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.

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.

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.

files, that make up a snapshot into a directory that contains only
these files. We hope that this will ease the handling of
snapshots. For now, this is useful in program
test_successive_overlap. So, in program extraction_eddies, create the
shapefiles in a directory called Snapshot. As we cannot create the
directory from Fortran (in Fortran 2003, it becomes possible in
Fortran 2008), we have to wrap the Fortran executable in a shell
script "extraction_eddies.sh". In the same way, read from a directory
Snapshot_old in programs test_read_eddy and test_read_snapshot and
create scripts "test_read_eddy.sh" and "test_read_snapshot.sh".

Reference the shell scripts "extraction_eddies.sh",
"test_read_eddy.sh" and "test_read_snapshot.sh" in JSON test files.

In program test_successive_overlap, finally read two snapshots, from
directories Snapshot_1 and Snapshot_2. Pass to successive_overlap the
date of the second snapshot. Use new variables corner_deg and step_deg
to avoid converting to rad twice.

Create directory Snapshot in Tests/Input/Region_4/2006_01_01.

Stdin to Input. Two input dir provided for in tests.json: $input_dir
and $large_input_dir.

Rename everywhere variable nearby_extr to outside_points to avoid
confusion with function nearby_extr. Rename file "nearby_extr.csv" to
"outside_points.csv".

In procedure nearby_extr, include in the selection extrema with
different sign, even if they do not have sufficient amplitude.

Bug fix in read_eddy: use the value of read attribute to define
e%interpolated.

GPC_F and GPC must be used.

read_snapshot, assert that there is no duplicate tuple in
s%ind_extr. Since we are not sure of that, we must use a do construct
and not a forall in order to define s%extr_map.

Bug fix in program test_local_extrema: support missing values. Add
corresponding test.

Output s%ind_extr in program test_read_snapshot.