customize css of 'console' code (#15)

 * change background of 'console' code to distinguish
   it from 'python' code

 * remove contentui extension (not needed)
 * PRACE 2018:
    * add graph figure
    * add workflows figure

docs/_static/css/custom.css

@@ -0,0 +1,3 @@
+div.highlight-console div.highlight {
+    background-color: aliceblue;
+}

docs/conf.py

@@ -23,7 +23,7 @@
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.todo', 'sphinx.ext.imgmath', 'sphinx.ext.ifconfig', 'sphinx.ext.viewcode', 'IPython.sphinxext.ipython_console_highlighting', 'IPython.sphinxext.ipython_directive', 'sphinxcontrib.contentui', 'recommonmark']
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.todo', 'sphinx.ext.imgmath', 'sphinx.ext.ifconfig', 'sphinx.ext.viewcode', 'IPython.sphinxext.ipython_console_highlighting', 'IPython.sphinxext.ipython_directive', 'recommonmark']
 ipython_mplbackend = ""
 
 todo_include_todos = True
@@ -130,8 +130,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-# TEMPORARILY DISABLED
-#html_static_path = ['_static']
+html_static_path = ['_static']
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.
@@ -311,3 +310,7 @@
 #    nitpick_ignore.append((dtype, target))
 
 suppress_warnings = [ 'misc.highlighting_failure' ]
+
+
+def setup(app):
+    app.add_stylesheet('css/custom.css')

docs/pages/2018_PRACE_MaX/sections/calculations.md

@@ -8,13 +8,13 @@ The AiiDA daemon
 
 First of all, check that the AiiDA daemon is actually running. The AiiDA daemon is a program running all the time in the background, checking if new calculations appear and need to be submitted to the scheduler. The daemon also takes care of all the necessary operations before the calculation submission, and after the calculation has completed on the cluster. Type in the terminal
 
-``` bash
+```console
 verdi daemon status
 ```
 
 If the daemon is running, the output should look like
 
-``` bash
+```console
     Profile: default
     Daemon is running as PID 1650 since 2018-05-16 16:26:04
     Active workers [1]:
@@ -26,7 +26,7 @@ If the daemon is running, the output should look like
 
 If this is not the case, type in the terminal
 
-``` bash
+```console
 verdi daemon start
 ```
 
@@ -39,7 +39,7 @@ To launch a calculation, you will need to interact with AiiDA mainly in the `ver
 
 **The best way to run python scripts using AiiDA functionalities is to run them in a terminal by means of the command**
 
-``` bash
+```console
  verdi run <scriptname>
 ```
 
@@ -51,7 +51,7 @@ Every calculation sent to a cluster is linked to a code, which describes the exe
 
 Here `Code` is the general AiiDA class handling all possible codes, and `code` is a class instance tagged as `<codename>` (see the first part of the tutorial for listing all codes installed in your AiiDA machine). You might also want to list only the codes that define a default calculation plugin for the pw.x code of Quantum ESPRESSO. You can do this with the following command:
 
-``` bash
+```console
 verdi code list -p quantumespresso.pw
 ```
 
@@ -118,7 +118,7 @@ Moreover, PWscf also needs information on the pseudopotentials, specified by Upf
 
 You can list the preconfigured families from the command line:
 
-``` bash
+```console
  verdi data upf listfamilies
 ```
 
@@ -212,7 +212,7 @@ In the meantine, as soon as you submitted your calculation, the daemon picked it
 
 You can check the calculation status from the command line:
 
-``` bash
+```console
  verdi calculation list                                   
 ```
 
@@ -222,21 +222,21 @@ By now, it is possible that the calculation you submitted has already finished,
 
 To see also (your) calculations that have finished (and limit those only to the one created in the past day), use instead
 
-``` bash
+```console
  verdi calculation list -a -p1                                  
 ```
 
 as explained in the first section.
 
 To inspect the list of input files generated by the AiiDA (this can be done even when the calculation did not finish yet), type
 
-``` bash
+```console
  verdi calculation inputls <pk_number> -c
 ```
 
 with `pk_number` the pk number of your calculation. This will show the contents of the input directory (`-c` prints directories in colour). Then you can also check the content of the actual input file with
 
-``` bash
+```console
  verdi calculation inputcat <pk_number> | less
 ```
 
@@ -247,13 +247,13 @@ After all this work the calculation should end up in a FAILED Job state (last co
 
 A first way to proceed is the manual inspection of the output file of PWscf. You can visualize it with:
 
-``` bash
+```console
  verdi calculation outputcat <pk_number> | less
 ```
 
 This can be a good primer for problem inspection. For something more compact, you can also try to inspect the calculation log (from AiiDA):
 
-``` bash
+```console
  verdi calculation logshow <pk_number>
 ```
 
@@ -281,7 +281,7 @@ parameters_dict = {
 
 If you launch the modified script by typing
 
-``` bash
+```console
  verdi run test_pw.py
 ```
 

docs/pages/2018_PRACE_MaX/sections/preliminaries.md

@@ -1,3 +1,6 @@
+Preliminaries
+=============
+
 Instructions to SSH to the Amazon EC2 instance
 ----------------------------------------------
 
@@ -30,7 +33,7 @@ You should have received an IP address from the instructors, and two files with
 
 -   You can then `ssh` to the Amazon EC2 instance from the terminal, using simply
 
-    ``` bash
+    ```console
       ssh -X -C aiidatutorial
      
     ```
@@ -66,13 +69,13 @@ Before starting
 
 Once connected to your machine, type in the remote terminal
 
-``` bash
+```console
  workon aiida
 ```
 
 This will enable the virtual environment in which AiiDA is installed, allowing you to use AiiDA. Now type in the same bash
 
-``` bash
+```console
  jupyter notebook --no-browser
 ```
 

docs/pages/2018_PRACE_MaX/sections/querybuilder.md

@@ -3,13 +3,13 @@ Queries in AiiDA: The Querybuilder
 
 This part of the tutorial is provided only in interactive mode through a Jupyter notebook, which you will be able to run in your browser. To accomplish this we first need to start the Jupyter server, if you didn’t do it already at the very beginning of the tutorial. First make sure you are connected to the virtual machine with local forwarding enabled, as described in section [sec:sshintro]. Then, on the virtual machine, first make sure your are in the `aiida` virtual environment:
 
-``` bash
+```console
 workon aiida
 ```
 
 If the virtual environment is successfully loaded, your prompt should be prefixed with `(aiida)`. To finally launch the Jupyter server, execute the following commands:
 
-``` bash
+```console
 cd ~/examples/aiida-demos/tutorial/
 jupyter notebook --no-browser
 ```