clear lesson-check errors

Author: tkphd

_episodes/02-00-environment-modules.md renamed to _episodes/00-environment-modules.md

@@ -27,7 +27,7 @@ When Lola sits down to tackle her next project, she wants to get a feeling on wh
 ~~~
 $ python3
 ~~~
-{: .bash}
+{: .language-bash}
 
 ~~~
 bash: python3: command not found
@@ -55,7 +55,7 @@ Lena demonstrates that inside the folder where `fdate` was unzipped, it can be e
 ~~~
 $ ./fdate
 ~~~
-{: .bash}
+{: .language-bash}
 
 ~~~
 -----------------------------
@@ -69,7 +69,7 @@ However, when omitting the leading `./`, the command doesn't work anymore.
 ~~~
 $ fdate
 ~~~
-{: .bash}
+{: .language-bash}
 
 ~~~
 bash: fdate: command not found...
@@ -85,7 +85,7 @@ What is likely to happen in a good library: a sign will be put up which tells a
 ~~~
 $ echo ${PATH}
 ~~~
-{: .bash}
+{: .language-bash}
 
 which may yield something along the lines of:
 
@@ -101,7 +101,7 @@ To proceed and make `/home/lola/from_lena/fdate` available to `PATH`, Lena shows
 ~~~
 $ export PATH=${PATH}:/home/lola/from_lena/
 ~~~
-{: .bash}
+{: .language-bash}
 
 As you can see only directories (not paths to files) are added to `PATH` (similar to the example above where only signs to the fantasy corner and not to Harry Potter V are put up). 
 
@@ -112,7 +112,7 @@ As you can see only directories (not paths to files) are added to `PATH` (simila
 > ~~~~~
 > $ export PATH=/home/lola/from_lena/:${PATH}
 > ~~~~~
-> {: .bash}
+> {: .language-bash}
 > 
 > This means though that you have trust, that `/home/lola/from_lena/` does not contain applications which would shadow applications which are already accessible through `PATH`.
 >
@@ -155,7 +155,7 @@ As you can see only directories (not paths to files) are added to `PATH` (simila
 > $ cd /tmp
 > $ ls
 > ~~~~~
-> {: .bash} 
+> {: .language-bash} 
 > 
 > > ## Solution
 > > `fdate.zip` can be downloaded from [here]({{ page.root }}/code/02_parallel_jobs/fdate.zip). 
@@ -172,7 +172,7 @@ $ fdate
 $ cd /tmp
 $ fdate
 ~~~
-{: .bash}
+{: .language-bash}
 
 ~~~
 -----------------------------
@@ -191,7 +191,7 @@ To have a look, what software is available through the `module` system, a user i
 ~~~
 $ module available
 ~~~
-{: .bash}
+{: .language-bash}
 
 ~~~
 --------------------------------- /opt/modulefiles/ ---------------------------------------
@@ -206,7 +206,7 @@ The structure of each entry is usually the same `<software>/<version>`, where `s
 ~~~
 $ module load python/3.6.5
 ~~~
-{: .bash}
+{: .language-bash}
 
 ~~~
 python version 3.6.5 for x86_64 architecture loaded.
@@ -218,7 +218,7 @@ The exact content of the above differs from system to system and depends on how
 ~~~
 $ python --version             
 ~~~
-{: .bash}
+{: .language-bash}
 
 ~~~
 Python 3.6.5
@@ -233,7 +233,7 @@ Python 3.6.5
 > ~~~
 > $ python --version             
 > ~~~
-> {: .bash}
+> {: .language-bash}
 > 
 {: .callout }
 
@@ -242,14 +242,14 @@ The real hallmark of the module system comes with the facility to switch off app
 ~~~
 $ module unload python/3.6.5
 ~~~
-{: .bash}
+{: .language-bash}
 
 When one tries again now, the above mentioned effect is gone again:
 
 ~~~
 $ python --version
 ~~~
-{: .bash}
+{: .language-bash}
 
 ~~~
 Python 2.7.15
@@ -259,12 +259,15 @@ Python 2.7.15
 
 > ## The others do it too
 > 
-> The idea of programmatically changing the environment of a running terminal is offered by many other software stacks. In the python eco system, `virtualenv` is a prime example. of such. From the [`virtualenv` docs](https://virtualenv.pypa.io/en/stable/userguide/#activate-script):
+> The idea of programmatically changing the environment of a running terminal
+> is offered by many other software stacks. In the python eco system,
+> `virtualenv` is a prime example. of such. From the [`virtualenv`
+> docs](https://virtualenv.pypa.io/en/stable/userguide/#activate-script):
 >
 > ~~~~~
 > $ source bin/activate
 > ~~~~~
-> { .bash }
+> {: .language-bash}
 > 
 > "... This will change your $PATH so its first entry is the virtualenv’s bin/ directory. (You have to use source because it changes your shell environment in-place.)"
 > 
@@ -274,7 +277,7 @@ Python 2.7.15
 > $ conda create -n our_workshop python=3.6 numpy mpi4py line_profiler
 > $ source activate our_workshop
 > ~~~~~
-> { .bash }
+> {: .language-bash}
 >
 > The last line above changes the environment of the current shell, so that `python=3.6 numpy mpi4py line_profiler` are available.
 {: .callout }

_episodes/02-01-estimate-of-pi.md renamed to _episodes/01-estimate-of-pi.md

@@ -86,7 +86,7 @@ If need be, to install the profiler, please issue the following command:
 ~~~
 $ pip3 install line_profiler
 ~~~
-{: .language-bash }
+{: .language-bash}
 
 When this is done and your command line offers the `kernprof-3` executable, you are ready to go on. 
 
@@ -146,7 +146,7 @@ $ kernprof-3 -l ./serial_numpi_annotated.py 50000000
 [serial version] pi is 3.141728 from 50000000 samples
 Wrote profile results to serial_numpi_annotated.py.lprof
 ~~~
-{: .language-bash }
+{: .language-bash}
 
 You can see that the profiler just adds one line to the output, i.e. the last line. In order to view, the output we can use the `line_profile` module in python:
 
@@ -358,6 +358,8 @@ So this is a prime candidate for acceleration.
 > >     48                                               else:
 > >     49                                                   sys.exit(1)
 > > ~~~~~
+> > {: .output}
+> >
 > > The `word_count` function takes the longest time. Inside it, `re.split` hogs runtime the most.
 > {: .solution}
 {: .challenge}

_episodes/02-02-parallel-estimate.md renamed to _episodes/02-parallel-estimate.md

@@ -86,7 +86,7 @@ She tests her python program on a single input file. As she knows how long it'll
 ~~~
 {: .output}
 
-> ## The `bash` can do that too
+> ## The shell can do that too
 >
 > Filtering out any lines starting with `3.1` can be done with pure bash commands as well.
 > 

_episodes/02-03-a-paradigm-shift.md renamed to _episodes/03-a-paradigm-shift.md

@@ -6,36 +6,45 @@ permalink: /setup/
 
 ## Software requirements
 
-Please bring your laptop to the course. Your laptop should have a program called `ssh` or any clients thereof installed and ready for use.
+Please bring your laptop to the course. Your laptop should have a program
+called `ssh` or any clients thereof installed and ready for use.
 
 ### Linux
 
-Please make sure that ssh is in your PATH or to install ssh with your distribution's package manager (like xterm, terminal, konsole, etc. available as well).
+Please make sure that ssh is in your PATH or to install ssh with your
+distribution's package manager (like xterm, terminal, konsole, etc. available
+as well).
 
 ### macOS / OS X
 
-`ssh` is typically preinstalled, however be sure to have a terminal program (like e.g. [`iTerm`](https://www.iterm2.com/) available as well).
+`ssh` is typically preinstalled, however be sure to have a terminal program
+(like e.g. [`iTerm`](https://www.iterm2.com/) available as well).
 
 ### Windows
 
-It depends on your version of windows how and if you have to install a terminal and/or a ssh client. Typically, [putty](http://www.putty.org), [bitvise SSH](https://www.bitvise.com/ssh-client-download) or [mRemoteNG](https://mremoteng.org/) are a good choices.
+It depends on your version of windows how and if you have to install a terminal
+and/or a ssh client. Typically, [putty](http://www.putty.org), [bitvise
+SSH](https://www.bitvise.com/ssh-client-download) or
+[mRemoteNG](https://mremoteng.org/) are a good choices.
 
 
 ## Logging in
 
 In this lesson, we will be working on the command-line on a remote computer.
-This means that the commands we enter into the command-line will be run
-on a different computer than our laptop/workstation.
+This means that the commands we enter into the command-line will be run on a
+different computer than our laptop/workstation.
 
-The first step will be to connect to this computer.
-This is known as a remote login.
+The first step will be to connect to this computer. This is known as a remote
+login.
 
 If you run Mac OS X or any other Unix-based operating system on your machine,
 you can log in remotely by opening a terminal and using the `ssh` command:
 
 ~~~
 $ ssh username@{{ site.workshop_login_host }}
 ~~~
+{: .language-bash}
 
-Make sure to change `username` to the username you will have on the remote machine. Also, please change `{{ site.workshop_login_host }}` to what your instructors tells you.
-
+Make sure to change `username` to the username you will have on the remote
+machine. Also, please change `{{ site.workshop_login_host }}` to what your
+instructors tells you.