Type annotations, mypy config, pydoclint setup, and other changes

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

@@ -24,8 +24,6 @@ runs:
         environment-file: ${{ inputs.environment-file }}
         python-version: ${{ inputs.python-version }}
         channels: conda-forge
-        cache-environment: true
-        cache-downloads: true
     - name: MPI support
       if: ${{ ! (runner.os == 'Windows') }}
       run: conda install -c conda-forge mpich mpi4py

.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"

.github/workflows/ci.yml

@@ -5,11 +5,13 @@ on:
       - "master"
       - "test-me/*"
   pull_request:
-    branches:
-      - "*"
   schedule:
     - cron: "0 7 * * 1" # Run every Monday at 7:00 UTC
 
+concurrency:
+  group: branch-${{ github.head_ref }}
+  cancel-in-progress: true
+
 defaults:
   run:
     shell: bash -el {0}
@@ -81,3 +83,25 @@ jobs:
         with:
           name: Integration test report
           path: ${{ matrix.os }}_integration_test_report.html
+  typechecking:
+    name: mypy
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Setup Conda and parcels
+        uses: ./.github/actions/install-parcels
+        with:
+          environment-file: environment.yml
+      - run: conda install lxml # dep for report generation
+      - name: Typechecking
+        run: |
+          mypy --install-types --non-interactive parcels --cobertura-xml-report mypy_report
+      - name: Upload mypy coverage to Codecov
+        uses: codecov/codecov-action@v3.1.1
+        if: ${{ always() }} # Upload even on error of mypy
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: mypy_report/cobertura.xml
+          flags: mypy
+          fail_ci_if_error: false

.pre-commit-config.yaml

@@ -13,14 +13,27 @@ repos:
     rev: v0.5.6
     hooks:
       - id: ruff
-        args: [ --fix ]
+        args: [--fix, --show-fixes]
       - id: ruff
         name: ruff (isort jupyter)
         args: [--select, I, --fix]
-        types_or: [ jupyter ]
+        types_or: [jupyter]
       - id: ruff-format
         types_or: [ python, jupyter ]
   - repo: https://github.com/biomejs/pre-commit
     rev: v0.4.0
     hooks:
       - id: biome-format
+
+  # Ruff doesn't have full coverage of pydoclint https://github.com/astral-sh/ruff/issues/12434
+  - repo: https://github.com/PyCQA/flake8
+    rev: 7.0.0
+    hooks:
+      - id: flake8
+        name: pydoclint
+        files: "none"
+        # files: parcels/fieldset.py # put here instead of in config file due to https://github.com/pre-commit/pre-commit-hooks/issues/112#issuecomment-215613842
+        args:
+          - --select=DOC103 # TODO: Expand coverage to other codes
+        additional_dependencies:
+          - pydoclint[flake8]

README.md

@@ -1,12 +1,13 @@
 ## Parcels
 
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/OceanParcels/parcels/master?labpath=docs%2Fexamples%2Fparcels_tutorial.ipynb)
-[![unit-tests](https://github.com/OceanParcels/parcels/actions/workflows/unit-tests.yml/badge.svg)](https://github.com/OceanParcels/parcels/actions/workflows/unit-tests.yml)
-[![codecov](https://codecov.io/gh/OceanParcels/parcels/branch/master/graph/badge.svg)](https://codecov.io/gh/OceanParcels/parcels)
 [![Anaconda-release](https://anaconda.org/conda-forge/parcels/badges/version.svg)](https://anaconda.org/conda-forge/parcels/)
 [![Anaconda-date](https://anaconda.org/conda-forge/parcels/badges/latest_release_date.svg)](https://anaconda.org/conda-forge/parcels/)
 [![Zenodo](https://zenodo.org/badge/DOI/10.5281/zenodo.823561.svg)](https://doi.org/10.5281/zenodo.823561)
+[![Code style: Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/format.json)](https://github.com/astral-sh/ruff)
+[![unit-tests](https://github.com/OceanParcels/parcels/actions/workflows/ci.yml/badge.svg)](https://github.com/OceanParcels/parcels/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/OceanParcels/parcels/branch/master/graph/badge.svg)](https://codecov.io/gh/OceanParcels/parcels)
 [![CII Best Practices](https://bestpractices.coreinfrastructure.org/projects/5353/badge)](https://bestpractices.coreinfrastructure.org/projects/5353)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/OceanParcels/parcels/master?labpath=docs%2Fexamples%2Fparcels_tutorial.ipynb)
 
 **Parcels** (**P**robably **A** **R**eally **C**omputationally **E**fficient **L**agrangian **S**imulator) is a set of Python classes and methods to create customisable particle tracking simulations using output from Ocean Circulation models. Parcels can be used to track passive and active particulates such as water, plankton, [plastic](http://www.topios.org/) and [fish](https://github.com/Jacketless/IKAMOANA).
 

codecov.yml

@@ -13,6 +13,5 @@ comment:
   require_base: false
   require_head: true
   hide_project_coverage: true
-
 # When modifying this file, please validate using
 # curl -X POST --data-binary @codecov.yml https://codecov.io/validate

environment.yml

@@ -33,10 +33,13 @@ dependencies:
   - pytest-html
   - coverage
 
+  # Typing
+  - mypy
+  - types-tqdm
+  - types-psutil
+
   # Linting
-  - flake8>=2.1.0
   - pre_commit
-  - pydocstyle
 
   # Docs
   - ipython

parcels/_compat.py

@@ -0,0 +1,19 @@
+"""Import helpers for compatability between installations."""
+
+__all__ = ["MPI", "KMeans"]
+
+from typing import Any
+
+MPI: Any | None = None
+KMeans: Any | None = None
+
+try:
+    from mpi4py import MPI  # type: ignore[no-redef]
+except ModuleNotFoundError:
+    pass
+
+# KMeans is used in MPI. sklearn not installed by default
+try:
+    from sklearn.cluster import KMeans  # type: ignore[no-redef]
+except ModuleNotFoundError:
+    pass

parcels/_typing.py

@@ -0,0 +1,45 @@
+"""
+Typing support for Parcels.
+
+This module contains type aliases used throughout Parcels as well as functions that are
+used for runtime parameter validation (to ensure users are only using the right params).
+
+"""
+
+import ast
+import datetime
+import os
+from typing import Callable, Literal
+
+
+class ParcelsAST(ast.AST):
+    ccode: str
+
+
+InterpMethodOption = Literal[
+    "linear",
+    "nearest",
+    "freeslip",
+    "partialslip",
+    "bgrid_velocity",
+    "bgrid_w_velocity",
+    "cgrid_velocity",
+    "linear_invdist_land_tracer",
+    "nearest",
+    "bgrid_tracer",
+    "cgrid_tracer",
+]  # corresponds with `tracer_interp_method`
+InterpMethod = (
+    InterpMethodOption | dict[str, InterpMethodOption]
+)  # corresponds with `interp_method` (which can also be dict mapping field names to method)
+PathLike = str | os.PathLike
+Mesh = Literal["spherical", "flat"]  # corresponds with `mesh`
+VectorType = Literal["3D", "2D"] | None  # corresponds with `vector_type`
+ChunkMode = Literal["auto", "specific", "failsafe"]  # corresponds with `chunk_mode`
+GridIndexingType = Literal["pop", "mom5", "mitgcm", "nemo"]  # corresponds with `grid_indexing_type`
+UpdateStatus = Literal["not_updated", "first_updated", "updated"]  # corresponds with `update_status`
+TimePeriodic = float | datetime.timedelta | Literal[False]  # corresponds with `update_status`
+NetcdfEngine = Literal["netcdf4", "xarray", "scipy"]
+
+
+KernelFunction = Callable[..., None]

parcels/compilation/codecompiler.py

@@ -2,10 +2,7 @@
 import subprocess
 from struct import calcsize
 
-try:
-    from mpi4py import MPI
-except ModuleNotFoundError:
-    MPI = None
+from parcels._compat import MPI
 
 _tmp_dir = os.getcwd()
 

parcels/compilation/codegenerator.py

@@ -410,7 +410,7 @@ class KernelGenerator(ABC, ast.NodeVisitor):
 
     # Intrinsic variables that appear as function arguments
     kernel_vars = ["particle", "fieldset", "time", "output_time", "tol"]
-    array_vars = []
+    array_vars: list[str] = []
 
     def __init__(self, fieldset=None, ptype=JITParticle):
         self.fieldset = fieldset
@@ -419,7 +419,7 @@ def __init__(self, fieldset=None, ptype=JITParticle):
         self.vector_field_args = collections.OrderedDict()
         self.const_args = collections.OrderedDict()
 
-    def generate(self, py_ast, funcvars):
+    def generate(self, py_ast, funcvars: list[str]):
         # Replace occurrences of intrinsic objects in Python AST
         transformer = IntrinsicTransformer(self.fieldset, self.ptype)
         py_ast = transformer.visit(py_ast)
@@ -434,7 +434,7 @@ def generate(self, py_ast, funcvars):
         # Insert variable declarations for non-intrinsic variables
         # Make sure that repeated variables are not declared more than
         # once. If variables occur in multiple Kernels, give a warning
-        used_vars = []
+        used_vars: list[str] = []
         funcvars_copy = copy(funcvars)  # editing a list while looping over it is dangerous
         for kvar in funcvars:
             if kvar in used_vars + ["particle_dlon", "particle_dlat", "particle_ddepth"]: