Merge pull request #1350 from knutfrode/dev

[run-ex] Config general:coastline_approximation_precision is now acti…

examples/example_coastline_options.py

@@ -29,6 +29,7 @@
 o.add_reader([reader_osc])
 o.set_config('environment:fallback:y_sea_water_velocity', .2)
 o.set_config('general:coastline_action', 'stranding')
+o.set_config('general:coastline_approximation_precision', None)
 o.seed_elements(lon=12.2, lat=67.7, radius=5000, number=number, time=reader_osc.zero_time)
 o.run(duration=duration, time_step=time_step)
 print(f'Calculation time: {o.timing["total time"]}')
@@ -41,7 +42,7 @@
 # Coastline option "stranding" with higher precision
 # ==================================================
 #
-# By setting config "general:coastline_approximation_precision" to desired accuracy in degrees,
+# By setting config "general:coastline_approximation_precision" to desired accuracy in degrees (default is 0.01 as in this example),
 # a more exact coastline crossing is calculated by the deactivated particles.
 # Note that with a (too) large compuation time step, particles may still "jump" over islands.
 # An alternative to avoid this possibility is to use a smaller timestep for the simulation, though at a larger computational cost.

opendrift/models/basemodel/__init__.py

@@ -319,22 +319,18 @@ def __init__(self,
                                         'default': '', 'level': CONFIG_LEVEL_BASIC,
                                         'description': 'Name of simulation'},
             'general:coastline_action': {
-                'type':
-                'enum',
+                'type': 'enum',
                 'enum': ['none', 'stranding', 'previous'],
-                'default':
-                'stranding',
-                'level':
-                CONFIG_LEVEL_BASIC,
-                'description':
-                'None means that objects may also move over land. '
-                'stranding means that objects are deactivated if they hit land. '
-                'previous means that objects will move back to the previous location '
-                'if they hit land'
+                'default': 'stranding',
+                'level': CONFIG_LEVEL_BASIC,
+                'description': 'None means that objects may also move over land. '
+                    'stranding means that objects are deactivated if they hit land. '
+                    'previous means that objects will move back to the previous location '
+                    'if they hit land'
             },
             'general:coastline_approximation_precision': {
                 'type': 'float',
-                'default': None,
+                'default': 0.001,
                 'min': 0.0001,
                 'max': 0.005,
                 'units': 'degrees',

pyproject.toml

@@ -24,7 +24,7 @@ grib = ["cfgrib", "pygrib"]
 [tool.poetry.dependencies]
 python = ">=3.9,<3.13"
 matplotlib = ">=3.5"
-numpy = ">=1.23"
+numpy = "<=1.26.4"
 scipy = ">=1.9"
 netCDF4 = ">=1.6"
 pyproj = ">=2.3"
@@ -43,7 +43,7 @@ utm = ">=0.7"
 roaring-landmask = ">=0.7"
 requests = ">=2.28"
 pykdtree = ">=1.3"
-trajan = ">=0.1.3"
+trajan = ">=0.6.3"
 xhistogram = ">=0.3"
 #adios_db = "<1.2"
 copernicusmarine = ">=1.1.1"

tests/models/test_leeway.py

@@ -54,6 +54,7 @@ def test_leewayrun(tmpdir, test_data):
     object_type = 50  # FISHING-VESSEL-1
     reader_landmask = reader_global_landmask.Reader()
     lee.add_reader([reader_landmask])
+    lee.set_config('general:coastline_approximation_precision', None)
     lee.set_config('environment:fallback:x_wind', 0)
     lee.set_config('environment:fallback:y_wind', 10)
     lee.set_config('environment:fallback:x_sea_water_velocity', 0)
@@ -70,13 +71,16 @@ def test_leewayrun(tmpdir, test_data):
     asciif = tmpdir + '/leeway_ascii.txt'
     lee.export_ascii(asciif)
     asciitarget = test_data + "/generated/test_leewayrun_export_ascii.txt"
+    asciitarget2 = test_data + "/generated/test_leewayrun_export_ascii_v2.txt"
     from difflib import Differ
     with open(asciif) as file_1, open(asciitarget) as file_2:
         differ = Differ()
         for line in differ.compare(file_1.readlines(), file_2.readlines()):
             print(line)
     import filecmp
-    assert filecmp.cmp(asciif, asciitarget)
+    if not filecmp.cmp(asciif, asciitarget):
+        # Comparing with second versio of ASCII file, with slight numerical differences
+        assert filecmp.cmp(asciif, asciitarget2)
 
 def test_capsize():
     o = Leeway(loglevel=20)

tests/models/test_stranding.py

@@ -39,6 +39,7 @@ def test_stranding_3d(self):
         o.add_reader(reader_nordic)
         o.set_config('environment:fallback:y_wind', 10)  # Some wind for mixing
         o.set_config('general:coastline_action', 'stranding')
+        o.set_config('general:coastline_approximation_precision', None)
         o.set_config('vertical_mixing:timestep', 120)
         o.set_config('drift:max_speed', .1)
         o.seed_elements(lon=14.0, lat=68.15, radius=2000, number=100,
@@ -110,6 +111,7 @@ def test_stranding_options(self):
                     time_step = -900
                 o = OceanDrift(loglevel=50)
                 o.set_config('general:coastline_action', option)
+                o.set_config('general:coastline_approximation_precision', None)
                 o.add_reader([reader_osc, reader_global])
                 # Adding northwards drift
                 o.set_config('environment:constant:y_sea_water_velocity', .1)
@@ -128,7 +130,6 @@ def test_stranding_options(self):
                 self.assertIsNone(np.testing.assert_array_almost_equal(
                     el.lon, lons[i], 3))
 
-
     def test_interact_coastline_global(self):
         reader_global = reader_global_landmask.Reader()
 
@@ -144,6 +145,20 @@ def test_interact_coastline_global(self):
         self.assertAlmostEqual(lons[-2], 5.092, 2)
         self.assertAlmostEqual(lons[-1], 5.092, 2)
 
+    def test_stranding_approximation(self):
+        o = OceanDrift(loglevel=0)
+        o.set_config('environment:constant:x_sea_water_velocity', 1)
+        o.set_config('general:coastline_approximation_precision', None)
+        o.seed_elements(lon=4.55, lat=60, time=datetime.now())
+        o.run(steps=10)
+        o2 = OceanDrift(loglevel=0)
+        o2.set_config('environment:constant:x_sea_water_velocity', 1)
+        o2.set_config('general:coastline_approximation_precision', .001)
+        o2.seed_elements(lon=4.55, lat=60, time=datetime.now())
+        o2.run(steps=10)
+        self.assertAlmostEqual(o.elements_deactivated.lon[0], 5.066, 3)
+        self.assertAlmostEqual(o2.elements_deactivated.lon[0], 5.051, 3)
+
 
 if __name__ == '__main__':
     unittest.main()

tests/readers/test_shyfem.py

@@ -5,15 +5,22 @@
 from opendrift.models.oceandrift import OceanDrift
 
 ismar = 'https://iws.ismar.cnr.it/thredds/dodsC/emerge/shyfem_unstructured_adriatic.nc'
-
-
-def test_open():
+try:
     r = shyfem.Reader(ismar)
-    print(r)
-    # r.plot_mesh()
-    # plt.show()
+    shyfem_available = True
+except:
+    shyfem_available = False
+
+#def test_open():
+#    r = shyfem.Reader(ismar)
+#    print(r)
+#    # r.plot_mesh()
+#    # plt.show()
 
+need_shyfem = pytest.mark.skipif(shyfem_available == False,
+                                 reason='Shyfem sample file not available/readable from iws.ismar.cnr.it/thredds')
 
+@need_shyfem
 def test_get_variables(benchmark):
     r = shyfem.Reader(ismar)
 
@@ -28,11 +35,13 @@ def test_get_variables(benchmark):
     assert u.shape == (len(x),)
     assert len(u) == len(x)
 
+@need_shyfem
 def test_z_polarity():
     r = shyfem.Reader(ismar)
     assert r.zmax > r.zmin
     assert (r.z < 0).all()
 
+@need_shyfem
 def test_get_values():
     r = shyfem.Reader(ismar)