Merge pull request #1658 from OceanParcels/v/spec0

Drop Python 3.8, 3.9 support and expand CI unit testing

.github/actions/install-parcels/action.yml

@@ -7,6 +7,9 @@ inputs:
   environment-file:
     description: Conda environment file to use.
     default: environment.yml
+  python-version:
+    description: Python version to use.
+    default: ""
 runs:
   using: "composite"
   steps:
@@ -19,6 +22,7 @@ runs:
       uses: conda-incubator/setup-miniconda@v3
       with:
         environment-file: ${{ inputs.environment-file }}
+        python-version: ${{ inputs.python-version }}
         channels: conda-forge
         cache-environment: true
         cache-downloads: true

.github/workflows/pypi-release.yml

@@ -19,7 +19,7 @@ jobs:
       - uses: actions/setup-python@v3
         name: Install Python
         with:
-          python-version: 3.8
+          python-version: 3.10
 
       - name: Install dependencies
         run: |
@@ -54,7 +54,7 @@ jobs:
       - uses: actions/setup-python@v3
         name: Install Python
         with:
-          python-version: 3.8
+          python-version: 3.10
       - uses: actions/download-artifact@v3
         with:
           name: releases
@@ -102,7 +102,7 @@ jobs:
       - uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: parcels
-          python-version: 3.8
+          python-version: 3.10
           channels: conda-forge
       - run: conda install -c conda-forge c-compiler pip
       - run: pip install parcels --no-cache

.github/workflows/unit-tests.yml

@@ -16,22 +16,29 @@ defaults:
 
 jobs:
   unit-test:
-    name: Unittesting on ${{ matrix.os }} with python latest
+    name: Unittesting on ${{ matrix.os }} with python ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}-latest
     strategy:
       fail-fast: false
       matrix:
         os: [macos, ubuntu, windows]
+        python-version: ["3.12"]
+        include:
+          - os: ubuntu
+            python-version: "3.10"
+          - os: ubuntu
+            python-version: "3.11"
     steps:
       - name: Checkout
         uses: actions/checkout@v3
       - name: Setup Conda and parcels
         uses: ./.github/actions/install-parcels
         with:
           environment-file: environment.yml
+          python-version: ${{ matrix.python-version }}
       - name: Unit test
         run: |
-          coverage run -m pytest -v -s --html=${{ matrix.os }}_unit_test_report.html --self-contained-html tests
+          coverage run -m pytest -v -s --html=${{ matrix.os }}_${{ matrix.python-version }}_unit_test_report.html --self-contained-html tests
           coverage xml
       - name: Codecov
         uses: codecov/[email protected]
@@ -42,4 +49,4 @@ jobs:
         uses: actions/[email protected]
         with:
           name: Unittest report
-          path: ${{ matrix.os }}_unit_test_report.html
+          path: ${{ matrix.os }}_${{ matrix.python-version }}_unit_test_report.html

docs/installation.rst

@@ -1,7 +1,7 @@
 Basic installation
 ==================
 
-The simplest way to install the Parcels code is to use Anaconda and the `Parcels conda-forge package <https://anaconda.org/conda-forge/parcels>`_ with the latest release of Parcels. This package will automatically install all the requirements for a fully functional installation of Parcels. This is the “batteries-included” solution probably suitable for most users.
+The simplest way to install the Parcels code is to use Anaconda and the `Parcels conda-forge package <https://anaconda.org/conda-forge/parcels>`_ with the latest release of Parcels. This package will automatically install all the requirements for a fully functional installation of Parcels. This is the “batteries-included” solution probably suitable for most users. Note that we support Python 3.10 and higher.
 
 If you want to install the latest development version of Parcels and work with features that have not yet been officially released, you can follow the instructions for a `developer installation <#installation-for-developers>`_.
 

environment.yml

@@ -2,7 +2,7 @@ name: parcels
 channels:
   - conda-forge
 dependencies:
-  - python>=3.8
+  - python>=3.10
   - cgen
   - ffmpeg>=3.2.3
   - git

parcels/compilation/codegenerator.py

@@ -396,7 +396,7 @@ def visit_Assign(self, node):
             if len(t_elts) != len(v_elts):
                 raise AttributeError("Tuple lengths in assignment do not agree")
             node = [ast.Assign() for _ in t_elts]
-            for n, t, v in zip(node, t_elts, v_elts):
+            for n, t, v in zip(node, t_elts, v_elts, strict=True):
                 n.targets = [t]
                 n.value = v
         return node

parcels/field.py

@@ -569,7 +569,7 @@ def from_netcdf(
             # Pre-allocate data before reading files into buffer
             data_list = []
             ti = 0
-            for tslice, fname in zip(grid.timeslices, data_filenames):
+            for tslice, fname in zip(grid.timeslices, data_filenames, strict=True):
                 with _field_fb_class(
                     fname,
                     dimensions,
@@ -798,8 +798,8 @@ def calc_cell_edge_sizes(self):
 
                 x_conv = GeographicPolar() if self.grid.mesh == "spherical" else UnitConverter()
                 y_conv = Geographic() if self.grid.mesh == "spherical" else UnitConverter()
-                for y, (lat, dy) in enumerate(zip(self.grid.lat, np.gradient(self.grid.lat))):
-                    for x, (lon, dx) in enumerate(zip(self.grid.lon, np.gradient(self.grid.lon))):
+                for y, (lat, dy) in enumerate(zip(self.grid.lat, np.gradient(self.grid.lat), strict=False)):
+                    for x, (lon, dx) in enumerate(zip(self.grid.lon, np.gradient(self.grid.lon), strict=False)):
                         self.grid.cell_edge_sizes["x"][y, x] = x_conv.to_source(dx, lon, lat, self.grid.depth[0])
                         self.grid.cell_edge_sizes["y"][y, x] = y_conv.to_source(dy, lon, lat, self.grid.depth[0])
                 self.cell_edge_sizes = self.grid.cell_edge_sizes
@@ -2295,13 +2295,13 @@ def __init__(self, name, F, V=None, W=None):
                 ), "Components of a NestedField must be Field or VectorField"
                 self.append(Fi)
         elif W is None:
-            for i, Fi, Vi in zip(range(len(F)), F, V):
+            for i, Fi, Vi in zip(range(len(F)), F, V, strict=True):
                 assert isinstance(Fi, Field) and isinstance(
                     Vi, Field
                 ), "F, and V components of a NestedField must be Field"
                 self.append(VectorField(name + "_%d" % i, Fi, Vi))
         else:
-            for i, Fi, Vi, Wi in zip(range(len(F)), F, V, W):
+            for i, Fi, Vi, Wi in zip(range(len(F)), F, V, W, strict=True):
                 assert (
                     isinstance(Fi, Field) and isinstance(Vi, Field) and isinstance(Wi, Field)
                 ), "F, V and W components of a NestedField must be Field"

parcels/fieldset.py

@@ -280,7 +280,7 @@ def check_velocityfields(U, V, W):
 
         if isinstance(self.U, NestedField):
             w = self.W if hasattr(self, "W") else [None] * len(self.U)
-            for U, V, W in zip(self.U, self.V, w):
+            for U, V, W in zip(self.U, self.V, w, strict=True):
                 check_velocityfields(U, V, W)
         else:
             W = self.W if hasattr(self, "W") else None

parcels/interaction/neighborsearch/basehash.py

@@ -197,4 +197,4 @@ def hash_split(hash_ids, active_idx=None):
     unq_items = a_sorted[unq_first]
     unq_count = np.diff(np.nonzero(unq_first)[0])
     unq_idx = np.split(sort_idx, np.cumsum(unq_count))
-    return dict(zip(unq_items, unq_idx))
+    return dict(zip(unq_items, unq_idx, strict=True))

parcels/kernel.py

@@ -248,7 +248,7 @@ def __init__(
             fieldset = self.fieldset
             for f in self.vector_field_args.values():
                 Wname = f.W.ccode_name if f.W else "not_defined"
-                for sF_name, sF_component in zip([f.U.ccode_name, f.V.ccode_name, Wname], ["U", "V", "W"]):
+                for sF_name, sF_component in zip([f.U.ccode_name, f.V.ccode_name, Wname], ["U", "V", "W"], strict=True):
                     if sF_name not in self.field_args:
                         if sF_name != "not_defined":
                             self.field_args[sF_name] = getattr(f, sF_component)

pyproject.toml

@@ -8,13 +8,13 @@ description = "Framework for Lagrangian tracking of virtual ocean particles in t
 readme = "README.md"
 dynamic = ["version"]
 authors = [{name = "oceanparcels.org team"}]
-requires-python = ">=3.8"
+requires-python = ">=3.10"
 license = {file = "LICENSE.md"}
 classifiers = [
   "License :: OSI Approved :: MIT License",
-  "Programming Language :: Python :: 3.8",
-  "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
   "Operating System :: OS Independent",
   "Topic :: Scientific/Engineering",
   "Intended Audience :: Science/Research",
@@ -54,7 +54,7 @@ local_scheme = "no-local-version"
 python_files = ["test_*.py", "example_*.py", "*tutorial*"]
 
 [tool.ruff]
-target-version = "py38"
+target-version = "py310"
 line-length = 120
 
 [tool.ruff.lint]

tests/test_advection.py

@@ -352,8 +352,8 @@ def test_stationary_eddy(fieldset_stationary, mode, method, rtol, diffField, npa
     pset = ParticleSet(fieldset, pclass=pclass, lon=lon, lat=lat)
     pset.execute(kernel[method], dt=dt, endtime=endtime)
 
-    exp_lon = [truth_stationary(x, y, pset[0].time)[0] for x, y in zip(lon, lat)]
-    exp_lat = [truth_stationary(x, y, pset[0].time)[1] for x, y in zip(lon, lat)]
+    exp_lon = [truth_stationary(x, y, pset[0].time)[0] for x, y in zip(lon, lat, strict=True)]
+    exp_lat = [truth_stationary(x, y, pset[0].time)[1] for x, y in zip(lon, lat, strict=True)]
     assert np.allclose(pset.lon, exp_lon, rtol=rtol)
     assert np.allclose(pset.lat, exp_lat, rtol=rtol)
 
@@ -380,8 +380,8 @@ def test_stationary_eddy_vertical(mode, npart=1):
 
     pset = ParticleSet(fieldset, pclass=ptype[mode], lon=lon, lat=lat, depth=depth)
     pset.execute(AdvectionRK4_3D, dt=dt, endtime=endtime)
-    exp_lon = [truth_stationary(x, z, pset[0].time)[0] for x, z in zip(lon, depth)]
-    exp_depth = [truth_stationary(x, z, pset[0].time)[1] for x, z in zip(lon, depth)]
+    exp_lon = [truth_stationary(x, z, pset[0].time)[0] for x, z in zip(lon, depth, strict=True)]
+    exp_depth = [truth_stationary(x, z, pset[0].time)[1] for x, z in zip(lon, depth, strict=True)]
     print(pset, exp_lon)
     assert np.allclose(pset.lon, exp_lon, rtol=1e-5)
     assert np.allclose(pset.lat, lat, rtol=1e-5)
@@ -392,8 +392,8 @@ def test_stationary_eddy_vertical(mode, npart=1):
 
     pset = ParticleSet(fieldset, pclass=ptype[mode], lon=lon, lat=lat, depth=depth)
     pset.execute(AdvectionRK4_3D, dt=dt, endtime=endtime)
-    exp_depth = [truth_stationary(z, y, pset[0].time)[0] for z, y in zip(depth, lat)]
-    exp_lat = [truth_stationary(z, y, pset[0].time)[1] for z, y in zip(depth, lat)]
+    exp_depth = [truth_stationary(z, y, pset[0].time)[0] for z, y in zip(depth, lat, strict=True)]
+    exp_lat = [truth_stationary(z, y, pset[0].time)[1] for z, y in zip(depth, lat, strict=True)]
     assert np.allclose(pset.lon, lon, rtol=1e-5)
     assert np.allclose(pset.lat, exp_lat, rtol=1e-5)
     assert np.allclose(pset.depth, exp_depth, rtol=1e-5)
@@ -453,8 +453,8 @@ def test_moving_eddy(fieldset_moving, mode, method, rtol, diffField, npart=1):
     pset = ParticleSet(fieldset, pclass=pclass, lon=lon, lat=lat)
     pset.execute(kernel[method], dt=dt, endtime=endtime)
 
-    exp_lon = [truth_moving(x, y, t)[0] for x, y, t in zip(lon, lat, pset.time)]
-    exp_lat = [truth_moving(x, y, t)[1] for x, y, t in zip(lon, lat, pset.time)]
+    exp_lon = [truth_moving(x, y, t)[0] for x, y, t in zip(lon, lat, pset.time, strict=True)]
+    exp_lat = [truth_moving(x, y, t)[1] for x, y, t in zip(lon, lat, pset.time, strict=True)]
     assert np.allclose(pset.lon, exp_lon, rtol=rtol)
     assert np.allclose(pset.lat, exp_lat, rtol=rtol)
 
@@ -531,8 +531,8 @@ def test_decaying_eddy(fieldset_decaying, mode, method, rtol, diffField, npart=1
     pset = ParticleSet(fieldset, pclass=pclass, lon=lon, lat=lat)
     pset.execute(kernel[method], dt=dt, endtime=endtime)
 
-    exp_lon = [truth_decaying(x, y, t)[0] for x, y, t in zip(lon, lat, pset.time)]
-    exp_lat = [truth_decaying(x, y, t)[1] for x, y, t in zip(lon, lat, pset.time)]
+    exp_lon = [truth_decaying(x, y, t)[0] for x, y, t in zip(lon, lat, pset.time, strict=True)]
+    exp_lat = [truth_decaying(x, y, t)[1] for x, y, t in zip(lon, lat, pset.time, strict=True)]
     assert np.allclose(pset.lon, exp_lon, rtol=rtol)
     assert np.allclose(pset.lat, exp_lat, rtol=rtol)
 

tests/test_fieldset.py

@@ -156,7 +156,9 @@ def test_field_from_netcdf_variables():
         f3 = Field.from_netcdf(filename, variable, dims)
 
 
-@pytest.mark.parametrize("calendar, cftime_datetime", zip(_get_cftime_calendars(), _get_cftime_datetimes()))
+@pytest.mark.parametrize(
+    "calendar, cftime_datetime", zip(_get_cftime_calendars(), _get_cftime_datetimes(), strict=True)
+)
 def test_fieldset_nonstandardtime(
     calendar, cftime_datetime, tmpdir, filename="test_nonstandardtime.nc", xdim=4, ydim=6
 ):

tests/test_particlefile.py

@@ -322,17 +322,17 @@ def SampleP(particle, fieldset, time):
         assert (pxi0[p, 0] == 0) and (pxi0[p, -1] == pset[p].pxi0)  # check that particle has moved
         assert np.all(pxi1[p, :6] == 0)  # check that particle has not been sampled on grid 1 until time 6
         assert np.all(pxi1[p, 6:] > 0)  # check that particle has not been sampled on grid 1 after time 6
-        for xi, lon in zip(pxi0[p, 1:], lons[p, 1:]):
+        for xi, lon in zip(pxi0[p, 1:], lons[p, 1:], strict=True):
             assert fieldset.U.grid.lon[xi] <= lon < fieldset.U.grid.lon[xi + 1]
-        for xi, lon in zip(pxi1[p, 6:], lons[p, 6:]):
+        for xi, lon in zip(pxi1[p, 6:], lons[p, 6:], strict=True):
             assert fieldset.P.grid.lon[xi] <= lon < fieldset.P.grid.lon[xi + 1]
-        for yi, lat in zip(pyi[p, 1:], lats[p, 1:]):
+        for yi, lat in zip(pyi[p, 1:], lats[p, 1:], strict=True):
             assert fieldset.U.grid.lat[yi] <= lat < fieldset.U.grid.lat[yi + 1]
     ds.close()
 
 
 def test_set_calendar():
-    for _calendar_name, cf_datetime in zip(_get_cftime_calendars(), _get_cftime_datetimes()):
+    for _calendar_name, cf_datetime in zip(_get_cftime_calendars(), _get_cftime_datetimes(), strict=True):
         date = getattr(cftime, cf_datetime)(1990, 1, 1)
         assert _set_calendar(date.calendar) == date.calendar
     assert _set_calendar("np_datetime64") == "standard"

tests/test_particlesets.py

@@ -323,7 +323,7 @@ def test_pset_remove_index(fieldset, mode, npart=100):
     lon = np.linspace(0, 1, npart)
     lat = np.linspace(1, 0, npart)
     pset = ParticleSet(fieldset, lon=lon, lat=lat, pclass=ptype[mode], lonlatdepth_dtype=np.float64)
-    for ilon, ilat in zip(lon[::-1], lat[::-1]):
+    for ilon, ilat in zip(lon[::-1], lat[::-1], strict=True):
         assert pset[-1].lon == ilon
         assert pset[-1].lat == ilat
         pset.remove_indices(-1)
@@ -336,7 +336,7 @@ def test_pset_remove_particle(fieldset, mode, npart=100):
     lon = np.linspace(0, 1, npart)
     lat = np.linspace(1, 0, npart)
     pset = ParticleSet(fieldset, lon=lon, lat=lat, pclass=ptype[mode])
-    for ilon, ilat in zip(lon[::-1], lat[::-1]):
+    for ilon, ilat in zip(lon[::-1], lat[::-1], strict=True):
         assert pset.lon[-1] == ilon
         assert pset.lat[-1] == ilat
         pset.remove_indices(pset[-1])