Merge branch 'OceanParcels:master' into kdtree-with-nans

.github/ISSUE_TEMPLATE/general-issue.md

@@ -1,8 +1,7 @@
 ---
 name: Parcels feature requests, enhancements, or bug reporting
 about: Create an Issue about bugs in the Parcels codebase, or required improvements
-title: ''
-labels: ''
-assignees: ''
-
+title: ""
+labels: ""
+assignees: ""
 ---

.github/workflows/pypi-release.yaml

@@ -5,7 +5,7 @@ on:
       - published
   push:
     tags:
-      - 'v*'
+      - "v*"
   workflow_dispatch:
 
 jobs:
@@ -79,7 +79,6 @@ jobs:
           repository_url: https://test.pypi.org/legacy/
           verbose: true
 
-
   upload-to-pypi:
     needs: test-built-dist
     if: github.event_name == 'release'

.github/workflows/unit-tests.yml

@@ -22,7 +22,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [macos, ubuntu, windows]
-        include:  # TODO check if these can go?
+        include: # TODO check if these can go?
           - os: macos
             os-short: osx
           - os: ubuntu

.pre-commit-config.yaml

@@ -1,30 +1,34 @@
 repos:
--   repo: https://github.com/pre-commit/pre-commit-hooks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.5.0
     hooks:
-    -   id: trailing-whitespace
-    -   id: end-of-file-fixer
-    -   id: check-yaml
-    -   id: check-ast
-    -   id: check-json
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-ast
+      - id: check-json
         types: [text]
         files: \.(json|ipynb)$
--   repo: https://github.com/pycqa/flake8
-    rev: '6.1.0'
+  - repo: https://github.com/pycqa/flake8
+    rev: "6.1.0"
     hooks:
-    -   id: flake8
--   repo: https://github.com/pycqa/pydocstyle
-    rev: 6.3.0  # pick a git hash / tag to point to
+      - id: flake8
+  - repo: https://github.com/pycqa/pydocstyle
+    rev: 6.3.0 # pick a git hash / tag to point to
     hooks:
-    -   id: pydocstyle
--   repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.7.0
+      - id: pydocstyle
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.7.1
     hooks:
-    -   id: nbqa-black
-    -   id: nbqa-check-ast
-    -   id: nbqa-isort
--   repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+      - id: nbqa-black
+      - id: nbqa-check-ast
+      - id: nbqa-isort
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
     hooks:
-    -   id: isort
+      - id: isort
         name: isort (python)
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v3.1.0"
+    hooks:
+      - id: prettier

.prettierignore

@@ -0,0 +1 @@
+docs/_templates

CITATION.cff

@@ -1,20 +1,20 @@
 cff-version: 1.2.0
 message: "If you use this software, please cite it as below."
 authors:
-- family-names: "Van Sebille"
-  given-names: "Erik"
-  orcid: "https://orcid.org/0000-0003-2041-0704"
-- family-names: "Kehl"
-  given-names: "Christian"
-  orcid: "https://orcid.org/0000-0003-4200-1450"
-- family-names: "Lange"
-  given-names: "Michael"
-  orcid: "https://orcid.org/0000-0002-3232-0127"
-- family-names: "Delandmeter"
-  given-names: "Philippe"
-  orcid: "https://orcid.org/0000-0003-0100-5834"
-- name: "The Parcels contributors"
-  website: "https://github.com/OceanParcels/parcels/graphs/contributors"
+  - family-names: "Van Sebille"
+    given-names: "Erik"
+    orcid: "https://orcid.org/0000-0003-2041-0704"
+  - family-names: "Kehl"
+    given-names: "Christian"
+    orcid: "https://orcid.org/0000-0003-4200-1450"
+  - family-names: "Lange"
+    given-names: "Michael"
+    orcid: "https://orcid.org/0000-0002-3232-0127"
+  - family-names: "Delandmeter"
+    given-names: "Philippe"
+    orcid: "https://orcid.org/0000-0003-0100-5834"
+  - name: "The Parcels contributors"
+    website: "https://github.com/OceanParcels/parcels/graphs/contributors"
 title: "Parcels"
 version: 2.4.2
 doi: 10.5281/zenodo.8010997

CODE_OF_CONDUCT.md

@@ -8,19 +8,19 @@ In the interest of fostering an open and welcoming environment, we as contributo
 
 Examples of behavior that contributes to creating a positive environment include:
 
-* Using welcoming and inclusive language
-* Being respectful of differing viewpoints and experiences
-* Gracefully accepting constructive criticism
-* Focusing on what is best for the community
-* Showing empathy towards other community members
+- Using welcoming and inclusive language
+- Being respectful of differing viewpoints and experiences
+- Gracefully accepting constructive criticism
+- Focusing on what is best for the community
+- Showing empathy towards other community members
 
 Examples of unacceptable behavior by participants include:
 
-* The use of sexualized language or imagery and unwelcome sexual attention or advances
-* Trolling, insulting/derogatory comments, and personal or political attacks
-* Public or private harassment
-* Publishing others' private information, such as a physical or electronic address, without explicit permission
-* Other conduct which could reasonably be considered inappropriate in a professional setting
+- The use of sexualized language or imagery and unwelcome sexual attention or advances
+- Trolling, insulting/derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information, such as a physical or electronic address, without explicit permission
+- Other conduct which could reasonably be considered inappropriate in a professional setting
 
 ## Our Responsibilities
 

README.md

@@ -4,27 +4,26 @@
 
 ![Arctic-SO-medusaParticles](https://github.com/OceanParcels/oceanparcels_website/blob/master/images/homepage.gif)
 
-*Animation of virtual particles carried by ocean surface flow in the global oceans. The particles are advected with [Parcels](http://oceanparcels.org/) in data from the [NEMO Ocean Model](https://www.nemo-ocean.eu/).*
+_Animation of virtual particles carried by ocean surface flow in the global oceans. The particles are advected with [Parcels](http://oceanparcels.org/) in data from the [NEMO Ocean Model](https://www.nemo-ocean.eu/)._
 
 ### Parcels manuscript and code
 
 The manuscript detailing the first release of Parcels, version 0.9, has been published in [Geoscientific Model Development](https://www.geosci-model-dev.net/10/4175/2017/gmd-10-4175-2017.html) and can be cited as
 
-*Lange, M and E van Sebille (2017) Parcels v0.9: prototyping a Lagrangian Ocean Analysis framework for the petascale age. Geoscientific Model Development, 10, 4175-4186. https://doi.org/10.5194/gmd-2017-167*
+_Lange, M and E van Sebille (2017) Parcels v0.9: prototyping a Lagrangian Ocean Analysis framework for the petascale age. Geoscientific Model Development, 10, 4175-4186. https://doi.org/10.5194/gmd-2017-167_
 
 The manuscript detailing version 2.0 of Parcels is available at [Geoscientific Model Development](https://www.geosci-model-dev.net/12/3571/2019/gmd-12-3571-2019-discussion.html) and can be cited as:
 
-*Delandmeter, P and E van Sebille (2019) The Parcels v2.0 Lagrangian framework: new field interpolation schemes. Geoscientific Model Development, 12, 3571-3584. https://doi.org/10.5194/gmd-12-3571-2019*
+_Delandmeter, P and E van Sebille (2019) The Parcels v2.0 Lagrangian framework: new field interpolation schemes. Geoscientific Model Development, 12, 3571-3584. https://doi.org/10.5194/gmd-12-3571-2019_
 
 The manuscript detailing the performance of Parcels v2.4 is available at [Computers & Geosciences](https://doi.org/10.1016/j.cageo.2023.105322) and can be cited as:
 
-*Kehl, C, PD Nooteboom, MLA Kaandorp and E van Sebille (2023) Efficiently simulating Lagrangian particles in large-scale ocean flows — Data structures and their impact on geophysical applications, Computers and Geosciences, 175, 105322. https://doi.org/10.1016/j.cageo.2023.105322*
+_Kehl, C, PD Nooteboom, MLA Kaandorp and E van Sebille (2023) Efficiently simulating Lagrangian particles in large-scale ocean flows — Data structures and their impact on geophysical applications, Computers and Geosciences, 175, 105322. https://doi.org/10.1016/j.cageo.2023.105322_
 
 ### Further information
 
 See [oceanparcels.org](http://oceanparcels.org/) for further information about [installing](https://docs.oceanparcels.org/en/latest/installation.html) and [running](https://docs.oceanparcels.org/en/latest/documentation.html) the Parcels code, as well as extended [documentation](https://docs.oceanparcels.org/en/latest/reference.html) of the methods and classes.
 
-
 ### Launch Parcels Tutorials on [mybinder.org](https://mybinder.org/v2/gh/OceanParcels/parcels/master?labpath=docs%2Fexamples%2Fparcels_tutorial.ipynb)
 
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/OceanParcels/parcels/master?labpath=docs%2Fexamples%2Fparcels_tutorial.ipynb)

docs/contributing.md

@@ -5,41 +5,36 @@ Even if you don't want to contribute directly to the codebase, getting involved
 
 This document outlines some guidelines for contributing to the parcels codebase. If you have any questions or suggestions for how we can improve this document, please let us know.
 
-
 ## Getting Started
 
 To get started contributing to parcels, you'll need to install the developer version of Parcels following [our installation instructions](installation.rst#installation-for-developers). This will install the latest version of Parcels from the `master` branch of the repository.
 
 **Optional:** Setup `pre-commit` hooks by running `pre-commit install`. This ensures that code is formatted correctly before you commit it.
 
-
 ## Making Changes
 
 Once you have a working environment, you can start making changes to the code! Here are some general guidelines to follow when making changes:
 
-* Follow the [NumPy docstring conventions](https://numpydoc.readthedocs.io/en/latest/format.html) when adding or modifying docstrings.
-
-* Follow the [PEP 8](https://peps.python.org/pep-0008/) style guide when writing code. This codebase also uses [flake8](https://flake8.pycqa.org/en/latest/) and [isort](https://pycqa.github.io/isort/) to ensure a consistent code style (these tools are run automatically by pre-commit).
+- Follow the [NumPy docstring conventions](https://numpydoc.readthedocs.io/en/latest/format.html) when adding or modifying docstrings.
 
-* Use Git to manage your changes. Create a new branch for each feature or bug fix.
+- Follow the [PEP 8](https://peps.python.org/pep-0008/) style guide when writing code. This codebase also uses [flake8](https://flake8.pycqa.org/en/latest/) and [isort](https://pycqa.github.io/isort/) to ensure a consistent code style (these tools are run automatically by pre-commit).
 
-* Write clear commit messages that explain the changes you've made.
+- Use Git to manage your changes. Create a new branch for each feature or bug fix.
 
-* Include tests for any new code you write.
+- Write clear commit messages that explain the changes you've made.
 
-* Submit your changes as a pull request to the `master` branch, and wait for feedback!
+- Include tests for any new code you write.
 
+- Submit your changes as a pull request to the `master` branch, and wait for feedback!
 
 ```{note}
 Feel free to create an issue for your proposed feature or change to the codebase so that feedback can be given.
 Submitting a "draft pull request" is also a great way to give visibility to your branch during development, allowing for faster feedback.
 ```
 
-
 ## Working with documentation
 
 The documentation for this project is processed by Sphinx. To view documentation from your changes, you can run
 `sphinx-autobuild --ignore "*.zip" docs docs/_build` to create a server to automatically rebuild the documentation when you make changes.
 
-
 If you have any questions or issues while contributing to parcels, please feel free to [open a discussion](https://github.com/OceanParcels/parcels/discussions). Thank you for your contributions!

docs/examples/tutorial_timestamps.ipynb

@@ -155,7 +155,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Note, by the way, that adding the `time_periodic=True` argument to `Field.from_netcdf()` will also mean that the climatology can be cycled for multiple years.\n"
+    "Note, by the way, that adding the `time_periodic` argument to `Field.from_netcdf()` will also mean that the climatology can be cycled for multiple years.\n"
    ]
   },
   {

parcels/particlefile.py

@@ -142,7 +142,7 @@ def _create_variables_attribute_dict(self):
 
         if self.time_origin.calendar is not None:
             attrs['time']['units'] = "seconds since " + str(self.time_origin)
-            attrs['time']['calendar'] = 'standard' if self.time_origin.calendar == 'np_datetime64' else self.time_origin.calendar
+            attrs['time']['calendar'] = _set_calendar(self.time_origin.calendar)
 
         for vname in self.vars_to_write:
             if vname not in ['time', 'lat', 'lon', 'depth', 'id']:
@@ -183,7 +183,7 @@ def _extend_zarr_dims(self, Z, store, dtype, axis):
             if len(obs) == Z.shape[1]:
                 obs.append(np.arange(self.chunks[1])+obs[-1]+1)
         else:
-            extra_trajs = max(self.maxids - Z.shape[0], self.chunks[0])
+            extra_trajs = self.maxids - Z.shape[0]
             if len(Z.shape) == 2:
                 a = np.full((extra_trajs, Z.shape[1]), self.fill_value_map[dtype], dtype=dtype)
             else:
@@ -233,7 +233,7 @@ def write(self, pset, time, indices=None):
                 if (self.maxids > len(ids)) or (self.maxids > self.chunks[0]):
                     arrsize = (self.maxids, self.chunks[1])
                 else:
-                    arrsize = (len(ids), 1)
+                    arrsize = (len(ids), self.chunks[1])
                 ds = xr.Dataset(attrs=self.metadata, coords={"trajectory": ("trajectory", pids),
                                                              "obs": ("obs", np.arange(arrsize[1], dtype=np.int32))})
                 attrs = self._create_variables_attribute_dict()

tests/test_particlefile.py

@@ -244,6 +244,25 @@ def IncrLon(particle, fieldset, time):
     ds.close()
 
 
+@pytest.mark.parametrize('mode', ['scipy', 'jit'])
+@pytest.mark.parametrize('repeatdt', [1, 2])
+@pytest.mark.parametrize('nump', [1, 10])
+def test_pfile_chunks_repeatedrelease(fieldset, mode, repeatdt, nump, tmpdir):
+    runtime = 8
+    pset = ParticleSet(fieldset, pclass=ptype[mode], lon=np.zeros((nump, 1)),
+                       lat=np.zeros((nump, 1)), repeatdt=repeatdt)
+    outfilepath = tmpdir.join("pfile_chunks_repeatedrelease.zarr")
+    chunks = (20, 10)
+    pfile = pset.ParticleFile(outfilepath, outputdt=1, chunks=chunks)
+
+    def DoNothing(particle, fieldset, time):
+        pass
+
+    pset.execute(DoNothing, dt=1, runtime=runtime, output_file=pfile)
+    ds = xr.open_zarr(outfilepath)
+    assert ds['time'].shape == (int(nump*runtime/repeatdt), chunks[1])
+
+
 @pytest.mark.parametrize('mode', ['scipy', 'jit'])
 def test_write_timebackward(fieldset, mode, tmpdir):
     outfilepath = tmpdir.join("pfile_write_timebackward.zarr")