DOKU: Make examples more consistence (same path names,...)

[mscheinert]

Description

In the documentation there are several examples using certain paths and names. But they or not consistent throughout all sections.

E.g.: Step-1 in "Getting Started" uses My_Config and MyExp1 as names for the configuration and the experiment. But in the "Bundle Up" section, the Configuration is ORCA2_ICE and the experiment name is REF.

[lmicallef]

@mscheinert is ORCA2_ICE part of Nemo 4? Or is it used for experimental purposes? Also, REF is mentioned as the ‘experiment’ folder, what is the main purpose of REF? Will this contain, for example, the script for the functions, input.ini etc…? If yes, then I will need to make some modifications to the code.

[lmicallef]

Nemo Simsar Feedback:

• Getting Started Section *

Step 1:

Assuming the path to your copy of the NEMO repository reads $WORK/NEMO/release-4.0 and the configuration is "ORCA2_ICE" ,  let's go into the respective experiment folder of the simulation you want to publish e.g. “REF”

cd ~$WORK/NEMO/release-4.0/cfgs/ORCA2_ICE/REF

1.1 List input data files
First, we need a list of the required input data files for your simulation together with some detailed meta-data, like sources, references and check-sums. SIMSAR expects this list in a special file, the input.ini file. If this file does not exists yet, please create it and save in root.

? Do we still need the ‘important’ section? Are we making use of input.def?

4.3 typo (intention not intension)

The Simulation Package

Simulation Meta Data
Assemble the Meta-Data:
Typo: Most instead Mot

Create the README file with mkReadme.py
Experiment folder section:

Please, be aware, that currently the mkReadme.py and scriptMk.py expects you to be within the NEMO repository tree. If your experiment folder is outside of e.g. ~$WORK/NEMO/release-4.0/cfgs/ORCA2_ICE/REF, please consider finding a work-around by e.g. copying the necessary files temporarily into the NEMO repository tree (no need to copy the huge input data files, input.ini will be sufficient).

Step-by-Step Section:
5. (Add) If using GIT the full name is automatically extracted from .git config file
6. (Add) If using GIT the email is automatically extracted from .git config file

14. Typo (is instead of ist)

** Bundle up Section **

Checklist section

• Your experiment folder is complete, clean and ready.
• README.md is ready in the experiment folder. (In my opinion this is not necessary because the readme.md will be created through the script)
• mkReadme.py and scriptMk.py files are stored in the experiment folder
• input.ini is present and lists all necessary files.
• Depending which release you will using, it is necessary that either of these files(cfg.txt (or ref_cfgs.txt or work_cfgs.txt) is stored in the configuration. 

• Local git client is installed (git --version)
• You have access to a git remote server (maybe also to some group namespace)
• ...

(A) (1) - Shall we mention that release 3.6 includes CONFIG and release 4 includes CFGS?
- typo (folder not golder)
(A) (4) - typo (you’re not your’)

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Additional information

MacOS Catalina
If you are on macOS Catalina, the new default shell is zsh. You will instead need to run source <path to conda>/bin/activate followed by conda init zsh.

Note: wget and subversion modules do not work with pip3 if you are using Mac OS Catalina.

Install Wget:
In the terminal type: conda install -c conda-forge python-wget

Install subprocess:
In the terminal type: conda install -c anaconda svn

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[lmicallef]

• Update bundleup.md
• Update mkReadme.md
• Update simulation-meta.md
• Update gettingstarted.md

The above have been updated and modified accordingly. Awaiting approval.
(Additional Information section has not been included yet.)