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.

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

Add dummy argument `shp_triplet_dir` to procedure
`shp_triplet_create`. Motivation: program `eddy_graph` needs to create
one SHP triplet per MPI process.

Rename procedure `init_shapefiles` to `shp_triplet_create`.

Use the components for field identifiers of a variable of type
`shp_triplet` instead of storing these field identifiers in variables
of modules `init_shapefiles_m` and `read_field_indices_m`. The dummy
argument hshp of procedure `read_field_indices` becomes
`intent(inout)`.

Create derived type `shp_triplet`. Motivation: we need to manipulate
two triplets of shapefiles in program `eddy_graph`. Use everywhere a
variable of type `shp_triplet` instead of the three variables
`hshp_extremum`, `hshp_outermost`, `hshp_max_speed` when all three of
them appear. Rename character variable `shp_triplet` to
`shp_triplet_dir`.

In procedure `dispatch_snapshot`, rename dummy argument m to rank,
clearer.

Rename program `test_get_snapshot` to `test_get_dispatch_snap` and
make it call `dispatch_snapshot` instead of `send_snapshot`. The only
difference in result is that the program now writes files
`isolated_nodes.txt` and `number_eddies.csv`.

Check in program `test_overlap` that it is run on a single MPI process.

Change order of dummy arguments of procedure `get_snapshot` to make it
more convenient to call with keywords. Rename dummy argument m to
rank, clearer.

Bug fix in `short_tests_.json`: run `test_read_snapshot` and
`test_overlap` with `mpiexec -n 1`, else the programs may not be able
to read standard input.

On our way to a generalization of script `filter.py`: use a function
to define the filter.

In script `plot_snapshot.py`, accept a triplet of shapefiles without
`ishape_last.txt`.

Add a test for program `test_get_snapshot` where one of the processes
does a reception in procedure `get_snapshot`.

Bug fix in main unit `test_get_snapshot`: we send and receive date k.

Add script for concatenation of triplets of shapefiles.

Generalize script `plot_snapshot.py` to read a single date in a
triplet of shapefiles containing several dates.

Bug fix in `Tests/CMakeLists.txt`: missing source file.

Include four dates in `Tests/Input/Region_1/SHP_triplet_noise`, in
preparation for a test with `test_get_snapshot`. Main unit
`test_nearby_extr` must then read the number of shapes for the first
date in `ishape_last.txt`.

Prepare for a run of `test_get_snapshot` which receives a
snapshot. Generalize main unit `test_get_snapshot`: it is now
parallelized; it reads a date index from stdin; it sends a snapshot
from process 1 to process 0 if it is run with 2 processes.

The logic of the overlap program will be that all processes access the
triplet of input shapefiles. So modify subroutine
`read_field_indices`: process 0 reads field indices and broadcasts
them. This implies that programs `test_overlap`, `test_read_snapshot`
and `test_read_eddy` use MPI.

Generalize `algorithm.py`.

In program `test_send_recv`, read input SHP triplet from command line
instead of requiring it to be present in the current directory with
the name `SHP_triplet_old`. Generalize `test_send_recv`: read
`ishape_last` from file. In `test_send_recv`, all processes must now
access the triplet of shapefiles since process 0 reads field
indices. For the sake of uniformity, read and broadcast k1 from
process 0.

First compilation and test of procedure `get_snapshot`. Change order
of dummy arguments of procedure `get_snapshot`: make it more
convenient for call with keywords. Replace dummy arguments periodic
and `dist_lim` by dummy argument copy. Add dummy arguments
`ishape_last` and k1. Promote `hshp_extremum`, `hshp_outermost`,
`hshp_max_speed` from local variables to dummy arguments.

In program `test_read_snapshot`, read input SHP triplet from command
line instead of requiring it to be present in the current directory
with the name `SHP_triplet_old`.

Remove directory `Tests/Input/Region_1/SHP_triplet`, which was not used.

Change of idea: make date index an intent in argument of procedure
`read_snapshot`. Replace dummy arguments `ishape_first` and scalar
`ishape_last` by k1 and array `ishape_last`. It is now the task of
`read_snapshot` to find the ishapes to read. This seems clearer.

Change of idea: instead of storing `date_index` and `ishape_last` in a
file `contents.csv`, store only `ishape_last` in a file
`ishape_last.txt`. The `date_index` column was useless and it
complicated reading the file. The first value of `date_index` can be
read from one of the three DBF files. Also, to roll with the flow, let
the lower bound of `ishape_last` in main unit `test_overlap` be 1
instead of k1.

Change order of actual arguments of `dbf_read_attribute_03` following
revision of `Shapelib_03`.

Bug fix in procedure `dispatch_snapshot`: the rank of MPI processes is 0-based.

Bug fix: remove `extr_map_outermost.nc`, which was not used since
commit ad420d25.

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.

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`.

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`.

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.