This was used in old times to distinguish between triplets of
shapefiles. Now we have the philosophy of creating a dedicated
directory for a triplet. So the script `distribution_function.py` just
has to be run in the triplet directory.

The position for interpolated eddies is not in `shp_tr_dir`. We have
to read it from `SHP_triplet` in the current directory.

The shapefile reader does not abort with ishape == - 1. So use None instead.

For easier comparison between runs.

Plot trajectories using the Networkx graph instead of directly from
the CSV file. This allows grouping of edges by connected component,
with a different color for each component, and labeling each component
with its ancestor.

Only create Graphviz file if option `--gv` is specified.

For `read_eddy_graph`.

In preparation for creation of function `read_eddy`.

As this eddy field was created by filtering the global field of eddies
on the position of extrema, it is different for the first four dates
than the previous version: the eddies on the border are larger or
become valid. The previous version was created by first filtering the
Aviso data and then extracting the eddies.

Mark the interpolated eddies with a different shape in the output
Graphviz file.

Revert commit e8a607ef because now we are writing a file. We are
compelling the user to run this script in the directory containing the
input file so the output file does not get lost in the arborescence.

Encapsulate the drawing of the domain box in a function `plot_grid_bb`.

Add the ability to read a limited number of dates in program
`eddy_graph`. The default is to read all the dates.

Catch the error to display a more informative message.

Missing libraries in `target_link_libraries`. This appears now because
some links are now declared private in the libraries.

In `plot_snapshot.py`, read `grid_nml.txt` and draw a rectangle
showing the domain.

Generalize `filter.py` to act on a triplet of shapefiles containing
several dates, with renumber option. Create file `ishape_last.txt`.

Replace `loop_shp_append.py` by `loop_shp_tr_append.py`. Instead of
looping on years, we assume we are working on a single year. We could
call this script inside a loop on years in the shell. The advantage is
that we need to make fewer assumptions on the arborescence of
files. Also, we can make `loop_shp_tr_append.py` more general by
starting and ending at arbitrary days. We drop the timing that was in
`loop_shp_append.py`. We add the creation of file `ishape_last.txt`.

In script `shp_tr_append.sh`, assume that the directories contain
files `ishape_last.txt` and modify `ishape_last.txt` in the
destination directory.

In program `test_overlap`, read grid description from a file
`grid_nml.txt` in SHP triplet directory, instead of from standard
input. This is the same modification we made for program
`eddy_graph`. Modify input files accordingly.

Add grid description in a file `grid_nml.txt` in SHP triplets that
should be read by the program `eddy_graph`, instead of reading the
grid description from standard input.

Add test `Eddy_graph_r2md2`.

Replace script `mkdir_nproc.sh` by script
`eddy_graph.sh`. `eddy_graph.sh` is a wrapper script for program
`eddy_graph`. It includes the creation of output directories that was
done by `mkdir_nproc.sh`. `mkdir_nproc.sh` was only used for program
`eddy_graph`. There was the need to automate the concatenation of
output files for a run with several MPI processes.

Add a test for `eddy_graph`.

Improve the handling of the NetCDF Fortran library in cmake files.
Add the configuration of `eddy_graph_in.sh`.

In main program `eddy_graph`, do not write title lines in files
`unit_number_eddies` and `unit_edgelist` because these files are
concatenated for all the MPI processes by `eddy_graph.sh`. So the
title lines are added by `eddy_graph.sh`.

In script `plot_snapshot.py`, add dummy arguments to function snapshot
so that it does not use global variables and it can work after the
module is reloaded. Bug fix for the suptitle in function snapshot.

Add test for program `eddy_graph`. Add the corresponding input NetCDF
files and the corresponding dates in
`Tests/Input/Region_2/SHP_triplet`.

In script `read_eddy_graph.py`, create a pygraphviz graph and write
the corresponding file instead of directly plotting with
Matplotlib. Also, create subgraphs in the pygraphviz
graph. Motivation: aligning nodes with the same date. Moreover: it is
more convenient to visualize a graphviz file. Moreover, networkx
documentation seems to advise against relying on networkx's own
visualizing functionality.

In script `plot_snapshot.py`, add title with date index.

Rename `read_overlap.py` to `read_eddy_graph.py`.

Rename `loop_shpcat.py` to `loop_shp_append.py` and `shp_tr_cat.sh` to
`shp_tr_append.sh` because an analogy to the cat command is confusing:
the cat command does not modify its arguments and the result is in the
order of the arguments.

Import small NetCDF files in `Tests/Input/Region_1`.

Bug fix in `short_tests.json`: missing mpiexec for `test_read_eddy`.

New test `Eddy_graph_md2`, with corresponding input files.

Add test of `eddy_graph` with 2 processes.

Bug fix in main program `eddy_graph`: broadcast `dist_lim` and
periodic.

Added a trick to verify at the beginning of execution of program
`extraction_eddies` that the directory `SHP_triplet` exists.

Added a script to created as many directories as MPI processes, for
program `eddy_graph`.

Added stdout keys to JSON tests, so that the stdout files are not
named `mpiexec_stdout.txt`.

Added first test of program `eddy_graph`.

Bug fixes in main program `eddy_graph`. Add default value for
max_delta. Trim names of files and directories.

Following upgrade of `test_compare.py`, remove `mkdir_run.sh` and
write the mkdir command in the JSON tests files.

Add main program `eddy_graph`.

Change order of dummy arguments of `dispatch_snapshot` and overlap.