Merge pull request #13 from OceanParcels/code_cleanup_and_standardisa…

…tion

Code cleanup and standardisation

.flake8

@@ -0,0 +1,12 @@
+[flake8]
+ignore =
+    # missing whitespace around arithmetic operator
+    E226,
+    # do not use bare except, specify exception instead
+    E722,
+    # line break before binary operator
+    W503,
+    # line too long (82 > 79 characters)
+    E501,
+    # ‘from module import *’ used; unable to detect undefined names
+    F403,

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

@@ -0,0 +1,26 @@
+name: Setup Conda and install plasticparcels
+description: >
+  In-repo composite action to setup Conda and install parcels. Installation of parcels relies on
+  `setup.py` file being available in the root. For general setup of Anaconda environments, just use
+  the `mamba-org/setup-micromamba@v1` action (setting C variables as required), or the `conda-incubator/setup-miniconda` action.
+inputs:
+  environment-file:
+    description: Conda environment file to use.
+    default: environment.yml
+  environment-name:
+    description: Name to use for the Conda environment
+    default: test
+runs:
+  using: "composite"
+  steps:
+    - name: Install micromamba (${{ inputs.environment-file }})
+      uses: mamba-org/setup-micromamba@v1
+      with:
+        environment-file: ${{ inputs.environment-file }}
+        environment-name: ${{ inputs.environment-name }}
+        channels: conda-forge
+        cache-environment: true
+        cache-downloads: true
+    - name: Install parcels
+      run: pip install .
+      shell: bash -el {0}

.github/workflows/draft-pdf.yml

@@ -12,12 +12,12 @@ jobs:
         with:
           journal: joss
           # This should be the path to the paper within your repo.
-          paper-path: paper/paper.md
+          paper-path: docs/paper/paper.md
       - name: Upload
         uses: actions/upload-artifact@v1
         with:
           name: paper
           # This is the output path where Pandoc will write the compiled
           # PDF. Note, this should be the same directory as the input
           # paper.md
-          path: paper/paper.pdf
+          path: docs/paper/paper.pdf

.github/workflows/linting.yml

@@ -0,0 +1,19 @@
+name: linting
+on:
+  pull_request:
+  push:
+jobs:
+  linting:
+    name: Linting with flake8
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@master
+      - name: Python setup
+        run: |
+          pip install wheel
+          pip install flake8
+      - name: flake8
+        run: |
+          python -m flake8 plasticparcels
+          python -m flake8 tests

.github/workflows/unit_tests.yml

@@ -0,0 +1,28 @@
+name: unit-tests
+on:
+  pull_request:
+  push:
+  schedule:
+    - cron: "0 7 * * 1" # Run every Monday at 7:00 UTC
+
+defaults:
+  run:
+    shell: bash -el {0}
+
+jobs:
+  unit-test:
+    name: Unittesting on ubuntu with python latest
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Setup Conda and parcels
+        uses: ./.github/actions/install-plasticparcels
+        with:
+          environment-file: environment.yml
+          environment-name: py3_parcels
+      - name: Unit test
+        run: |
+          python -m pytest -v -s tests

.gitignore

@@ -1,5 +1,6 @@
-data/
-fig/
+input_data/
 **.code-workspace*
 **.DS_store**
 **.pyc**
+**.nc
+**.zarr

docs/examples/default_settings.json

@@ -0,0 +1,168 @@
+{
+    "use_3D": true,
+    "allow_time_extrapolation": false,
+    "verbose_delete": false,
+    "use_mixing": false,
+    "use_biofouling": false,
+    "use_stokes": false,
+    "use_wind": false,
+    "ocean": {
+        "modelname": "NEMO0083",
+        "directory": "/storage/shared/oceanparcels/input_data/MOi/",
+        "filename_style": "psy4v3r1/psy4v3r1-daily_",
+        "ocean_mesh": "domain_ORCA0083-N006/PSY4V3R1_mesh_hgr.nc",
+        "bathymetry_mesh": "domain_ORCA0083-N006/PSY4V3R1_mesh_zgr.nc",
+        "variables": {
+            "U": "vozocrtx",
+            "V": "vomecrty",
+            "W": "vovecrtz",
+            "conservative_temperature": "votemper",
+            "absolute_salinity": "vosaline"
+        },
+        "dimensions": {
+            "U": {
+                "lon": "glamf",
+                "lat": "gphif",
+                "depth": "depthw",
+                "time": "time_counter"
+            },
+            "V": {
+                "lon": "glamf",
+                "lat": "gphif",
+                "depth": "depthw",
+                "time": "time_counter"
+            },
+            "W": {
+                "lon": "glamf",
+                "lat": "gphif",
+                "depth": "depthw",
+                "time": "time_counter"
+            },
+            "conservative_temperature": {
+                "lon": "glamf",
+                "lat": "gphif",
+                "depth": "depthw",
+                "time": "time_counter"
+            },
+            "absolute_salinity": {
+                "lon": "glamf",
+                "lat": "gphif",
+                "depth": "depthw",
+                "time": "time_counter"
+            }
+        },
+        "indices": {},
+        "bathymetry_variables": {
+            "bathymetry": "mbathy"
+        },
+        "bathymetry_dimensions": {
+            "lon": "nav_lon",
+            "lat": "nav_lat"
+        },
+        "mixing_variables": {
+            "mixing_kz": "votkeavt"
+        },
+        "mixing_dimensions": {
+            "lon": "glamf",
+            "lat": "gphif",
+            "depth": "depthw",
+            "time": "time_counter"
+        }
+    },
+    "bgc": {
+        "directory": "/storage/shared/oceanparcels/input_data/MOi/",
+        "filename_style": "biomer4v2r1/biomer4v2r1-weekly_",
+        "bgc_mesh": "domain_ORCA025-N006/mesh_hgr_PSY4V3_deg.nc",
+        "variables": {
+            "pp_phyto": "nppv",
+            "bio_nanophy": "phy",
+            "bio_diatom": "phy2"
+        },
+        "dimensions": {
+            "pp_phyto": {
+                "lon": "glamf",
+                "lat": "gphif",
+                "depth": "depthw",
+                "time": "time_counter"
+            },
+            "bio_nanophy": {
+                "lon": "glamf",
+                "lat": "gphif",
+                "depth": "depthw",
+                "time": "time_counter"
+            },
+            "bio_diatom": {
+                "lon": "glamf",
+                "lat": "gphif",
+                "depth": "depthw",
+                "time": "time_counter"
+            }
+        },
+        "indices": {},
+        "constants": {
+            "biofilm_density": 1388.0,
+            "algae_cell_volume": 2e-16,
+            "K": 1.3805834190672156e-23,
+            "R20": 1.1574074074074074e-06,
+            "Q10": 2.13,
+            "Gamma": 2.0,
+            "carbon_molecular_weight": 12.0,
+            "collision_probability": 1.0,
+            "algae_mortality_rate": 1.0,
+            "algae_respiration_f": 1.0
+        }
+    },
+    "stokes": {
+        "directory": "/storage/shared/oceanparcels/output_data/data_Michael/ERA5/waves/",
+        "filename_style": "ERA5_global_waves_monthly_",
+        "variables": {
+            "Stokes_U": "ust",
+            "Stokes_V": "vst",
+            "wave_Tp": "pp1d"
+        },
+        "dimensions": {
+            "lat": "latitude",
+            "lon": "longitude",
+            "time": "time"
+        },
+        "indices": {}
+    },
+    "wind": {
+        "directory": "/storage/shared/oceanparcels/output_data/data_Michael/ERA5/wind/",
+        "filename_style": "ERA5_global_wind_monthly_",
+        "variables": {
+            "Wind_U": "u10",
+            "Wind_V": "v10"
+        },
+        "dimensions": {
+            "lat": "latitude",
+            "lon": "longitude",
+            "time": "time"
+        },
+        "indices": {}
+    },
+    "unbeaching": {
+        "directory": "input_data/NEMO0083/",
+        "filename": "land_current_NEMO0083.nc",
+        "variables": {
+            "unbeach_U": "land_current_u",
+            "unbeach_V": "land_current_v"
+        },
+        "dimensions": {
+            "lat": "lat",
+            "lon": "lon"
+        }
+    },
+    "simulation": {
+        "start_date": null,
+        "runtime": null,
+        "dt_write": null,
+        "dt_timestep": null
+    },
+    "release_maps": {
+        "coastal": "input_data/NEMO0083/coastal_population_MPW_NEMO0083.csv",
+        "rivers": "input_data/NEMO0083/river_emissions_NEMO0083.csv",
+        "fisheries": "input_data/NEMO0083/agg_data_fisheries_info.csv",
+        "global_concentrations": null
+    }
+}