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.

>= 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.

than extr_map /= i.

Preparing to remove the coding of sufficient amplitude in extr_map: do
not use anywhere the sign of extr_map, use the component suff_amp of
the type eddy instead.

In program test_successive_overlap, I would rather not use default
values for namelist variables.

Add a larger test for successive_overlap, to have eddies wih
insufficient amplitude in the region.

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.

Bug fix in test_set_max_speed: forgot conversion to rad.

set_all_outerm and in get_snapshot.

procedure get_snapshot. The idea is that, in this branch, nearby_extr
will eventually include extrema depending not only on them having
sufficient amplitude but also on their cyclonicity. Both pieces of
information cannot be simply encoded in extr_map. The downside is that
we compute needlessly nearby_extr if e%radius4 == 1 in set_max_speed.

procedure set_all_outerm. The idea is that, in this branch,
nearby_extr will eventually include extrema depending not only on them
having sufficient amplitude but also on their cyclonicity. Both pieces
of information cannot be simply encoded in extr_map.

title lines in "edgelist_1.csv". Add python script reading
"edgelist_1.csv" into a NetworkX graph.

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.

be useful for testing successive_overlap.

for upcoming procedure read_snapshot.

Bug fix in procedure rossby_number: e%speed_cont could be null.

multi-polygon. This is a useful test because, in successive_overlap,
the intersection of two polygons may give a multi-polygon.

specifying polygon in source code.

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.

to 1e4, safer too.

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.

instead of defining the component ssh to the ssh of the extremum or to
the ssh of the outermost contour, use a missing value flag
(1e4). Also, when radius4 >= 2 and the max speed contour is the
outermost contour, use missing value flag in the ssh component of max
speed contour instead of ssh on outermost contour. This makes clearer
output.

Add function null_ssh_contour.

In procedure get_1_outerm, simplify the comparison of level_try and
level_good. So we do not need any longer the dummy argument
ssh_extremum.

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.

and signalling NaN so we cannot use the -ffpe-trap=invalid option.

Accept that we might not be able to compute the mean speed on the
outermost contour: there might be undefined values of velocity
around. In that case just use the contour coming from
max_speed_contour_ssh.

Add quiver_key in plot_snapshot.py.

New test for region 5.

procedure set_all_outerm. So do not define and output null max-speed
contours.

Bug fix in program test_set_all_outerm: take into account missing
values in ADT.

Make plot_snapshot.py work even if there is no max-speed contour
shapefile. So we can use plot_snapshot.py on results of program
test_set_all_outerm.

For ssh, missing value is huge(0.). We have to take a large value
because Contour_531 has an argument zmax for missing values. For
velocity, missing value is a quiet NaN. We have to take this because
we need to know if the interpolation procedure in mean_speed has not
used any missing value and we do not want to alter the interpolation
procedure itself.

In local_extrema, we accept as local extrema only points with 8 valid
values around them.

When we look for the maximum speed contour, we are hoping that good
contours do not englobe missing values. If this happens, the program
aborts.

When computing the mean speed on a contour, we are hoping that the
interpolation of speed on contour points does not use missing
values. If this happens, the program aborts.

Draw coastlines in plot_snaphot.py. At the same time, this allows the
use of any projection.

because the order is not obvious.

In test_mean_speed and test_set_max_speed, do not read primary
variables with nf95_gw_var so the primary variables are allowed to
have or not a degenerate dimension.

set_all_outerm. Thus, we have the clearer intent(out) for argument s
of set_all_outerm. Also, this prepares a possible replacement of
set_all_outerm by a procedure from the Topology toolkit.

Create test program for procedure set_all_outerm.

with some components intent(in) and one component intent(out) was less
clear. Also, replace argument ind_targ_extr by argument i. This is
simpler both in get_1_outerm and in set_all_outerm.

There is now no need to use an eddy in test_get_1_outerm.