Disable coverage on kernels across codebase

used the following regex:
def .*\(particle, fieldset, time\):$

test

Author: VeckoTheGecko

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()

parcels/application_kernels/EOSseawaterproperties.py

@@ -5,7 +5,7 @@
 __all__ = ["AdiabticTemperatureGradient", "PressureFromLatDepth", "PtempFromTemp", "TempFromPtemp", "UNESCODensity"]
 
 
-def PressureFromLatDepth(particle, fieldset, time):
+def PressureFromLatDepth(particle, fieldset, time):  # pragma: no cover
     """
     Calculates pressure in dbars from depth in meters and latitude.
 
@@ -28,7 +28,7 @@ def PressureFromLatDepth(particle, fieldset, time):
     particle.pressure = ((1 - C1) - math.pow(((math.pow((1 - C1), 2)) - (8.84e-6 * particle.depth)), 0.5)) / 4.42e-6
 
 
-def AdiabticTemperatureGradient(particle, fieldset, time):
+def AdiabticTemperatureGradient(particle, fieldset, time):  # pragma: no cover
     """Calculates adiabatic temperature gradient as per UNESCO 1983 routines.
 
 
@@ -81,7 +81,7 @@ def AdiabticTemperatureGradient(particle, fieldset, time):
     )
 
 
-def PtempFromTemp(particle, fieldset, time):
+def PtempFromTemp(particle, fieldset, time):  # pragma: no cover
     """
     Calculates potential temperature as per UNESCO 1983 report.
 
@@ -188,7 +188,7 @@ def PtempFromTemp(particle, fieldset, time):
     particle.potemp = (th + (del_th - 2 * q) / 6) / 1.00024
 
 
-def TempFromPtemp(particle, fieldset, time):
+def TempFromPtemp(particle, fieldset, time):  # pragma: no cover
     """
     Calculates temperature from potential temperature at the reference
     pressure PR and in situ pressure P.
@@ -295,7 +295,7 @@ def TempFromPtemp(particle, fieldset, time):
     particle.temp = (th + (del_th - 2 * q) / 6) / 1.00024
 
 
-def UNESCODensity(particle, fieldset, time):
+def UNESCODensity(particle, fieldset, time):  # pragma: no cover
     # This is a kernel which calculates the UNESCO density
     # (https://link.springer.com/content/pdf/bbm%3A978-3-319-18908-6%2F1.pdf),
     # from pressure, temperature and salinity.

parcels/application_kernels/TEOSseawaterdensity.py

@@ -5,7 +5,7 @@
 __all__ = ["PolyTEOS10_bsq"]
 
 
-def PolyTEOS10_bsq(particle, fieldset, time):
+def PolyTEOS10_bsq(particle, fieldset, time):  # pragma: no cover
     """Calculates density based on the polyTEOS10-bsq algorithm from Appendix A.2 of
     https://www.sciencedirect.com/science/article/pii/S1463500315000566
     requires fieldset.abs_salinity and fieldset.cons_temperature Fields in the fieldset

parcels/application_kernels/advection.py

@@ -14,7 +14,7 @@
 ]
 
 
-def AdvectionRK4(particle, fieldset, time):
+def AdvectionRK4(particle, fieldset, time):  # pragma: no cover
     """Advection of particles using fourth-order Runge-Kutta integration."""
     (u1, v1) = fieldset.UV[particle]
     lon1, lat1 = (particle.lon + u1 * 0.5 * particle.dt, particle.lat + v1 * 0.5 * particle.dt)
@@ -27,7 +27,7 @@ def AdvectionRK4(particle, fieldset, time):
     particle_dlat += (v1 + 2 * v2 + 2 * v3 + v4) / 6.0 * particle.dt  # noqa
 
 
-def AdvectionRK4_3D(particle, fieldset, time):
+def AdvectionRK4_3D(particle, fieldset, time):  # pragma: no cover
     """Advection of particles using fourth-order Runge-Kutta integration including vertical velocity."""
     (u1, v1, w1) = fieldset.UVW[particle]
     lon1 = particle.lon + u1 * 0.5 * particle.dt
@@ -47,7 +47,7 @@ def AdvectionRK4_3D(particle, fieldset, time):
     particle_ddepth += (w1 + 2 * w2 + 2 * w3 + w4) / 6 * particle.dt  # noqa
 
 
-def AdvectionRK4_3D_CROCO(particle, fieldset, time):
+def AdvectionRK4_3D_CROCO(particle, fieldset, time):  # pragma: no cover
     """Advection of particles using fourth-order Runge-Kutta integration including vertical velocity.
     This kernel assumes the vertical velocity is the 'w' field from CROCO output and works on sigma-layers.
     """
@@ -92,14 +92,14 @@ def AdvectionRK4_3D_CROCO(particle, fieldset, time):
     ) / 6
 
 
-def AdvectionEE(particle, fieldset, time):
+def AdvectionEE(particle, fieldset, time):  # pragma: no cover
     """Advection of particles using Explicit Euler (aka Euler Forward) integration."""
     (u1, v1) = fieldset.UV[particle]
     particle_dlon += u1 * particle.dt  # noqa
     particle_dlat += v1 * particle.dt  # noqa
 
 
-def AdvectionRK45(particle, fieldset, time):
+def AdvectionRK45(particle, fieldset, time):  # pragma: no cover
     """Advection of particles using adaptive Runge-Kutta 4/5 integration.
 
     Note that this kernel requires a Particle Class that has an extra Variable 'next_dt'
@@ -161,7 +161,7 @@ def AdvectionRK45(particle, fieldset, time):
         return StatusCode.Repeat
 
 
-def AdvectionAnalytical(particle, fieldset, time):
+def AdvectionAnalytical(particle, fieldset, time):  # pragma: no cover
     """Advection of particles using 'analytical advection' integration.
 
     Based on Ariane/TRACMASS algorithm, as detailed in e.g. Doos et al (https://doi.org/10.5194/gmd-10-1733-2017).