc file 'software/python.md' contains an unrecognized relative link 'Python versions', it was left as is.
INFO    -  Doc file 'software/r.md' contains an unrecognized relative link 'swcarpentry.github.io/r-novice-inflammation/', it was left as is.
INFO    -  Doc file 'cluster_guides/start_interactive_node.md' contains a link '#when-to-use-an-interactive node', but there is no such anchor on this page.
INFO    -  Doc file 'software/beast2.md' contains a link '../getting_started/login_rackham.md#remote-desktop-via-a-ThinLinc client', but the doc
           'getting_started/login_rackham.md' does not contain an anchor '#remote-desktop-via-a-ThinLinc client'.
INFO    -  Doc file 'software/beast2.md' contains a link '../getting_started/login_rackham.md#remote-desktop-via-the-web', but the doc
           'getting_started/login_rackham.md' does not contain an anchor '#remote-desktop-via-the-web'.
INFO    -  Doc file 'software/install.md' contains a link 'compiling_parallel.md#overview-of-available-compilers-from-gcc-and-intel-and-compatible-mpi-libraries', but
           the doc 'software/compiling_parallel.md' does not contain an anchor '#overview-of-available-compilers-from-gcc-and-intel-and-compatible-mpi-libraries'.
INFO    -  Doc file 'software/jobstats.md' contains a link '#jobstats---plot', but there is no such anchor on this page.
INFO    -  Doc file 'software/python_venv.md' contains a link '../software/python.md#loading-python-modules', but the doc 'software/python.md' does not contain an
           anchor '#loading-python-modules'.

docs/cluster_guides/start_interactive_node.md

@@ -12,7 +12,7 @@ tags:
 Below we describe the general ideas of using an interactive node:
 
 - [the types of nodes](#types-of-nodes)
-- [When to use an interactive node](#when-to-use-an-interactive node)
+- [When to use an interactive node](#when-to-use-an-interactive-node)
 
 To start an interactive node on specific cluster:
 

docs/software/beast2.md

@@ -248,9 +248,9 @@ beast -beagle_info
 This problem seems to be related to not having a proper X server installed.
 In this case, [SSH X forwarding](ssh_x_forwarding.md) works to the extent
 that SSH is able to show [`xeyes`](../software/xeyes.md), yet fails to show BEAUti.
-Also, [using the remote desktop via a ThinLinc client](../getting_started/login_rackham.md#remote-desktop-via-a-ThinLinc client) fails.
+Also, [using the remote desktop via a ThinLinc client](../getting_started/login_rackham_remote_desktop_local_thinlinc_client.md) fails.
 
-A solution may be to [use the remote desktop via the web](../getting_started/login_rackham.md#remote-desktop-via-the-web)
+A solution may be to [use the remote desktop via the web](../getting_started/login_rackham_remote_desktop_website.md)
 
 ???- question "How does that look like?"
 

docs/software/install.md

@@ -142,7 +142,7 @@ container.
 - You may have your own code that you want to run on UPPMAX.
 - [Guide for compiling **serial** programs](compiling_serial.md)
 - [Guide for compiling **parallel** programs](compiling_parallel.md)
-    - [Available **combinations** of compilers and parallel libraries](compiling_parallel.md#overview-of-available-compilers-from-gcc-and-intel-and-compatible-mpi-libraries)
+    - [Available **combinations** of compilers and parallel libraries](parallel_comb.md)
 - [User guide for debuggers](../software/debuggers.md)
 - [User guide for profilers](../software/profilers.md)
 

docs/software/jobstats.md

@@ -9,7 +9,7 @@ for jobs submitted to the [Slurm](../cluster_guides/slurm.md) job queue.
 
 At this page, it is described:
 
-- [`jobstats --plot`](#jobstats---plot): How to use is `jobstats --plot` to see resource use in a graphical plot
+- [`jobstats --plot`](#jobstats-plot): How to use is `jobstats --plot` to see resource use in a graphical plot
 - [Efficient use](#efficient-use): How to use your resources efficiently
 - [Examples](#examples): Examples of ineffective resource use plots
 - Other `jobstats` functionality

docs/software/python.md

@@ -5,7 +5,7 @@
 Welcome to the UPPMAX Python user guide.
 
 We describe [what Python is](#what-is-python)
-and that there are [multiple Python versions](Python versions).
+and that there are [multiple Python versions](#python-versions).
 
 Then, we show how to [load Python](#loading-python)
 and to [load Python packages](#loading-python-packages)

docs/software/python_venv.md

@@ -32,7 +32,7 @@ which has these steps:
 The first step is described at
 ['Loading Python'](../software/python.md#loading-python)
 and
-['Loading Python package modules'](../software/python.md#loading-python-modules).
+['Loading Python package modules'](../software/python.md#loading-python-package-modules).
 
 ???- question "Just show me how to do this"
 
@@ -42,7 +42,7 @@ and
     module load python/3.11.8
     ```
 
-    Here is how to [load a Python package module](../software/python.md#loading-python-modules):
+    Here is how to [load a Python package module](../software/python.md#loading-python-package-modules):
 
     ```bash
     module load python_ML_packages/3.11.8-cpu

docs/software/r.md

@@ -291,7 +291,7 @@ A large number of R packages are available as part of the R_packages/3.3.0 modul
 
 [The Carpentries](https://carpentries.org/) teaches basic lab skills for research computing, such as:
 
-- [Programming with R](swcarpentry.github.io/r-novice-inflammation/)
+- [Programming with R](https://swcarpentry.github.io/r-novice-inflammation/)
 - [R for reproducible scientific analysis](https://swcarpentry.github.io/r-novice-gapminder)
 
 ### Experienced R courses