This notebook introduces you to the [atmodat checker](https://github.com/AtMoDat/atmodat_data_checker) which contains checks to ensure compliance with the ATMODAT Standard.
> Its core functionality is based on the [IOOS compliance checker](https://github.com/ioos/compliance-checker). The ATMODAT Standard Compliance Checker library makes use of [cc-yaml](https://github.com/cedadev/cc-yaml), which provides a plugin for the IOOS compliance checker that generates check suites from YAML descriptions. Furthermore, the Compliance Check Library is used as the basis to define generic, reusable compliance checks.
In addition, the compliance to the **CF Conventions 1.4 or higher** is verified with the [CF checker](https://github.com/cedadev/cf-checker).
**Option 2: Create a kernel with checker libraries to work with jupyter notebooks**
With `ipykernel` you can install a *kernel* which can be used within a jupyter server like [jupyterhub](https://jupyterhub.dkrz.de). `ipykernel` creates the kernel based on the activated environment.
```bash
module load python3/unstable
#The following line activates the quality-assurance environment mit den checker libraries so that you can execute them with shell commands:
If you run this command from within a jupyter server, you have to restart the jupyterserver afterwards to be able to select the new *quality checker* kernel.
**Expert mode**: Running the jupyter server from a different environment than the environment in which atmodat is installed
Make sure that you:
1. Install the `cfunits` package to the jupyter environment via `conda install cfunits -c conda-forge -p $jupyterenv` and restart the kernel.
1. Add the atmodat environment to the `PATH` environment variable inside the notebook. Otherwise, the notebook's shell does not find the application `run_checks`. You can modify environment variables with the `os` package and its command `os.envrion`. The environment of the kernel can be found with `sys` and `sys.executable`. The following block sets the environment variable `PATH` correctly:
The results of the performed checks are provided in the checker_output directory. By default, `run_checks` assumes writing permissions in the path where the atmodat checker is installed. If this is not the case, you must specify an output directory where you possess writing permissions with the `-op output_path`.
In the following block, we set the *output path* to the current working directory which we get via the bash command `pwd`. We apply `run_checks` for the `exp_file` which we downloaded in the chapter before.
Now, we have a directory `atmodat_checker_output` in the `op`. For each run of `run_checks`, a new directory is created inside of `op` named by the timestamp. Additionally, a directory *latest* always shows the output of the most recent run.
The short summary contains information about versions, the timestamp of execution, the ratio of passed checks on attributes and errors written by the CF checker.
- cfchecks routine only issues a warning/information message if variable metadata are completely missing.
- Zero errors in the cfchecks routine does not necessarily mean that a data file is CF compliant!
We can also have a look into the detailled output including the exact error message in the *long_summary_* files which are subdivided into severe levels.
We can also only provide a directory instead of a file as an argument with the option `-p`. The checker will find all `.nc` files inside that directory.
