Replace positional argument template by optional argument. This
argument is now needed only in case we process several dates, since
the first date is now read from the NetCDF file.

The script may abort because of wrong arguments. It is better not to
have touched anything in that case.

Following commit 4792f83f.

To ease use of call with keywords.

Even for a run with a single MPI process, otherwise execution will not
work on some systems (jean-zay).

Replace `/proju/lmd-oce/data/AVISO/DT_2018/2006/01` by
`$large_input_dir`.

Move the definition of colors out of the loop on shapes, since the
orientation is now the same for all shapes.

Instead of `Inst_eddies_5`, which no longer exists because we now
create separate SHPC for each orientation.

Clearer for the user.

`h_region_1.nc` is no longer in the repository, since commit d023fd3f.

This SHPC was made with an old version of `inst_eddies`: it contained
cyclones and anticyclones output together. We create a test `Region_6`
instead.

The orientation is no longer a DBF field.

Instead of `d_init`, `ishape_last` and `reader_extr`.

Instead of readers. Preparing for extension to receive orientation.

Instead of `readers_all`.

Instead of several pieces of it. Clearer and more concise.

Instead of several values of the handler dictionary. Clearer and more concise.

Instead of tuple. Preparing for extensions to return orientation and
to deal with several SHPC.

Because variables in `grid_nml` should be all defined in the input file.

With separated orientations.

Since `Inst_eddies_loop` is in the same series of tests as
`Nearby_extr`, take it from `$PWD` rather than `$tests_old_dir`.

We now impose that all eddies in an SHPC have the same
orientation. Remove field `extr_cycl` from the derived type shpc and
add field cyclone to shpc. When reading an eddy, give it the
orientation of its SHPC. Add argument cyclone to procedure
`shpc_create`. Create a file `orientation.txt` in each SHPC. When
writing an eddy, check that its orientation matches that of the SHPC.

Rename triplet to collection, `shp_tr` to shpc, shpt to shpc in
comments, identifiers and file names.

Do not specify the orientation as a command line argument of
`report_graph_int.py`. As in commit 292305e.

For test `Report_graph_cyclo`.

Do not specify the orientation as a command line argument of
`report_graph.py`. We are reverting commit 0ca2da8c because now
edgelists and SHPC for interpolated eddies are normally in separate
directories, and edgelist is normally just `edgelist.csv`.