Fixing parcels inputs and warnings

Author: erikvansebille

environment.yml

@@ -8,7 +8,7 @@ dependencies:
   - pyproj >= 3, < 4
   - sortedcontainers == 2.4.0
   - opensimplex == 0.4.5
-  - numpy >=1, < 2
+  - numpy >=2.1
   - pydantic >=2, <3
   - pip
   - pyyaml

pyproject.toml

@@ -68,7 +68,10 @@ filterwarnings = [
   "error",
   "default::DeprecationWarning",
   "error::DeprecationWarning:virtualship",
-  "ignore:ParticleSet is empty.*:RuntimeWarning" # TODO: Probably should be ignored in the source code
+  "ignore:ParticleSet is empty.*:RuntimeWarning", # TODO: Probably should be ignored in the source code
+  "ignore:divide by zero encountered in divide:RuntimeWarning",
+  "ignore:invalid value encountered in add:RuntimeWarning",
+  "ignore:This is an alpha version of Parcels v4*:UserWarning",
 ]
 log_cli_level = "INFO"
 testpaths = [

src/virtualship/instruments/adcp.py

@@ -3,8 +3,7 @@
 from pathlib import Path
 
 import numpy as np
-from parcels import FieldSet, ParticleSet, Variable
-from parcels.particle import Particle
+from parcels import FieldSet, Particle, ParticleSet, Variable
 
 from virtualship.models import Spacetime
 

src/virtualship/instruments/argo_float.py

@@ -6,13 +6,13 @@
 
 import numpy as np
 from parcels import (
-    AdvectionRK4,
     FieldSet,
+    Particle,
     ParticleSet,
     StatusCode,
     Variable,
 )
-from parcels.particle import Particle
+from parcels.kernels import AdvectionRK4
 
 from virtualship.models import Spacetime
 

src/virtualship/instruments/ctd.py

@@ -5,9 +5,8 @@
 from pathlib import Path
 
 import numpy as np
-from parcels import FieldSet, ParticleSet, Variable
-from parcels.particle import Particle
-from parcels.tools import StatusCode
+from parcels import FieldSet, Particle, ParticleSet, Variable
+from parcels._core.statuscodes import StatusCode
 
 from virtualship.models import Spacetime
 

src/virtualship/instruments/ctd_bgc.py

@@ -5,9 +5,8 @@
 from pathlib import Path
 
 import numpy as np
-from parcels import FieldSet, ParticleSet, Variable
-from parcels.particle import Particle
-from parcels.tools import StatusCode
+from parcels import FieldSet, Particle, ParticleSet, Variable
+from parcels._core.statuscodes import StatusCode
 
 from virtualship.models import Spacetime
 

src/virtualship/instruments/drifter.py

@@ -5,9 +5,9 @@
 from pathlib import Path
 
 import numpy as np
-from parcels import AdvectionRK4, FieldSet, ParticleSet, Variable
-from parcels.particle import Particle
-from parcels.tools import StatusCode
+from parcels import FieldSet, Particle, ParticleFile, ParticleSet, Variable
+from parcels.kernels import AdvectionRK4
+from parcels._core.statuscodes import StatusCode
 
 from virtualship.models import Spacetime
 

src/virtualship/instruments/ship_underwater_st.py

@@ -3,8 +3,7 @@
 from pathlib import Path
 
 import numpy as np
-from parcels import FieldSet, ParticleSet, Variable
-from parcels.particle import Particle
+from parcels import FieldSet, Particle, ParticleSet, Variable
 
 from virtualship.models import Spacetime
 

src/virtualship/instruments/xbt.py

@@ -5,9 +5,8 @@
 from pathlib import Path
 
 import numpy as np
-from parcels import FieldSet, ParticleSet, Variable
-from parcels.particle import Particle
-from parcels.tools import StatusCode
+from parcels import FieldSet, Particle, ParticleSet, Variable
+from parcels._core.statuscodes import StatusCode
 
 from virtualship.models import Spacetime