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Merge branch 'v4-dev' into feature/from_fesom2
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‎.github/workflows/additional.yml‎

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@@ -13,7 +13,7 @@ jobs:
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shell: bash -l {0}
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steps:
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- uses: actions/checkout@v4
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- uses: actions/checkout@v5
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- name: Setup micromamba
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uses: mamba-org/setup-micromamba@v2
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with:
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shell: bash -l {0}
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steps:
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- uses: actions/checkout@v4
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- uses: actions/checkout@v4
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- uses: actions/checkout@v5
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- uses: actions/checkout@v5
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- uses: prefix-dev/[email protected]
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- run: pixi run docs-linkcheck

‎.github/workflows/cache-pixi-lock.yml‎

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@@ -2,6 +2,9 @@ name: Generate and cache Pixi lockfile
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on:
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workflow_call:
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inputs:
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pixi-version:
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type: string
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outputs:
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cache-id:
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description: "The lock file contents"
@@ -17,6 +20,7 @@ jobs:
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- uses: actions/checkout@v5
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with:
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fetch-depth: 0
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submodules: recursive
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- name: Get current date
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id: date
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run: echo "date=$(date +'%Y-%m-%d')" >> "$GITHUB_OUTPUT"
@@ -25,11 +29,11 @@ jobs:
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with:
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path: |
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pixi.lock
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key: ${{ steps.date.outputs.date }}_${{hashFiles('pixi.toml')}}
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key: ${{ steps.date.outputs.date }}_${{inputs.pixi-version}}_${{hashFiles('pixi.toml')}}
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- uses: prefix-dev/[email protected]
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if: ${{ !steps.restore.outputs.cache-hit }}
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with:
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pixi-version: v0.56.0
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pixi-version: ${{ inputs.pixi-version }}
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run-install: false
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- name: Run pixi lock
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if: ${{ !steps.restore.outputs.cache-hit }}
@@ -42,7 +46,7 @@ jobs:
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pixi.lock
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key: ${{ steps.restore.outputs.cache-primary-key }}
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- name: Upload pixi.lock
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uses: actions/upload-artifact@v4
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uses: actions/upload-artifact@v5
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with:
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name: pixi-lock
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path: pixi.lock

‎.github/workflows/ci.yml‎

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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu] #, mac, windows] # TODO v4: Re-enable windows and mac
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os: [ubuntu, mac, windows]
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pixi-environment: [test-latest]
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include:
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- os: ubuntu
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pixi-environment: "test-py311"
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- os: ubuntu
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pixi-environment: "test-py313"
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- os: ubuntu
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pixi-environment: "test-minimum"
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steps:
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- uses: actions/checkout@v4
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- uses: actions/checkout@v5
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- name: Restore cached pixi lockfile
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uses: actions/cache/restore@v4
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id: restore-pixi-lock
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with:
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enableCrossOsArchive: true
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path: |
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pixi.lock
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key: ${{ needs.cache-pixi-lock.outputs.cache-id }}
@@ -52,14 +55,14 @@ jobs:
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run: |
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pixi run -e ${{ matrix.pixi-environment }} tests -v -s --cov=parcels --cov-report=xml --html="${{ env.COVERAGE_REPORT }}" --self-contained-html
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- name: Codecov
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uses: codecov/codecov-action@v5.3.1
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uses: codecov/codecov-action@v5.5.1
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env:
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CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
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with:
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flags: unit-tests
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- name: Upload test results
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if: ${{ always() }} # Always run this step, even if tests fail
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uses: actions/upload-artifact@v4
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uses: actions/upload-artifact@v5
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with:
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name: Unittest report ${{ matrix.os }}-${{ matrix.pixi-environment }}
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path: ${{ env.COVERAGE_REPORT }}
@@ -80,11 +83,12 @@ jobs:
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- os: ubuntu
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python-version: "3.11"
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steps:
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- uses: actions/checkout@v4
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- uses: actions/checkout@v5
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- name: Restore cached pixi lockfile
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uses: actions/cache/restore@v4
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id: restore-pixi-lock
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with:
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enableCrossOsArchive: true
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path: |
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pixi.lock
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key: ${{ needs.cache-pixi-lock.outputs.cache-id }}
@@ -96,14 +100,14 @@ jobs:
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run: |
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pixi run test-notebooks -v -s --html="${{ env.COVERAGE_REPORT }}" --self-contained-html --cov=parcels --cov-report=xml
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- name: Codecov
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uses: codecov/codecov-action@v5.3.1
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uses: codecov/codecov-action@v5.5.1
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env:
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CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
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with:
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flags: integration-tests
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- name: Upload test results
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if: ${{ always() }} # Always run this step, even if tests fail
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uses: actions/upload-artifact@v4
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uses: actions/upload-artifact@v5
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with:
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name: Integration test report ${{ matrix.os }}-${{ matrix.pixi-environment }}
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path: ${{ env.COVERAGE_REPORT }}
@@ -115,7 +119,7 @@ jobs:
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- typechecking
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steps:
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- name: Merge Artifacts
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uses: actions/upload-artifact/merge@v4
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uses: actions/upload-artifact/merge@v5
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with:
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name: Testing reports
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pattern: "* report *"
@@ -127,7 +131,7 @@ jobs:
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needs: [cache-pixi-lock]
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steps:
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- name: Checkout
130-
uses: actions/checkout@v4
134+
uses: actions/checkout@v5
131135
- name: Restore cached pixi lockfile
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uses: actions/cache/restore@v4
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id: restore-pixi-lock
@@ -144,7 +148,7 @@ jobs:
144148
pixi run typing --non-interactive --html-report mypy-report
145149
- name: Upload test results
146150
if: ${{ always() }} # Upload even on mypy error
147-
uses: actions/upload-artifact@v4
151+
uses: actions/upload-artifact@v5
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with:
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name: Mypy report
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path: mypy-report

‎.github/workflows/nightly.yml‎

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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: actions/checkout@v5
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- name: Build conda package
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uses: prefix-dev/[email protected].19
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uses: prefix-dev/[email protected].34
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with:
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recipe-path: .github/ci/recipe.yaml
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‎.github/workflows/pypi-release.yml‎

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runs-on: ubuntu-latest
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if: github.repository == 'Parcels-code/parcels'
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steps:
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- uses: actions/checkout@v4
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- uses: actions/checkout@v5
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with:
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fetch-depth: 0
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- uses: actions/setup-python@v5
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- uses: actions/setup-python@v6
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name: Install Python
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with:
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python-version: "3.11"
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else
4343
echo "✅ Looks good"
4444
fi
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- uses: actions/upload-artifact@v4
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- uses: actions/upload-artifact@v5
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with:
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name: releases
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path: dist
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needs: build-artifacts
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runs-on: ubuntu-latest
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steps:
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- uses: actions/setup-python@v5
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- uses: actions/setup-python@v6
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name: Install Python
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with:
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python-version: "3.11"
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- uses: actions/download-artifact@v4
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- uses: actions/download-artifact@v6
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with:
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name: releases
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path: dist
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if: github.event_name == 'release'
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runs-on: ubuntu-latest
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steps:
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- uses: actions/download-artifact@v4
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- uses: actions/download-artifact@v6
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with:
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name: releases
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path: dist

‎.pre-commit-config.yaml‎

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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v5.0.0
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rev: v6.0.0
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hooks:
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- id: trailing-whitespace
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- id: end-of-file-fixer
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types: [text]
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files: \.(json|ipynb)$
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.12.5
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rev: v0.14.2
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hooks:
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- id: ruff
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name: ruff lint (.py)

‎docs/community/v4-migration.md‎

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@@ -34,3 +34,12 @@ Version 4 of Parcels is unreleased at the moment. The information in this migrat
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- Particlefiles should be created by `ParticleFile(...)` instead of `pset.ParticleFile(...)`
3636
- The `name` argument in `ParticleFile` has been replaced by `store` and can now be a string, a Path or a zarr store.
37+
38+
## Field
39+
40+
- `Field.eval()` returns an array of floats instead of a single float (related to the vectorization)
41+
- `Field.eval()` does not throw OutOfBounds or other errors
42+
43+
## GridSet
44+
45+
- `GridSet` is now a list, so change `fieldset.gridset.grids[0]` to `fieldset.gridset[0]`.

‎docs/documentation/index.md‎

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@@ -42,7 +42,7 @@ The tutorials written for Parcels v3 are currently being updated for Parcels v4.
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:name: tutorial-kernels
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<!-- ../examples/tutorial_diffusion.ipynb -->
45-
<!-- ../examples/tutorial_sampling.ipynb -->
45+
../examples/tutorial_sampling.ipynb
4646
<!-- ../examples/tutorial_particle_field_interaction.ipynb -->
4747
<!-- ../examples/tutorial_interaction.ipynb -->
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<!-- ../examples/tutorial_analyticaladvection.ipynb -->

‎docs/examples/tutorial_Argofloats.ipynb‎

Lines changed: 17 additions & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -41,11 +41,9 @@
4141
"\n",
4242
" def SinkingPhase(p):\n",
4343
" \"\"\"Phase 0: Sinking with vertical_speed until depth is driftdepth\"\"\"\n",
44-
" p.ddepth += vertical_speed * dt\n",
45-
" p.cycle_phase = np.where(p.depth + p.ddepth >= driftdepth, 1, p.cycle_phase)\n",
46-
" p.ddepth = np.where(\n",
47-
" p.depth + p.ddepth >= driftdepth, driftdepth - p.depth, p.ddepth\n",
48-
" )\n",
44+
" p.dz += vertical_speed * dt\n",
45+
" p.cycle_phase = np.where(p.z + p.dz >= driftdepth, 1, p.cycle_phase)\n",
46+
" p.dz = np.where(p.z + p.dz >= driftdepth, driftdepth - p.z, p.dz)\n",
4947
"\n",
5048
" SinkingPhase(particles[particles.cycle_phase == 0])\n",
5149
"\n",
@@ -67,11 +65,9 @@
6765
"\n",
6866
" def SecondSinkingPhase(p):\n",
6967
" \"\"\"Phase 2: Sinking further to maxdepth\"\"\"\n",
70-
" p.ddepth += vertical_speed * dt\n",
71-
" p.cycle_phase = np.where(p.depth + p.ddepth >= maxdepth, 3, p.cycle_phase)\n",
72-
" p.ddepth = np.where(\n",
73-
" p.depth + p.ddepth >= maxdepth, maxdepth - p.depth, p.ddepth\n",
74-
" )\n",
68+
" p.dz += vertical_speed * dt\n",
69+
" p.cycle_phase = np.where(p.z + p.dz >= maxdepth, 3, p.cycle_phase)\n",
70+
" p.dz = np.where(p.z + p.dz >= maxdepth, maxdepth - p.z, p.dz)\n",
7571
"\n",
7672
" SecondSinkingPhase(particles[particles.cycle_phase == 2])\n",
7773
"\n",
@@ -81,15 +77,13 @@
8177
"\n",
8278
" def RisingPhase(p):\n",
8379
" \"\"\"Phase 3: Rising with vertical_speed until at surface\"\"\"\n",
84-
" p.ddepth -= vertical_speed * dt\n",
85-
" p.temp = fieldset.thetao[p.time, p.depth, p.lat, p.lon]\n",
86-
" p.cycle_phase = np.where(\n",
87-
" p.depth + p.ddepth <= fieldset.mindepth, 4, p.cycle_phase\n",
88-
" )\n",
89-
" p.ddepth = np.where(\n",
90-
" p.depth + p.ddepth <= fieldset.mindepth,\n",
91-
" fieldset.mindepth - p.depth,\n",
92-
" p.ddepth,\n",
80+
" p.dz -= vertical_speed * dt\n",
81+
" p.temp = fieldset.thetao[p.time, p.z, p.lat, p.lon]\n",
82+
" p.cycle_phase = np.where(p.z + p.dz <= fieldset.mindepth, 4, p.cycle_phase)\n",
83+
" p.dz = np.where(\n",
84+
" p.z + p.dz <= fieldset.mindepth,\n",
85+
" fieldset.mindepth - p.z,\n",
86+
" p.dz,\n",
9387
" )\n",
9488
"\n",
9589
" RisingPhase(particles[particles.cycle_phase == 3])\n",
@@ -163,7 +157,7 @@
163157
" pclass=ArgoParticle,\n",
164158
" lon=[32],\n",
165159
" lat=[-31],\n",
166-
" depth=[fieldset.mindepth],\n",
160+
" z=[fieldset.mindepth],\n",
167161
")\n",
168162
"\n",
169163
"# combine Argo vertical movement kernel with built-in Advection kernel\n",
@@ -174,7 +168,7 @@
174168
" ArgoPhase4,\n",
175169
" ArgoPhase5,\n",
176170
" ArgoPhase6,\n",
177-
" parcels.AdvectionRK4,\n",
171+
" parcels.kernels.AdvectionRK4,\n",
178172
"]\n",
179173
"\n",
180174
"# Create a ParticleFile object to store the output\n",
@@ -209,9 +203,7 @@
209203
"metadata": {},
210204
"outputs": [],
211205
"source": [
212-
"ds_out = xr.open_zarr(\n",
213-
" output_file.store, decode_times=False\n",
214-
") # TODO fix without using decode_times=False\n",
206+
"ds_out = xr.open_zarr(output_file.store)\n",
215207
"x = ds_out[\"lon\"][:].squeeze()\n",
216208
"y = ds_out[\"lat\"][:].squeeze()\n",
217209
"z = ds_out[\"z\"][:].squeeze()\n",
@@ -268,7 +260,7 @@
268260
],
269261
"metadata": {
270262
"kernelspec": {
271-
"display_name": "parcels-v4",
263+
"display_name": "test-notebooks",
272264
"language": "python",
273265
"name": "python3"
274266
},

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