The NanoFASE data module is a collection of Python scripts that are used to compile input data for the model. It is recommended to use these scripts over and above manually compiling the NetCDF and constants namelist file required by the model, as the data module scripts take care of deriving a variety of secondary derived variables, amongst other reasons.
+The NanoFASE data module (nfdata) is a Python library that is used to compile input data for the model. It is recommended to use this library over and above manually compiling the NetCDF and constants namelist file required by the model, as the data module scripts take care of deriving a variety of secondary derived variables, amongst other reasons.
The library can be found on GitHub.
Note
-The data module is currently only available as standalone scripts, rather than a Python package. This means that you must manually download the repository and set up a computational environment (install the correct packages) to be able to run the scripts, as detailed below. In the future, we will create a Python package from these scripts to ease this process.
-Clone a copy of the repository from GitHub:
-$ git clone git@github.com:NERC-CEH/nanofase-data.git
-$ cd nanofase-data
+The easiest way to use the library is to install it from PyPI. For example, using pip:
+$ pip install nfdata
-Use Conda (or Mamba) to create a new environmental and install the required packages:
-$ conda env create -f environment.yaml
-$ conda activate nanofase-data
-
+
+Note
+We are currently working on a Conda package for the library - watch this space!
-If you don’t want to use Conda/Mamba, then the environment.yaml file lists the packages that need to be installed.
Basic usage#
-The main script is nanofase_data.py:
-(nanofase-data) $ python nanofase_data.py --help
-usage: nanofase_data.py [-h] [--output OUTPUT] {create,edit,constants} file
+Once installed, the library can be run via the command line using the nfdata command:
+$ nfdata --help
+usage: nfdata [-h] [--output OUTPUT] {create,edit,constants} file
Compile or edit data for the NanoFASE model.
@@ -484,7 +478,7 @@ Basic usage
Creating a new dataset#
Specifying the “create” option compiles a new NetCDF dataset and Fortran namelist constant file:
-(nanofase-data) $ python nanofase_data.py create /path/to/config.create.yaml
+$ nfdata create /path/to/config.create.yaml
An annotated example config file is given: config.create.example.yaml. The file is quite self-explanatory, but a full description is given below.
@@ -493,7 +487,7 @@ Creating a new dataset
Editing an existing dataset#
To edit an existing NetCDF dataset, specify the “edit” option:
-(nanofase-data) $ python nanofase_data.py edit /path/to/config.edit.yaml
+$ nfdata edit /path/to/config.edit.yaml
An annotated example config file is given: config.edit.example.yaml. This is similar (but not identical) in format to the creation config file, except only those variables you with to edit should be specified (all other variables are left as-is). Documentation for the config file is provided below.
@@ -503,7 +497,7 @@ Editing an existing dataset
Only creating a new constants file#
To simply convert a constants YAML file to a Fortran namelist file, you can use the constants option:
-(nanofase-data) $ python nanofase_data.py constants /path/to/constants.yaml -o /path/to/constants.nml
+$ nfdata constants /path/to/constants.yaml -o /path/to/constants.nml
No config file is required. The location of the newly created constants file is given by the -o or --output argument.