Configure Ruff, add pre-commit, remove flake isort and pydocstyle

Ruff replaces flake isort and pydocstyle

.pre-commit-config.yaml

@@ -0,0 +1,16 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: trailing-whitespace
+      # - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-json
+        types: [text]
+        files: \.(json|ipynb)$
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.5.6
+    hooks:
+      - id: ruff
+        args: [ --fix ]
+      # - id: ruff-format

environment.yml

@@ -9,3 +9,4 @@ dependencies:
   # Testing
   - pytest
   - coverage
+  - pre_commit

plasticparcels/constructors.py

@@ -10,7 +10,7 @@
 
 
 def create_hydrodynamic_fieldset(settings):
-    """ A constructor method to create a Parcels.Fieldset from hydrodynamic model data
+    """A constructor method to create a Parcels.Fieldset from hydrodynamic model data
 
     Parameters
     ----------
@@ -22,7 +22,6 @@ def create_hydrodynamic_fieldset(settings):
     fieldset
         A parcels.FieldSet object
     """
-
     # Location of hydrodynamic data
     dirread_model = os.path.join(settings['ocean']['directory'], settings['ocean']['filename_style'])
 
@@ -87,7 +86,7 @@ def create_hydrodynamic_fieldset(settings):
 
 
 def create_fieldset(settings):
-    """ A constructor method to create a Parcels.Fieldset with all fields necessary for a plasticparcels simulation
+    """A constructor method to create a Parcels.Fieldset with all fields necessary for a plasticparcels simulation
 
     Parameters
     ----------
@@ -99,7 +98,6 @@ def create_fieldset(settings):
     fieldset
         A parcels.FieldSet object
     """
-
     # First create the hydrodynamic fieldset
     fieldset = create_hydrodynamic_fieldset(settings)
 
@@ -203,7 +201,7 @@ def create_fieldset(settings):
 
 
 def create_particleset(fieldset, settings, release_locations):
-    """ A constructor method to create a Parcels.ParticleSet for a plasticparcels simulation
+    """A constructor method to create a Parcels.ParticleSet for a plasticparcels simulation
 
     Parameters
     ----------
@@ -219,7 +217,6 @@ def create_particleset(fieldset, settings, release_locations):
     particleset
         A parcels.ParticleSet object
     """
-
     # Set the longitude, latitude, and plastic amount per particle
     lons = np.array(release_locations['lons'])
     lats = np.array(release_locations['lats'])
@@ -271,7 +268,7 @@ def create_particleset(fieldset, settings, release_locations):
 
 
 def create_particleset_from_map(fieldset, settings):
-    """ A constructor method to create a Parcels.ParticleSet for a plasticparcels simulation from one of the available initialisation maps
+    """A constructor method to create a Parcels.ParticleSet for a plasticparcels simulation from one of the available initialisation maps
 
     Parameters
     ----------
@@ -285,7 +282,6 @@ def create_particleset_from_map(fieldset, settings):
     particleset
         A parcels.ParticleSet object
     """
-
     # Load release type information
     release_type = settings['release']['initialisation_type']
 
@@ -326,7 +322,7 @@ def create_particleset_from_map(fieldset, settings):
 
 
 def create_kernel(fieldset):
-    """ A constructor method to create a list of kernels for a plasticparcels simulation
+    """A constructor method to create a list of kernels for a plasticparcels simulation
 
     Parameters
     ----------

plasticparcels/kernels.py

@@ -36,7 +36,6 @@ def StokesDrift(particle, fieldset, time):
 
 
     """
-
     # Sample the U / V components of Stokes drift
     stokes_U = fieldset.Stokes_U[time, particle.depth, particle.lat, particle.lon]
     stokes_V = fieldset.Stokes_V[time, particle.depth, particle.lat, particle.lon]
@@ -96,7 +95,6 @@ def WindageDrift(particle, fieldset, time):
         None
 
     """
-
     # Sample ocean velocities
     (ocean_U, ocean_V) = fieldset.UV[particle]
     ocean_speed = math.sqrt(ocean_U**2 + ocean_V**2)
@@ -226,14 +224,13 @@ def SettlingVelocity(particle, fieldset, time):
         - Must run before any kernel that uses the particle.settling_velocty variable
 
 
-    References:
+    References
     ----------
     [1] Dietrich (1982) - https://doi.org/10.1029/WR018i006p01615
     [2] Kooi et al. (2017) - https://doi.org/10.1021/acs.est.6b04702
 
     TODO: Add units to each variable, and the TODO's below.
     """
-
     # Define constants and sample fieldset variables
     g = fieldset.G  # gravitational acceleration [m s-2]
     seawater_density = particle.seawater_density  # [kg m-3]
@@ -276,7 +273,7 @@ def SettlingVelocity(particle, fieldset, time):
 
 
 def Biofouling(particle, fieldset, time):
-    """ Settling velocity due to biofouling kernel
+    """Settling velocity due to biofouling kernel
 
     Description
     ----------
@@ -339,14 +336,13 @@ def Biofouling(particle, fieldset, time):
 
 
 
-    References:
+    References
     ----------
     [1] Dietrich (1982) - https://doi.org/10.1029/WR018i006p01615
     [2] Kooi et al. (2017) - https://doi.org/10.1021/acs.est.6b04702
     [3] Menden-Deuer and Lessard (2000) - https://doi.org/10.4319/lo.2000.45.3.0569
     [4] Bernard and Remond (2012) - https://doi.org/10.1016/j.biortech.2012.07.022
     """
-
     # Define constants and algal properties, and sample fieldset variables
     # g = fieldset.G  # gravitational acceleration [m s-2]
     # k = fieldset.K  # Boltzmann constant [m2 kg d-2 K-1] now [s-2] (=1.3804E-23)
@@ -467,7 +463,7 @@ def Biofouling(particle, fieldset, time):
 
 
 def PolyTEOS10_bsq(particle, fieldset, time):
-    """ A seawater density kernel
+    """A seawater density kernel
 
     Description:
     ----------
@@ -487,7 +483,8 @@ def PolyTEOS10_bsq(particle, fieldset, time):
     Order of Operations:
         This kernel must be run before any kernel that requires particle.seawater_density
 
-    References:
+    References
+    ----------
      Roquet, F., Madec, G., McDougall, T. J., Barker, P. M., 2014: Accurate
       polynomial expressions for the density and specific volume of
       seawater using the TEOS-10 standard. Ocean Modelling.
@@ -496,7 +493,6 @@ def PolyTEOS10_bsq(particle, fieldset, time):
       temperature and density of seawater.  Journal of Atmospheric and
       Oceanic Technology, 20, 730-741.
     """
-
     Z = - particle.depth  # note: use negative depths!
     SA = fieldset.absolute_salinity[time, particle.depth, particle.lat, particle.lon]
     CT = fieldset.conservative_temperature[time, particle.depth, particle.lat, particle.lon]
@@ -569,7 +565,7 @@ def PolyTEOS10_bsq(particle, fieldset, time):
 
 
 def VerticalMixing(particle, fieldset, time):
-    """ A markov-0 kernel for vertical mixing
+    """A markov-0 kernel for vertical mixing
 
     Description:
         A simple verticle mixing kernel that uses a markov-0 process to determine the vertical displacement of a particle.
@@ -587,7 +583,6 @@ def VerticalMixing(particle, fieldset, time):
 
     NOTES: previously called markov_0_mixing
     """
-
     # Sample the ocean vertical eddy diffusivity field KZ
     delta_z = 0.5  # [m], used to compute the gradient of kz using a forward-difference
     kz = fieldset.mixing_kz[time, particle.depth, particle.lat, particle.lon]
@@ -633,7 +628,7 @@ def VerticalMixing(particle, fieldset, time):
 
 
 def unbeaching(particle, fieldset, time):
-    """ A kernel to unbeach particles"""
+    """A kernel to unbeach particles"""
     # Measure the velocity field at the final particle location
     (vel_u, vel_v, vel_w) = fieldset.UVW[time, particle.depth + particle_ddepth, particle.lat + particle_dlat, particle.lon + particle_dlon]  # noqa
 
@@ -670,8 +665,8 @@ def checkThroughBathymetry(particle, fieldset, time):
 # @date: 2023-08-09
 
 def periodicBC(particle, fieldset, time):
-    """ Kernel to keep the particle between [-180,180] longitude
-        To be run after all movement kernels
+    """Kernel to keep the particle between [-180,180] longitude
+    To be run after all movement kernels
     """
     if particle.lon + particle_dlon <= -180.:  # noqa
         particle_dlon += 360.  # noqa
@@ -680,7 +675,7 @@ def periodicBC(particle, fieldset, time):
 
 
 def checkErrorThroughSurface(particle, fieldset, time):
-    """ Kernel to set the particle depth to the particle surface if it goes through the surface
+    """Kernel to set the particle depth to the particle surface if it goes through the surface
     """
     if particle.state == StatusCode.ErrorThroughSurface:
         # particle_ddepth = - particle.depth # Set so that final depth = 0  # TODO why not use this instead of delete?
@@ -689,7 +684,7 @@ def checkErrorThroughSurface(particle, fieldset, time):
 
 
 def deleteParticle(particle, fieldset, time):
-    """ Kernel for deleting particles if they throw an error other than through the surface
+    """Kernel for deleting particles if they throw an error other than through the surface
     """
     if particle.state >= 50 and particle.state != StatusCode.ErrorThroughSurface:
         particle.delete()

plasticparcels/scripts/create_masks.py

@@ -2,12 +2,12 @@
 
 
 """
-    TODO:
-    Come back to this on the advice from Daan:
+TODO:
+Come back to this on the advice from Daan:
 
-    https://www.mercator-ocean.eu/static-files-description/
-    Mask files can be found in /storage2/oceanparcels/data/input_data/MOi/domain_ORCA0083-N006/
-    These are downloaded directly from MOi - where though?
+https://www.mercator-ocean.eu/static-files-description/
+Mask files can be found in /storage2/oceanparcels/data/input_data/MOi/domain_ORCA0083-N006/
+These are downloaded directly from MOi - where though?
 
 
 """
@@ -37,10 +37,9 @@ def NEMO_select_section(extent, lon, lat, val):
 
 
 def to_netcdf(output_filename, data, data_name, lons, lats, explanation=''):
-    '''
+    """
     All data is written to netcdf files to speed up computations
-    '''
-
+    """
     dict_data = {}
     for data_, name_ in zip(data, data_name):
         dict_data[name_] = (["x", "y"], data_)
@@ -58,9 +57,9 @@ def to_netcdf(output_filename, data, data_name, lons, lats, explanation=''):
 
 
 def get_mask_land(field, lons, lats, outfile='./tmp_mask_land'):
-    '''
+    """
     Mask with true on land cells, false on ocean cells
-    '''
+    """
     if os.path.exists(outfile):
         ds = xr.open_dataset(outfile)
         mask_land = np.array(ds['mask_land'], dtype=bool)
@@ -120,7 +119,6 @@ def create_displacement_field(landmask, lons, lats, double_cell=False, outfile='
 
     Output: two 2D arrays, one for each camponent of the velocity.
     """
-
     if os.path.exists(outfile):
         ds = xr.open_dataset(outfile)
         v_x = np.array(ds['land_current_u'], dtype=float)
@@ -165,9 +163,9 @@ def create_displacement_field(landmask, lons, lats, double_cell=False, outfile='
 
 
 def get_mask_coast(mask_land, lons, lats, outfile='./tmp_mask_coast'):
-    '''
+    """
     calculate the coast mask. With coastal cells, we mean cells in the water, adjacent to land
-    '''
+    """
     if os.path.exists(outfile):
         ds = xr.open_dataset(outfile)
         mask_coast = np.array(ds['mask_coast'], dtype=bool)

plasticparcels/scripts/create_release_maps.py

@@ -39,7 +39,6 @@ def create_coastal_mpw_jambeck_release_map(mask_coast_filepath, coords_filepath,
 
     Parameters
     ----------
-
     mask_coast_filepath : str
         File path to the coastal mask generated in ...py TODO
     coords_filepath : str
@@ -66,7 +65,6 @@ def create_coastal_mpw_jambeck_release_map(mask_coast_filepath, coords_filepath,
     coastal_density_mpw_df
         A pandas dataframe containing the coastal grid cells, associated countries, and associated mismanaged plastic waste in kg/day.
     """
-
     # Open the Natural Earth coastline vector dataset
     shpfilename = shpreader.natural_earth(resolution='50m',
                                           category='cultural',
@@ -406,7 +404,6 @@ def create_global_concentrations_kaandorp_release_map(mask_land_filepath, mask_c
     We match this data to the model coastal and ocean cells for a better coverage release.
     We use only the 2020 data for all plastic class sizes, and for the ocean cells we only use the surface 0-5m depth.
     """
-
     # Load in the data and select year 2020, all plastic sizes, and for ocean concentrations take the surface layer
     ds = xr.open_dataset(kaandorp_filepath)
     beach = ds['concentration_beach_mass_log10'].sel({'size_nominal': 'all', 'time': 2020})

plasticparcels/utils.py

@@ -57,7 +57,6 @@ def distance(lon1, lat1, lon2, lat2):
     Calculate the great circle distance between two points
     on the earth (specified in decimal degrees)
     """
-
     # Convert decimal degrees to Radians:
     lon1r = np.radians(lon1)
     lat1r = np.radians(lat1)
@@ -100,7 +99,7 @@ def get_coords_from_polygon(shape):
 
 
 def load_settings(filename):
-    """ A function to load a settings file in json format"""
+    """A function to load a settings file in json format"""
     with open(filename, "r") as file:
         settings = json.load(file)
     return settings
@@ -126,7 +125,6 @@ def download_plasticparcels_dataset(dataset: str, settings, data_home=None):
     dataset_folder : Path
         Path to the folder containing the downloaded dataset files.
     """
-
     plasticparcels_data_files = {
         "NEMO0083": [
             (("release_maps", "coastal"), "coastal_population_MPW_NEMO0083.csv"),