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.

Generalize `read_snapshot`. Add dummy argments `ishape_first` and
`ishape_last`. This allows getting a snaphot from a triplet of
shapefiles containing several snapshots. Consequence: move the call to
`shp_get_info_03` from `read_snapshot` to `test_overlap`,
`test_read_snapshot` and `test_send_recv`.

Remove opening and closing of shapefiles from procedure
`get_snapshot`. Since a triplet of shapefiles can contain several
snapshots, we do not want to open and close the same shapefiles
several times from the same MPI process.

Pass argument copy to `read_snapshot` rather than arguments periodic
and `dist_lim`. Motivation: do not recompute copy at each call of
`read_snapshot`. `read_snapshot` is going to be called many times in
overlap program, with always the same value of copy. And we do not
need the values of periodic and `dist_lim` separately in
`read_snapshot`.

Complete `send_snapshot` and `recv_snapshot` by sending and receiving
an entire snapshot. So we need nlon, nlat and copy in `recv_snapshot`
to allocate `extr_map`. It is better to pass arguments nlon, nlat and
copy than sending and receiving the shape of `extr_map` with MPI, of
course, since the shape is the same for all snapshots. In program
`test_send_recv`, write the entire received snaphot.

Bug fix in `Tests/CMakeLists.txt`: several targets missed
`${netcdff_INCLUDE_DIR}`.

Create procedure `write_snapshot` from code in main program
`test_read_snapshot`, because we need to do this also in program
`test_send_recv`. Note the dissymmetry with `read_snapshot`, which
does not include the opening and closing of the shapefiles. That is
because we anticipate calling `read_snapshot` several times with the
same shapefiles in program overlap.

Change order of dummy arguments of procedure `write_extr_map`. More
convenient for calling it with keywords from `write_snapshot`.

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.

Fill in procedures `receive_snapshot` and `send_snapshot`. This is
just a beginning with part of an eddy. Add test program.

hsp arguments in procedure `read_snapshot` can be declared with
`intent(in)` since they are `intent(in)` in `read_eddy` since commit d815bf76.

Bug fixes in procedure `get_snapshot`: remove duplicated declaration
of nlon, nlat; add argument `dist_lim`, which must be passed to `read_snapshot`.

In procedure `get_snapshot`, read the triplet of shapefiles from a
directory named with the date index (for the now moment, we will see
later for something more efficient). Check that the date index in the
shapefiles is the date index required.

In procedure `get_var`, take advantage of new procedure `nf95_get_missing`.

Update input files for program `test_overlap` because the program now
reads `delta_in` and `delta_out`.

Add a test for the logic of `delta_in` and `delta_out` in subroutine
overlap. Add corresponding input snapshots.

Add possiblity of specifying `delta_in` and `delta_out` in program
`test_overlap`.

Add possibility to renumber eddies in script `filter.py`.

Read `SHP_triplet` directories as arguments in script `filter.py`.

Move directory `Tests/Input/Extraction_eddies_region_5` to
`Tests/Input/Region_5_2006_01_01`.

Bug fix in procedure overlap: `delta_out` and `delta_in` should not increase.

In script `eddy_dump.py`, do not assume that there is a single date
index. So find ishape by iterating through values of date index and
eddy index.

Add a test of overlap in `short_tests.json`.

In procedure `write_eddy`, no need of special treatment for
interpolated eddy: the outermost contours and max-speed contours are
defined as null.

Read name of input file on the command line in script `read_overlap.py`.

Add tests with program `test_overlap` in `short_tests.json`.

Bug fix in main unit `test_overlap`: we have to call
`init_interpolated_eddy`.  In main unit `test_overlap`, change the
initial value of `flow(2:max_delta)%number_eddies` for more clarity in
the results. Bug fix in main unit `test_overlap`: valid isolated
eddies of snasphot 2 are in `flow(max_delta + 1)`, not `flow(2)`.

Rename `test_successive_overlap` to `test_overlap`: we will also use
it for non-successive overlap. Accordingly, add an input variable
`max_delta` and change the size of flow to `max_delta` + 1. We read
from snapshots `flow(1)` and `flow(max_delta + 1)`. For
`flow(2:max_delta)`, we only need to define the component
`number_eddies`.

In tests, remove use of `$test_old_dir`, use data from
`$src_dir/Tests/Input` instead. Motivation: run tests for the first
time more easily.

Change the order of dummy arguments of `write_overlap`.

Add tests for program `test_write_overlap`. In program
`test_write_overlap`, make the eddy identifiers distinct.

Create procedure `init_interpolated_eddy` so that initialization is
not repeated needlessly at each call of `write_overlap`. (Problem was
mentioned in message of commit 10f339d2.)

Use `SHP_triplet` instead of Snapshot for the name of the directory
containing the three shapefiles extremum, `outermost_contour` and
`max_speed_contour`. This is meant as a general name, analogous to a
new file type. Generally, the shapefiles may contain eddies at
different dates, not just a snapshot.

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.

Bug fix in procedure overlap: procedure `interpolate_eddy` does not
exist any longer.

In tests, remove use of `$test_old_dir`, use data from
`$src_dir/Tests/Input` instead. Motivation: run tests for the first
time more easily.

Change order of dummy arguments of procedure
`write_overlap`. Motivation: call with keywords in
`test_write_overlap`.

Add main program `test_write_overlap` and corresponding tests in
`short_tests.json`.

New script `triplet_dump.sh`.

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`.

Remove procedure `interpolate_eddy`. I realized that the longitude of
one of the overlapping eddies must be shifted. It seemed awkward to
pass variable m from overlap as an argument to
`interpolate_eddy`. Passing separately the useful components of
overlapping eddies made the procedure bulky, not worth creating for
three lines of computation.

As a consequence, inline the interpolation of eddies in procedure
overlap. An advantage is that part of the processing that was in
`interpolate_eddy` can migrate out of the interpolation loop.

As another consequence, remove program `test_interpolate_eddy` and
correponding test.

Upgrade procedure `candidate_overlap` to deal with non-successive
overlap. Add dummy argument delta.

Make the program `test_interpolate_eddy` more comfortable to use by
reading a directory on the command line.

Create main program `test_interpolate_eddy`. Add corresponding test in
`short_tests.json`. Add corresponding input files.

Move dummy arguments k and i of procedure `write_eddy` to the end of
dummy argument list: keyword association more likely for these.

Follow upgrade of `Shapelib_03`: move argument associated to dummy
argument hshp of `shp_open_03` to the beginning of argument list.

Use `dbf_read_attribute_03` instead of dbfreadattribute in procedure
`read_eddy`. This also allows us to avoid the intermediary real
`c_double` variable. Modify intent of hshp arguments, taking also
advantage of upgrade of `shp_read_object_03` in `Shapelib_03`.

Create general script `mkdir_run.sh` to replace specific
scripts `extraction_eddies.sh`, `test_read_snapshot.sh`,
`test_read_eddy.sh` and to run `test_successive_overlap`.

Replace `$input_dir` by `$src_dir/Tests/Input` in
`*_tests.json`. Motivation: we also need `src_dir` to point to
`mkdir_run.sh`.

Replace `intent(inout)` by `intent(in)` for shpfileobject arguments in
`write_eddy`. This requires an updated version of `Shapelib_03`.

Changing my mind, `interpolate_eddy` only interpolates, it does not
write the interpolated eddy, this seems clearer. So it can be a
function instead of a subroutine and we call `write_eddy` from
overlap. We need to add arguments `hshp_extremum`, `hshp_outermost`
and `hshp_max_speed` to overlap. The main program
`test_successive_overlap` now has to create shapefiles.

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.

for which `delta_out` == 1 and eddies for which `delta_in` == 1. This
is redundant with information in file `edgelist.csv`. I have checked
in test `Successive_overlap_global` that eddies for which `delta_out`
== 1 correspond to column i1 (sorted, unique) and eddies for which
`delta_in` == 1 correspond to column i2 (sorted, unique).

Take into account new policy in `filter.py`: the names of the three
shapefiles are always the same and form a unit in a snaphot directory.

Rename `compil_prod_dir`to `build_dir` in JSON test files. Add a test
of `successive_overlap` with global grid, normal resolution.