Thus remove too component interpolated of derived type eddy and
component `extr_interp` of derived type shpc.

We now impose that all eddies in an SHPC have the same
orientation. Remove field `extr_cycl` from the derived type shpc and
add field cyclone to shpc. When reading an eddy, give it the
orientation of its SHPC. Add argument cyclone to procedure
`shpc_create`. Create a file `orientation.txt` in each SHPC. When
writing an eddy, check that its orientation matches that of the SHPC.

Rename triplet to collection, `shp_tr` to shpc, shpt to shpc in
comments, identifiers and file names.

`read_eddy.f90`, `read_field_indices.f90` and `shp_tr_open.f90` will
become common to Overlap and `Inst_eddies` because they will be used
in `Inst_eddies/Tests/test_set_max_speed.f90`. So there are now enough
common files to justify a new directory.

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

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 `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)`.

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.

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

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.)

hard-coding them.

Remove component twice of type eddy, no longer needed.

init_shapefiles. This allows us to have variables for DBF field
numbers, as module variables. We avoid the burden of passing this
large number of variables as arguments to write_eddy. Safer to have
variables for DBF field numbers than relying on the order of those
fields.

Remove file_list. This was a duplication of information.

Use named constant for missing max speed value. It is used in two procedures.

src_test_get_snapshot.

Move field speed from DBF file max_speed_contour to DBF file extremum
because it can be associated to either the contour in
outermost_contour or in max_speed_contour.

of local variable radius in procedure set_max_speed. Add corresponding
column in outermost_contour DBF file. This is just a diagnostic of the
workings of get_snapshot. Clearer to have this output than having
special meaning in components ssh and area of speed_cont.

weight. So, in procedure set_max_speed, in case radius equals 1, set
e%max_speed to the speed on the outermost contour instead of zero.

In procedure set_max_speed, in case the highest speed is on the
outermost contour, set e%speed_cont%polyline to null_polyline instead
of e%out_cont%polyline. This saves main memory and there is less
copying to do.

speed_cont can now be null even if max_speed is not zero so change
test for null shape in procedure write_eddy.

It appears that the shapelib C library cannot write a NaN value to a
dbf file, so write 1e4 instead.

Bug fix in plot_snapshot.py.

to out_cont and speed_cont (shorter names).

Propagate change in shapelib_03: shp_append_simple_object_03 to
shp_append_object_03.

program behavior.

In plot_snapshot.py, no need to accumulate all content of shapefile
extremum_1, just process it record by record, as for other shapefiles.

contour.

Read whole NetCDF files in program test_set_outermost_contour instead
of specifying a reading window. Simpler to prepare a file outside
the Fortran program, as in program test_local_extrema. Also, compute
step from read longitude and latitude.

contour no longer means that the eddy is interpolated.

low-amplitude threshold, min_amp.

Add component suff_amp to derived type eddy. Write this component in
extremum_$m.dbf.

In shapefiles, write positions of vertices in degrees rather than
radians.

test_get_snapshot reads the whole domain of input NetCDF files instead
of selecting a window through a namelist. This is clearer and more
convenient. Same in test_get_snapshot.py, test_local_extrema and
test_local_extrema.py.

In test_get_snapshot.py, annotate extrema instead of inserting a
legend.

More correct names: radian_per_degree to deg_over_rad,
degree_per_radian to rad_over_deg.