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`.

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 `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.

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: 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.

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.

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)`.

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.

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`.

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

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.

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.

splitting and merging.

`snapshot`. Also, move calls to `ax.gridlines` and `ax.coastlines`
inside function `snapshot`. These changes allow us to call `snapshot`
in a new figure.

Move `Region4/2006_01_01` to `Region4_2006_01_01` and
`Region4/2006_01_02` to `Region4_2006_01_02`.

Add a test of `successive_overlap` for a larger region, for which the
identifying numbers of the connected eddies are not the same for all
edges. Add corresponding input files.

Bug fix in main program `test_successive_overlap`.

snapshots in the same figure: useful for visualizing overlaps. So move
lines plotting a snapshot inside a new function called
snapshot and add option `--dashed`.

Remove the option `-e` of `plot_snaphot.py` and add directory argument
instead. The idea is that we now consider the three shapefiles as a
whole, they should always be alone in a dedicated directory.

Move the three shapefiles of `Tests/Input/Region_4/2006_01_02` to a
dedicated directory.

In `plot_snapshot.py`, netCDF variables for wind are now expected to be
called ugos and vgos.

Add a test for overlap of two different 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.

overlap, we will have to read a set of three shapefiles, extremum,
outermost_contour and max_speed_contour, containing several
snapshots. We do not want to re-read field indices for each snapshot.

Rename u, v to ugos, vgos in NetCDF files.

vgos, lon to longitude, lat to latitude.

Add a test for successive_overlap with periodic grid.

Add snapshot for region 4 at a different date, in input files, for a
new test of successive_overlap.

targetted a single main program.

In script plot_snapshot.py, with option --light, do not plot invalid
outermost contours.

spherical_polygon_area to spher_polygon_area.

In procedure max_speed_contour_ssh, instead of aborting when the speed
is not defined, continue with missing_ssh. Found such a case in
November 29th, 2015 data. Added corresponding test. In procedure
set_max_speed, if max_speed_contour_ssh returns missing_ssh then we
just take the outermost contour as max-speed contour.

outside_points(1, :) if necessary in procedure get_snapshot; read
max_radius at run-time. Add a corresponding test.

procedure so it can be used by program test_set_all_outerm.

Move dummy argument corner of set_all_outerm to last position.

Bug fix in procedure get_snapshot: urc(2) must always be lower than
nlat, even if periodic is true. Fix the same bug in procedure
set_all_outerm: llc(2) >= 1 and urc(2) <= nlat even if periodic is true.

Bug fix in procedure set_all_outerm: the lower bound of dummy argument
ssh is not always 1.

Make script examine_ssh_values.py work for a periodic domain.

Make program test_set_all_outerm work for a periodic
domain. max_radius is now chosen at run-time (we must change it for
a very coarse grid). Add a corresponding test.

In written shapefiles, replace field "area" by field "r_eq_area",
that is radius of disk of equal area. This is a smaller number so it
needs fewer characters, especially for a global coarse grid.

reading and spares some disk space: we can reduce the size of the
field from 20 to 14 characters. We do not loose precision with this
reduction because the order of magnitude of the area is 1e3 km2 or
more so the decimal part of the field was 0. Accordingly, change the
are for a null contour from - 1 to - 1e6 m2.

Bug fix in program test_set_max_speed. No need for width 20 for field "speed".

validity of an eddy depending not only on its amplitude but also its
surface. (Note that, in this version, the component valid is redundant: one
can simply test the component out_cont%n_points.)

>= 0 everywhere outside of procedure local_extrema.

In test Nearby_extr, use output from Get_snapshot_region_1_noise since
we now use suff_amp in extremum shapefile.