fixed merge conflict

Author: rswamina

CODE_OF_CONDUCT.md

@@ -1,3 +1,7 @@
+---
+layout: page
+title: "Contributor Code of Conduct"
+---
 # Contributor Code of Conduct
 
 As contributors and maintainers of this tutorial,

CONTRIBUTING.md

@@ -51,6 +51,12 @@ There are many ways to contribute:
   [maintainers][tutorial-maintainers] have final say over what gets merged into
   the tutorial.
 
+* Information on how to write a software carpentry lesson,
+  can be found [here](https://carpentries.github.io/lesson-example/).
+
+* Guidelines on how to develop a software carpentry style curriculum
+  can be found [here](https://carpentries.github.io/curriculum-development/).
+
 ## Tutorial guidelines
 
 This section demonstrates all the instructions for developing a lesson in the
@@ -176,4 +182,4 @@ Please see [information][contact-info] on how to subscribe to user mailing list.
 [swc-lesson-organization]: https://carpentries.github.io/lesson-example/03-organization/index.html
 [swc-lesson-formatting]: https://carpentries.github.io/lesson-example/04-formatting/index.html
 [user-engagement]: https://github.com/orgs/ESMValGroup/teams/userengagementteam
-[contact-info]: https://docs.esmvaltool.org/en/latest/community/contact.html#user-mailing-list
+[contact-info]: https://docs.esmvaltool.org/en/latest/introduction.html#user-mailing-list

README.md

@@ -1,8 +1,10 @@
 # ESMValTool Tutorial
 
-[![Join the chat at
-https://gitter.im/ESMValGroup/Tutorial](https://badges.gitter.im/ESMValGroup/Tutorial.svg)](https://gitter.im/ESMValGroup/Tutorial?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3974592.svg)](https://doi.org/10.5281/zenodo.3974592)
+[![Join the chat at https://gitter.im/ESMValGroup/Tutorial](
+https://badges.gitter.im/ESMValGroup/Tutorial.svg)](
+https://gitter.im/ESMValGroup/Tutorial)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3974592.svg)](
+https://doi.org/10.5281/zenodo.3974592)
 
 
 [ESMValTool Tutorial][tutorial-site] is an open-source project in
@@ -42,4 +44,4 @@ To cite this tutorial, please use the information available at
 [tutorial-repo]: https://esmvalgroup.github.io/ESMValTool_Tutorial/
 [tutorial-site]: https://esmvalgroup.github.io/ESMValTool_Tutorial
 [user-engagement]: https://github.com/orgs/ESMValGroup/teams/userengagementteam
-[contact-info]: https://docs.esmvaltool.org/en/latest/community/contact.html#user-mailing-list
+[contact-info]: https://docs.esmvaltool.org/en/latest/introduction.html#user-mailing-list

_config.yml

@@ -31,7 +31,7 @@ kind: "lesson"
 repository: <USERNAME>/<PROJECT>
 
 # Email address, no mailto:
-email: "esmvaltool@listserv.dfn.de"
+email: "esmvaltool_user_engagement_team@listserv.dfn.de"
 
 # Sites.
 amy_site: "https://amy.carpentries.org/workshops"
@@ -50,9 +50,9 @@ training_site: "https://carpentries.github.io/instructor-training"
 workshop_repo: "https://github.com/carpentries/workshop-template"
 workshop_site: "https://carpentries.github.io/workshop-template"
 cc_by_human: "https://creativecommons.org/licenses/by/4.0/"
-ea_github: "https://github.com/escience-academy/"
-ea_pages: "https://github.com/escience-academy/escience-academy.github.io"
-ea_site: "https://escience-academy.github.io"
+esmvaltool_site: "https://www.esmvaltool.org/"
+esmvaltool_rtd: "https://esmvaltool.readthedocs.io"
+esmvaltool_github: "https://github.com/ESMValGroup"
 
 # Surveys.
 pre_survey: "https://carpentries.typeform.com/to/wi32rS?slug="

_episodes/01-introduction.md _episodes/00-introduction.md_episodes/01-introduction.md renamed to _episodes/00-introduction.md

@@ -64,7 +64,8 @@ documentation:
     - lastname_firstname
 
 datasets:
-  - {dataset: HadGEM2-ES, project: CMIP5, exp: historical, mip: Amon, ensemble: r1i1p1, start_year: 1960, end_year: 2005}
+  - {dataset: HadGEM2-ES, project: CMIP5, exp: historical, mip: Amon, 
+     ensemble: r1i1p1, start_year: 1960, end_year: 2005}
 
 preprocessors:
   global_mean:
@@ -88,8 +89,9 @@ diagnostics:
 >
 > > ## Solution
 > > The keys are explained in the ESMValTool documentation, in the `Recipe 
->>  section `, under
-> [datasets](https://docs.esmvaltool.org/projects/esmvalcore/en/latest/recipe/overview.html#recipe-section-datasets)
+> >  section `, under
+> [datasets](https://docs.esmvaltool.org/projects/esmvalcore/en/latest/recipe/
+overview.html#recipe-section-datasets)
 > {: .solution}
 {: .challenge}
 

_episodes/01-quickstart.md

@@ -0,0 +1,110 @@
+---
+title: "Quickstart guide"
+teaching: 2
+exercises: 8
+questions:
+
+- "What is the purpose of the quickstart guide?"
+- "How do I load and check the ESMValTool environment?"
+- "How do I configure ESMValTool?"
+- "How do I run a recipe?"
+
+objectives:
+
+- "Understand the purpose of the quickstart guide"
+- "Load and check the ESMValTool environment"
+- "Configure ESMValTool"
+- "Run a recipe"
+
+keypoints:
+
+- "The purpose of the quickstart guide is to enable a user of ESMValTool
+  to run ESMValTool as quickly as possible without having to go through the  
+  whole tutorial"
+- "Use the `module load` command to load the ESMValTool environment, 
+  see the [installation]({{ page.root }}{% link _episodes/02-installation.md %}) 
+  episode for more details and use `esmvaltool --help` to check the ESMValTool 
+  environment"
+- "Use `esmvaltool config get_config_user` to create the ESMValTool user 
+  configuration file"
+- "Use `esmvaltool run <recipe>.yml` to run a recipe"
+---
+>
+> This quickstart guide is compatible with ESMValTool v2.6.0.
+ {: .callout}
+
+> ## What is the purpose of the quickstart guide?
+>
+> - The purpose of the quickstart guide is to enable a user of ESMValTool to
+>   run ESMValTool as quickly as possible by making the bare minimum number of 
+>   changes.
+{: .discussion}
+
+> ## How do I load and check the ESMValTool environment?
+>
+> - For this quickstart guide, an assumption is made that ESMValTool has 
+>   already been installed at the site where ESMValTool will be run. If this is
+>   not the case, see the [Installation][lesson-installation] episode in this
+>   tutorial.
+> 
+> - Load the ESMValTool environment by following the instructions at
+>   [ESMValTool: Pre-installed versions on HPC clusters / other 
+>   servers][activate-environment].
+>
+> - Check the ESMValTool environment by accessing the help for ESMValTool:
+>
+>     ~~~
+>     esmvaltool --help
+>     ~~~
+>     {: .language-bash}
+{: .challenge}
+
+> ## How do I configure ESMValTool?
+>
+> - Create the ESMValTool user configuration file (the file is written by 
+>   default to `~/.esmvaltool/config-user.yml`):
+>
+>     ~~~
+>     esmvaltool config get_config_user
+>     ~~~
+>     {: .language-bash}
+> 
+> - Edit the ESMValTool user configuration file using your favourite text editor
+>   to uncomment the lines relating to the site where ESMValTool will be run.
+>
+> - For more details about the ESMValTool user configuration file see the
+>   [Configuration][lesson-configuration] episode in this tutorial.
+{: .challenge}
+
+> ## How do I run a recipe?
+> 
+> - Run the example Python recipe:
+> 
+>   ~~~
+>   esmvaltool run examples/recipe_python.yml 
+>   ~~~
+>   {: .language-bash}
+>
+> - Wait for the recipe to complete. If the recipe completes successfully, the
+>   last line printed to screen at the end of the log will look something like: 
+>
+>    ~~~
+>    YYYY-MM-DD HH:mm:SS, NNN UTC [NNNNN] INFO    Run was successful
+>    ~~~
+>    {: .language-bash}
+>
+> - View the output of the recipe by opening the HTML file produced by 
+>   ESMValTool (the location of this file is printed to screen near the end of
+>   the log):
+>
+>   ~~~
+>   YYYY-MM-DD HH:mm:SS, NNN UTC [NNNNN] INFO    Wrote recipe output to:
+>   file:///$HOME/esmvaltool_output/recipe_python_<date>_<time>/index.html
+>   ~~~
+>   {: .language-bash}
+>
+> - For more details about running recipes see the
+>   [Running your first recipe][lesson-recipe] episode in this tutorial.
+{: .challenge}
+
+{% include links.md %}

_episodes/02-installation.md

@@ -30,15 +30,18 @@ depending on your level of expertise or involvement with ESMValTool and
 associated software such as GitHub and Mamba.
 
 1. If you have access to a server where ESMValTool is already installed
-as a module, for e.g., the [CEDA JASMIN](https://help.jasmin.ac.uk/article/4955-community-software-esmvaltool)
+as a module, for e.g., the [CEDA JASMIN](https://help.jasmin.ac.uk/article
+/4955-community-software-esmvaltool)
 server, you can simply load the module with the following command:
 ~~~bash
 module load esmvaltool
 ~~~
-After loading ``esmvaltool``, we can start using ESMValTool right away. Please see the [next lesson]({{ page.root }}{% link _episodes/03-configuration.md %}). 
+After loading ``esmvaltool``, we can start using ESMValTool right away. Please
+ see the [next lesson]({{ page.root }}{% link _episodes/03-configuration.md %}). 
 2. If you would like to install ESMValTool as a mamba package, then this lesson
 will tell you how!
-3. If you would like to start experimenting with existing diagnostics or contributing to ESMvalTool, please see the instructions for 
+3. If you would like to start experimenting with existing diagnostics or 
+contributing to ESMvalTool, please see the instructions for 
 source installation in the lesson [Development and
 contribution]({{ page.root }}{% link _episodes/07-development-setup.md %}) and
 in the [documentation](https://docs.esmvaltool.org/en/latest/quickstart/installation.html).
@@ -62,7 +65,8 @@ in the [documentation](https://docs.esmvaltool.org/en/latest/quickstart/installa
 ESMValTool is distributed using [Mamba](https://mamba.readthedocs.io/en/latest/index.html).
 To install mamba on ``Linux`` or ``MacOSX``, follow the  instructions below:
 
-1.  Please download the installation file for the latest Mamba version [here](https://github.com/conda-forge/miniforge#mambaforge).
+1.  Please download the installation file for the latest Mamba version 
+[here](https://github.com/conda-forge/miniforge#mambaforge).
 
 2.  Next, run the installer from the place where you downloaded it:
 
@@ -98,7 +102,8 @@ To install mamba on ``Linux`` or ``MacOSX``, follow the  instructions below:
     This should show the path to your mamba executable, e.g. `~/mambaforge/bin/mamba`.
 
 For more information about installing mamba,
-see [the mamba installation documentation](https://docs.esmvaltool.org/en/latest/quickstart/installation.html#mamba-installation).
+see [the mamba installation documentation](https://docs.esmvaltool.org/en
+/latest/quickstart/installation.html#mamba-installation).
 
 ### Install the ESMValTool package
 
@@ -121,18 +126,22 @@ mamba create --name esmvaltool esmvaltool 'python=3.10'
 ```
 
 On MacOSX ESMValTool functionalities in Julia, NCL, and R are not supported. To install
-a Mamba environment on MacOSX, please refer to specific [information](https://docs.esmvaltool.org/en/latest/quickstart/installation.html#installation-on-macosx).
+a Mamba environment on MacOSX, please refer to specific [information](https://
+docs.esmvaltool.org/en/latest/quickstart/installation.html#installation-on-
+macosx).
 
 This will create a new [Mamba
-environment](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html)
+environment](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks
+/manage-environments.html)
 called `esmvaltool`, with the ESMValTool package and all of its dependencies
 installed in it.
 
 
 > ## Common issues
 >
 > You find a list of common installation problems and their solutions in the 
-> [documentation](https://docs.esmvaltool.org/en/latest/quickstart/installation.html#common-installation-problems-and-their-solutions).
+> [documentation](https://docs.esmvaltool.org/en/latest/quickstart/installation
+.html#common-installation-problems-and-their-solutions).
 >
 {: .callout}
 
@@ -219,8 +228,8 @@ to display the command line help.
 > > {: .bash}
 > > The version of ESMValTool installed should be displayed on the screen as:
 > > ~~~
-> > ESMValCore: 2.5.0
-> > ESMValTool: 2.5.0
+> > ESMValCore: 2.6.0
+> > ESMValTool: 2.6.0
 > > ~~~
 > > {: .output}
 > {: .solution}

_episodes/03-configuration.md

@@ -140,7 +140,8 @@ file are mentioned below. For example, CMIP is used for a dataset from
 the Climate Model Intercomparison Project whereas OBS may be 
 used for an observational dataset.
 More information about the projects used in ESMValTool is available in the 
-[documentation](https://docs.esmvaltool.org/projects/esmvalcore/en/latest/quickstart/find_data.html).
+[documentation](https://docs.esmvaltool.org/projects/esmvalcore/en/latest/
+quickstart/find_data.html).
 When using ESMValTool on your own machine, you can create a directory to download 
 climate model data or observation data sets and let the tool use data from there. 
 It is also possible to ask 
@@ -222,7 +223,8 @@ removing the machine specific lines should be sufficient to access input data.
 >>```
 >>
 >> - For more information about setting the rootpath, see also the ESMValTool
->> [documentation](https://docs.esmvaltool.org/projects/esmvalcore/en/latest/quickstart/find_data.html).
+>> [documentation](https://docs.esmvaltool.org/projects/esmvalcore/en/latest/
+quickstart/find_data.html).
 > {: .solution}
 {: .challenge}
 
@@ -236,7 +238,8 @@ The ``drs`` setting describes the file structure for several projects (e.g.
 CMIP6, CMIP5, obs4mips, OBS6, OBS) on several key machines
 (e.g. BADC, CP4CDS, DKRZ, ETHZ, SMHI, BSC). For more
 information about ``drs``, you can visit the ESMValTool documentation on
-[Data Reference Syntax (DRS)](https://docs.esmvaltool.org/projects/esmvalcore/en/latest/quickstart/find_data.html#cmor-drs).
+[Data Reference Syntax (DRS)](https://docs.esmvaltool.org/projects/esmvalcore/
+en/latest/quickstart/find_data.html#cmor-drs).
 
 > ## Set the correct drs
 >
@@ -299,7 +302,9 @@ information about ``drs``, you can visit the ESMValTool documentation on
 >> 2. Observational data are organized in Tiers depending on their level of
 >>    public availability. Therefore the default directory must be structured
 >>    accordingly with sub-directories `TierX` e.g. Tier1, Tier2 or Tier3, even
->>    when `drs: default`. More details can be found in the [documentation](https://docs.esmvaltool.org/projects/esmvalcore/en/latest/quickstart/find_data.html#observational-data).
+>>    when `drs: default`. More details can be found in the 
+[documentation](https://docs.esmvaltool.org/projects/esmvalcore/en/latest/
+quickstart/find_data.html#observational-data).
 >>
 > {: .solution}
 {: .challenge}
@@ -319,7 +324,8 @@ if you want to feed some additional data (e.g. shape files) to your recipe.
 > auxiliary_data_dir: ~/auxiliary_data
 > ```
 > See more information in ESMValTool
-[document](https://docs.esmvaltool.org/projects/ESMValCore/en/latest/quickstart/configure.html?highlight=auxiliary_data#user-configuration-file).
+[document](https://docs.esmvaltool.org/projects/ESMValCore/en/latest/quickstart
+/configure.html?highlight=auxiliary_data#user-configuration-file).
 {: .callout}
 
 > ## Number of parallel tasks