# FILE_PATHS

This required field, defines where any input files can be found and where the results of the computation are to be stored.

## Example from FILE_PATHS from a Fit Script

    FILE_PATHS:
        # path to input comma separated value file in popy data format
        input_data_file: builtin_fit_example_data.csv

        # Output folder - results of computation stored here
        output_folder: auto

        # Temp folder - temporary files stored here
        temp_folder: auto

        # Output file extension - determines graphical output file format.
        output_file_ext: ['svg', 'pdf']

        # Solution containing f[X] values from a previous run.
        input_solution_file: none

## Main FILE_PATH Fields

### input_file

Required path to input a .csv file in popy data format:-

    input_data_file: builtin_fit_example_data.csv

Note that this field is required and the .csv file must exist else PoPy will throw an error message.

### output_folder

Optional field that specifies the output folder, where the results of computation are stored.

The default is:-

    output_folder: auto

Using auto will specify an output folder based on the script name. E.g if your script is called ‘my_fit_script.pyml’, the output folder will be:-

    my_fit_script.pyml.output

Using auto is safest, as then it is impossible to over-write the output from other scripts.

### temp_folder

Optional field that specifies the temp folder, where temporary functions generated by PoPy are stored.

The default is:-

    temp_folder: auto

The default folder name is ‘_temp’ within the output_folder. If you have a script named ‘my_fit_script.pyml’ and miss out the ‘output_folder’ and ‘temp_folder’ you will end up with temporary functions in this folder:-

    my_fit_script.pyml.output
        /fit
            /_temp

Note the subfolders within ‘_temp’ have random names, this is to avoid re-using old temporary functions if the same script is run twice (and altered slightly).

### output_file_ext

This is an optional list of file types to output when plotting. The default is:-

    output_file_ext: ['svg']

This outputs plots in .svg format, which stands for scalable vector graphics, see:-

https://en.wikipedia.org/wiki/Scalable_Vector_Graphics

.svg is a good format because it can be displayed at any resolution without being pixelated. For example if you used .png or any other raster format.

The input is a Python list. This is to enable you to output plots in multiple formats. For example many of the documentation examples use the following:-

    output_file_ext: ['svg', 'pdf']

To generate plots in .svg and also .pdf format. We do this with the documentation so that the HTML documentation can display .svg and the pdf version can use .pdf plots.

### input_solution_file

This field is only available in the Fit Script. It is an optional link to a ‘solution.pyml’ file to initialise the `f[X]` starting values during a fit. The default is:-

    input_solution_file: none

This does nothing and uses the `f[X]` starting values specified in the EFFECTS section of the script.

If a solution file is specified, e.g.:-

    input_solution_file: ./previous_fit_script.pyml_output/fit/solN/solution.pyml

Then the ‘solution.pyml’ file will be loaded, specifically the ‘fx_params.csv’ part of the solution.

    FILE_PATHS:
        fx_params_path: fx_params.csv

The `f[X]` params are used as new starting values.

You can use the ‘input_solution_file’ to restart a Fit Script from a previous fitting script. This is useful if the previous script fails, for example if the machine is accidentally switched off or some other system failure.