Bug fix: do not provide standard input for `inst_eddies_Aviso.py`, it
does not read it.

Because `$tests_old_dir/Extraction_eddies_region_5/SHPC` is opened
with `SHPC_class` in test `Plot_eddy_contours_window`, which will
create `n_slices.txt`, so there will always be this file only in
`$tests_old_dir/Extraction_eddies_region_5/SHPC`.

We import in the test infrastructure the experiment `Inst_eddies_4`
because we want to no longer keep invalid contours, so we will need to
update the experiment.

Changing my mind. In an SHPC, store shapefiles in
"Slice_{slice}/{orientation}" instead of
"{orientation}/Slice_{slice}". Two reasons: easier to store accessory
files from running `inst_eddies`, such as `perf_report` and output
from Torque submission script; clearer that a slice should contain the
same dates for both orientations.

Assume that a slice is in a directory
"{shpc_dir}/{orientation}/Slice_{slice}" where shpc_dir can be any
name, orientation is "Anticyclones" or "Cyclones" and slice is an
integer. Do not read or create any longer a file "orientation.txt" in
the slice directory. Add procedure `get_slice_dir`. Add dummy
arguments cyclone and slice to procedure `shpc_open`. Add dummy
argument slice to procedure `shpc_create`.

Rename `main_nml` to `config_nml` in module `config_m`.

Extract code from program `inst_eddies` into new procedure `input_ssh`.

Add tests for a case where the speed is not defined on a whole segment.

Following update of `test_compare.py`.

We can make a symbolic link or copy to `$large_input_dir`.

Following modifications of `CMakeLists.txt` files.

When there are more than 3 input files. We recover the convenience of
commit b34b85a8, with the underlying generality of commit d365e754.

Provide list of input files as arguments of `inst_eddies.py`,
following commit 8e0c03e1.

For programs `inst_eddies` and `test_get_1_outerm`, following commits
9a59d13 and 9dc139d.

Following commit b0e3ce55.

In commit d5e89eb9, the test was added with the useless key
"input". Now, after commit 29c37646, the useless key is the key "required".

Now that `inst_eddies` reads `main_nml` only on the first date, we do
not need to create a file `main_nml.txt` before running
`inst_eddies.py`. `inst_eddies.py` can just read `main_nml` from
standard input.

Replace positional argument template by optional argument. This
argument is now needed only in case we process several dates, since
the first date is now read from the NetCDF file.

Replace `/proju/lmd-oce/data/AVISO/DT_2018/2006/01` by
`$large_input_dir`.

This SHPC was made with an old version of `inst_eddies`: it contained
cyclones and anticyclones output together. We create a test `Region_6`
instead.

Make it 15 days long because we want to use it in place of
`Overlap/Tests/Input/Region_2_SHPC`.

Create separate collections of shapefiles for cyclones and anticyclones.

Preparing for two collections of shapefiles. We create the
procedure `write_nml` so we will be able to call it twice. But it
needs to access the namelist. So the namelist must be at the module level.

Take into account new structure of repository in JSon test files.

Also split the tests, Fortran source files, Python files and JSon
files. Keep at the top level the files used in both `Inst_eddies` and
Overlap.

Motivations for the split:

- The top directory contained many files.

- It may be useful to compile only one of the two sub-projects. For
example, only `Inst_eddies` on Ciclad, where MPI 3 is not available.

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.

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`.

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`.

Create general script `mkdir_run.sh` to replace specific
scripts `extraction_eddies.sh`, `test_read_snapshot.sh`,
`test_read_eddy.sh` and to run `test_successive_overlap`.

Replace `$input_dir` by `$src_dir/Tests/Input` in
`*_tests.json`. Motivation: we also need `src_dir` to point to
`mkdir_run.sh`.

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.

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.