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Merge pull request #13 from OceanParcels/code_cleanup_and_standardisation
Code cleanup and standardisation
2 parents d748b97 + 903d479 commit 23d4e5a

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‎.flake8‎

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[flake8]
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ignore =
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# missing whitespace around arithmetic operator
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E226,
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# do not use bare except, specify exception instead
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E722,
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# line break before binary operator
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W503,
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# line too long (82 > 79 characters)
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E501,
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# ‘from module import *’ used; unable to detect undefined names
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F403,

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

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name: Setup Conda and install plasticparcels
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description: >
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In-repo composite action to setup Conda and install parcels. Installation of parcels relies on
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`setup.py` file being available in the root. For general setup of Anaconda environments, just use
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the `mamba-org/setup-micromamba@v1` action (setting C variables as required), or the `conda-incubator/setup-miniconda` action.
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inputs:
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environment-file:
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description: Conda environment file to use.
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default: environment.yml
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environment-name:
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description: Name to use for the Conda environment
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default: test
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runs:
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using: "composite"
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steps:
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- name: Install micromamba (${{ inputs.environment-file }})
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uses: mamba-org/setup-micromamba@v1
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with:
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environment-file: ${{ inputs.environment-file }}
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environment-name: ${{ inputs.environment-name }}
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channels: conda-forge
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cache-environment: true
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cache-downloads: true
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- name: Install parcels
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run: pip install .
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shell: bash -el {0}

‎.github/workflows/draft-pdf.yml‎

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with:
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journal: joss
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# This should be the path to the paper within your repo.
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paper-path: paper/paper.md
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paper-path: docs/paper/paper.md
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- name: Upload
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uses: actions/upload-artifact@v1
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with:
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name: paper
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# This is the output path where Pandoc will write the compiled
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# PDF. Note, this should be the same directory as the input
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# paper.md
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path: paper/paper.pdf
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path: docs/paper/paper.pdf

‎.github/workflows/linting.yml‎

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name: linting
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on:
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pull_request:
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push:
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jobs:
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linting:
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name: Linting with flake8
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@master
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- name: Python setup
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run: |
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pip install wheel
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pip install flake8
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- name: flake8
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run: |
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python -m flake8 plasticparcels
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python -m flake8 tests

‎.github/workflows/unit_tests.yml‎

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name: unit-tests
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on:
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pull_request:
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push:
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schedule:
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- cron: "0 7 * * 1" # Run every Monday at 7:00 UTC
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defaults:
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run:
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shell: bash -el {0}
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jobs:
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unit-test:
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name: Unittesting on ubuntu with python latest
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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steps:
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- name: Checkout
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uses: actions/checkout@v3
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- name: Setup Conda and parcels
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uses: ./.github/actions/install-plasticparcels
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with:
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environment-file: environment.yml
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environment-name: py3_parcels
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- name: Unit test
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run: |
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python -m pytest -v -s tests

‎.gitignore‎

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data/
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fig/
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input_data/
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**.code-workspace*
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**.DS_store**
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**.pyc**
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**.nc
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**.zarr

‎README.md‎

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‎docs/examples/default_settings.json‎

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{
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"use_3D": true,
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"allow_time_extrapolation": false,
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"verbose_delete": false,
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"use_mixing": false,
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"use_biofouling": false,
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"use_stokes": false,
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"use_wind": false,
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"ocean": {
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"modelname": "NEMO0083",
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"directory": "/storage/shared/oceanparcels/input_data/MOi/",
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"filename_style": "psy4v3r1/psy4v3r1-daily_",
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"ocean_mesh": "domain_ORCA0083-N006/PSY4V3R1_mesh_hgr.nc",
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"bathymetry_mesh": "domain_ORCA0083-N006/PSY4V3R1_mesh_zgr.nc",
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"variables": {
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"U": "vozocrtx",
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"V": "vomecrty",
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"W": "vovecrtz",
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"conservative_temperature": "votemper",
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"absolute_salinity": "vosaline"
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},
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"dimensions": {
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"U": {
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"lon": "glamf",
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"lat": "gphif",
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"depth": "depthw",
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"time": "time_counter"
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},
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"V": {
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"lon": "glamf",
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"lat": "gphif",
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"depth": "depthw",
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"time": "time_counter"
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},
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"W": {
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"lon": "glamf",
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"lat": "gphif",
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"depth": "depthw",
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"time": "time_counter"
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},
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"conservative_temperature": {
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"lon": "glamf",
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"lat": "gphif",
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"depth": "depthw",
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"time": "time_counter"
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},
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"absolute_salinity": {
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"lon": "glamf",
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"lat": "gphif",
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"depth": "depthw",
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"time": "time_counter"
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}
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},
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"indices": {},
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"bathymetry_variables": {
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"bathymetry": "mbathy"
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},
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"bathymetry_dimensions": {
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"lon": "nav_lon",
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"lat": "nav_lat"
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},
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"mixing_variables": {
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"mixing_kz": "votkeavt"
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},
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"mixing_dimensions": {
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"lon": "glamf",
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"lat": "gphif",
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"depth": "depthw",
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"time": "time_counter"
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}
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},
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"bgc": {
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"directory": "/storage/shared/oceanparcels/input_data/MOi/",
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"filename_style": "biomer4v2r1/biomer4v2r1-weekly_",
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"bgc_mesh": "domain_ORCA025-N006/mesh_hgr_PSY4V3_deg.nc",
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"variables": {
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"pp_phyto": "nppv",
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"bio_nanophy": "phy",
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"bio_diatom": "phy2"
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},
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"dimensions": {
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"pp_phyto": {
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"lon": "glamf",
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"lat": "gphif",
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"depth": "depthw",
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"time": "time_counter"
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},
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"bio_nanophy": {
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"lon": "glamf",
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"lat": "gphif",
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"depth": "depthw",
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"time": "time_counter"
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},
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"bio_diatom": {
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"lon": "glamf",
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"lat": "gphif",
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"depth": "depthw",
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"time": "time_counter"
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}
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},
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"indices": {},
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"constants": {
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"biofilm_density": 1388.0,
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"algae_cell_volume": 2e-16,
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"K": 1.3805834190672156e-23,
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"R20": 1.1574074074074074e-06,
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"Q10": 2.13,
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"Gamma": 2.0,
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"carbon_molecular_weight": 12.0,
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"collision_probability": 1.0,
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"algae_mortality_rate": 1.0,
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"algae_respiration_f": 1.0
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}
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},
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"stokes": {
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"directory": "/storage/shared/oceanparcels/output_data/data_Michael/ERA5/waves/",
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"filename_style": "ERA5_global_waves_monthly_",
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"variables": {
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"Stokes_U": "ust",
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"Stokes_V": "vst",
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"wave_Tp": "pp1d"
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},
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"dimensions": {
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"lat": "latitude",
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"lon": "longitude",
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"time": "time"
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},
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"indices": {}
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},
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"wind": {
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"directory": "/storage/shared/oceanparcels/output_data/data_Michael/ERA5/wind/",
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"filename_style": "ERA5_global_wind_monthly_",
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"variables": {
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"Wind_U": "u10",
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"Wind_V": "v10"
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},
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"dimensions": {
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"lat": "latitude",
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"lon": "longitude",
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"time": "time"
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},
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"indices": {}
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},
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"unbeaching": {
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"directory": "input_data/NEMO0083/",
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"filename": "land_current_NEMO0083.nc",
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"variables": {
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"unbeach_U": "land_current_u",
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"unbeach_V": "land_current_v"
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},
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"dimensions": {
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"lat": "lat",
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"lon": "lon"
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}
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},
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"simulation": {
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"start_date": null,
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"runtime": null,
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"dt_write": null,
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"dt_timestep": null
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},
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"release_maps": {
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"coastal": "input_data/NEMO0083/coastal_population_MPW_NEMO0083.csv",
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"rivers": "input_data/NEMO0083/river_emissions_NEMO0083.csv",
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"fisheries": "input_data/NEMO0083/agg_data_fisheries_info.csv",
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"global_concentrations": null
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}
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}

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