Experimental/type for run configuration

Overhaul the input/config setup. Introduces derived types to deal with the configuration of components of the code (one type per namelist). The primary motivation for this is to make it easier to override the configuration of the code in a programmatic way. This is of key importance for our unit testing, but also enables interesting uses of the code.

The use of a consistent type to define the inputs enables us to construct automatically generated documentation relating to the inputs and the default values etc. See https://gyrokinetics.gitlab.io/gs2/page/namelists/index.html for what this looks like (another PR is required to port existing documentation from the wiki into the source code so that this generated documentation is complete).

Note: Currently this PR also contains all the changes in 8.0.2-RC that are not yet in next. This will become cleaner once v8.0.2 is released and merged into next.

• Add an abstract type to represent config options

• Add an example config type for the run_parameters module

• Make use of config instance in run_parameters

• Make config_internal module level rather than routine level.

  If this is then exposed it offers a way to set the default configuration state to be used when the appropriate init routine doesn't pass in a configuration object.

• Rename run_parameters_config to run_parameters_config_type

• Switch to specifying defaults at initialisation time

  Make reset force state to "clean"/empty object

• Remove stray character

• Move run_parameters_config_type to run_parameters

• Remove empty config_types module

• Remove initialised requirement from write_run_parameters_config

• Move the init code into the abstract type as it is generic

• Add a comment

• Add config type for theta_grid_gridgen_knobs

• Correct format for run_parameters

• Initially adding salpha namelist

• Make some allocations in theta_grid safer

• Add helper script for working with config types

  Allows auto generation of the standard routines associated with the config types by detecting the relevant information from the config type declarations in the source file.

  Can also be used to produce new config types etc. if desired.

• Ensure failing tests are reported on gitlab

• Fix intent

• Add config type for theta_grid_knobs

• Add config type for theta_grid_file_knobs

• Add config type for theta_grid_parameters

• Add config type for theta_grid_eik_knobs

  Note this shows one way to set "smart" defaults

• Make sure config types are reset when module is reset

• Make sure rpexist populated on all processors

• Ensure only proc0 calls eikcoefs for now

• Make sure we also setup theta_grid_gridgen

• Bugfix: Ensure all procs participate in read_parameters type setup

• Add extra output to placeholder text

• Fix bug to identify defaults with no space

• Add config type for kt_grids_single

• Add config type for kt_grids_range_parameters.

• Add config type for kt_grids_specified and kt_grids_specified_element

• Make sure we cleanup kt_grids_specified module

• Remove unused namelist

• Add config type for kt_grids_box

• Add config type for kt_grids

  Add a consistency check for config elements

• Fix routine names

• Make sure to close indexed namelists

  Also provide workaround for get_indexed_namelist not trimming the input namelist string. Should change this routine to use trim but for now just ensure trimmed string is passed.

• Add config types for species namelists

• Update config placeholder generator for index fixes

• Add config type for le_grids

• Add config types for the dist_fn namelists

• Add config type for fields knobs

• Add config type for reinit knobs

• Add config type for layouts_knobs

• Add config type for collisions_knobs

• Add config type for hyper_knobs

• Add config type for nonlinear_terms_knobs

• Add complex to list of valid types

• Expand write_key_val type handling

• Add config type for init_g_knobs

• Add config type for antenna driver/stir namelists

• Add config type for parameter_scan_knobs

• Make sure parameter scan config is reset

• Fix init_g smart default

• Add config type for ballstab_knobs

• Add config type for eigval_knobs

• Add config type for gs2_diagnostics

• Improve handling of smart defaults

  Only set now if the config object hasn't been initialised

• Remove unused namelist

• Add config type for ingen

• Add config type for normalisations

• Make sure config is reset in ingen

• Add config type for optimisation_config

  This allows us to replace the ruby based generation with just the fortran source file.

• Add config type for gs2_init

• Add config type for new diagnostics config

• Add routine to write markdown table from config instance

• Add namelist documentation

• Enable cleaner reuse of namelist documentation

• Remove mistaken lines

• Update documentation slightly

• TO REVERT: Allow manual to build on experimental branch for testing

• Join long comments with space rather than newline

• Add custom css for namelist tables

• Some hacking to finally get namelist tables rendering correctly

• Fix formatting of individual namelist pages

• Try to ensure namelist page always has namelists in the same order

• Make table highlighting use blues from theme

• Add table of contents for namelist page

• Split python code for generating placeholder text and namelist documentation

• Expand gitignore to ignore placeholders files

• Add helper python tool for finding files matching a pattern in paths recursively

  Can act as a simplified and perhaps more portable version of find.

• Make doc rule automatically update the namelist documentation

• Split run_parameters config type to more closely match namelists

  Helps improve consistency with other config types.

• Removing auto-generated namelist documentation

• Expose config_type definitions

• Add meta data to config types for requires_index status

  Currently just in generator/parser script

• Add indexed meta data to all config types

• Add constructor to config templates

• Add constructors for all types

• Add write_default_input_file program

  Writes an input file containing every option set to the default value

• Change logic about namelist header formatting

  Allow arbitrary index to be indexed

• Bugfix for get_all_matching_files

• Tweak auto generated documentation setup to allow to be ignored and removed automatically

• Avoid generating dependency file for a few more make targets

• Make config generation treat indexed types better

• Start to change the naming convention of the config types

• Adopt improved config type naming convention

• Try to provide mechanism to pass in config types in all appropriate module init routines

• Bugfix: Ensure theta_grid_params is reset correctly

• Prevent shadowing in gridgen config setup

• Fix previous commit -- remove different set of shadowing

• Add setters for config types

• Report which file is being processed in the config generator code

• Remove non-ascii character

• Remove two more non-ascii characters