diff --git a/.github/link-checker-config.json b/.github/link-checker-config.json new file mode 100644 index 00000000..07aa05c4 --- /dev/null +++ b/.github/link-checker-config.json @@ -0,0 +1,13 @@ +{ + "projectBaseUrl":"${https://github.com/ESMValGroup/ESMValTool_Tutorial}", + "ignorePatterns": [ + { + "pattern": "^http://example.net" + } + ], + "timeout": "20s", + "retryOn429": true, + "retryCount": 5, + "fallbackRetryDelay": "30s", + "aliveStatusCodes": [200, 206] +} diff --git a/.github/workflows/link-checker.yml b/.github/workflows/link-checker.yml new file mode 100644 index 00000000..6c853b62 --- /dev/null +++ b/.github/workflows/link-checker.yml @@ -0,0 +1,17 @@ +name: Check Markdown links + +on: [pull_request] + +jobs: + markdown-link-check: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@master + - uses: gaurav-nelson/github-action-markdown-link-check@v1 + with: + use-quiet-mode: 'yes' + use-verbose-mode: 'yes' + config-file: 'link-checker-config.json' + file-path: './README.md, ./LICENSE.md, ./CONTRIBUTING.md, ./CODE_OF_CONDUCT.md, ./aio.md, ./index.md, ./reference.md, ./setup.md' + + diff --git a/_episodes/09-cmorization.md b/_episodes/09-cmorization.md index c131c96e..6b58674e 100644 --- a/_episodes/09-cmorization.md +++ b/_episodes/09-cmorization.md @@ -123,6 +123,12 @@ run the CMORizer scripts: esmvaltool data format --config_file ``` +The options `--start` and `--end` can be added to command above to restrict the +formatting of raw data to a time range. They will be ignored if a specific +dataset does not support (i.e. because it is provided as a single file). +Valid formats are `YYYY`, `YYYYMM`, `YYYYMMDD`. The same way is also applicable for +the option `esmvaltool data download`. + The ``config-user.yml`` is the file in which we define the different data paths, see the episode on [Configuration]({{ page.root }}{% link _episodes/03-configuration.md %}). In the ``rootpath`` of your ``config-user.yml``, make sure to add the right @@ -193,6 +199,12 @@ You can also see the path where ESMValTool stores the reformatting script: have a look at this file if you want. The script also uses a configuration file: `~/ESMValTool/esmvaltool/cmorizers/data/cmor_config/FLUXCOM.yml`. +To get help on CMORizer commands, run the tool with: + +```bash +esmvaltool data --help +``` + ## Make a test recipe To verify that the data is correctly CMORized, we will make a simple test diff --git a/fig/flowchart_setup.png b/fig/flowchart_setup.png new file mode 100644 index 00000000..11682b61 Binary files /dev/null and b/fig/flowchart_setup.png differ diff --git a/setup.md b/setup.md index 4b27bffe..2d95a748 100644 --- a/setup.md +++ b/setup.md @@ -34,6 +34,33 @@ ESMValTool code. - git: [https://swcarpentry.github.io/git-novice/](https://swcarpentry.github.io/git-novice/) +![Data flow with ESMValTool](../fig/flowchart_setup.png) + +### Using your own machine + +Please skip this section if you are not going to use ESMValTool on your +local machine and go [here](#github-account-advanced). + +If you are planning on running ESMValTool on your own machine, please make sure +that you are able to download CMIP data and that you have a few GB of space +available to install conda and ESMValTool, but also enough to make a copy of some +data (~125MB) needed for this tutorial. + +You can use ESMValTool to automatically download data needed for test recipes. +Please see the [Configuration][lesson-configuration] episode +or the [configuration file documentation][config-file] for more information. +This the recommended option as it has the advantage that data is +stored in subdirectories, and features such as wildcards and recording +the version of the data will work automatically. + +Alternatively, you can run the following command using +[wget](https://en.wikipedia.org/wiki/Wget): + +~~~shell +wget --no-clobber --input-file \ + https://github.com/ESMValGroup/ESMValTool_Tutorial/raw/main/data/dataset.urls \ + --directory-prefix $HOME/esmvaltool_tutorial/data/ +~~~ ## Access to CMIP and Observational data and a suitable compute cluster @@ -227,33 +254,6 @@ be found [here](https://docs.dkrz.de/doc/levante/running-jobs/index.html). Congratulations! Please go here [here](#github-account-advanced) next. -### Using your own machine - -Please skip this section if you are not going to use ESMValTool on your -local machine and go [here](#github-account-advanced). - -If you are planning on running ESMValTool on your own machine, please make sure -that you are able to download CMIP data and that you have a few GB of space -available to install conda and ESMValTool, but also enough to make a copy of some -data (~125MB) needed for this tutorial. - -You can use ESMValTool to automatically download data needed for test recipes. -Please see the [Configuration][lesson-configuration] episode -or the [configuration file documentation][config-file] for more information. -This the recommended option as it has the advantage that data is -stored in subdirectories, and features such as wildcards and recording -the version of the data will work automatically. - -Alternatively, you can run the following command using -[wget](https://en.wikipedia.org/wiki/Wget): - -~~~shell -wget --no-clobber --input-file \ - https://github.com/ESMValGroup/ESMValTool_Tutorial/raw/main/data/dataset.urls \ - --directory-prefix $HOME/esmvaltool_tutorial/data/ -~~~ - - ## GitHub account (Advanced) You don’t need a github account to participate in the tutorial. However, if you