Fix duplicate label due to includes

.gitlab-ci.yml

@@ -3,10 +3,9 @@ image: alpine
 pages:
   script:
   - apk --no-cache add py3-pip python3-dev
-  - pip install sphinx sphinx_rtd_theme
+  - pip install sphinx sphinx_rtd_theme recommonmark
   - apk --no-cache add make
   - make html
-  - make html  # fix some toc/include related warnings
   - mkdir public
   - mv _build/html/* public/
   artifacts:

conf.py

@@ -31,14 +31,11 @@ import sphinx_rtd_theme
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = []
+extensions = ['recommonmark']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
-# The suffix(es) of source filenames.
-# You can specify multiple suffix as a list of string:
-source_suffix = ['.rst', '.md']
 
 # The encoding of source files.
 #source_encoding = 'utf-8-sig'
@@ -119,7 +116,6 @@ html_theme = "sphinx_rtd_theme"
 
 # Add any paths that contain custom themes here, relative to this directory.
 #html_theme_path = []
-html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".

rm/general.rst

+.. _rm_general:
+
 General
 =======
 
@@ -23,10 +25,10 @@ will find documentation and example commands for both systems.
 Queues/Partitions
 -----------------
 
-The RM usually manages a number of queues (they are called partitions for
-Slurm) and they can hold thousands of jobs that are subject to execution. Once
-you prepared a Job (:ref:`torque_jobs`, :ref:`slurm_jobs`) you can place them
-inside a queue. All jobs of all users are going to the same central
+The RM usually manages a number of queues (partitions for Slurm) and they can
+hold thousands of jobs that are subject to execution. Once you prepared a Job
+(:ref:`Torque Jobs <torque_jobs>`, :ref:`Slurm Jobs <slurm_jobs>`) you can
+place them inside a queue. All jobs of all users are going to the same central
 queue(s):
 
 .. image:: ../img/queue.svg

rm/slurm.rst

@@ -11,10 +11,10 @@ nodes from Torque to SLURM to motivate everyone to familiarize with the new syst
 **Users familiar with Torque** can check out the :ref:`slurm_transition` for a quick start:
 
 
-.. include:: slurm/transition.rst
-.. include:: slurm/jobs.rst
-.. include:: slurm/commands.rst
-.. include:: slurm/resources.rst
-.. include:: slurm/gpus.rst
+.. include:: slurm/transition.inc
+.. include:: slurm/jobs.inc
+.. include:: slurm/commands.inc
+.. include:: slurm/resources.inc
+.. include:: slurm/gpus.inc
 
 .. _SLURM: https://slurm.schedmd.com/

rm/slurm/gpus.rst → rm/slurm/gpus.inc

+.. _gpu_list:
+
 using GPUs
 ----------
 

rm/torque.rst

-.. _torque:
+.. _torque_index:
 
 Torque **(End-Of-Life)**
 ========================
@@ -10,7 +10,7 @@ the open source product Maui, which hadn't seen an update for many years and
 became incompatible to some of the more recent feature of Torque.
 
 
-.. include:: torque/jobs.rst
-.. include:: torque/commands.rst
-.. include:: torque/dependencies.rst
-.. include:: torque/resources.rst
+.. include:: torque/jobs.inc
+.. include:: torque/commands.inc
+.. include:: torque/dependencies.inc
+.. include:: torque/resources.inc

rm/torque/dependencies.rst → rm/torque/dependencies.inc

@@ -18,7 +18,7 @@ dependency systems to specify the structure of the three stages so you only
 have to submit once.
 
 Submit Example
-~~~~~~~~~~~~~~
+++++++++++++++
 
 Every time you submit a job with qsub you can add a dependency list to that job
 and ask to only run on certain conditions. For instance, to run job 5 only