The programs in this project do not depend directly on them. If they
are secondary dependencies, it is the responsibilty of the primary
dependencies to find them.

Only three files were left in cmake, not enough to justify a directory.

Change of philosophy. We do not force the choice of compiler options
from the project, we leave them to the user at configuration. We just
need to display a warning for the option `-ffpe-trap=invalid`.

Move the call to `find_package` for EZMPI to
`Overlap/CMakeLists.txt`. We are reverting in part commit f04aea8b
since `test_set_max_speed` no longer uses MPI.

Note that programs `test_max_speed_contour_ssh` and `test_weight`
depend on fortranGIS through the module derived_types. Compilation
worked without linking to fortranGIS because objects used by
`test_max_speed_contour_ssh` and `test_weight` in
derived types do not use fortranGIS.

Following commit e741203 of `GPC_F`. We have to add this
`find_package` of GPC in `Detection_eddies` because `GPC_F` now
declares a dependency on the abstract target GPC.

Assuming the englobing project builds the corresponding librairies.

Use higher level procedures in main program
`test_set_max_speed`. Allows to read easily more information: cyclone,
`ssh_extremum`, `coord_extr` from the shapefiles. So we do not ask
this information to the user. The drawback is that we have to call
MPI (because of `read_field_indices`) even if we do not really use
it. We move the calls to `find_package` for EZMPI and `GPC_F` to the
top-level `CMakeLists.txt` since these libraries are now necessary in
both `Inst_eddies` and Overlap.

Create and use module FindNetCDF_Fortran, modeling on FindNetCDF.

Move Fortran source files used in tests of both parts, `Inst_eddies`
and Overlap, to directory Tests at root of repository.

Also split the tests, Fortran source files, Python files and JSon
files. Keep at the top level the files used in both `Inst_eddies` and
Overlap.

Motivations for the split:

- The top directory contained many files.

- It may be useful to compile only one of the two sub-projects. For
example, only `Inst_eddies` on Ciclad, where MPI 3 is not available.

To avoid inadvertant modification of `eddy_graph.sh` instead of
`eddy_graph_in.sh`.

Motivation: we are going to split the edge list file into two files.

`unit_edgelist` was just transmitted by procedure overlap from main
program unit to `write_overlap`. So now overlap does not see
`unit_edgelist`. Further motivation: we are going to split the edge
list file into two files.

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

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`.

Add main program `eddy_graph`.

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

Rename files and identifiers: change `"shp_triplet"` to `"shp_tr"`.

Rename procedure `init_shapefiles` to `shp_triplet_create`.

Organize better the directory `Input`: create sub-directories for regions.

Big change: use SHP triplets that can contain several snapshots. So
program `test_overlap` reads a single SHP triplet. The dates that
`test_overlap` should read are now specified in the input
namelist. SHP triplet directory must now contain a file named
`contents.csv`. `test_overlap` reads `contents.csv` into variables k1
and `ishape_last`. So there is no longer any need to read the number
of entities in one of the shapefiles.

For each region, concatenate SHP triplets for dates 2006/01/01 and
2006/01/02.

Read namelist from process 0 in program `test_send_recv`: it is
simpler since it is the default setting of mpiexec and I do not see
any drawback.

In programs `test_read_snapshot` and `test_send_recv`, just hard code
for now the ishapes we want to read in the SHP triplet.

Simplify cmake files, taking advantage of improved packaging of
libraries. This also much simplifies the configuration process: the
user typically has only two directories to specify: `CMAKE_PREFIX_PATH` and
`fortrangis_INCLUDE_DIR`. Also `Shapelib_03` no longer depends on EZMPI,
since revision 129a0cc.

Add test for `test_send_recv`.

We need the dummy version of EZMPI for sequential programs linking
with `Shapelib_03`.

Replace `include_directories` by `target_include_directories` in
`Tests/CMakeLists.txt`. Motivation: some targets do no use ezmpi. This
implies adding directories to `target_include_directories` for
`extraction_eddies`.

In `send_snapshot` and `recv_snapshot`, send and receive a whole
eddy. Read and write a snapshot in `test_send_recv`.

In procedures `recv_snapshot` and `send_snapshot`, use library EZMPI
instead of MPI directly.

Rename `receive_snapshot` to `recv_snapshot` for consistency with MPI
calls. In procedure `send_snapshot`, invert order of dummy arguments
tag and dest for consistency with MPI calls.

Add options for the NAG compiler.

Replace `target_include_directories` by `include_directories` in
`Tests/CMakeLists.txt`. The file was becoming too long.

Remove unused items in use statements.

Bug fix in `Tests/Input/successive_overlap_region_5_nml.txt`: remove a comma.

Add `.cmake` files. The idea is to have a build system independent of
the environment. This allows us to have a customized version of
`ConfigureCompilerFlags.cmake` without the `-ffpe-trap=invalid`
option.

Move the inner part of procedure overlap to a separate procedure
`write_overlap`. overlap was too complex with 6 nested constructs. The
downside is that the initialization of `e` is repeated for every
non-successive overlap. If necessary, we can later add an
initialization on first entry (but an initialization at declaration is
not possible). `write_overlap` has some consistency: all the arguments
are `intent(in)`, scalars or small vectors of intrinsic type, and
`write_overlap` only writes to files. All modifications to flow are
done outside of `write_overlap`.

Prepare for overlap of eddies at non-successive dates:

- add argument `delta_out` to procedure `candidate_overlap` (not yet
used);
- add procedure `interpolate_eddy` (empty for now);
- rename `successive_overlap` to overlap because the procedure will handle both
cases, successive dates and non-successive dates;
- generalize procedure overlap to handle delta between dates.

`settings.mk` in GNUmakefile.

Bug fix in procedure `dispatch_snapshot`: an isolated eddy is a valid eddy.

In script `plot_snapshot.py`, in function snaphot, replace argument ax
with argument `new_figure` so the user does not have to call figure
and `axes(projection = projection)`. Add argument light to function
snapshot so we can call snapshot with light set to False for a second
snapshot. Add a test to only read `h.nc` when we need it.

In script `read_overlap.py`, print more information: number of nodes,
number of edges, number of nodes with at least one successor, number
of nodes with at least one predecessor, splitting events, merging
events.

In script `stat.py`, use the convention that shapefiles are grouped in
a directory instead of identifying a set of shapefiles by the end of
their basename.

In main program `test_successive_overlap`, we know that `delta_in` for
snapshot 1 and `delta_out` for snapshot 2 are `huge(0)` so do not test
this. Print eddy identifiers in a single line. Add the printing of
identifiers of isolated eddies.

Tests/CMakeLists.txt. This is more concise since we can merge them
with target_sources.

Bug fix: missing source file successive_overlap.f90 for target
test_read_snapshot.