From 561502318bdb029d6047445107907bff0765b5f9 Mon Sep 17 00:00:00 2001
From: Lionel GUEZ <guez@lmd.ens.fr>
Date: Fri, 26 Feb 2021 08:55:27 +0100
Subject: [PATCH] Split arborescence into `Inst_eddies` and Overlap

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.
---
 Analysis/short_tests.json                     |  69 +++
 CMakeLists.txt                                |  41 +-
 Convert_Matlab/short_tests.json               |  40 ++
 Inst_eddies/CMakeLists.txt                    |  16 +
 Inst_eddies/Tests/CMakeLists.txt              | 103 ++++
 {Tests => Inst_eddies/Tests}/long_tests.json  |  14 +-
 Inst_eddies/Tests/short_tests.json            | 358 ++++++++++++++
 .../Tests}/test_get_1_outerm.f90              |   0
 .../Tests}/test_good_contour.f90              |   0
 .../Tests}/test_inside_4.f90                  |   0
 .../Tests}/test_local_extrema.f90             |   0
 .../Tests}/test_local_extrema.py              |   0
 .../Tests}/test_max_speed_contour_ssh.f90     |   0
 .../Tests}/test_mean_speed.f90                |   0
 .../Tests}/test_mean_speed.py                 |   0
 .../Tests}/test_nearby_extr.f90               |   0
 .../Tests}/test_set_all_outerm.f90            |   0
 .../Tests}/test_set_max_speed.f90             |   0
 .../get_1_outerm.f90                          |   0
 get_var.f90 => Inst_eddies/get_var.f90        |   0
 .../good_contour.f90                          |   0
 inside_4.f90 => Inst_eddies/inside_4.f90      |   0
 .../inst_eddies.f90                           |   0
 .../local_extrema.f90                         |   0
 .../max_speed_contour_ssh.f90                 |   0
 mean_speed.f90 => Inst_eddies/mean_speed.f90  |   0
 .../nearby_extr.f90                           |   0
 .../set_all_outerm.f90                        |   0
 .../set_max_speed.f90                         |   0
 Overlap/CMakeLists.txt                        |  22 +
 Overlap/Tests/CMakeLists.txt                  | 116 +++++
 .../Tests}/Input/Eurec4A_OA/Nanti.mat         | Bin
 .../Tests}/Input/Eurec4A_OA/Ncyclo.mat        | Bin
 .../Input/Eurec4A_OA/adt_2019-12-15.mat       | Bin
 .../Tests}/Input/Eurec4A_OA/date_num.mat      | Bin
 .../Tests}/Input/Eurec4A_OA/id_child_anti.mat | Bin
 .../Input/Eurec4A_OA/id_child_cyclo.mat       | Bin
 .../Tests}/Input/Get_1_outerm/test.json       |   0
 .../Input/Get_1_outerm/test_get_1_outerm.dbf  | Bin
 .../Input/Get_1_outerm/test_get_1_outerm.shp  | Bin
 .../Input/Get_1_outerm/test_get_1_outerm.shx  | Bin
 .../Get_1_outerm/test_get_1_outerm_stdout.txt |   0
 .../Input/Get_1_outerm_noise_2_8/test.json    |   0
 .../test_get_1_outerm.dbf                     | Bin
 .../test_get_1_outerm.shp                     | Bin
 .../test_get_1_outerm.shx                     | Bin
 .../test_get_1_outerm_stdout.txt              |   0
 .../SHP_triplet/extremum.dbf                  | Bin
 .../SHP_triplet/extremum.shp                  | Bin
 .../SHP_triplet/extremum.shx                  | Bin
 .../SHP_triplet/grid_nml.txt                  |   0
 .../SHP_triplet/ishape_last.txt               |   0
 .../SHP_triplet/max_speed_contour.dbf         | Bin
 .../SHP_triplet/max_speed_contour.shp         | Bin
 .../SHP_triplet/max_speed_contour.shx         | Bin
 .../SHP_triplet/outermost_contour.dbf         | Bin
 .../SHP_triplet/outermost_contour.shp         | Bin
 .../SHP_triplet/outermost_contour.shx         | Bin
 .../mkdir_run_stdout.txt                      |   0
 .../Extraction_eddies_periodic/test.json      |   0
 .../Tests}/Input/Global/NSO_in.txt            |   0
 .../Input/Global/h_2006_01_01_coarse.nc       | Bin
 .../Input/Global/successive_overlap_in.txt    |   0
 .../Input/Global/uv_2006_01_01_coarse.nc      | Bin
 .../Tests}/Input/NSO_delta_in.txt             |   0
 .../Input/Region_1/Local_extrema/extr_map.nc  | Bin
 .../Input/Region_1/Local_extrema/test.json    |   0
 .../Local_extrema/test_local_extrema.csv      |   0
 .../test_local_extrema_stdout.txt             |   0
 .../Region_1/SHP_triplet_noise/extremum.dbf   | Bin
 .../Region_1/SHP_triplet_noise/extremum.shp   | Bin
 .../Region_1/SHP_triplet_noise/extremum.shx   | Bin
 .../Region_1/SHP_triplet_noise/grid_nml.txt   |   0
 .../SHP_triplet_noise/ishape_last.txt         |   0
 .../SHP_triplet_noise/max_speed_contour.dbf   | Bin
 .../SHP_triplet_noise/max_speed_contour.shp   | Bin
 .../SHP_triplet_noise/max_speed_contour.shx   | Bin
 .../SHP_triplet_noise/mkdir_run_stdout.txt    |   0
 .../SHP_triplet_noise/outermost_contour.dbf   | Bin
 .../SHP_triplet_noise/outermost_contour.shp   | Bin
 .../SHP_triplet_noise/outermost_contour.shx   | Bin
 .../Region_1/SHP_triplet_noise/test.json      |   0
 .../Input/Region_1/get_snapshot_nml.txt       |   0
 .../Input/Region_1/get_snapshot_recv_nml.txt  |   0
 {Tests => Overlap/Tests}/Input/Region_1/h.nc  | Bin
 .../Input/Region_1/huv_region_1_2006_01_02.nc | Bin
 .../Input/Region_1/huv_region_1_2006_01_03.nc | Bin
 .../Input/Region_1/huv_region_1_2006_01_04.nc | Bin
 .../Tests}/Input/Region_1/outside_points.csv  |   0
 .../Region_1/outside_points_get_1_outerm.csv  |   0
 .../outside_points_get_1_outerm_noise_2.csv   |   0
 {Tests => Overlap/Tests}/Input/Region_1/uv.nc | Bin
 .../Input/Region_2/SHP_triplet/extremum.dbf   | Bin
 .../Input/Region_2/SHP_triplet/extremum.shp   | Bin
 .../Input/Region_2/SHP_triplet/extremum.shx   | Bin
 .../Input/Region_2/SHP_triplet/grid_nml.txt   |   0
 .../Region_2/SHP_triplet/ishape_last.txt      |   0
 .../SHP_triplet/max_speed_contour.dbf         | Bin
 .../SHP_triplet/max_speed_contour.shp         | Bin
 .../SHP_triplet/max_speed_contour.shx         | Bin
 .../SHP_triplet/outermost_contour.dbf         | Bin
 .../SHP_triplet/outermost_contour.shp         | Bin
 .../SHP_triplet/outermost_contour.shx         | Bin
 {Tests => Overlap/Tests}/Input/Region_2/h.nc  | Bin
 .../Input/Region_2/successive_overlap_in.txt  |   0
 {Tests => Overlap/Tests}/Input/Region_2/uv.nc | Bin
 .../Region_4/Eddies_region_4/extremum.dbf     | Bin
 .../Region_4/Eddies_region_4/extremum.shp     | Bin
 .../Region_4/Eddies_region_4/extremum.shx     | Bin
 .../Region_4/Eddies_region_4/grid_nml.txt     |   0
 .../Region_4/Eddies_region_4/ishape_last.txt  |   0
 .../Eddies_region_4/max_speed_contour.dbf     | Bin
 .../Eddies_region_4/max_speed_contour.shp     | Bin
 .../Eddies_region_4/max_speed_contour.shx     | Bin
 .../Eddies_region_4/outermost_contour.dbf     | Bin
 .../Eddies_region_4/outermost_contour.shp     | Bin
 .../Eddies_region_4/outermost_contour.shx     | Bin
 .../Tests}/Input/Region_4/NSODS_in.txt        |   0
 .../Input/Region_4/dt_region_4_2006_01_02.nc  | Bin
 .../Region_4/extraction_eddies_stdout.txt     |   0
 {Tests => Overlap/Tests}/Input/Region_4/h.nc  | Bin
 .../Region_4/non_successive_overlap_in.txt    |   0
 .../Input/Region_4/read_snapshot_nml.txt      |   0
 {Tests => Overlap/Tests}/Input/Region_4/uv.nc | Bin
 .../Tests}/Input/Region_5/NSO_in.txt          |   0
 .../Tests}/Input/Region_5/SOR5OD_in.txt       |   0
 .../Tests}/Input/Region_5/SOR5_in.txt         |   0
 {Tests => Overlap/Tests}/Input/Region_5/h.nc  | Bin
 {Tests => Overlap/Tests}/Input/Region_5/uv.nc | Bin
 .../Input/Region_6_SHP_triplet/extremum.dbf   | Bin
 .../Input/Region_6_SHP_triplet/extremum.shp   | Bin
 .../Input/Region_6_SHP_triplet/extremum.shx   | Bin
 .../Input/Region_6_SHP_triplet/grid_nml.txt   |   0
 .../Region_6_SHP_triplet/ishape_last.txt      |   0
 .../max_speed_contour.dbf                     | Bin
 .../max_speed_contour.shp                     | Bin
 .../max_speed_contour.shx                     | Bin
 .../outermost_contour.dbf                     | Bin
 .../outermost_contour.shp                     | Bin
 .../outermost_contour.shx                     | Bin
 {Tests => Overlap/Tests}/Input/SODS_in.txt    |   0
 .../Tests}/Input/empty_outside_points.csv     |   0
 {Tests => Overlap/Tests}/Input/example.nc     | Bin
 .../Tests}/Input/good_contour.txt             |   0
 .../Tests}/Input/good_contour_2.txt           |   0
 {Tests => Overlap/Tests}/Input/h_outermost.nc | Bin
 {Tests => Overlap/Tests}/Input/h_region_3.nc  | Bin
 .../Tests}/Input/huv_2015_11_29.nc            | Bin
 .../Tests}/Input/inside_4_false_nml.txt       |   0
 .../Tests}/Input/inside_4_true_nml.txt        |   0
 .../Tests}/Input/no_good_contour.txt          |   0
 .../Tests}/Input/outermost_contour_alt.dbf    | Bin
 .../Tests}/Input/outermost_contour_alt.shp    | Bin
 .../Tests}/Input/outermost_contour_alt.shx    | Bin
 .../Tests}/Input/outermost_eddy_5.dbf         | Bin
 .../Tests}/Input/outermost_eddy_5.shp         | Bin
 .../Tests}/Input/outermost_eddy_5.shx         | Bin
 .../Tests}/Input/outside_points_1.csv         |   0
 .../Tests}/Input/outside_points_2.csv         |   0
 .../Tests}/Input/successive_overlap_in.txt    |   0
 .../Input/successive_overlap_periodic_in.txt  |   0
 .../Tests}/Input/tri_square_hole.dbf          | Bin
 .../Tests}/Input/tri_square_hole.shp          | Bin
 .../Tests}/Input/tri_square_hole.shx          | Bin
 {Tests => Overlap/Tests}/Input/triangle.dbf   | Bin
 {Tests => Overlap/Tests}/Input/triangle.shp   | Bin
 {Tests => Overlap/Tests}/Input/triangle.shx   | Bin
 .../Tests}/Input/uv_outermost.nc              | Bin
 {Tests => Overlap/Tests}/Input/uv_region_3.nc | Bin
 .../Input/write_overlap_delta_3_nml.txt       |   0
 .../Input/write_overlap_different_nml.txt     |   0
 .../Input/write_overlap_shifting_nml.txt      |   0
 Overlap/Tests/long_tests.json                 |  14 +
 {Tests => Overlap/Tests}/short_tests.json     | 465 ------------------
 .../Tests}/test_get_dispatch_snap.f90         |   0
 {Tests => Overlap/Tests}/test_overlap.f90     |   0
 {Tests => Overlap/Tests}/test_read_eddy.f90   |   0
 .../Tests}/test_read_snapshot.f90             |   0
 {Tests => Overlap/Tests}/test_send_recv.f90   |   0
 .../Tests}/test_spher_polygon_area.f90        |   0
 {Tests => Overlap/Tests}/test_weight.f90      |   0
 .../Tests}/test_write_overlap.f90             |   0
 {Tests => Overlap/Tests}/write_snapshot.f90   |   0
 .../candidate_overlap.f90                     |   0
 .../dispatch_snapshot.f90                     |   0
 eddy_graph.f90 => Overlap/eddy_graph.f90      |   0
 eddy_graph_in.sh => Overlap/eddy_graph_in.sh  |   0
 get_snapshot.f90 => Overlap/get_snapshot.f90  |   0
 overlap.f90 => Overlap/overlap.f90            |   0
 read_eddy.f90 => Overlap/read_eddy.f90        |   0
 .../read_field_indices.f90                    |   0
 .../read_snapshot.f90                         |   0
 .../recv_snapshot.f90                         |   0
 .../send_snapshot.f90                         |   0
 shp_tr_open.f90 => Overlap/shp_tr_open.f90    |   0
 .../spher_polygon_area.f90                    |   0
 unit_edge_m.f90 => Overlap/unit_edge_m.f90    |   0
 weight.f90 => Overlap/weight.f90              |   0
 write_edge.f90 => Overlap/write_edge.f90      |   0
 .../write_overlap.f90                         |   0
 Tests/CMakeLists.txt                          | 211 --------
 short_tests.json                              |   6 +
 ...e_area.f90 => test_spher_polyline_area.f90 |   0
 .../write_extr_map.f90 => write_extr_map.f90  |   0
 204 files changed, 753 insertions(+), 722 deletions(-)
 create mode 100644 Analysis/short_tests.json
 create mode 100644 Convert_Matlab/short_tests.json
 create mode 100644 Inst_eddies/CMakeLists.txt
 create mode 100644 Inst_eddies/Tests/CMakeLists.txt
 rename {Tests => Inst_eddies/Tests}/long_tests.json (79%)
 create mode 100644 Inst_eddies/Tests/short_tests.json
 rename {Tests => Inst_eddies/Tests}/test_get_1_outerm.f90 (100%)
 rename {Tests => Inst_eddies/Tests}/test_good_contour.f90 (100%)
 rename {Tests => Inst_eddies/Tests}/test_inside_4.f90 (100%)
 rename {Tests => Inst_eddies/Tests}/test_local_extrema.f90 (100%)
 rename {Tests => Inst_eddies/Tests}/test_local_extrema.py (100%)
 rename {Tests => Inst_eddies/Tests}/test_max_speed_contour_ssh.f90 (100%)
 rename {Tests => Inst_eddies/Tests}/test_mean_speed.f90 (100%)
 rename {Tests => Inst_eddies/Tests}/test_mean_speed.py (100%)
 rename {Tests => Inst_eddies/Tests}/test_nearby_extr.f90 (100%)
 rename {Tests => Inst_eddies/Tests}/test_set_all_outerm.f90 (100%)
 rename {Tests => Inst_eddies/Tests}/test_set_max_speed.f90 (100%)
 rename get_1_outerm.f90 => Inst_eddies/get_1_outerm.f90 (100%)
 rename get_var.f90 => Inst_eddies/get_var.f90 (100%)
 rename good_contour.f90 => Inst_eddies/good_contour.f90 (100%)
 rename inside_4.f90 => Inst_eddies/inside_4.f90 (100%)
 rename inst_eddies.f90 => Inst_eddies/inst_eddies.f90 (100%)
 rename local_extrema.f90 => Inst_eddies/local_extrema.f90 (100%)
 rename max_speed_contour_ssh.f90 => Inst_eddies/max_speed_contour_ssh.f90 (100%)
 rename mean_speed.f90 => Inst_eddies/mean_speed.f90 (100%)
 rename nearby_extr.f90 => Inst_eddies/nearby_extr.f90 (100%)
 rename set_all_outerm.f90 => Inst_eddies/set_all_outerm.f90 (100%)
 rename set_max_speed.f90 => Inst_eddies/set_max_speed.f90 (100%)
 create mode 100644 Overlap/CMakeLists.txt
 create mode 100644 Overlap/Tests/CMakeLists.txt
 rename {Tests => Overlap/Tests}/Input/Eurec4A_OA/Nanti.mat (100%)
 rename {Tests => Overlap/Tests}/Input/Eurec4A_OA/Ncyclo.mat (100%)
 rename {Tests => Overlap/Tests}/Input/Eurec4A_OA/adt_2019-12-15.mat (100%)
 rename {Tests => Overlap/Tests}/Input/Eurec4A_OA/date_num.mat (100%)
 rename {Tests => Overlap/Tests}/Input/Eurec4A_OA/id_child_anti.mat (100%)
 rename {Tests => Overlap/Tests}/Input/Eurec4A_OA/id_child_cyclo.mat (100%)
 rename {Tests => Overlap/Tests}/Input/Get_1_outerm/test.json (100%)
 rename {Tests => Overlap/Tests}/Input/Get_1_outerm/test_get_1_outerm.dbf (100%)
 rename {Tests => Overlap/Tests}/Input/Get_1_outerm/test_get_1_outerm.shp (100%)
 rename {Tests => Overlap/Tests}/Input/Get_1_outerm/test_get_1_outerm.shx (100%)
 rename {Tests => Overlap/Tests}/Input/Get_1_outerm/test_get_1_outerm_stdout.txt (100%)
 rename {Tests => Overlap/Tests}/Input/Get_1_outerm_noise_2_8/test.json (100%)
 rename {Tests => Overlap/Tests}/Input/Get_1_outerm_noise_2_8/test_get_1_outerm.dbf (100%)
 rename {Tests => Overlap/Tests}/Input/Get_1_outerm_noise_2_8/test_get_1_outerm.shp (100%)
 rename {Tests => Overlap/Tests}/Input/Get_1_outerm_noise_2_8/test_get_1_outerm.shx (100%)
 rename {Tests => Overlap/Tests}/Input/Get_1_outerm_noise_2_8/test_get_1_outerm_stdout.txt (100%)
 rename {Tests => Overlap/Tests}/Input/Global/Extraction_eddies_periodic/SHP_triplet/extremum.dbf (100%)
 rename {Tests => Overlap/Tests}/Input/Global/Extraction_eddies_periodic/SHP_triplet/extremum.shp (100%)
 rename {Tests => Overlap/Tests}/Input/Global/Extraction_eddies_periodic/SHP_triplet/extremum.shx (100%)
 rename {Tests => Overlap/Tests}/Input/Global/Extraction_eddies_periodic/SHP_triplet/grid_nml.txt (100%)
 rename {Tests => Overlap/Tests}/Input/Global/Extraction_eddies_periodic/SHP_triplet/ishape_last.txt (100%)
 rename {Tests => Overlap/Tests}/Input/Global/Extraction_eddies_periodic/SHP_triplet/max_speed_contour.dbf (100%)
 rename {Tests => Overlap/Tests}/Input/Global/Extraction_eddies_periodic/SHP_triplet/max_speed_contour.shp (100%)
 rename {Tests => Overlap/Tests}/Input/Global/Extraction_eddies_periodic/SHP_triplet/max_speed_contour.shx (100%)
 rename {Tests => Overlap/Tests}/Input/Global/Extraction_eddies_periodic/SHP_triplet/outermost_contour.dbf (100%)
 rename {Tests => Overlap/Tests}/Input/Global/Extraction_eddies_periodic/SHP_triplet/outermost_contour.shp (100%)
 rename {Tests => Overlap/Tests}/Input/Global/Extraction_eddies_periodic/SHP_triplet/outermost_contour.shx (100%)
 rename {Tests => Overlap/Tests}/Input/Global/Extraction_eddies_periodic/mkdir_run_stdout.txt (100%)
 rename {Tests => Overlap/Tests}/Input/Global/Extraction_eddies_periodic/test.json (100%)
 rename {Tests => Overlap/Tests}/Input/Global/NSO_in.txt (100%)
 rename {Tests => Overlap/Tests}/Input/Global/h_2006_01_01_coarse.nc (100%)
 rename {Tests => Overlap/Tests}/Input/Global/successive_overlap_in.txt (100%)
 rename {Tests => Overlap/Tests}/Input/Global/uv_2006_01_01_coarse.nc (100%)
 rename {Tests => Overlap/Tests}/Input/NSO_delta_in.txt (100%)
 rename {Tests => Overlap/Tests}/Input/Region_1/Local_extrema/extr_map.nc (100%)
 rename {Tests => Overlap/Tests}/Input/Region_1/Local_extrema/test.json (100%)
 rename {Tests => Overlap/Tests}/Input/Region_1/Local_extrema/test_local_extrema.csv (100%)
 rename {Tests => Overlap/Tests}/Input/Region_1/Local_extrema/test_local_extrema_stdout.txt (100%)
 rename {Tests => Overlap/Tests}/Input/Region_1/SHP_triplet_noise/extremum.dbf (100%)
 rename {Tests => Overlap/Tests}/Input/Region_1/SHP_triplet_noise/extremum.shp (100%)
 rename {Tests => Overlap/Tests}/Input/Region_1/SHP_triplet_noise/extremum.shx (100%)
 rename {Tests => Overlap/Tests}/Input/Region_1/SHP_triplet_noise/grid_nml.txt (100%)
 rename {Tests => Overlap/Tests}/Input/Region_1/SHP_triplet_noise/ishape_last.txt (100%)
 rename {Tests => Overlap/Tests}/Input/Region_1/SHP_triplet_noise/max_speed_contour.dbf (100%)
 rename {Tests => Overlap/Tests}/Input/Region_1/SHP_triplet_noise/max_speed_contour.shp (100%)
 rename {Tests => Overlap/Tests}/Input/Region_1/SHP_triplet_noise/max_speed_contour.shx (100%)
 rename {Tests => Overlap/Tests}/Input/Region_1/SHP_triplet_noise/mkdir_run_stdout.txt (100%)
 rename {Tests => Overlap/Tests}/Input/Region_1/SHP_triplet_noise/outermost_contour.dbf (100%)
 rename {Tests => Overlap/Tests}/Input/Region_1/SHP_triplet_noise/outermost_contour.shp (100%)
 rename {Tests => Overlap/Tests}/Input/Region_1/SHP_triplet_noise/outermost_contour.shx (100%)
 rename {Tests => Overlap/Tests}/Input/Region_1/SHP_triplet_noise/test.json (100%)
 rename {Tests => Overlap/Tests}/Input/Region_1/get_snapshot_nml.txt (100%)
 rename {Tests => Overlap/Tests}/Input/Region_1/get_snapshot_recv_nml.txt (100%)
 rename {Tests => Overlap/Tests}/Input/Region_1/h.nc (100%)
 rename {Tests => Overlap/Tests}/Input/Region_1/huv_region_1_2006_01_02.nc (100%)
 rename {Tests => Overlap/Tests}/Input/Region_1/huv_region_1_2006_01_03.nc (100%)
 rename {Tests => Overlap/Tests}/Input/Region_1/huv_region_1_2006_01_04.nc (100%)
 rename {Tests => Overlap/Tests}/Input/Region_1/outside_points.csv (100%)
 rename {Tests => Overlap/Tests}/Input/Region_1/outside_points_get_1_outerm.csv (100%)
 rename {Tests => Overlap/Tests}/Input/Region_1/outside_points_get_1_outerm_noise_2.csv (100%)
 rename {Tests => Overlap/Tests}/Input/Region_1/uv.nc (100%)
 rename {Tests => Overlap/Tests}/Input/Region_2/SHP_triplet/extremum.dbf (100%)
 rename {Tests => Overlap/Tests}/Input/Region_2/SHP_triplet/extremum.shp (100%)
 rename {Tests => Overlap/Tests}/Input/Region_2/SHP_triplet/extremum.shx (100%)
 rename {Tests => Overlap/Tests}/Input/Region_2/SHP_triplet/grid_nml.txt (100%)
 rename {Tests => Overlap/Tests}/Input/Region_2/SHP_triplet/ishape_last.txt (100%)
 rename {Tests => Overlap/Tests}/Input/Region_2/SHP_triplet/max_speed_contour.dbf (100%)
 rename {Tests => Overlap/Tests}/Input/Region_2/SHP_triplet/max_speed_contour.shp (100%)
 rename {Tests => Overlap/Tests}/Input/Region_2/SHP_triplet/max_speed_contour.shx (100%)
 rename {Tests => Overlap/Tests}/Input/Region_2/SHP_triplet/outermost_contour.dbf (100%)
 rename {Tests => Overlap/Tests}/Input/Region_2/SHP_triplet/outermost_contour.shp (100%)
 rename {Tests => Overlap/Tests}/Input/Region_2/SHP_triplet/outermost_contour.shx (100%)
 rename {Tests => Overlap/Tests}/Input/Region_2/h.nc (100%)
 rename {Tests => Overlap/Tests}/Input/Region_2/successive_overlap_in.txt (100%)
 rename {Tests => Overlap/Tests}/Input/Region_2/uv.nc (100%)
 rename {Tests => Overlap/Tests}/Input/Region_4/Eddies_region_4/extremum.dbf (100%)
 rename {Tests => Overlap/Tests}/Input/Region_4/Eddies_region_4/extremum.shp (100%)
 rename {Tests => Overlap/Tests}/Input/Region_4/Eddies_region_4/extremum.shx (100%)
 rename {Tests => Overlap/Tests}/Input/Region_4/Eddies_region_4/grid_nml.txt (100%)
 rename {Tests => Overlap/Tests}/Input/Region_4/Eddies_region_4/ishape_last.txt (100%)
 rename {Tests => Overlap/Tests}/Input/Region_4/Eddies_region_4/max_speed_contour.dbf (100%)
 rename {Tests => Overlap/Tests}/Input/Region_4/Eddies_region_4/max_speed_contour.shp (100%)
 rename {Tests => Overlap/Tests}/Input/Region_4/Eddies_region_4/max_speed_contour.shx (100%)
 rename {Tests => Overlap/Tests}/Input/Region_4/Eddies_region_4/outermost_contour.dbf (100%)
 rename {Tests => Overlap/Tests}/Input/Region_4/Eddies_region_4/outermost_contour.shp (100%)
 rename {Tests => Overlap/Tests}/Input/Region_4/Eddies_region_4/outermost_contour.shx (100%)
 rename {Tests => Overlap/Tests}/Input/Region_4/NSODS_in.txt (100%)
 rename {Tests => Overlap/Tests}/Input/Region_4/dt_region_4_2006_01_02.nc (100%)
 rename {Tests => Overlap/Tests}/Input/Region_4/extraction_eddies_stdout.txt (100%)
 rename {Tests => Overlap/Tests}/Input/Region_4/h.nc (100%)
 rename {Tests => Overlap/Tests}/Input/Region_4/non_successive_overlap_in.txt (100%)
 rename {Tests => Overlap/Tests}/Input/Region_4/read_snapshot_nml.txt (100%)
 rename {Tests => Overlap/Tests}/Input/Region_4/uv.nc (100%)
 rename {Tests => Overlap/Tests}/Input/Region_5/NSO_in.txt (100%)
 rename {Tests => Overlap/Tests}/Input/Region_5/SOR5OD_in.txt (100%)
 rename {Tests => Overlap/Tests}/Input/Region_5/SOR5_in.txt (100%)
 rename {Tests => Overlap/Tests}/Input/Region_5/h.nc (100%)
 rename {Tests => Overlap/Tests}/Input/Region_5/uv.nc (100%)
 rename {Tests => Overlap/Tests}/Input/Region_6_SHP_triplet/extremum.dbf (100%)
 rename {Tests => Overlap/Tests}/Input/Region_6_SHP_triplet/extremum.shp (100%)
 rename {Tests => Overlap/Tests}/Input/Region_6_SHP_triplet/extremum.shx (100%)
 rename {Tests => Overlap/Tests}/Input/Region_6_SHP_triplet/grid_nml.txt (100%)
 rename {Tests => Overlap/Tests}/Input/Region_6_SHP_triplet/ishape_last.txt (100%)
 rename {Tests => Overlap/Tests}/Input/Region_6_SHP_triplet/max_speed_contour.dbf (100%)
 rename {Tests => Overlap/Tests}/Input/Region_6_SHP_triplet/max_speed_contour.shp (100%)
 rename {Tests => Overlap/Tests}/Input/Region_6_SHP_triplet/max_speed_contour.shx (100%)
 rename {Tests => Overlap/Tests}/Input/Region_6_SHP_triplet/outermost_contour.dbf (100%)
 rename {Tests => Overlap/Tests}/Input/Region_6_SHP_triplet/outermost_contour.shp (100%)
 rename {Tests => Overlap/Tests}/Input/Region_6_SHP_triplet/outermost_contour.shx (100%)
 rename {Tests => Overlap/Tests}/Input/SODS_in.txt (100%)
 rename {Tests => Overlap/Tests}/Input/empty_outside_points.csv (100%)
 rename {Tests => Overlap/Tests}/Input/example.nc (100%)
 rename {Tests => Overlap/Tests}/Input/good_contour.txt (100%)
 rename {Tests => Overlap/Tests}/Input/good_contour_2.txt (100%)
 rename {Tests => Overlap/Tests}/Input/h_outermost.nc (100%)
 rename {Tests => Overlap/Tests}/Input/h_region_3.nc (100%)
 rename {Tests => Overlap/Tests}/Input/huv_2015_11_29.nc (100%)
 rename {Tests => Overlap/Tests}/Input/inside_4_false_nml.txt (100%)
 rename {Tests => Overlap/Tests}/Input/inside_4_true_nml.txt (100%)
 rename {Tests => Overlap/Tests}/Input/no_good_contour.txt (100%)
 rename {Tests => Overlap/Tests}/Input/outermost_contour_alt.dbf (100%)
 rename {Tests => Overlap/Tests}/Input/outermost_contour_alt.shp (100%)
 rename {Tests => Overlap/Tests}/Input/outermost_contour_alt.shx (100%)
 rename {Tests => Overlap/Tests}/Input/outermost_eddy_5.dbf (100%)
 rename {Tests => Overlap/Tests}/Input/outermost_eddy_5.shp (100%)
 rename {Tests => Overlap/Tests}/Input/outermost_eddy_5.shx (100%)
 rename {Tests => Overlap/Tests}/Input/outside_points_1.csv (100%)
 rename {Tests => Overlap/Tests}/Input/outside_points_2.csv (100%)
 rename {Tests => Overlap/Tests}/Input/successive_overlap_in.txt (100%)
 rename {Tests => Overlap/Tests}/Input/successive_overlap_periodic_in.txt (100%)
 rename {Tests => Overlap/Tests}/Input/tri_square_hole.dbf (100%)
 rename {Tests => Overlap/Tests}/Input/tri_square_hole.shp (100%)
 rename {Tests => Overlap/Tests}/Input/tri_square_hole.shx (100%)
 rename {Tests => Overlap/Tests}/Input/triangle.dbf (100%)
 rename {Tests => Overlap/Tests}/Input/triangle.shp (100%)
 rename {Tests => Overlap/Tests}/Input/triangle.shx (100%)
 rename {Tests => Overlap/Tests}/Input/uv_outermost.nc (100%)
 rename {Tests => Overlap/Tests}/Input/uv_region_3.nc (100%)
 rename {Tests => Overlap/Tests}/Input/write_overlap_delta_3_nml.txt (100%)
 rename {Tests => Overlap/Tests}/Input/write_overlap_different_nml.txt (100%)
 rename {Tests => Overlap/Tests}/Input/write_overlap_shifting_nml.txt (100%)
 create mode 100644 Overlap/Tests/long_tests.json
 rename {Tests => Overlap/Tests}/short_tests.json (59%)
 rename {Tests => Overlap/Tests}/test_get_dispatch_snap.f90 (100%)
 rename {Tests => Overlap/Tests}/test_overlap.f90 (100%)
 rename {Tests => Overlap/Tests}/test_read_eddy.f90 (100%)
 rename {Tests => Overlap/Tests}/test_read_snapshot.f90 (100%)
 rename {Tests => Overlap/Tests}/test_send_recv.f90 (100%)
 rename {Tests => Overlap/Tests}/test_spher_polygon_area.f90 (100%)
 rename {Tests => Overlap/Tests}/test_weight.f90 (100%)
 rename {Tests => Overlap/Tests}/test_write_overlap.f90 (100%)
 rename {Tests => Overlap/Tests}/write_snapshot.f90 (100%)
 rename candidate_overlap.f90 => Overlap/candidate_overlap.f90 (100%)
 rename dispatch_snapshot.f90 => Overlap/dispatch_snapshot.f90 (100%)
 rename eddy_graph.f90 => Overlap/eddy_graph.f90 (100%)
 rename eddy_graph_in.sh => Overlap/eddy_graph_in.sh (100%)
 rename get_snapshot.f90 => Overlap/get_snapshot.f90 (100%)
 rename overlap.f90 => Overlap/overlap.f90 (100%)
 rename read_eddy.f90 => Overlap/read_eddy.f90 (100%)
 rename read_field_indices.f90 => Overlap/read_field_indices.f90 (100%)
 rename read_snapshot.f90 => Overlap/read_snapshot.f90 (100%)
 rename recv_snapshot.f90 => Overlap/recv_snapshot.f90 (100%)
 rename send_snapshot.f90 => Overlap/send_snapshot.f90 (100%)
 rename shp_tr_open.f90 => Overlap/shp_tr_open.f90 (100%)
 rename spher_polygon_area.f90 => Overlap/spher_polygon_area.f90 (100%)
 rename unit_edge_m.f90 => Overlap/unit_edge_m.f90 (100%)
 rename weight.f90 => Overlap/weight.f90 (100%)
 rename write_edge.f90 => Overlap/write_edge.f90 (100%)
 rename write_overlap.f90 => Overlap/write_overlap.f90 (100%)
 delete mode 100644 Tests/CMakeLists.txt
 create mode 100644 short_tests.json
 rename Tests/test_spher_polyline_area.f90 => test_spher_polyline_area.f90 (100%)
 rename Tests/write_extr_map.f90 => write_extr_map.f90 (100%)

diff --git a/Analysis/short_tests.json b/Analysis/short_tests.json
new file mode 100644
index 00000000..8322db41
--- /dev/null
+++ b/Analysis/short_tests.json
@@ -0,0 +1,69 @@
+[
+    {
+	"title": "Report_graph_cyclo",
+	"command":
+	[
+	    "$src_dir/Analysis/report_graph.py", "--gv", "--interp",
+	    "--merging", "cyclo"
+	],
+	"required":
+	[
+	    "$tests_old_dir/EGr2nd15md4np3/edgelist_cyclo.csv",
+	    "$tests_old_dir/EGr2nd15md4np3/SHP_triplet"
+	]
+    },
+    {
+	"title": "Report_graph_anti",
+	"command":
+	[
+	    "$src_dir/Analysis/report_graph.py", "--gv", "--interp",
+	    "--merging", "anti"
+	],
+	"required":
+	[
+	    "$tests_old_dir/EGr2nd15md4np3/edgelist_anti.csv",
+	    "$tests_old_dir/EGr2nd15md4np3/SHP_triplet"
+	]
+    },
+    {
+	"title": "Plot_traj",
+	"command":
+	[
+	    "$src_dir/Analysis/plot_traj.py",
+	    "$src_dir/Tests/Input/Region_2/SHP_triplet", "--save=png"
+	],
+	"required":
+	[
+	    "$tests_old_dir/EGr2nd15md4np3/edgelist_anti.csv",
+	    "$tests_old_dir/EGr2nd15md4np3/edgelist_cyclo.csv",
+	    "$tests_old_dir/EGr2nd15md4np3/SHP_triplet"
+	]
+    },
+    {
+	"title": "Plot_eddy_contours",
+	"command":
+	[
+	    "$src_dir/Analysis/plot_eddy_contours.py",
+	    "$src_dir/Tests/Input/Region_6_SHP_triplet", "--save=png"
+	]
+    },
+    {
+	"title": "Animation",
+	"command":
+	[
+	    "$src_dir/Analysis/plot_eddy_contours.py",
+	    "--anim", "20454", "20455",
+	    "--light", "$src_dir/Tests/Input/Region_6_SHP_triplet"
+	]
+    },
+    {
+	"title": "Plot_eddy_contours_Mat",
+	"description":
+	"plot_eddy_contours.py on a file coming from the Matlab program.",
+	"command":
+	[
+	    "$src_dir/Analysis/plot_eddy_contours.py",
+	    "$tests_old_dir/Mat_v6_to_shapefiles/Snapshot_cyclo", "--save=png"
+	]
+    }
+]    
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 2cde5dea..0c4ebd76 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,49 +1,24 @@
 cmake_minimum_required(VERSION 3.18)
 project(Detection_eddies LANGUAGES Fortran)
 set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR})
-
 find_package(NR_util REQUIRED CONFIG)
 find_package(Jumble REQUIRED CONFIG)
 find_package(NetCDF95 REQUIRED CONFIG)
 find_package(Contour_531 REQUIRED CONFIG)
-find_package(EZMPI REQUIRED CONFIG)
 find_package(Shapelib_03 REQUIRED CONFIG)
 find_package(Geometry REQUIRED CONFIG)
 find_package(Numer_Rec_95 REQUIRED CONFIG)
-find_package(GPC_F REQUIRED CONFIG)
 find_package(NetCDF REQUIRED)
 include(FindPkgConfig)
 pkg_check_modules(netcdf-fortran IMPORTED_TARGET netcdf-fortran)
-
 find_path(fortrangis_INCLUDE_DIR shapelib.mod REQUIRED)
-
-add_executable(inst_eddies inst_eddies.f90 write_eddy.f90
-  local_extrema.f90 set_max_speed.f90 get_1_outerm.f90 max_speed_contour_ssh.f90
-  good_contour.f90 spher_polyline_area.f90 mean_speed.f90 inside_4.f90
-  set_all_outerm.f90 derived_types.f90 shp_tr_create.f90 nearby_extr.f90
-  get_var.f90 shp_tr_close.f90)
-
-target_include_directories(inst_eddies PRIVATE
-  ${fortrangis_INCLUDE_DIR})
-
-target_link_libraries(inst_eddies PRIVATE contour_531 geometry netcdf95
-  shapelib_03 numer_rec_95 nr_util jumble)
-
-add_executable(eddy_graph eddy_graph.f90 shp_tr_open.f90
-  shp_tr_create.f90 get_snapshot.f90 overlap.f90 dispatch_snapshot.f90
-  shp_tr_close.f90 read_field_indices.f90 read_snapshot.f90
-  recv_snapshot.f90 candidate_overlap.f90 spher_polygon_area.f90
-  spher_polyline_area.f90 write_overlap.f90 weight.f90
-  send_snapshot.f90 read_eddy.f90 write_eddy.f90 derived_types.f90
-  unit_edge_m.f90 write_edge.f90)
-
-target_include_directories(eddy_graph PRIVATE ${fortrangis_INCLUDE_DIR})
-
-target_link_libraries(eddy_graph PRIVATE ezmpi jumble shapelib_03
-  contour_531 gpc_f geometry nr_util)
-
-include(Tests/CMakeLists.txt)
 include(ConfigureCompilerFlags)  
 include(TAGS)
-configure_file(eddy_graph_in.sh eddy_graph.sh @ONLY)
-execute_process(COMMAND chmod -w eddy_graph.sh)
+add_subdirectory(Inst_eddies)
+add_subdirectory(Overlap)
+
+add_executable(test_spher_polyline_area
+  ${CMAKE_SOURCE_DIR}/spher_polyline_area.f90
+  ${CMAKE_CURRENT_LIST_DIR}/test_spher_polyline_area.f90)
+
+target_link_libraries(test_spher_polyline_area geometry contour_531 nr_util)
diff --git a/Convert_Matlab/short_tests.json b/Convert_Matlab/short_tests.json
new file mode 100644
index 00000000..771dce66
--- /dev/null
+++ b/Convert_Matlab/short_tests.json
@@ -0,0 +1,40 @@
+[
+    {
+	"title": "Graph_from_Matlab_v6_cyclo",
+	"command": ["$src_dir/Convert_Matlab/overlap_v6.py", "cyclo"],
+	"required":
+	[
+	    "$src_dir/Tests/Input/Eurec4A_OA/id_child_cyclo.mat",
+	    "$src_dir/Tests/Input/Eurec4A_OA/Ncyclo.mat",
+	    "$src_dir/Tests/Input/Eurec4A_OA/date_num.mat"
+	]
+    },
+    {
+	"title": "Graph_from_Matlab_v6_anti",
+	"command": ["$src_dir/Convert_Matlab/overlap_v6.py", "anti"],
+	"required":
+	[
+	    "$src_dir/Tests/Input/Eurec4A_OA/id_child_anti.mat",
+	    "$src_dir/Tests/Input/Eurec4A_OA/Nanti.mat",
+	    "$src_dir/Tests/Input/Eurec4A_OA/date_num.mat"
+	]
+    },
+    {
+	"title": "Mat_v6_to_shapefiles",
+	"command":
+	[
+	    "$src_dir/Convert_Matlab/inst_eddies_v6.py",
+	    "/data/lmd-oce/EUREC4A_OA/DATA_SAT_NewExport_Atalante/TOEddies/Eddies/adt_2019-12-15.mat",
+	    "2019-12-16"
+	],
+	"required": ["$src_dir/Convert_Matlab/inst_eddies.m"]
+    },
+    {
+	"title": "Mat_HDF5_to_shapefiles",
+	"command":
+	[
+	    "$src_dir/Convert_Matlab/inst_eddies_HDF5.py",
+	    "$src_dir/Tests/Input/Eurec4A_OA/adt_2019-12-15.mat"
+	]
+    }
+]    
diff --git a/Inst_eddies/CMakeLists.txt b/Inst_eddies/CMakeLists.txt
new file mode 100644
index 00000000..5af01bad
--- /dev/null
+++ b/Inst_eddies/CMakeLists.txt
@@ -0,0 +1,16 @@
+add_executable(inst_eddies inst_eddies.f90
+  ${CMAKE_SOURCE_DIR}/write_eddy.f90 local_extrema.f90
+  set_max_speed.f90 get_1_outerm.f90 max_speed_contour_ssh.f90
+  good_contour.f90 ${CMAKE_SOURCE_DIR}/spher_polyline_area.f90
+  mean_speed.f90 inside_4.f90 set_all_outerm.f90
+  ${CMAKE_SOURCE_DIR}/derived_types.f90
+  ${CMAKE_SOURCE_DIR}/shp_tr_create.f90 nearby_extr.f90 get_var.f90
+  ${CMAKE_SOURCE_DIR}/shp_tr_close.f90)
+
+target_include_directories(inst_eddies PRIVATE
+  ${fortrangis_INCLUDE_DIR})
+
+target_link_libraries(inst_eddies PRIVATE contour_531 geometry netcdf95
+  shapelib_03 numer_rec_95 nr_util jumble)
+
+include(Tests/CMakeLists.txt)
diff --git a/Inst_eddies/Tests/CMakeLists.txt b/Inst_eddies/Tests/CMakeLists.txt
new file mode 100644
index 00000000..a4284803
--- /dev/null
+++ b/Inst_eddies/Tests/CMakeLists.txt
@@ -0,0 +1,103 @@
+# test_get_1_outerm
+
+add_executable(test_get_1_outerm good_contour.f90
+  ${CMAKE_SOURCE_DIR}/derived_types.f90 get_1_outerm.f90
+  ${CMAKE_SOURCE_DIR}/spher_polyline_area.f90
+  ${CMAKE_CURRENT_LIST_DIR}/test_get_1_outerm.f90)
+
+target_link_libraries(test_get_1_outerm geometry netcdf95 shapelib_03
+  contour_531 nr_util jumble)
+
+target_include_directories(test_get_1_outerm PRIVATE
+  ${fortrangis_INCLUDE_DIR})
+
+# test_set_all_outerm
+
+add_executable(test_set_all_outerm
+  ${CMAKE_SOURCE_DIR}/derived_types.f90 set_all_outerm.f90
+  local_extrema.f90 get_1_outerm.f90 good_contour.f90
+  ${CMAKE_SOURCE_DIR}/spher_polyline_area.f90 nearby_extr.f90
+  get_var.f90 ${CMAKE_CURRENT_LIST_DIR}/test_set_all_outerm.f90)
+
+target_link_libraries(test_set_all_outerm geometry netcdf95
+  numer_rec_95 shapelib_03 contour_531 jumble nr_util)
+
+target_include_directories(test_set_all_outerm PRIVATE
+  ${fortrangis_INCLUDE_DIR})
+
+# test_good_contour
+
+add_executable(test_good_contour good_contour.f90
+  ${CMAKE_CURRENT_LIST_DIR}/test_good_contour.f90)
+
+target_link_libraries(test_good_contour geometry netcdf95 shapelib_03
+  contour_531 jumble nr_util)
+
+target_include_directories(test_good_contour PRIVATE
+  ${fortrangis_INCLUDE_DIR})
+
+# test_inside_4
+
+add_executable(test_inside_4 inside_4.f90
+  ${CMAKE_CURRENT_LIST_DIR}/test_inside_4.f90)
+
+target_link_libraries(test_inside_4 geometry shapelib_03 jumble)
+target_include_directories(test_inside_4 PRIVATE ${fortrangis_INCLUDE_DIR})
+
+# test_mean_speed
+
+add_executable(test_mean_speed mean_speed.f90
+  ${CMAKE_CURRENT_LIST_DIR}/test_mean_speed.f90)
+
+target_link_libraries(test_mean_speed numer_rec_95 netcdf95
+  shapelib_03 contour_531 nr_util)
+
+target_include_directories(test_mean_speed PRIVATE
+  ${fortrangis_INCLUDE_DIR})
+
+# test_max_speed_contour_ssh
+
+add_executable(test_max_speed_contour_ssh
+  ${CMAKE_SOURCE_DIR}/derived_types.f90 max_speed_contour_ssh.f90
+  get_var.f90
+  ${CMAKE_CURRENT_LIST_DIR}/test_max_speed_contour_ssh.f90)
+
+target_link_libraries(test_max_speed_contour_ssh netcdf95 contour_531
+  jumble nr_util)
+
+target_include_directories(test_max_speed_contour_ssh PRIVATE
+  ${fortrangis_INCLUDE_DIR})
+
+# test_nearby_extr
+
+add_executable(test_nearby_extr nearby_extr.f90
+  ${CMAKE_SOURCE_DIR}/derived_types.f90
+  ${CMAKE_CURRENT_LIST_DIR}/test_nearby_extr.f90)
+
+target_link_libraries(test_nearby_extr netcdf95 shapelib_03
+  contour_531 jumble nr_util)
+
+target_include_directories(test_nearby_extr PRIVATE
+  ${fortrangis_INCLUDE_DIR})
+
+# test_local_extrema
+
+add_executable(test_local_extrema local_extrema.f90
+  ${CMAKE_CURRENT_LIST_DIR}/test_local_extrema.f90
+  ${CMAKE_SOURCE_DIR}/write_extr_map.f90)
+
+target_link_libraries(test_local_extrema netcdf95 nr_util jumble)
+
+# test_set_max_speed
+
+add_executable(test_set_max_speed
+  ${CMAKE_SOURCE_DIR}/derived_types.f90 set_max_speed.f90
+  good_contour.f90 max_speed_contour_ssh.f90 mean_speed.f90
+  ${CMAKE_SOURCE_DIR}/spher_polyline_area.f90 inside_4.f90
+  ${CMAKE_CURRENT_LIST_DIR}/test_set_max_speed.f90)
+
+target_link_libraries(test_set_max_speed geometry numer_rec_95
+  netcdf95 shapelib_03 contour_531 jumble nr_util)
+
+target_include_directories(test_set_max_speed PRIVATE ${fortrangis_INCLUDE_DIR})
+
diff --git a/Tests/long_tests.json b/Inst_eddies/Tests/long_tests.json
similarity index 79%
rename from Tests/long_tests.json
rename to Inst_eddies/Tests/long_tests.json
index 193c3e75..b5d17726 100644
--- a/Tests/long_tests.json
+++ b/Inst_eddies/Tests/long_tests.json
@@ -29,17 +29,5 @@
 		     "$src_dir/Tests/Input/Region_5/uv.nc"],
 	"input": "&main_nml /\n",
 	"description": "Same as Extraction_eddies_region_4 with larger domain."
-    },
-    {
-        "input": "&MAIN_NML max_delta = 4 /\n",
-        "title": "EGg",
-        "stdout": "eddy_graph_stdout.txt",
-        "command": [
-            "env",
-            "mpiexec=$mpiexec",
-            "$build_dir/eddy_graph.sh",
-            "1",
-            "$large_input_dir/SHP_triplet_global"
-        ]
     }
-]
+]    
diff --git a/Inst_eddies/Tests/short_tests.json b/Inst_eddies/Tests/short_tests.json
new file mode 100644
index 00000000..de0fb286
--- /dev/null
+++ b/Inst_eddies/Tests/short_tests.json
@@ -0,0 +1,358 @@
+[
+    {
+        "input": "&main_nml /\n",
+        "title": "Get_1_outerm",
+        "required": [
+            "$src_dir/Tests/Input/Region_1/h.nc",
+            [
+                "$src_dir/Tests/Input/Region_1/outside_points_get_1_outerm.csv",
+                "outside_points.csv"
+            ]
+        ],
+        "command": "$build_dir/test_get_1_outerm"
+    },
+    {
+        "description": "Assume insufficient amplitude for extrema 2 and 8. Even if extremum 8 does not have a particularly small amplitude, we just want to see the target extremum, 6, grow its outermost contour compared to the case without minimum amplitude.",
+        "input": "&main_nml /\n",
+        "title": "Get_1_outerm_noise_2_8",
+        "required": [
+            "$src_dir/Tests/Input/Region_1/h.nc",
+            "$src_dir/Tests/Input/Region_1/outside_points.csv"
+        ],
+        "command": "$build_dir/test_get_1_outerm"
+    },
+    {
+        "description": "Negative value for extremum 2.",
+        "input": "&main_nml /\n",
+        "title": "Get_1_outerm_noise_2",
+        "required": [
+            "$src_dir/Tests/Input/Region_1/h.nc",
+            [
+                "$src_dir/Tests/Input/Region_1/outside_points_get_1_outerm_noise_2.csv",
+                "outside_points.csv"
+            ]
+        ],
+        "command": "$build_dir/test_get_1_outerm"
+    },
+    {
+        "description": "3 contours at that level. 2 contain the inside point, one of which contains the 2 outside points.",
+        "required": [
+            [
+                "$src_dir/Tests/Input/outside_points_1.csv",
+                "outside_points.csv"
+            ]
+        ],
+        "title": "Good_contour",
+        "command": [
+            "$build_dir/test_good_contour",
+            "$src_dir/Tests/Input/example.nc"
+        ],
+        "stdin_filename": "$src_dir/Tests/Input/good_contour.txt"
+    },
+    {
+        "description": "Select another good contour. Case where one of the contours tested does not contain inside point.",
+        "required": [
+            [
+                "$src_dir/Tests/Input/outside_points_2.csv",
+                "outside_points.csv"
+            ]
+        ],
+        "title": "Good_contour_2",
+        "command": [
+            "$build_dir/test_good_contour",
+            "$src_dir/Tests/Input/example.nc"
+        ],
+        "stdin_filename": "$src_dir/Tests/Input/good_contour_2.txt"
+    },
+    {
+        "required": [
+            [
+                "$src_dir/Tests/Input/outside_points_1.csv",
+                "outside_points.csv"
+            ]
+        ],
+        "title": "No_good_contour",
+        "command": [
+            "$build_dir/test_good_contour",
+            "$src_dir/Tests/Input/example.nc"
+        ],
+        "stdin_filename": "$src_dir/Tests/Input/no_good_contour.txt"
+    },
+    {
+        "stdin_filename": "$src_dir/Tests/Input/inside_4_true_nml.txt",
+        "title": "Inside_4_true",
+        "command": [
+            "$build_dir/test_inside_4",
+            "$src_dir/Tests/Input/outermost_eddy_5"
+        ]
+    },
+    {
+        "stdin_filename": "$src_dir/Tests/Input/inside_4_false_nml.txt",
+        "title": "Inside_4_false",
+        "command": [
+            "$build_dir/test_inside_4",
+            "$src_dir/Tests/Input/outermost_eddy_5"
+        ]
+    },
+    {
+        "input": "f",
+        "title": "Local_extrema",
+        "command": [
+            "$build_dir/test_local_extrema",
+            "$src_dir/Tests/Input/Region_1/h.nc"
+        ]
+    },
+    {
+        "description": "With a larger region than in test Local_extrema.",
+        "input": "f",
+        "title": "Local_extrema_larger",
+        "command": [
+            "$build_dir/test_local_extrema",
+            "$src_dir/Tests/Input/Region_2/h.nc"
+        ]
+    },
+    {
+        "input": "f\n",
+        "description": "With input file containing missing values.",
+        "title": "Local_extrema_missing",
+        "command": [
+            "$build_dir/test_local_extrema",
+            "$src_dir/Tests/Input/Region_4/h.nc"
+        ]
+    },
+    {
+        "description": "Same as Local_extrema but with periodicity. The data is actually regional so there is a discontinuity in the field and the longitude grid assuming periodicity is not regular.",
+        "input": "t\n",
+        "title": "Local_extrema_periodic",
+        "command": [
+            "$build_dir/test_local_extrema",
+            "$src_dir/Tests/Input/Region_1/h.nc"
+        ]
+    },
+    {
+        "description": "The data is really global so there is no discontinuity in the field and the longitude grid assuming periodicity is regular.",
+        "input": "t\n",
+        "title": "Local_extrema_periodic_2",
+        "command": [
+            "$build_dir/test_local_extrema",
+            "$src_dir/Tests/Input/Global/h_2006_01_01_coarse.nc"
+        ]
+    },
+    {
+        "input": "&main_nml /\n",
+        "title": "Max_speed_contour_ssh",
+        "command": [
+            "$build_dir/test_max_speed_contour_ssh",
+            "$src_dir/Tests/Input/Region_1/h.nc",
+            "$src_dir/Tests/Input/Region_1/uv.nc"
+        ]
+    },
+    {
+        "description": "direction = 2",
+        "input": "&main_nml IND_EXTR= 4,14/\n",
+        "title": "Max_speed_contour_ssh_north",
+        "command": [
+            "$build_dir/test_max_speed_contour_ssh",
+            "$src_dir/Tests/Input/Region_1/h.nc",
+            "$src_dir/Tests/Input/Region_1/uv.nc"
+        ]
+    },
+    {
+        "description": "Missing value in speed.",
+        "input": "&main_nml IND_EXTR= 3, 4/\n",
+        "title": "Max_speed_contour_ssh_missing",
+        "command": [
+            "$build_dir/test_max_speed_contour_ssh",
+            "$src_dir/Tests/Input/huv_2015_11_29.nc",
+            "$src_dir/Tests/Input/huv_2015_11_29.nc"
+        ]
+    },
+    {
+        "input": "&main_nml /\n",
+        "title": "Mean_speed",
+        "required": [
+            "$src_dir/Tests/Input/Region_1/uv.nc",
+            [
+                "$src_dir/Tests/Input/Get_1_outerm/test_get_1_outerm.shp",
+                "contour.shp"
+            ],
+            [
+                "$src_dir/Tests/Input/Get_1_outerm/test_get_1_outerm.dbf",
+                "contour.dbf"
+            ],
+            [
+                "$src_dir/Tests/Input/Get_1_outerm/test_get_1_outerm.shx",
+                "contour.shx"
+            ]
+        ],
+        "command": "$build_dir/test_mean_speed"
+    },
+    {
+        "input": "&main_nml /\n",
+        "title": "Mean_speed_alt",
+        "required": [
+            "$src_dir/Tests/Input/Region_1/uv.nc",
+            [
+                "$src_dir/Tests/Input/outermost_contour_alt.shp",
+                "contour.shp"
+            ],
+            [
+                "$src_dir/Tests/Input/outermost_contour_alt.dbf",
+                "contour.dbf"
+            ],
+            [
+                "$src_dir/Tests/Input/outermost_contour_alt.shx",
+                "contour.shx"
+            ]
+        ],
+        "command": "$build_dir/test_mean_speed"
+    },
+    {
+        "input": "&main_nml /\n",
+        "required": [
+            [
+                "$src_dir/Tests/Input/h_outermost.nc",
+                "h.nc"
+            ],
+            [
+                "$src_dir/Tests/Input/uv_outermost.nc",
+                "uv.nc"
+            ],
+            [
+                "$src_dir/Tests/Input/empty_outside_points.csv",
+                "outside_points.csv"
+            ],
+            "$src_dir/Tests/Input/Get_1_outerm/test_get_1_outerm.*"
+        ],
+        "title": "Set_max_speed",
+        "command": "$build_dir/test_set_max_speed"
+    },
+    {
+        "input": "&MAIN_NML IND_TARG_EXTR=19,11 /\n",
+        "required": [
+            "$src_dir/Tests/Input/Region_1/h.nc",
+            "$src_dir/Tests/Input/Region_1/uv.nc",
+            "$src_dir/Tests/Input/Region_1/outside_points.csv",
+            "$src_dir/Tests/Input/Get_1_outerm_noise_2_8/test_get_1_outerm.*"
+        ],
+        "title": "Set_max_speed_noise",
+        "command": "$build_dir/test_set_max_speed"
+    },
+    {
+        "input": "&main_nml min_amp = 0./\n",
+        "required": [
+            "$src_dir/Tests/Input/Region_1/h.nc",
+            "$src_dir/Tests/Input/Region_1/uv.nc"
+        ],
+        "title": "Extraction_eddies_region_1",
+        "commands": [
+            [
+                "mkdir",
+                "SHP_triplet"
+            ],
+            "$build_dir/inst_eddies"
+        ]
+    },
+    {
+        "description": "Same as Extraction_eddies_region_1 but with non-zero minimal amplitude.",
+        "input": "&main_nml /\n",
+        "required": [
+            "$src_dir/Tests/Input/Region_1/h.nc",
+            "$src_dir/Tests/Input/Region_1/uv.nc"
+        ],
+        "title": "Extraction_eddies_region_1_noise",
+        "commands": [
+            [
+                "mkdir",
+                "SHP_triplet"
+            ],
+            "$build_dir/inst_eddies"
+        ]
+    },
+    {
+        "input": "&main_nml min_amp = 0./\n",
+        "required": [
+            "$src_dir/Tests/Input/Region_2/h.nc",
+            "$src_dir/Tests/Input/Region_2/uv.nc"
+        ],
+        "title": "Extraction_eddies_region_2",
+        "commands": [
+            [
+                "mkdir",
+                "SHP_triplet"
+            ],
+            "$build_dir/inst_eddies"
+        ]
+    },
+    {
+        "input": "&main_nml /\n",
+        "required": [
+            "$src_dir/Tests/Input/Region_2/h.nc",
+            "$src_dir/Tests/Input/Region_2/uv.nc"
+        ],
+        "title": "Extraction_eddies_region_2_noise",
+        "commands": [
+            [
+                "mkdir",
+                "SHP_triplet"
+            ],
+            "$build_dir/inst_eddies"
+        ]
+    },
+    {
+        "description": "Part of the domain has missing values.",
+        "input": "&main_nml /\n",
+        "required": [
+            "$src_dir/Tests/Input/Region_4/h.nc",
+            "$src_dir/Tests/Input/Region_4/uv.nc"
+        ],
+        "title": "Extraction_eddies_region_4",
+        "commands": [
+            [
+                "mkdir",
+                "SHP_triplet"
+            ],
+            "$build_dir/inst_eddies"
+        ]
+    },
+    {
+        "required": [
+            "$src_dir/Tests/Input/Region_1/SHP_triplet_noise/extremum.*",
+            "$src_dir/Tests/Input/Region_1/SHP_triplet_noise/ishape_last.txt",
+            "$src_dir/Tests/Input/Region_1/Local_extrema/extr_map.nc"
+        ],
+        "title": "Nearby_extr",
+        "command": "$build_dir/test_nearby_extr"
+    },
+    {
+        "description": "test_set_all_outerm with periodicity.",
+        "input": "&main_nml MAX_RADIUS = 4, 4/\n",
+        "title": "Set_all_outerm_periodic",
+        "command": [
+            "$build_dir/test_set_all_outerm",
+            "$src_dir/Tests/Input/Global/h_2006_01_01_coarse.nc"
+        ]
+    },
+    {
+        "description": "Periodic domain.",
+        "input": "&main_nml min_amp = 0., MAX_RADIUS = 4, 4/\n",
+        "required": [
+            [
+                "$src_dir/Tests/Input/Global/h_2006_01_01_coarse.nc",
+                "h.nc"
+            ],
+            [
+                "$src_dir/Tests/Input/Global/uv_2006_01_01_coarse.nc",
+                "uv.nc"
+            ]
+        ],
+        "title": "Extraction_eddies_periodic",
+        "commands": [
+            [
+                "mkdir",
+                "SHP_triplet"
+            ],
+            "$build_dir/inst_eddies"
+        ]
+    },
+]
diff --git a/Tests/test_get_1_outerm.f90 b/Inst_eddies/Tests/test_get_1_outerm.f90
similarity index 100%
rename from Tests/test_get_1_outerm.f90
rename to Inst_eddies/Tests/test_get_1_outerm.f90
diff --git a/Tests/test_good_contour.f90 b/Inst_eddies/Tests/test_good_contour.f90
similarity index 100%
rename from Tests/test_good_contour.f90
rename to Inst_eddies/Tests/test_good_contour.f90
diff --git a/Tests/test_inside_4.f90 b/Inst_eddies/Tests/test_inside_4.f90
similarity index 100%
rename from Tests/test_inside_4.f90
rename to Inst_eddies/Tests/test_inside_4.f90
diff --git a/Tests/test_local_extrema.f90 b/Inst_eddies/Tests/test_local_extrema.f90
similarity index 100%
rename from Tests/test_local_extrema.f90
rename to Inst_eddies/Tests/test_local_extrema.f90
diff --git a/Tests/test_local_extrema.py b/Inst_eddies/Tests/test_local_extrema.py
similarity index 100%
rename from Tests/test_local_extrema.py
rename to Inst_eddies/Tests/test_local_extrema.py
diff --git a/Tests/test_max_speed_contour_ssh.f90 b/Inst_eddies/Tests/test_max_speed_contour_ssh.f90
similarity index 100%
rename from Tests/test_max_speed_contour_ssh.f90
rename to Inst_eddies/Tests/test_max_speed_contour_ssh.f90
diff --git a/Tests/test_mean_speed.f90 b/Inst_eddies/Tests/test_mean_speed.f90
similarity index 100%
rename from Tests/test_mean_speed.f90
rename to Inst_eddies/Tests/test_mean_speed.f90
diff --git a/Tests/test_mean_speed.py b/Inst_eddies/Tests/test_mean_speed.py
similarity index 100%
rename from Tests/test_mean_speed.py
rename to Inst_eddies/Tests/test_mean_speed.py
diff --git a/Tests/test_nearby_extr.f90 b/Inst_eddies/Tests/test_nearby_extr.f90
similarity index 100%
rename from Tests/test_nearby_extr.f90
rename to Inst_eddies/Tests/test_nearby_extr.f90
diff --git a/Tests/test_set_all_outerm.f90 b/Inst_eddies/Tests/test_set_all_outerm.f90
similarity index 100%
rename from Tests/test_set_all_outerm.f90
rename to Inst_eddies/Tests/test_set_all_outerm.f90
diff --git a/Tests/test_set_max_speed.f90 b/Inst_eddies/Tests/test_set_max_speed.f90
similarity index 100%
rename from Tests/test_set_max_speed.f90
rename to Inst_eddies/Tests/test_set_max_speed.f90
diff --git a/get_1_outerm.f90 b/Inst_eddies/get_1_outerm.f90
similarity index 100%
rename from get_1_outerm.f90
rename to Inst_eddies/get_1_outerm.f90
diff --git a/get_var.f90 b/Inst_eddies/get_var.f90
similarity index 100%
rename from get_var.f90
rename to Inst_eddies/get_var.f90
diff --git a/good_contour.f90 b/Inst_eddies/good_contour.f90
similarity index 100%
rename from good_contour.f90
rename to Inst_eddies/good_contour.f90
diff --git a/inside_4.f90 b/Inst_eddies/inside_4.f90
similarity index 100%
rename from inside_4.f90
rename to Inst_eddies/inside_4.f90
diff --git a/inst_eddies.f90 b/Inst_eddies/inst_eddies.f90
similarity index 100%
rename from inst_eddies.f90
rename to Inst_eddies/inst_eddies.f90
diff --git a/local_extrema.f90 b/Inst_eddies/local_extrema.f90
similarity index 100%
rename from local_extrema.f90
rename to Inst_eddies/local_extrema.f90
diff --git a/max_speed_contour_ssh.f90 b/Inst_eddies/max_speed_contour_ssh.f90
similarity index 100%
rename from max_speed_contour_ssh.f90
rename to Inst_eddies/max_speed_contour_ssh.f90
diff --git a/mean_speed.f90 b/Inst_eddies/mean_speed.f90
similarity index 100%
rename from mean_speed.f90
rename to Inst_eddies/mean_speed.f90
diff --git a/nearby_extr.f90 b/Inst_eddies/nearby_extr.f90
similarity index 100%
rename from nearby_extr.f90
rename to Inst_eddies/nearby_extr.f90
diff --git a/set_all_outerm.f90 b/Inst_eddies/set_all_outerm.f90
similarity index 100%
rename from set_all_outerm.f90
rename to Inst_eddies/set_all_outerm.f90
diff --git a/set_max_speed.f90 b/Inst_eddies/set_max_speed.f90
similarity index 100%
rename from set_max_speed.f90
rename to Inst_eddies/set_max_speed.f90
diff --git a/Overlap/CMakeLists.txt b/Overlap/CMakeLists.txt
new file mode 100644
index 00000000..e3569b1e
--- /dev/null
+++ b/Overlap/CMakeLists.txt
@@ -0,0 +1,22 @@
+find_package(EZMPI REQUIRED CONFIG)
+find_package(GPC_F REQUIRED CONFIG)
+
+add_executable(eddy_graph eddy_graph.f90 shp_tr_open.f90
+  ${CMAKE_SOURCE_DIR}/shp_tr_create.f90 get_snapshot.f90 overlap.f90
+  dispatch_snapshot.f90 ${CMAKE_SOURCE_DIR}/shp_tr_close.f90
+  read_field_indices.f90 read_snapshot.f90 recv_snapshot.f90
+  candidate_overlap.f90 spher_polygon_area.f90
+  ${CMAKE_SOURCE_DIR}/spher_polyline_area.f90 write_overlap.f90
+  weight.f90 send_snapshot.f90 read_eddy.f90
+  ${CMAKE_SOURCE_DIR}/write_eddy.f90
+  ${CMAKE_SOURCE_DIR}/derived_types.f90 unit_edge_m.f90
+  write_edge.f90)
+
+target_include_directories(eddy_graph PRIVATE ${fortrangis_INCLUDE_DIR})
+
+target_link_libraries(eddy_graph PRIVATE ezmpi jumble shapelib_03
+  contour_531 gpc_f geometry nr_util)
+
+configure_file(eddy_graph_in.sh eddy_graph.sh @ONLY)
+execute_process(COMMAND chmod -w ${CMAKE_CURRENT_BINARY_DIR}/eddy_graph.sh)
+include(Tests/CMakeLists.txt)
diff --git a/Overlap/Tests/CMakeLists.txt b/Overlap/Tests/CMakeLists.txt
new file mode 100644
index 00000000..f4be416e
--- /dev/null
+++ b/Overlap/Tests/CMakeLists.txt
@@ -0,0 +1,116 @@
+# test_overlap
+
+add_executable(test_overlap ${CMAKE_SOURCE_DIR}/derived_types.f90
+  overlap.f90 read_snapshot.f90 spher_polygon_area.f90
+  ${CMAKE_SOURCE_DIR}/spher_polyline_area.f90 weight.f90 read_eddy.f90
+  read_field_indices.f90 candidate_overlap.f90
+  ${CMAKE_SOURCE_DIR}/write_eddy.f90
+  ${CMAKE_SOURCE_DIR}/shp_tr_create.f90 write_overlap.f90
+  ${CMAKE_CURRENT_LIST_DIR}/test_overlap.f90 shp_tr_open.f90
+  ${CMAKE_SOURCE_DIR}/shp_tr_close.f90 unit_edge_m.f90 write_edge.f90)
+
+target_link_libraries(test_overlap shapelib_03 geometry contour_531
+  gpc_f ezmpi nr_util jumble)
+
+target_include_directories(test_overlap PRIVATE ${fortrangis_INCLUDE_DIR})
+
+# test_read_snapshot
+
+add_executable(test_read_snapshot
+  ${CMAKE_SOURCE_DIR}/derived_types.f90
+  ${CMAKE_SOURCE_DIR}/shp_tr_create.f90 read_snapshot.f90
+  ${CMAKE_SOURCE_DIR}/write_eddy.f90 read_eddy.f90
+  read_field_indices.f90
+  ${CMAKE_CURRENT_LIST_DIR}/test_read_snapshot.f90
+  ${CMAKE_SOURCE_DIR}/write_extr_map.f90
+  ${CMAKE_CURRENT_LIST_DIR}/write_snapshot.f90 shp_tr_open.f90
+  ${CMAKE_SOURCE_DIR}/shp_tr_close.f90)
+
+target_link_libraries(test_read_snapshot netcdf95 shapelib_03
+  contour_531 gpc_f ezmpi nr_util jumble)
+
+target_include_directories(test_read_snapshot PRIVATE
+  ${fortrangis_INCLUDE_DIR})
+
+# test_spher_polygon_area
+
+add_executable(test_spher_polygon_area spher_polygon_area.f90
+  ${CMAKE_SOURCE_DIR}/spher_polyline_area.f90
+  ${CMAKE_CURRENT_LIST_DIR}/test_spher_polygon_area.f90)
+
+target_link_libraries(test_spher_polygon_area geometry shapelib_03
+  jumble gpc_f nr_util)
+
+target_include_directories(test_spher_polygon_area PRIVATE
+  ${fortrangis_INCLUDE_DIR})
+
+# test_weight
+
+add_executable(test_weight weight.f90 ${CMAKE_SOURCE_DIR}/derived_types.f90
+  ${CMAKE_CURRENT_LIST_DIR}/test_weight.f90)
+
+target_link_libraries(test_weight contour_531 nr_util)
+target_include_directories(test_weight PRIVATE ${fortrangis_INCLUDE_DIR})
+  
+# test_read_eddy
+
+add_executable(test_read_eddy ${CMAKE_SOURCE_DIR}/derived_types.f90
+  ${CMAKE_SOURCE_DIR}/shp_tr_create.f90 read_eddy.f90
+  ${CMAKE_SOURCE_DIR}/write_eddy.f90 read_field_indices.f90
+  ${CMAKE_CURRENT_LIST_DIR}/test_read_eddy.f90 shp_tr_open.f90
+  ${CMAKE_SOURCE_DIR}/shp_tr_close.f90)
+
+target_link_libraries(test_read_eddy shapelib_03 contour_531 gpc_f
+  ezmpi nr_util)
+
+target_include_directories(test_read_eddy PRIVATE ${fortrangis_INCLUDE_DIR})
+
+# test_write_overlap
+
+add_executable(test_write_overlap
+  ${CMAKE_SOURCE_DIR}/derived_types.f90
+  ${CMAKE_SOURCE_DIR}/shp_tr_create.f90
+  ${CMAKE_SOURCE_DIR}/write_eddy.f90 write_overlap.f90
+  ${CMAKE_CURRENT_LIST_DIR}/test_write_overlap.f90
+  ${CMAKE_SOURCE_DIR}/shp_tr_close.f90 unit_edge_m.f90 write_edge.f90)
+
+target_link_libraries(test_write_overlap shapelib_03 contour_531 nr_util jumble)
+target_include_directories(test_write_overlap PRIVATE ${fortrangis_INCLUDE_DIR})
+
+# test_send_recv
+
+find_package(MPI REQUIRED)
+
+add_executable(test_send_recv
+  ${CMAKE_CURRENT_LIST_DIR}/test_send_recv.f90 send_snapshot.f90
+  recv_snapshot.f90 read_field_indices.f90 read_snapshot.f90
+  ${CMAKE_SOURCE_DIR}/write_eddy.f90
+  ${CMAKE_SOURCE_DIR}/shp_tr_create.f90 read_eddy.f90
+  ${CMAKE_CURRENT_LIST_DIR}/write_snapshot.f90
+  ${CMAKE_SOURCE_DIR}/write_extr_map.f90
+  ${CMAKE_SOURCE_DIR}/derived_types.f90 shp_tr_open.f90
+  ${CMAKE_SOURCE_DIR}/shp_tr_close.f90)
+
+target_link_libraries(test_send_recv PRIVATE MPI::MPI_Fortran
+  shapelib_03 ezmpi nr_util contour_531 gpc_f netcdf95 jumble)
+
+target_include_directories(test_send_recv PRIVATE
+  ${fortrangis_INCLUDE_DIR})
+
+# test_get_dispatch_snap
+
+add_executable(test_get_dispatch_snap
+  ${CMAKE_CURRENT_LIST_DIR}/test_get_dispatch_snap.f90
+  get_snapshot.f90 dispatch_snapshot.f90 read_field_indices.f90
+  ${CMAKE_CURRENT_LIST_DIR}/write_snapshot.f90 read_snapshot.f90
+  recv_snapshot.f90 ${CMAKE_SOURCE_DIR}/shp_tr_create.f90
+  ${CMAKE_SOURCE_DIR}/write_eddy.f90
+  ${CMAKE_SOURCE_DIR}/write_extr_map.f90 read_eddy.f90
+  send_snapshot.f90 ${CMAKE_SOURCE_DIR}/derived_types.f90
+  shp_tr_open.f90 ${CMAKE_SOURCE_DIR}/shp_tr_close.f90)
+
+target_link_libraries(test_get_dispatch_snap shapelib_03 jumble contour_531
+  ezmpi netcdf95 gpc_f nr_util)
+
+target_include_directories(test_get_dispatch_snap PRIVATE
+  ${fortrangis_INCLUDE_DIR})
diff --git a/Tests/Input/Eurec4A_OA/Nanti.mat b/Overlap/Tests/Input/Eurec4A_OA/Nanti.mat
similarity index 100%
rename from Tests/Input/Eurec4A_OA/Nanti.mat
rename to Overlap/Tests/Input/Eurec4A_OA/Nanti.mat
diff --git a/Tests/Input/Eurec4A_OA/Ncyclo.mat b/Overlap/Tests/Input/Eurec4A_OA/Ncyclo.mat
similarity index 100%
rename from Tests/Input/Eurec4A_OA/Ncyclo.mat
rename to Overlap/Tests/Input/Eurec4A_OA/Ncyclo.mat
diff --git a/Tests/Input/Eurec4A_OA/adt_2019-12-15.mat b/Overlap/Tests/Input/Eurec4A_OA/adt_2019-12-15.mat
similarity index 100%
rename from Tests/Input/Eurec4A_OA/adt_2019-12-15.mat
rename to Overlap/Tests/Input/Eurec4A_OA/adt_2019-12-15.mat
diff --git a/Tests/Input/Eurec4A_OA/date_num.mat b/Overlap/Tests/Input/Eurec4A_OA/date_num.mat
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rename from Tests/Input/Region_2/SHP_triplet/outermost_contour.shp
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diff --git a/Tests/Input/Region_2/SHP_triplet/outermost_contour.shx b/Overlap/Tests/Input/Region_2/SHP_triplet/outermost_contour.shx
similarity index 100%
rename from Tests/Input/Region_2/SHP_triplet/outermost_contour.shx
rename to Overlap/Tests/Input/Region_2/SHP_triplet/outermost_contour.shx
diff --git a/Tests/Input/Region_2/h.nc b/Overlap/Tests/Input/Region_2/h.nc
similarity index 100%
rename from Tests/Input/Region_2/h.nc
rename to Overlap/Tests/Input/Region_2/h.nc
diff --git a/Tests/Input/Region_2/successive_overlap_in.txt b/Overlap/Tests/Input/Region_2/successive_overlap_in.txt
similarity index 100%
rename from Tests/Input/Region_2/successive_overlap_in.txt
rename to Overlap/Tests/Input/Region_2/successive_overlap_in.txt
diff --git a/Tests/Input/Region_2/uv.nc b/Overlap/Tests/Input/Region_2/uv.nc
similarity index 100%
rename from Tests/Input/Region_2/uv.nc
rename to Overlap/Tests/Input/Region_2/uv.nc
diff --git a/Tests/Input/Region_4/Eddies_region_4/extremum.dbf b/Overlap/Tests/Input/Region_4/Eddies_region_4/extremum.dbf
similarity index 100%
rename from Tests/Input/Region_4/Eddies_region_4/extremum.dbf
rename to Overlap/Tests/Input/Region_4/Eddies_region_4/extremum.dbf
diff --git a/Tests/Input/Region_4/Eddies_region_4/extremum.shp b/Overlap/Tests/Input/Region_4/Eddies_region_4/extremum.shp
similarity index 100%
rename from Tests/Input/Region_4/Eddies_region_4/extremum.shp
rename to Overlap/Tests/Input/Region_4/Eddies_region_4/extremum.shp
diff --git a/Tests/Input/Region_4/Eddies_region_4/extremum.shx b/Overlap/Tests/Input/Region_4/Eddies_region_4/extremum.shx
similarity index 100%
rename from Tests/Input/Region_4/Eddies_region_4/extremum.shx
rename to Overlap/Tests/Input/Region_4/Eddies_region_4/extremum.shx
diff --git a/Tests/Input/Region_4/Eddies_region_4/grid_nml.txt b/Overlap/Tests/Input/Region_4/Eddies_region_4/grid_nml.txt
similarity index 100%
rename from Tests/Input/Region_4/Eddies_region_4/grid_nml.txt
rename to Overlap/Tests/Input/Region_4/Eddies_region_4/grid_nml.txt
diff --git a/Tests/Input/Region_4/Eddies_region_4/ishape_last.txt b/Overlap/Tests/Input/Region_4/Eddies_region_4/ishape_last.txt
similarity index 100%
rename from Tests/Input/Region_4/Eddies_region_4/ishape_last.txt
rename to Overlap/Tests/Input/Region_4/Eddies_region_4/ishape_last.txt
diff --git a/Tests/Input/Region_4/Eddies_region_4/max_speed_contour.dbf b/Overlap/Tests/Input/Region_4/Eddies_region_4/max_speed_contour.dbf
similarity index 100%
rename from Tests/Input/Region_4/Eddies_region_4/max_speed_contour.dbf
rename to Overlap/Tests/Input/Region_4/Eddies_region_4/max_speed_contour.dbf
diff --git a/Tests/Input/Region_4/Eddies_region_4/max_speed_contour.shp b/Overlap/Tests/Input/Region_4/Eddies_region_4/max_speed_contour.shp
similarity index 100%
rename from Tests/Input/Region_4/Eddies_region_4/max_speed_contour.shp
rename to Overlap/Tests/Input/Region_4/Eddies_region_4/max_speed_contour.shp
diff --git a/Tests/Input/Region_4/Eddies_region_4/max_speed_contour.shx b/Overlap/Tests/Input/Region_4/Eddies_region_4/max_speed_contour.shx
similarity index 100%
rename from Tests/Input/Region_4/Eddies_region_4/max_speed_contour.shx
rename to Overlap/Tests/Input/Region_4/Eddies_region_4/max_speed_contour.shx
diff --git a/Tests/Input/Region_4/Eddies_region_4/outermost_contour.dbf b/Overlap/Tests/Input/Region_4/Eddies_region_4/outermost_contour.dbf
similarity index 100%
rename from Tests/Input/Region_4/Eddies_region_4/outermost_contour.dbf
rename to Overlap/Tests/Input/Region_4/Eddies_region_4/outermost_contour.dbf
diff --git a/Tests/Input/Region_4/Eddies_region_4/outermost_contour.shp b/Overlap/Tests/Input/Region_4/Eddies_region_4/outermost_contour.shp
similarity index 100%
rename from Tests/Input/Region_4/Eddies_region_4/outermost_contour.shp
rename to Overlap/Tests/Input/Region_4/Eddies_region_4/outermost_contour.shp
diff --git a/Tests/Input/Region_4/Eddies_region_4/outermost_contour.shx b/Overlap/Tests/Input/Region_4/Eddies_region_4/outermost_contour.shx
similarity index 100%
rename from Tests/Input/Region_4/Eddies_region_4/outermost_contour.shx
rename to Overlap/Tests/Input/Region_4/Eddies_region_4/outermost_contour.shx
diff --git a/Tests/Input/Region_4/NSODS_in.txt b/Overlap/Tests/Input/Region_4/NSODS_in.txt
similarity index 100%
rename from Tests/Input/Region_4/NSODS_in.txt
rename to Overlap/Tests/Input/Region_4/NSODS_in.txt
diff --git a/Tests/Input/Region_4/dt_region_4_2006_01_02.nc b/Overlap/Tests/Input/Region_4/dt_region_4_2006_01_02.nc
similarity index 100%
rename from Tests/Input/Region_4/dt_region_4_2006_01_02.nc
rename to Overlap/Tests/Input/Region_4/dt_region_4_2006_01_02.nc
diff --git a/Tests/Input/Region_4/extraction_eddies_stdout.txt b/Overlap/Tests/Input/Region_4/extraction_eddies_stdout.txt
similarity index 100%
rename from Tests/Input/Region_4/extraction_eddies_stdout.txt
rename to Overlap/Tests/Input/Region_4/extraction_eddies_stdout.txt
diff --git a/Tests/Input/Region_4/h.nc b/Overlap/Tests/Input/Region_4/h.nc
similarity index 100%
rename from Tests/Input/Region_4/h.nc
rename to Overlap/Tests/Input/Region_4/h.nc
diff --git a/Tests/Input/Region_4/non_successive_overlap_in.txt b/Overlap/Tests/Input/Region_4/non_successive_overlap_in.txt
similarity index 100%
rename from Tests/Input/Region_4/non_successive_overlap_in.txt
rename to Overlap/Tests/Input/Region_4/non_successive_overlap_in.txt
diff --git a/Tests/Input/Region_4/read_snapshot_nml.txt b/Overlap/Tests/Input/Region_4/read_snapshot_nml.txt
similarity index 100%
rename from Tests/Input/Region_4/read_snapshot_nml.txt
rename to Overlap/Tests/Input/Region_4/read_snapshot_nml.txt
diff --git a/Tests/Input/Region_4/uv.nc b/Overlap/Tests/Input/Region_4/uv.nc
similarity index 100%
rename from Tests/Input/Region_4/uv.nc
rename to Overlap/Tests/Input/Region_4/uv.nc
diff --git a/Tests/Input/Region_5/NSO_in.txt b/Overlap/Tests/Input/Region_5/NSO_in.txt
similarity index 100%
rename from Tests/Input/Region_5/NSO_in.txt
rename to Overlap/Tests/Input/Region_5/NSO_in.txt
diff --git a/Tests/Input/Region_5/SOR5OD_in.txt b/Overlap/Tests/Input/Region_5/SOR5OD_in.txt
similarity index 100%
rename from Tests/Input/Region_5/SOR5OD_in.txt
rename to Overlap/Tests/Input/Region_5/SOR5OD_in.txt
diff --git a/Tests/Input/Region_5/SOR5_in.txt b/Overlap/Tests/Input/Region_5/SOR5_in.txt
similarity index 100%
rename from Tests/Input/Region_5/SOR5_in.txt
rename to Overlap/Tests/Input/Region_5/SOR5_in.txt
diff --git a/Tests/Input/Region_5/h.nc b/Overlap/Tests/Input/Region_5/h.nc
similarity index 100%
rename from Tests/Input/Region_5/h.nc
rename to Overlap/Tests/Input/Region_5/h.nc
diff --git a/Tests/Input/Region_5/uv.nc b/Overlap/Tests/Input/Region_5/uv.nc
similarity index 100%
rename from Tests/Input/Region_5/uv.nc
rename to Overlap/Tests/Input/Region_5/uv.nc
diff --git a/Tests/Input/Region_6_SHP_triplet/extremum.dbf b/Overlap/Tests/Input/Region_6_SHP_triplet/extremum.dbf
similarity index 100%
rename from Tests/Input/Region_6_SHP_triplet/extremum.dbf
rename to Overlap/Tests/Input/Region_6_SHP_triplet/extremum.dbf
diff --git a/Tests/Input/Region_6_SHP_triplet/extremum.shp b/Overlap/Tests/Input/Region_6_SHP_triplet/extremum.shp
similarity index 100%
rename from Tests/Input/Region_6_SHP_triplet/extremum.shp
rename to Overlap/Tests/Input/Region_6_SHP_triplet/extremum.shp
diff --git a/Tests/Input/Region_6_SHP_triplet/extremum.shx b/Overlap/Tests/Input/Region_6_SHP_triplet/extremum.shx
similarity index 100%
rename from Tests/Input/Region_6_SHP_triplet/extremum.shx
rename to Overlap/Tests/Input/Region_6_SHP_triplet/extremum.shx
diff --git a/Tests/Input/Region_6_SHP_triplet/grid_nml.txt b/Overlap/Tests/Input/Region_6_SHP_triplet/grid_nml.txt
similarity index 100%
rename from Tests/Input/Region_6_SHP_triplet/grid_nml.txt
rename to Overlap/Tests/Input/Region_6_SHP_triplet/grid_nml.txt
diff --git a/Tests/Input/Region_6_SHP_triplet/ishape_last.txt b/Overlap/Tests/Input/Region_6_SHP_triplet/ishape_last.txt
similarity index 100%
rename from Tests/Input/Region_6_SHP_triplet/ishape_last.txt
rename to Overlap/Tests/Input/Region_6_SHP_triplet/ishape_last.txt
diff --git a/Tests/Input/Region_6_SHP_triplet/max_speed_contour.dbf b/Overlap/Tests/Input/Region_6_SHP_triplet/max_speed_contour.dbf
similarity index 100%
rename from Tests/Input/Region_6_SHP_triplet/max_speed_contour.dbf
rename to Overlap/Tests/Input/Region_6_SHP_triplet/max_speed_contour.dbf
diff --git a/Tests/Input/Region_6_SHP_triplet/max_speed_contour.shp b/Overlap/Tests/Input/Region_6_SHP_triplet/max_speed_contour.shp
similarity index 100%
rename from Tests/Input/Region_6_SHP_triplet/max_speed_contour.shp
rename to Overlap/Tests/Input/Region_6_SHP_triplet/max_speed_contour.shp
diff --git a/Tests/Input/Region_6_SHP_triplet/max_speed_contour.shx b/Overlap/Tests/Input/Region_6_SHP_triplet/max_speed_contour.shx
similarity index 100%
rename from Tests/Input/Region_6_SHP_triplet/max_speed_contour.shx
rename to Overlap/Tests/Input/Region_6_SHP_triplet/max_speed_contour.shx
diff --git a/Tests/Input/Region_6_SHP_triplet/outermost_contour.dbf b/Overlap/Tests/Input/Region_6_SHP_triplet/outermost_contour.dbf
similarity index 100%
rename from Tests/Input/Region_6_SHP_triplet/outermost_contour.dbf
rename to Overlap/Tests/Input/Region_6_SHP_triplet/outermost_contour.dbf
diff --git a/Tests/Input/Region_6_SHP_triplet/outermost_contour.shp b/Overlap/Tests/Input/Region_6_SHP_triplet/outermost_contour.shp
similarity index 100%
rename from Tests/Input/Region_6_SHP_triplet/outermost_contour.shp
rename to Overlap/Tests/Input/Region_6_SHP_triplet/outermost_contour.shp
diff --git a/Tests/Input/Region_6_SHP_triplet/outermost_contour.shx b/Overlap/Tests/Input/Region_6_SHP_triplet/outermost_contour.shx
similarity index 100%
rename from Tests/Input/Region_6_SHP_triplet/outermost_contour.shx
rename to Overlap/Tests/Input/Region_6_SHP_triplet/outermost_contour.shx
diff --git a/Tests/Input/SODS_in.txt b/Overlap/Tests/Input/SODS_in.txt
similarity index 100%
rename from Tests/Input/SODS_in.txt
rename to Overlap/Tests/Input/SODS_in.txt
diff --git a/Tests/Input/empty_outside_points.csv b/Overlap/Tests/Input/empty_outside_points.csv
similarity index 100%
rename from Tests/Input/empty_outside_points.csv
rename to Overlap/Tests/Input/empty_outside_points.csv
diff --git a/Tests/Input/example.nc b/Overlap/Tests/Input/example.nc
similarity index 100%
rename from Tests/Input/example.nc
rename to Overlap/Tests/Input/example.nc
diff --git a/Tests/Input/good_contour.txt b/Overlap/Tests/Input/good_contour.txt
similarity index 100%
rename from Tests/Input/good_contour.txt
rename to Overlap/Tests/Input/good_contour.txt
diff --git a/Tests/Input/good_contour_2.txt b/Overlap/Tests/Input/good_contour_2.txt
similarity index 100%
rename from Tests/Input/good_contour_2.txt
rename to Overlap/Tests/Input/good_contour_2.txt
diff --git a/Tests/Input/h_outermost.nc b/Overlap/Tests/Input/h_outermost.nc
similarity index 100%
rename from Tests/Input/h_outermost.nc
rename to Overlap/Tests/Input/h_outermost.nc
diff --git a/Tests/Input/h_region_3.nc b/Overlap/Tests/Input/h_region_3.nc
similarity index 100%
rename from Tests/Input/h_region_3.nc
rename to Overlap/Tests/Input/h_region_3.nc
diff --git a/Tests/Input/huv_2015_11_29.nc b/Overlap/Tests/Input/huv_2015_11_29.nc
similarity index 100%
rename from Tests/Input/huv_2015_11_29.nc
rename to Overlap/Tests/Input/huv_2015_11_29.nc
diff --git a/Tests/Input/inside_4_false_nml.txt b/Overlap/Tests/Input/inside_4_false_nml.txt
similarity index 100%
rename from Tests/Input/inside_4_false_nml.txt
rename to Overlap/Tests/Input/inside_4_false_nml.txt
diff --git a/Tests/Input/inside_4_true_nml.txt b/Overlap/Tests/Input/inside_4_true_nml.txt
similarity index 100%
rename from Tests/Input/inside_4_true_nml.txt
rename to Overlap/Tests/Input/inside_4_true_nml.txt
diff --git a/Tests/Input/no_good_contour.txt b/Overlap/Tests/Input/no_good_contour.txt
similarity index 100%
rename from Tests/Input/no_good_contour.txt
rename to Overlap/Tests/Input/no_good_contour.txt
diff --git a/Tests/Input/outermost_contour_alt.dbf b/Overlap/Tests/Input/outermost_contour_alt.dbf
similarity index 100%
rename from Tests/Input/outermost_contour_alt.dbf
rename to Overlap/Tests/Input/outermost_contour_alt.dbf
diff --git a/Tests/Input/outermost_contour_alt.shp b/Overlap/Tests/Input/outermost_contour_alt.shp
similarity index 100%
rename from Tests/Input/outermost_contour_alt.shp
rename to Overlap/Tests/Input/outermost_contour_alt.shp
diff --git a/Tests/Input/outermost_contour_alt.shx b/Overlap/Tests/Input/outermost_contour_alt.shx
similarity index 100%
rename from Tests/Input/outermost_contour_alt.shx
rename to Overlap/Tests/Input/outermost_contour_alt.shx
diff --git a/Tests/Input/outermost_eddy_5.dbf b/Overlap/Tests/Input/outermost_eddy_5.dbf
similarity index 100%
rename from Tests/Input/outermost_eddy_5.dbf
rename to Overlap/Tests/Input/outermost_eddy_5.dbf
diff --git a/Tests/Input/outermost_eddy_5.shp b/Overlap/Tests/Input/outermost_eddy_5.shp
similarity index 100%
rename from Tests/Input/outermost_eddy_5.shp
rename to Overlap/Tests/Input/outermost_eddy_5.shp
diff --git a/Tests/Input/outermost_eddy_5.shx b/Overlap/Tests/Input/outermost_eddy_5.shx
similarity index 100%
rename from Tests/Input/outermost_eddy_5.shx
rename to Overlap/Tests/Input/outermost_eddy_5.shx
diff --git a/Tests/Input/outside_points_1.csv b/Overlap/Tests/Input/outside_points_1.csv
similarity index 100%
rename from Tests/Input/outside_points_1.csv
rename to Overlap/Tests/Input/outside_points_1.csv
diff --git a/Tests/Input/outside_points_2.csv b/Overlap/Tests/Input/outside_points_2.csv
similarity index 100%
rename from Tests/Input/outside_points_2.csv
rename to Overlap/Tests/Input/outside_points_2.csv
diff --git a/Tests/Input/successive_overlap_in.txt b/Overlap/Tests/Input/successive_overlap_in.txt
similarity index 100%
rename from Tests/Input/successive_overlap_in.txt
rename to Overlap/Tests/Input/successive_overlap_in.txt
diff --git a/Tests/Input/successive_overlap_periodic_in.txt b/Overlap/Tests/Input/successive_overlap_periodic_in.txt
similarity index 100%
rename from Tests/Input/successive_overlap_periodic_in.txt
rename to Overlap/Tests/Input/successive_overlap_periodic_in.txt
diff --git a/Tests/Input/tri_square_hole.dbf b/Overlap/Tests/Input/tri_square_hole.dbf
similarity index 100%
rename from Tests/Input/tri_square_hole.dbf
rename to Overlap/Tests/Input/tri_square_hole.dbf
diff --git a/Tests/Input/tri_square_hole.shp b/Overlap/Tests/Input/tri_square_hole.shp
similarity index 100%
rename from Tests/Input/tri_square_hole.shp
rename to Overlap/Tests/Input/tri_square_hole.shp
diff --git a/Tests/Input/tri_square_hole.shx b/Overlap/Tests/Input/tri_square_hole.shx
similarity index 100%
rename from Tests/Input/tri_square_hole.shx
rename to Overlap/Tests/Input/tri_square_hole.shx
diff --git a/Tests/Input/triangle.dbf b/Overlap/Tests/Input/triangle.dbf
similarity index 100%
rename from Tests/Input/triangle.dbf
rename to Overlap/Tests/Input/triangle.dbf
diff --git a/Tests/Input/triangle.shp b/Overlap/Tests/Input/triangle.shp
similarity index 100%
rename from Tests/Input/triangle.shp
rename to Overlap/Tests/Input/triangle.shp
diff --git a/Tests/Input/triangle.shx b/Overlap/Tests/Input/triangle.shx
similarity index 100%
rename from Tests/Input/triangle.shx
rename to Overlap/Tests/Input/triangle.shx
diff --git a/Tests/Input/uv_outermost.nc b/Overlap/Tests/Input/uv_outermost.nc
similarity index 100%
rename from Tests/Input/uv_outermost.nc
rename to Overlap/Tests/Input/uv_outermost.nc
diff --git a/Tests/Input/uv_region_3.nc b/Overlap/Tests/Input/uv_region_3.nc
similarity index 100%
rename from Tests/Input/uv_region_3.nc
rename to Overlap/Tests/Input/uv_region_3.nc
diff --git a/Tests/Input/write_overlap_delta_3_nml.txt b/Overlap/Tests/Input/write_overlap_delta_3_nml.txt
similarity index 100%
rename from Tests/Input/write_overlap_delta_3_nml.txt
rename to Overlap/Tests/Input/write_overlap_delta_3_nml.txt
diff --git a/Tests/Input/write_overlap_different_nml.txt b/Overlap/Tests/Input/write_overlap_different_nml.txt
similarity index 100%
rename from Tests/Input/write_overlap_different_nml.txt
rename to Overlap/Tests/Input/write_overlap_different_nml.txt
diff --git a/Tests/Input/write_overlap_shifting_nml.txt b/Overlap/Tests/Input/write_overlap_shifting_nml.txt
similarity index 100%
rename from Tests/Input/write_overlap_shifting_nml.txt
rename to Overlap/Tests/Input/write_overlap_shifting_nml.txt
diff --git a/Overlap/Tests/long_tests.json b/Overlap/Tests/long_tests.json
new file mode 100644
index 00000000..319c6f42
--- /dev/null
+++ b/Overlap/Tests/long_tests.json
@@ -0,0 +1,14 @@
+[
+    {
+        "input": "&MAIN_NML max_delta = 4 /\n",
+        "title": "EGg",
+        "stdout": "eddy_graph_stdout.txt",
+        "command": [
+            "env",
+            "mpiexec=$mpiexec",
+            "$build_dir/eddy_graph.sh",
+            "1",
+            "$large_input_dir/SHP_triplet_global"
+        ]
+    }
+]
diff --git a/Tests/short_tests.json b/Overlap/Tests/short_tests.json
similarity index 59%
rename from Tests/short_tests.json
rename to Overlap/Tests/short_tests.json
index 34c9d94b..9491089e 100644
--- a/Tests/short_tests.json
+++ b/Overlap/Tests/short_tests.json
@@ -1,301 +1,8 @@
 [
-    {
-        "description": "3 contours at that level. 2 contain the inside point, one of which contains the 2 outside points.",
-        "required": [
-            [
-                "$src_dir/Tests/Input/outside_points_1.csv",
-                "outside_points.csv"
-            ]
-        ],
-        "title": "Good_contour",
-        "command": [
-            "$build_dir/test_good_contour",
-            "$src_dir/Tests/Input/example.nc"
-        ],
-        "stdin_filename": "$src_dir/Tests/Input/good_contour.txt"
-    },
-    {
-        "description": "Select another good contour. Case where one of the contours tested does not contain inside point.",
-        "required": [
-            [
-                "$src_dir/Tests/Input/outside_points_2.csv",
-                "outside_points.csv"
-            ]
-        ],
-        "title": "Good_contour_2",
-        "command": [
-            "$build_dir/test_good_contour",
-            "$src_dir/Tests/Input/example.nc"
-        ],
-        "stdin_filename": "$src_dir/Tests/Input/good_contour_2.txt"
-    },
-    {
-        "required": [
-            [
-                "$src_dir/Tests/Input/outside_points_1.csv",
-                "outside_points.csv"
-            ]
-        ],
-        "title": "No_good_contour",
-        "command": [
-            "$build_dir/test_good_contour",
-            "$src_dir/Tests/Input/example.nc"
-        ],
-        "stdin_filename": "$src_dir/Tests/Input/no_good_contour.txt"
-    },
-    {
-        "input": "f",
-        "title": "Local_extrema",
-        "command": [
-            "$build_dir/test_local_extrema",
-            "$src_dir/Tests/Input/Region_1/h.nc"
-        ]
-    },
-    {
-        "description": "With a larger region than in test Local_extrema.",
-        "input": "f",
-        "title": "Local_extrema_larger",
-        "command": [
-            "$build_dir/test_local_extrema",
-            "$src_dir/Tests/Input/Region_2/h.nc"
-        ]
-    },
-    {
-        "input": "&main_nml /\n",
-        "title": "Get_1_outerm",
-        "required": [
-            "$src_dir/Tests/Input/Region_1/h.nc",
-            [
-                "$src_dir/Tests/Input/Region_1/outside_points_get_1_outerm.csv",
-                "outside_points.csv"
-            ]
-        ],
-        "command": "$build_dir/test_get_1_outerm"
-    },
-    {
-        "description": "Assume insufficient amplitude for extrema 2 and 8. Even if extremum 8 does not have a particularly small amplitude, we just want to see the target extremum, 6, grow its outermost contour compared to the case without minimum amplitude.",
-        "input": "&main_nml /\n",
-        "title": "Get_1_outerm_noise_2_8",
-        "required": [
-            "$src_dir/Tests/Input/Region_1/h.nc",
-            "$src_dir/Tests/Input/Region_1/outside_points.csv"
-        ],
-        "command": "$build_dir/test_get_1_outerm"
-    },
-    {
-        "description": "Negative value for extremum 2.",
-        "input": "&main_nml /\n",
-        "title": "Get_1_outerm_noise_2",
-        "required": [
-            "$src_dir/Tests/Input/Region_1/h.nc",
-            [
-                "$src_dir/Tests/Input/Region_1/outside_points_get_1_outerm_noise_2.csv",
-                "outside_points.csv"
-            ]
-        ],
-        "command": "$build_dir/test_get_1_outerm"
-    },
-    {
-        "input": "&main_nml /\n",
-        "title": "Max_speed_contour_ssh",
-        "command": [
-            "$build_dir/test_max_speed_contour_ssh",
-            "$src_dir/Tests/Input/Region_1/h.nc",
-            "$src_dir/Tests/Input/Region_1/uv.nc"
-        ]
-    },
-    {
-        "description": "direction = 2",
-        "input": "&main_nml IND_EXTR= 4,14/\n",
-        "title": "Max_speed_contour_ssh_north",
-        "command": [
-            "$build_dir/test_max_speed_contour_ssh",
-            "$src_dir/Tests/Input/Region_1/h.nc",
-            "$src_dir/Tests/Input/Region_1/uv.nc"
-        ]
-    },
-    {
-        "description": "Missing value in speed.",
-        "input": "&main_nml IND_EXTR= 3, 4/\n",
-        "title": "Max_speed_contour_ssh_missing",
-        "command": [
-            "$build_dir/test_max_speed_contour_ssh",
-            "$src_dir/Tests/Input/huv_2015_11_29.nc",
-            "$src_dir/Tests/Input/huv_2015_11_29.nc"
-        ]
-    },
-    {
-        "input": "&main_nml /\n",
-        "title": "Mean_speed",
-        "required": [
-            "$src_dir/Tests/Input/Region_1/uv.nc",
-            [
-                "$src_dir/Tests/Input/Get_1_outerm/test_get_1_outerm.shp",
-                "contour.shp"
-            ],
-            [
-                "$src_dir/Tests/Input/Get_1_outerm/test_get_1_outerm.dbf",
-                "contour.dbf"
-            ],
-            [
-                "$src_dir/Tests/Input/Get_1_outerm/test_get_1_outerm.shx",
-                "contour.shx"
-            ]
-        ],
-        "command": "$build_dir/test_mean_speed"
-    },
-    {
-        "input": "&main_nml /\n",
-        "title": "Mean_speed_alt",
-        "required": [
-            "$src_dir/Tests/Input/Region_1/uv.nc",
-            [
-                "$src_dir/Tests/Input/outermost_contour_alt.shp",
-                "contour.shp"
-            ],
-            [
-                "$src_dir/Tests/Input/outermost_contour_alt.dbf",
-                "contour.dbf"
-            ],
-            [
-                "$src_dir/Tests/Input/outermost_contour_alt.shx",
-                "contour.shx"
-            ]
-        ],
-        "command": "$build_dir/test_mean_speed"
-    },
-    {
-        "input": "&main_nml /\n",
-        "required": [
-            [
-                "$src_dir/Tests/Input/h_outermost.nc",
-                "h.nc"
-            ],
-            [
-                "$src_dir/Tests/Input/uv_outermost.nc",
-                "uv.nc"
-            ],
-            [
-                "$src_dir/Tests/Input/empty_outside_points.csv",
-                "outside_points.csv"
-            ],
-            "$src_dir/Tests/Input/Get_1_outerm/test_get_1_outerm.*"
-        ],
-        "title": "Set_max_speed",
-        "command": "$build_dir/test_set_max_speed"
-    },
-    {
-        "input": "&MAIN_NML IND_TARG_EXTR=19,11 /\n",
-        "required": [
-            "$src_dir/Tests/Input/Region_1/h.nc",
-            "$src_dir/Tests/Input/Region_1/uv.nc",
-            "$src_dir/Tests/Input/Region_1/outside_points.csv",
-            "$src_dir/Tests/Input/Get_1_outerm_noise_2_8/test_get_1_outerm.*"
-        ],
-        "title": "Set_max_speed_noise",
-        "command": "$build_dir/test_set_max_speed"
-    },
-    {
-        "input": "&main_nml min_amp = 0./\n",
-        "required": [
-            "$src_dir/Tests/Input/Region_1/h.nc",
-            "$src_dir/Tests/Input/Region_1/uv.nc"
-        ],
-        "title": "Extraction_eddies_region_1",
-        "commands": [
-            [
-                "mkdir",
-                "SHP_triplet"
-            ],
-            "$build_dir/inst_eddies"
-        ]
-    },
-    {
-        "description": "Same as Extraction_eddies_region_1 but with non-zero minimal amplitude.",
-        "input": "&main_nml /\n",
-        "required": [
-            "$src_dir/Tests/Input/Region_1/h.nc",
-            "$src_dir/Tests/Input/Region_1/uv.nc"
-        ],
-        "title": "Extraction_eddies_region_1_noise",
-        "commands": [
-            [
-                "mkdir",
-                "SHP_triplet"
-            ],
-            "$build_dir/inst_eddies"
-        ]
-    },
-    {
-        "input": "&main_nml min_amp = 0./\n",
-        "required": [
-            "$src_dir/Tests/Input/Region_2/h.nc",
-            "$src_dir/Tests/Input/Region_2/uv.nc"
-        ],
-        "title": "Extraction_eddies_region_2",
-        "commands": [
-            [
-                "mkdir",
-                "SHP_triplet"
-            ],
-            "$build_dir/inst_eddies"
-        ]
-    },
-    {
-        "input": "&main_nml /\n",
-        "required": [
-            "$src_dir/Tests/Input/Region_2/h.nc",
-            "$src_dir/Tests/Input/Region_2/uv.nc"
-        ],
-        "title": "Extraction_eddies_region_2_noise",
-        "commands": [
-            [
-                "mkdir",
-                "SHP_triplet"
-            ],
-            "$build_dir/inst_eddies"
-        ]
-    },
-    {
-        "stdin_filename": "$src_dir/Tests/Input/inside_4_true_nml.txt",
-        "title": "Inside_4_true",
-        "command": [
-            "$build_dir/test_inside_4",
-            "$src_dir/Tests/Input/outermost_eddy_5"
-        ]
-    },
-    {
-        "stdin_filename": "$src_dir/Tests/Input/inside_4_false_nml.txt",
-        "title": "Inside_4_false",
-        "command": [
-            "$build_dir/test_inside_4",
-            "$src_dir/Tests/Input/outermost_eddy_5"
-        ]
-    },
-    {
-        "description": "Part of the domain has missing values.",
-        "input": "&main_nml /\n",
-        "required": [
-            "$src_dir/Tests/Input/Region_4/h.nc",
-            "$src_dir/Tests/Input/Region_4/uv.nc"
-        ],
-        "title": "Extraction_eddies_region_4",
-        "commands": [
-            [
-                "mkdir",
-                "SHP_triplet"
-            ],
-            "$build_dir/inst_eddies"
-        ]
-    },
     {
         "title": "Weight",
         "command": "$build_dir/test_weight"
     },
-    {
-        "title": "Spher_polyline_area",
-        "command": "$build_dir/test_spher_polyline_area"
-    },
     {
         "title": "Spher_polygon_area",
         "command": [
@@ -351,15 +58,6 @@
             ]
         ]
     },
-    {
-        "input": "f\n",
-        "description": "With input file containing missing values.",
-        "title": "Local_extrema_missing",
-        "command": [
-            "$build_dir/test_local_extrema",
-            "$src_dir/Tests/Input/Region_4/h.nc"
-        ]
-    },
     {
         "stdin_filename": "$src_dir/Tests/Input/successive_overlap_in.txt",
         "description": "Overlap of a snapshot with itself.",
@@ -379,15 +77,6 @@
             ]
         ]
     },
-    {
-        "required": [
-            "$src_dir/Tests/Input/Region_1/SHP_triplet_noise/extremum.*",
-            "$src_dir/Tests/Input/Region_1/SHP_triplet_noise/ishape_last.txt",
-            "$src_dir/Tests/Input/Region_1/Local_extrema/extr_map.nc"
-        ],
-        "title": "Nearby_extr",
-        "command": "$build_dir/test_nearby_extr"
-    },
     {
         "stdin_filename": "$src_dir/Tests/Input/Region_5/SOR5OD_in.txt",
         "description": "Same as Successive_overlap, but with larger domain: region 5 instead of region 4.",
@@ -407,55 +96,6 @@
             ]
         ]
     },
-    {
-        "description": "Same as Local_extrema but with periodicity. The data is actually regional so there is a discontinuity in the field and the longitude grid assuming periodicity is not regular.",
-        "input": "t\n",
-        "title": "Local_extrema_periodic",
-        "command": [
-            "$build_dir/test_local_extrema",
-            "$src_dir/Tests/Input/Region_1/h.nc"
-        ]
-    },
-    {
-        "description": "The data is really global so there is no discontinuity in the field and the longitude grid assuming periodicity is regular.",
-        "input": "t\n",
-        "title": "Local_extrema_periodic_2",
-        "command": [
-            "$build_dir/test_local_extrema",
-            "$src_dir/Tests/Input/Global/h_2006_01_01_coarse.nc"
-        ]
-    },
-    {
-        "description": "test_set_all_outerm with periodicity.",
-        "input": "&main_nml MAX_RADIUS = 4, 4/\n",
-        "title": "Set_all_outerm_periodic",
-        "command": [
-            "$build_dir/test_set_all_outerm",
-            "$src_dir/Tests/Input/Global/h_2006_01_01_coarse.nc"
-        ]
-    },
-    {
-        "description": "Periodic domain.",
-        "input": "&main_nml min_amp = 0., MAX_RADIUS = 4, 4/\n",
-        "required": [
-            [
-                "$src_dir/Tests/Input/Global/h_2006_01_01_coarse.nc",
-                "h.nc"
-            ],
-            [
-                "$src_dir/Tests/Input/Global/uv_2006_01_01_coarse.nc",
-                "uv.nc"
-            ]
-        ],
-        "title": "Extraction_eddies_periodic",
-        "commands": [
-            [
-                "mkdir",
-                "SHP_triplet"
-            ],
-            "$build_dir/inst_eddies"
-        ]
-    },
     {
         "stdin_filename": "$src_dir/Tests/Input/successive_overlap_periodic_in.txt",
         "description": "Overlap of a snapshot with itself. Global coarse grid.",
@@ -1031,110 +671,5 @@
             "3",
             "$large_input_dir/SHP_triplet_region_5"
         ]
-    },
-    {
-	"title": "Graph_from_Matlab_v6_cyclo",
-	"command": ["$src_dir/Convert_Matlab/overlap_v6.py", "cyclo"],
-	"required":
-	[
-	    "$src_dir/Tests/Input/Eurec4A_OA/id_child_cyclo.mat",
-	    "$src_dir/Tests/Input/Eurec4A_OA/Ncyclo.mat",
-	    "$src_dir/Tests/Input/Eurec4A_OA/date_num.mat"
-	]
-    },
-    {
-	"title": "Graph_from_Matlab_v6_anti",
-	"command": ["$src_dir/Convert_Matlab/overlap_v6.py", "anti"],
-	"required":
-	[
-	    "$src_dir/Tests/Input/Eurec4A_OA/id_child_anti.mat",
-	    "$src_dir/Tests/Input/Eurec4A_OA/Nanti.mat",
-	    "$src_dir/Tests/Input/Eurec4A_OA/date_num.mat"
-	]
-    },
-    {
-	"title": "Report_graph_cyclo",
-	"command":
-	[
-	    "$src_dir/Analysis/report_graph.py", "--gv", "--interp",
-	    "--merging", "cyclo"
-	],
-	"required":
-	[
-	    "$tests_old_dir/EGr2nd15md4np3/edgelist_cyclo.csv",
-	    "$tests_old_dir/EGr2nd15md4np3/SHP_triplet"
-	]
-    },
-    {
-	"title": "Report_graph_anti",
-	"command":
-	[
-	    "$src_dir/Analysis/report_graph.py", "--gv", "--interp",
-	    "--merging", "anti"
-	],
-	"required":
-	[
-	    "$tests_old_dir/EGr2nd15md4np3/edgelist_anti.csv",
-	    "$tests_old_dir/EGr2nd15md4np3/SHP_triplet"
-	]
-    },
-    {
-	"title": "Plot_traj",
-	"command":
-	[
-	    "$src_dir/Analysis/plot_traj.py",
-	    "$src_dir/Tests/Input/Region_2/SHP_triplet", "--save=png"
-	],
-	"required":
-	[
-	    "$tests_old_dir/EGr2nd15md4np3/edgelist_anti.csv",
-	    "$tests_old_dir/EGr2nd15md4np3/edgelist_cyclo.csv",
-	    "$tests_old_dir/EGr2nd15md4np3/SHP_triplet"
-	]
-    },
-    {
-	"title": "Mat_v6_to_shapefiles",
-	"command":
-	[
-	    "$src_dir/Convert_Matlab/inst_eddies_v6.py",
-	    "/data/lmd-oce/EUREC4A_OA/DATA_SAT_NewExport_Atalante/TOEddies/Eddies/adt_2019-12-15.mat",
-	    "2019-12-16"
-	],
-	"required": ["$src_dir/Convert_Matlab/inst_eddies.m"]
-    },
-    {
-	"title": "Plot_eddy_contours",
-	"command":
-	[
-	    "$src_dir/Analysis/plot_eddy_contours.py",
-	    "$src_dir/Tests/Input/Region_6_SHP_triplet", "--save=png"
-	]
-    },
-    {
-	"title": "Animation",
-	"command":
-	[
-	    "$src_dir/Analysis/plot_eddy_contours.py",
-	    "--anim", "20454", "20455",
-	    "--light", "$src_dir/Tests/Input/Region_6_SHP_triplet"
-	]
-    },
-    {
-	"title": "Mat_HDF5_to_shapefiles",
-	"command":
-	[
-	    "$src_dir/Convert_Matlab/inst_eddies_HDF5.py",
-	    "$src_dir/Tests/Input/Eurec4A_OA/adt_2019-12-15.mat"
-	]
-    },
-    {
-	"title": "Plot_eddy_contours_Mat",
-	"description":
-	"plot_eddy_contours.py on a file coming from the Matlab program.",
-	"command":
-	[
-	    "$src_dir/Analysis/plot_eddy_contours.py",
-	    "$tests_old_dir/Mat_v6_to_shapefiles/Snapshot_cyclo", "--save=png"
-	]
     }
 ]
diff --git a/Tests/test_get_dispatch_snap.f90 b/Overlap/Tests/test_get_dispatch_snap.f90
similarity index 100%
rename from Tests/test_get_dispatch_snap.f90
rename to Overlap/Tests/test_get_dispatch_snap.f90
diff --git a/Tests/test_overlap.f90 b/Overlap/Tests/test_overlap.f90
similarity index 100%
rename from Tests/test_overlap.f90
rename to Overlap/Tests/test_overlap.f90
diff --git a/Tests/test_read_eddy.f90 b/Overlap/Tests/test_read_eddy.f90
similarity index 100%
rename from Tests/test_read_eddy.f90
rename to Overlap/Tests/test_read_eddy.f90
diff --git a/Tests/test_read_snapshot.f90 b/Overlap/Tests/test_read_snapshot.f90
similarity index 100%
rename from Tests/test_read_snapshot.f90
rename to Overlap/Tests/test_read_snapshot.f90
diff --git a/Tests/test_send_recv.f90 b/Overlap/Tests/test_send_recv.f90
similarity index 100%
rename from Tests/test_send_recv.f90
rename to Overlap/Tests/test_send_recv.f90
diff --git a/Tests/test_spher_polygon_area.f90 b/Overlap/Tests/test_spher_polygon_area.f90
similarity index 100%
rename from Tests/test_spher_polygon_area.f90
rename to Overlap/Tests/test_spher_polygon_area.f90
diff --git a/Tests/test_weight.f90 b/Overlap/Tests/test_weight.f90
similarity index 100%
rename from Tests/test_weight.f90
rename to Overlap/Tests/test_weight.f90
diff --git a/Tests/test_write_overlap.f90 b/Overlap/Tests/test_write_overlap.f90
similarity index 100%
rename from Tests/test_write_overlap.f90
rename to Overlap/Tests/test_write_overlap.f90
diff --git a/Tests/write_snapshot.f90 b/Overlap/Tests/write_snapshot.f90
similarity index 100%
rename from Tests/write_snapshot.f90
rename to Overlap/Tests/write_snapshot.f90
diff --git a/candidate_overlap.f90 b/Overlap/candidate_overlap.f90
similarity index 100%
rename from candidate_overlap.f90
rename to Overlap/candidate_overlap.f90
diff --git a/dispatch_snapshot.f90 b/Overlap/dispatch_snapshot.f90
similarity index 100%
rename from dispatch_snapshot.f90
rename to Overlap/dispatch_snapshot.f90
diff --git a/eddy_graph.f90 b/Overlap/eddy_graph.f90
similarity index 100%
rename from eddy_graph.f90
rename to Overlap/eddy_graph.f90
diff --git a/eddy_graph_in.sh b/Overlap/eddy_graph_in.sh
similarity index 100%
rename from eddy_graph_in.sh
rename to Overlap/eddy_graph_in.sh
diff --git a/get_snapshot.f90 b/Overlap/get_snapshot.f90
similarity index 100%
rename from get_snapshot.f90
rename to Overlap/get_snapshot.f90
diff --git a/overlap.f90 b/Overlap/overlap.f90
similarity index 100%
rename from overlap.f90
rename to Overlap/overlap.f90
diff --git a/read_eddy.f90 b/Overlap/read_eddy.f90
similarity index 100%
rename from read_eddy.f90
rename to Overlap/read_eddy.f90
diff --git a/read_field_indices.f90 b/Overlap/read_field_indices.f90
similarity index 100%
rename from read_field_indices.f90
rename to Overlap/read_field_indices.f90
diff --git a/read_snapshot.f90 b/Overlap/read_snapshot.f90
similarity index 100%
rename from read_snapshot.f90
rename to Overlap/read_snapshot.f90
diff --git a/recv_snapshot.f90 b/Overlap/recv_snapshot.f90
similarity index 100%
rename from recv_snapshot.f90
rename to Overlap/recv_snapshot.f90
diff --git a/send_snapshot.f90 b/Overlap/send_snapshot.f90
similarity index 100%
rename from send_snapshot.f90
rename to Overlap/send_snapshot.f90
diff --git a/shp_tr_open.f90 b/Overlap/shp_tr_open.f90
similarity index 100%
rename from shp_tr_open.f90
rename to Overlap/shp_tr_open.f90
diff --git a/spher_polygon_area.f90 b/Overlap/spher_polygon_area.f90
similarity index 100%
rename from spher_polygon_area.f90
rename to Overlap/spher_polygon_area.f90
diff --git a/unit_edge_m.f90 b/Overlap/unit_edge_m.f90
similarity index 100%
rename from unit_edge_m.f90
rename to Overlap/unit_edge_m.f90
diff --git a/weight.f90 b/Overlap/weight.f90
similarity index 100%
rename from weight.f90
rename to Overlap/weight.f90
diff --git a/write_edge.f90 b/Overlap/write_edge.f90
similarity index 100%
rename from write_edge.f90
rename to Overlap/write_edge.f90
diff --git a/write_overlap.f90 b/Overlap/write_overlap.f90
similarity index 100%
rename from write_overlap.f90
rename to Overlap/write_overlap.f90
diff --git a/Tests/CMakeLists.txt b/Tests/CMakeLists.txt
deleted file mode 100644
index ab5947d2..00000000
--- a/Tests/CMakeLists.txt
+++ /dev/null
@@ -1,211 +0,0 @@
-# test_max_speed_contour_ssh
-
-add_executable(test_max_speed_contour_ssh derived_types.f90
-  max_speed_contour_ssh.f90 get_var.f90
-  ${CMAKE_CURRENT_LIST_DIR}/test_max_speed_contour_ssh.f90)
-
-target_link_libraries(test_max_speed_contour_ssh netcdf95 contour_531
-  jumble nr_util)
-
-target_include_directories(test_max_speed_contour_ssh PRIVATE
-  ${fortrangis_INCLUDE_DIR})
-
-# test_nearby_extr
-
-add_executable(test_nearby_extr nearby_extr.f90 derived_types.f90
-  ${CMAKE_CURRENT_LIST_DIR}/test_nearby_extr.f90)
-
-target_link_libraries(test_nearby_extr netcdf95 shapelib_03
-  contour_531 jumble nr_util)
-
-target_include_directories(test_nearby_extr PRIVATE
-  ${fortrangis_INCLUDE_DIR})
-
-# test_overlap
-
-add_executable(test_overlap derived_types.f90 overlap.f90
-  read_snapshot.f90 spher_polygon_area.f90 spher_polyline_area.f90
-  weight.f90 read_eddy.f90 read_field_indices.f90
-  candidate_overlap.f90 write_eddy.f90 shp_tr_create.f90
-  write_overlap.f90 ${CMAKE_CURRENT_LIST_DIR}/test_overlap.f90
-  shp_tr_open.f90 shp_tr_close.f90 unit_edge_m.f90 write_edge.f90)
-
-target_link_libraries(test_overlap shapelib_03 geometry contour_531
-  gpc_f ezmpi nr_util jumble)
-
-target_include_directories(test_overlap PRIVATE ${fortrangis_INCLUDE_DIR})
-
-# test_read_snapshot
-
-add_executable(test_read_snapshot derived_types.f90
-  shp_tr_create.f90 read_snapshot.f90 write_eddy.f90
-  read_eddy.f90 read_field_indices.f90
-  ${CMAKE_CURRENT_LIST_DIR}/test_read_snapshot.f90
-  ${CMAKE_CURRENT_LIST_DIR}/write_extr_map.f90
-  ${CMAKE_CURRENT_LIST_DIR}/write_snapshot.f90 shp_tr_open.f90
-  shp_tr_close.f90)
-
-target_link_libraries(test_read_snapshot netcdf95 shapelib_03
-  contour_531 gpc_f ezmpi nr_util jumble)
-
-target_include_directories(test_read_snapshot PRIVATE
-  ${fortrangis_INCLUDE_DIR})
-
-# test_spher_polygon_area
-
-add_executable(test_spher_polygon_area spher_polygon_area.f90
-  spher_polyline_area.f90
-  ${CMAKE_CURRENT_LIST_DIR}/test_spher_polygon_area.f90)
-
-target_link_libraries(test_spher_polygon_area geometry shapelib_03
-  jumble gpc_f nr_util)
-
-target_include_directories(test_spher_polygon_area PRIVATE
-  ${fortrangis_INCLUDE_DIR})
-
-# test_local_extrema
-
-add_executable(test_local_extrema local_extrema.f90
-  ${CMAKE_CURRENT_LIST_DIR}/test_local_extrema.f90
-  ${CMAKE_CURRENT_LIST_DIR}/write_extr_map.f90)
-
-target_link_libraries(test_local_extrema netcdf95 nr_util jumble)
-
-# test_set_max_speed
-
-add_executable(test_set_max_speed derived_types.f90 set_max_speed.f90
-  good_contour.f90 max_speed_contour_ssh.f90 mean_speed.f90
-  spher_polyline_area.f90 inside_4.f90
-  ${CMAKE_CURRENT_LIST_DIR}/test_set_max_speed.f90)
-
-target_link_libraries(test_set_max_speed geometry numer_rec_95
-  netcdf95 shapelib_03 contour_531 jumble nr_util)
-
-target_include_directories(test_set_max_speed PRIVATE ${fortrangis_INCLUDE_DIR})
-
-# test_weight
-
-add_executable(test_weight weight.f90 derived_types.f90
-  ${CMAKE_CURRENT_LIST_DIR}/test_weight.f90)
-
-target_link_libraries(test_weight contour_531 nr_util)
-target_include_directories(test_weight PRIVATE ${fortrangis_INCLUDE_DIR})
-  
-# test_read_eddy
-
-add_executable(test_read_eddy derived_types.f90 shp_tr_create.f90
-  read_eddy.f90 write_eddy.f90 read_field_indices.f90
-  ${CMAKE_CURRENT_LIST_DIR}/test_read_eddy.f90 shp_tr_open.f90
-  shp_tr_close.f90)
-
-target_link_libraries(test_read_eddy shapelib_03 contour_531 gpc_f
-  ezmpi nr_util)
-
-target_include_directories(test_read_eddy PRIVATE ${fortrangis_INCLUDE_DIR})
-
-# test_get_1_outerm
-
-add_executable(test_get_1_outerm good_contour.f90 derived_types.f90
-  get_1_outerm.f90 spher_polyline_area.f90
-  ${CMAKE_CURRENT_LIST_DIR}/test_get_1_outerm.f90)
-
-target_link_libraries(test_get_1_outerm geometry netcdf95 shapelib_03
-  contour_531 nr_util jumble)
-
-target_include_directories(test_get_1_outerm PRIVATE
-  ${fortrangis_INCLUDE_DIR})
-
-# test_set_all_outerm
-
-add_executable(test_set_all_outerm derived_types.f90 set_all_outerm.f90
-  local_extrema.f90 get_1_outerm.f90 good_contour.f90 spher_polyline_area.f90
-  nearby_extr.f90 get_var.f90
-  ${CMAKE_CURRENT_LIST_DIR}/test_set_all_outerm.f90)
-
-target_link_libraries(test_set_all_outerm geometry netcdf95
-  numer_rec_95 shapelib_03 contour_531 jumble nr_util)
-
-target_include_directories(test_set_all_outerm PRIVATE
-  ${fortrangis_INCLUDE_DIR})
-
-# test_good_contour
-
-add_executable(test_good_contour good_contour.f90
-  ${CMAKE_CURRENT_LIST_DIR}/test_good_contour.f90)
-
-target_link_libraries(test_good_contour geometry netcdf95 shapelib_03
-  contour_531 jumble nr_util)
-
-target_include_directories(test_good_contour PRIVATE
-  ${fortrangis_INCLUDE_DIR})
-
-# test_inside_4
-
-add_executable(test_inside_4 inside_4.f90
-  ${CMAKE_CURRENT_LIST_DIR}/test_inside_4.f90)
-
-target_link_libraries(test_inside_4 geometry shapelib_03 jumble)
-target_include_directories(test_inside_4 PRIVATE ${fortrangis_INCLUDE_DIR})
-
-# test_mean_speed
-
-add_executable(test_mean_speed mean_speed.f90
-  ${CMAKE_CURRENT_LIST_DIR}/test_mean_speed.f90)
-
-target_link_libraries(test_mean_speed numer_rec_95 netcdf95
-  shapelib_03 contour_531 nr_util)
-
-target_include_directories(test_mean_speed PRIVATE
-  ${fortrangis_INCLUDE_DIR})
-
-# test_spher_polyline_area
-
-add_executable(test_spher_polyline_area spher_polyline_area.f90
-  ${CMAKE_CURRENT_LIST_DIR}/test_spher_polyline_area.f90)
-
-target_link_libraries(test_spher_polyline_area geometry contour_531 nr_util)
-
-# test_write_overlap
-
-add_executable(test_write_overlap derived_types.f90 shp_tr_create.f90
-  write_eddy.f90 write_overlap.f90
-  ${CMAKE_CURRENT_LIST_DIR}/test_write_overlap.f90 shp_tr_close.f90
-  unit_edge_m.f90 write_edge.f90)
-
-target_link_libraries(test_write_overlap shapelib_03 contour_531 nr_util jumble)
-target_include_directories(test_write_overlap PRIVATE ${fortrangis_INCLUDE_DIR})
-
-# test_send_recv
-
-find_package(MPI REQUIRED)
-
-add_executable(test_send_recv
-  ${CMAKE_CURRENT_LIST_DIR}/test_send_recv.f90 send_snapshot.f90
-  recv_snapshot.f90 read_field_indices.f90 read_snapshot.f90
-  write_eddy.f90 shp_tr_create.f90 read_eddy.f90
-  ${CMAKE_CURRENT_LIST_DIR}/write_snapshot.f90
-  ${CMAKE_CURRENT_LIST_DIR}/write_extr_map.f90 derived_types.f90
-  shp_tr_open.f90 shp_tr_close.f90)
-
-target_link_libraries(test_send_recv PRIVATE MPI::MPI_Fortran
-  shapelib_03 ezmpi nr_util contour_531 gpc_f netcdf95 jumble)
-
-target_include_directories(test_send_recv PRIVATE
-  ${fortrangis_INCLUDE_DIR})
-
-# test_get_dispatch_snap
-
-add_executable(test_get_dispatch_snap
-  ${CMAKE_CURRENT_LIST_DIR}/test_get_dispatch_snap.f90
-  get_snapshot.f90 dispatch_snapshot.f90 read_field_indices.f90
-  ${CMAKE_CURRENT_LIST_DIR}/write_snapshot.f90 read_snapshot.f90
-  recv_snapshot.f90 shp_tr_create.f90 write_eddy.f90
-  ${CMAKE_CURRENT_LIST_DIR}/write_extr_map.f90 read_eddy.f90
-  send_snapshot.f90 derived_types.f90 shp_tr_open.f90
-  shp_tr_close.f90)
-
-target_link_libraries(test_get_dispatch_snap shapelib_03 jumble contour_531
-  ezmpi netcdf95 gpc_f nr_util)
-
-target_include_directories(test_get_dispatch_snap PRIVATE
-  ${fortrangis_INCLUDE_DIR})
diff --git a/short_tests.json b/short_tests.json
new file mode 100644
index 00000000..ef75bedb
--- /dev/null
+++ b/short_tests.json
@@ -0,0 +1,6 @@
+[
+    {
+        "title": "Spher_polyline_area",
+        "command": "$build_dir/test_spher_polyline_area"
+    }
+]    
diff --git a/Tests/test_spher_polyline_area.f90 b/test_spher_polyline_area.f90
similarity index 100%
rename from Tests/test_spher_polyline_area.f90
rename to test_spher_polyline_area.f90
diff --git a/Tests/write_extr_map.f90 b/write_extr_map.f90
similarity index 100%
rename from Tests/write_extr_map.f90
rename to write_extr_map.f90
-- 
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