Merge branch 'fix_croco_multifiles_csw' of https://github.com/OceanParcels/parcels into fix_croco_multifiles_csw

Author: erikvansebille

.binder/environment.yml

@@ -3,3 +3,4 @@ channels:
   - conda-forge
 dependencies:
   - parcels
+  - trajan

.github/ci/min-core-deps.yml

@@ -20,7 +20,6 @@ dependencies:
   - pymbolic=2022.1
   - pytest=7.1
   - scipy=1.9
-  - trajan=0.1
   - tqdm=4.64
   - xarray=2022.6
   - zarr=2.12

.gitignore

@@ -1,7 +1,6 @@
 build/*
 docs/_build/*
 docs/_downloads
-gh-pages/*
 lib/
 bin/
 parcels_examples
@@ -19,15 +18,13 @@ out-*
 .DS_store
 
 .vscode
-.idea/*
 .env
 Profile.prof
 **/.ipynb_checkpoints/*
 .cache/*
-.pytest_cache/*
 .eggs/*
 parcels.egg-info/*
 dist/parcels*.egg
-parcels/examples/particle*.png
 parcels/_version_setup.py
-/.pytest_cache/
+.pytest_cache
+.coverage

docs/examples/example_dask_chunk_OCMs.py

@@ -17,7 +17,7 @@ def compute_nemo_particle_advection(fieldset, mode):
     lonp = 2.5 * np.ones(npart)
     latp = [i for i in 52.0 + (-1e-3 + np.random.rand(npart) * 2.0 * 1e-3)]
 
-    def periodicBC(particle, fieldSet, time):
+    def periodicBC(particle, fieldSet, time):  # pragma: no cover
         if particle.lon > 15.0:
             particle_dlon -= 15.0  # noqa
         if particle.lon < 0:
@@ -652,7 +652,7 @@ class MyParticle(ptype[mode]):
 
     pset = parcels.ParticleSet(fieldset, pclass=MyParticle, lon=2.5, lat=52)
 
-    def Sample2D(particle, fieldset, time):
+    def Sample2D(particle, fieldset, time):  # pragma: no cover
         particle.sample_var_curvilinear += fieldset.nav_lon[
             time, particle.depth, particle.lat, particle.lon
         ]

docs/examples/example_globcurrent.py

@@ -129,7 +129,7 @@ def test_globcurrent_time_periodic(mode, rundays):
             fieldset, pclass=MyParticle, lon=25, lat=-35, time=fieldset.U.grid.time[0]
         )
 
-        def SampleU(particle, fieldset, time):
+        def SampleU(particle, fieldset, time):  # pragma: no cover
             u, v = fieldset.UV[time, particle.depth, particle.lat, particle.lon]
             particle.sample_var += u
 
@@ -255,7 +255,7 @@ def test_globcurrent_startparticles_between_time_arrays(mode, dt, with_starttime
 
     MyParticle = ptype[mode].add_variable("sample_var", initial=0.0)
 
-    def SampleP(particle, fieldset, time):
+    def SampleP(particle, fieldset, time):  # pragma: no cover
         particle.sample_var += fieldset.P[
             time, particle.depth, particle.lat, particle.lon
         ]
@@ -288,7 +288,7 @@ def test_globcurrent_particle_independence(mode, rundays=5):
     fieldset = set_globcurrent_fieldset()
     time0 = fieldset.U.grid.time[0]
 
-    def DeleteP0(particle, fieldset, time):
+    def DeleteP0(particle, fieldset, time):  # pragma: no cover
         if particle.id == 0:
             particle.delete()
 
@@ -353,7 +353,7 @@ def test_error_outputdt_not_multiple_dt(mode, tmpdir):
     pset = parcels.ParticleSet(fieldset, pclass=ptype[mode], lon=[0], lat=[0])
     ofile = pset.ParticleFile(name=filepath, outputdt=timedelta(days=1))
 
-    def DoNothing(particle, fieldset, time):
+    def DoNothing(particle, fieldset, time):  # pragma: no cover
         pass
 
     with pytest.raises(ValueError):

docs/examples/example_mitgcm.py

@@ -29,7 +29,7 @@ def run_mitgcm_zonally_reentrant(mode: Literal["scipy", "jit"], path: Path):
     fieldset.add_periodic_halo(zonal=True)
     fieldset.add_constant("domain_width", 1000000)
 
-    def periodicBC(particle, fieldset, time):
+    def periodicBC(particle, fieldset, time):  # pragma: no cover
         if particle.lon < 0:
             particle_dlon += fieldset.domain_width  # noqa
         elif particle.lon > fieldset.domain_width:

docs/examples/example_moving_eddies.py

@@ -269,7 +269,7 @@ def test_periodic_and_computeTimeChunk_eddies(mode):
         fieldset=fieldset, pclass=ptype[mode], lon=[3.3, 3.3], lat=[46.0, 47.8]
     )
 
-    def periodicBC(particle, fieldset, time):
+    def periodicBC(particle, fieldset, time):  # pragma: no cover
         if particle.lon < fieldset.halo_west:
             particle_dlon += fieldset.halo_east - fieldset.halo_west  # noqa
         elif particle.lon > fieldset.halo_east:
@@ -279,7 +279,7 @@ def periodicBC(particle, fieldset, time):
         elif particle.lat > fieldset.halo_north:
             particle_dlat -= fieldset.halo_north - fieldset.halo_south
 
-    def slowlySouthWestward(particle, fieldset, time):
+    def slowlySouthWestward(particle, fieldset, time):  # pragma: no cover
         particle_dlon -= 5 * particle.dt / 1e5  # noqa
         particle_dlat -= 3 * particle.dt / 1e5  # noqa
 

docs/examples/example_nemo_curvilinear.py

@@ -47,7 +47,7 @@ def run_nemo_curvilinear(mode, outfile, advtype="RK4"):
         latp = np.linspace(-70, 70, npart)
         runtime = timedelta(days=15)
 
-    def periodicBC(particle, fieldSet, time):
+    def periodicBC(particle, fieldSet, time):  # pragma: no cover
         if particle.lon > 180:
             particle_dlon -= 360  # noqa
 

docs/examples/example_peninsula.py

@@ -91,7 +91,7 @@ def peninsula_fieldset(xdim, ydim, mesh="flat", grid_type="A"):
     return fieldset
 
 
-def UpdateP(particle, fieldset, time):
+def UpdateP(particle, fieldset, time):  # pragma: no cover
     if time == 0:
         particle.p_start = fieldset.P[time, particle.depth, particle.lat, particle.lon]
     particle.p = fieldset.P[time, particle.depth, particle.lat, particle.lon]

docs/examples/example_stommel.py

@@ -77,13 +77,13 @@ def stommel_fieldset(xdim=200, ydim=200, grid_type="A"):
     return fieldset
 
 
-def UpdateP(particle, fieldset, time):
+def UpdateP(particle, fieldset, time):  # pragma: no cover
     if time == 0:
         particle.p_start = fieldset.P[time, particle.depth, particle.lat, particle.lon]
     particle.p = fieldset.P[time, particle.depth, particle.lat, particle.lon]
 
 
-def AgeP(particle, fieldset, time):
+def AgeP(particle, fieldset, time):  # pragma: no cover
     particle.age += particle.dt
     if particle.age > fieldset.maxage:
         particle.delete()