roms-tools 1.6.1__tar.gz → 1.6.2__tar.gz

roms_tools-1.6.2/.github/workflows/tests.yaml

@@ -0,0 +1,106 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  test-without-dask:
+    name: ${{ matrix.python-version }}-build-without-dask
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Create conda environment
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          cache-downloads: true
+          cache-environment: true
+          micromamba-version: 'latest'
+          environment-file: ci/environment.yml
+          create-args: |
+            python=${{ matrix.python-version }}
+          cache-key: micromamba-${{ matrix.python-version }}-${{ runner.os }}
+
+      - name: Conda info
+        run: conda info
+
+      - name: Install roms-tools
+        shell: micromamba-shell {0}
+        run: |
+           python -V
+           python -m pip install -e . --force-reinstall
+
+      - name: Running Tests without Dask
+        shell: bash -l {0}
+        run: |
+           python -V
+           coverage run --rcfile=coverage.toml -m pytest --verbose roms_tools/tests/*
+
+      - name: Get coverage report
+        shell: bash -l {0}
+        run: |
+          coverage report -m
+          coverage xml
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v4.0.1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          flags: unittests # optional
+
+  test-with-dask:
+    name: 3.13-build-with-dask
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.13"]
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Create conda environment
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          cache-downloads: true
+          cache-environment: true
+          micromamba-version: 'latest'
+          environment-file: ci/environment.yml
+          create-args: |
+            python=${{ matrix.python-version }}
+          cache-key: micromamba-${{ matrix.python-version }}-${{ runner.os }}
+
+      - name: Conda info
+        run: conda info
+
+      - name: Install roms-tools
+        shell: micromamba-shell {0}
+        run: |
+           python -V
+           python -m pip install -e .[dask]  --force-reinstall
+
+      - name: Running Tests with Dask
+        shell: bash -l {0}
+        run: |
+           python -V
+           coverage run --rcfile=coverage.toml -m pytest --use_dask --verbose roms_tools/tests/*
+
+      - name: Get coverage report
+        shell: bash -l {0}
+        run: |
+          coverage report -m
+          coverage xml
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v4.0.1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          flags: unittests # optional

roms_tools-1.6.2/PKG-INFO

@@ -0,0 +1,133 @@
+Metadata-Version: 2.1
+Name: roms-tools
+Version: 1.6.2
+Summary: Tools for running and analysing UCLA-ROMS simulations
+Author-email: Nora Loose <nora.loose@gmail.com>, Thomas Nicholas <tom@cworthy.org>
+License: Apache-2
+Project-URL: Home, https://github.com/CWorthy-ocean/roms-tools
+Project-URL: Documentation, https://roms-tools.readthedocs.io/en/latest/
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: xarray>=2022.6.0
+Requires-Dist: numpy
+Requires-Dist: pooch
+Requires-Dist: matplotlib
+Requires-Dist: cartopy
+Requires-Dist: packaging
+Requires-Dist: scipy
+Requires-Dist: gcm_filters
+Requires-Dist: netcdf4
+Requires-Dist: PyYAML
+Requires-Dist: pyamg
+Requires-Dist: bottleneck
+Provides-Extra: dask
+Requires-Dist: dask; extra == "dask"
+
+# ROMS-Tools
+[![Conda version](https://img.shields.io/conda/vn/conda-forge/roms-tools.svg)](https://anaconda.org/conda-forge/roms-tools)
+[![PyPI version](https://img.shields.io/pypi/v/roms-tools.svg)](https://pypi.org/project/roms-tools/)
+[![codecov](https://codecov.io/gh/CWorthy-ocean/roms-tools/graph/badge.svg?token=5S1oNu39xE)](https://codecov.io/gh/CWorthy-ocean/roms-tools)
+[![Documentation Status](https://readthedocs.org/projects/roms-tools/badge/?version=latest)](https://roms-tools.readthedocs.io/en/latest/?badge=latest)
+![Run Tests](https://github.com/CWorthy-ocean/roms-tools/actions/workflows/tests.yaml/badge.svg)
+![Supported Python Versions](https://img.shields.io/pypi/pyversions/roms-tools)
+
+
+## Overview
+
+A suite of python tools for setting up a [ROMS](https://github.com/CESR-lab/ucla-roms) simulation.
+
+<mark>**DISCLAIMER**: This project is **ALPHA** and will be **EXPERIMENTAL** at least throughout Fall 2024. We do not recommend to use this software before this ALPHA development and test phase is completed.</mark>
+
+## Installation
+
+### Installation from conda forge
+
+```bash
+conda install -c conda-forge roms-tools
+```
+
+This command installs `ROMS-Tools` along with its `dask` dependency.
+
+### Installation from pip
+
+```bash
+pip install roms-tools
+```
+
+If you want to use `ROMS-Tools` together with dask (which we recommend), you can
+install `ROMS-Tools` along with the additional dependency via:
+
+```bash
+pip install roms-tools[dask]
+```
+
+### Installation from GitHub
+
+To obtain the latest development version, first clone the source repository:
+
+```bash
+git clone https://github.com/CWorthy-ocean/roms-tools.git
+cd roms-tools
+```
+
+Next, install and activate the following conda environment:
+
+```bash
+conda env create -f ci/environment.yml
+conda activate romstools-test
+```
+
+Finally, install `ROMS-Tools` in the same environment:
+
+```bash
+pip install -e .
+```
+
+If you want to use `ROMS-Tools` together with dask (which we recommend), you can
+install `ROMS-Tools` along with the additional dependency via:
+
+```bash
+pip install -e .[dask]
+```
+
+
+### Run the tests
+
+Before running the tests, you can activate the conda environment created in the previous section:
+
+```bash
+conda activate romstools-test
+```
+
+Check the installation of `ROMS-Tools` has worked by running the test suite
+```bash
+cd roms-tools
+pytest
+```
+
+## Getting Started
+
+To learn how to use `ROMS-Tools`, check out the [documentation](https://roms-tools.readthedocs.io/en/latest/).
+
+## Feedback and contributions
+
+**If you find a bug, have a feature suggestion, or any other kind of feedback, please start a Discussion.**
+
+We also accept contributions in the form of Pull Requests.
+
+
+## See also
+
+- [ROMS source code](https://github.com/CESR-lab/ucla-roms)
+- [C-Star](https://github.com/CWorthy-ocean/C-Star)

roms_tools-1.6.2/conftest.py

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+import pytest
+from datetime import datetime
+from roms_tools import (
+    Grid,
+    TidalForcing,
+    InitialConditions,
+    BoundaryForcing,
+    SurfaceForcing,
+)
+from roms_tools.setup.datasets import (
+    GLORYSDataset,
+    ERA5Dataset,
+    CESMBGCDataset,
+    CESMBGCSurfaceForcingDataset,
+    TPXODataset,
+)
+from roms_tools.setup.download import download_test_data
+import hashlib
+
+
+def pytest_addoption(parser):
+    parser.addoption(
+        "--overwrite",
+        action="append",
+        default=[],
+        help="Specify which fixtures to overwrite. Use 'all' to overwrite all fixtures.",
+    )
+    parser.addoption(
+        "--use_dask", action="store_true", default=False, help="Run tests with Dask"
+    )
+
+
+def pytest_configure(config):
+    if "all" in config.getoption("--overwrite"):
+        # If 'all' is specified, overwrite everything
+        config.option.overwrite = ["all"]
+
+
+@pytest.fixture(scope="session")
+def use_dask(request):
+    return request.config.getoption("--use_dask")
+
+
+@pytest.fixture(scope="session")
+def grid():
+
+    grid = Grid(nx=1, ny=1, size_x=100, size_y=100, center_lon=-20, center_lat=0, rot=0)
+
+    return grid
+
+
+@pytest.fixture(scope="session")
+def grid_that_straddles_dateline():
+
+    grid = Grid(nx=1, ny=1, size_x=100, size_y=100, center_lon=0, center_lat=0, rot=20)
+
+    return grid
+
+
+@pytest.fixture(scope="session")
+def tidal_forcing(request, use_dask):
+
+    grid = Grid(
+        nx=3, ny=3, size_x=1500, size_y=1500, center_lon=235, center_lat=25, rot=-20
+    )
+    fname = download_test_data("TPXO_regional_test_data.nc")
+
+    return TidalForcing(
+        grid=grid, source={"name": "TPXO", "path": fname}, ntides=1, use_dask=use_dask
+    )
+
+
+@pytest.fixture(scope="session")
+def initial_conditions(request, use_dask):
+    """Fixture for creating an InitialConditions object."""
+
+    grid = Grid(
+        nx=2,
+        ny=2,
+        size_x=500,
+        size_y=1000,
+        center_lon=0,
+        center_lat=55,
+        rot=10,
+        N=3,  # number of vertical levels
+        theta_s=5.0,  # surface control parameter
+        theta_b=2.0,  # bottom control parameter
+        hc=250.0,  # critical depth
+    )
+
+    fname = download_test_data("GLORYS_coarse_test_data.nc")
+
+    return InitialConditions(
+        grid=grid,
+        ini_time=datetime(2021, 6, 29),
+        source={"path": fname, "name": "GLORYS"},
+        use_dask=use_dask,
+    )
+
+
+@pytest.fixture(scope="session")
+def initial_conditions_with_bgc(request, use_dask):
+    """Fixture for creating an InitialConditions object."""
+
+    grid = Grid(
+        nx=2,
+        ny=2,
+        size_x=500,
+        size_y=1000,
+        center_lon=0,
+        center_lat=55,
+        rot=10,
+        N=3,  # number of vertical levels
+        theta_s=5.0,  # surface control parameter
+        theta_b=2.0,  # bottom control parameter
+        hc=250.0,  # critical depth
+    )
+
+    fname = download_test_data("GLORYS_coarse_test_data.nc")
+    fname_bgc = download_test_data("CESM_regional_test_data_one_time_slice.nc")
+
+    return InitialConditions(
+        grid=grid,
+        ini_time=datetime(2021, 6, 29),
+        source={"path": fname, "name": "GLORYS"},
+        bgc_source={"path": fname_bgc, "name": "CESM_REGRIDDED"},
+        use_dask=use_dask,
+    )
+
+
+@pytest.fixture(scope="session")
+def initial_conditions_with_bgc_from_climatology(request, use_dask):
+    """Fixture for creating an InitialConditions object."""
+
+    grid = Grid(
+        nx=2,
+        ny=2,
+        size_x=500,
+        size_y=1000,
+        center_lon=0,
+        center_lat=55,
+        rot=10,
+        N=3,  # number of vertical levels
+        theta_s=5.0,  # surface control parameter
+        theta_b=2.0,  # bottom control parameter
+        hc=250.0,  # critical depth
+    )
+
+    fname = download_test_data("GLORYS_coarse_test_data.nc")
+    fname_bgc = download_test_data("CESM_regional_test_data_climatology.nc")
+
+    return InitialConditions(
+        grid=grid,
+        ini_time=datetime(2021, 6, 29),
+        source={"path": fname, "name": "GLORYS"},
+        bgc_source={
+            "path": fname_bgc,
+            "name": "CESM_REGRIDDED",
+            "climatology": True,
+        },
+        use_dask=use_dask,
+    )
+
+
+@pytest.fixture(scope="session")
+def boundary_forcing(request, use_dask):
+    """Fixture for creating a BoundaryForcing object."""
+
+    grid = Grid(
+        nx=2,
+        ny=2,
+        size_x=500,
+        size_y=1000,
+        center_lon=0,
+        center_lat=55,
+        rot=10,
+        N=3,  # number of vertical levels
+        theta_s=5.0,  # surface control parameter
+        theta_b=2.0,  # bottom control parameter
+        hc=250.0,  # critical depth
+    )
+
+    fname = download_test_data("GLORYS_coarse_test_data.nc")
+
+    return BoundaryForcing(
+        grid=grid,
+        start_time=datetime(2021, 6, 29),
+        end_time=datetime(2021, 6, 30),
+        source={"name": "GLORYS", "path": fname},
+        apply_2d_horizontal_fill=True,
+        use_dask=use_dask,
+    )
+
+
+@pytest.fixture(scope="session")
+def bgc_boundary_forcing_from_climatology(request, use_dask):
+    """Fixture for creating a BoundaryForcing object."""
+
+    grid = Grid(
+        nx=2,
+        ny=2,
+        size_x=500,
+        size_y=1000,
+        center_lon=0,
+        center_lat=55,
+        rot=10,
+        N=3,  # number of vertical levels
+        theta_s=5.0,  # surface control parameter
+        theta_b=2.0,  # bottom control parameter
+        hc=250.0,  # critical depth
+    )
+
+    fname_bgc = download_test_data("CESM_regional_coarse_test_data_climatology.nc")
+
+    return BoundaryForcing(
+        grid=grid,
+        start_time=datetime(2021, 6, 29),
+        end_time=datetime(2021, 6, 30),
+        source={"path": fname_bgc, "name": "CESM_REGRIDDED", "climatology": True},
+        type="bgc",
+        apply_2d_horizontal_fill=True,
+        use_dask=use_dask,
+    )
+
+
+@pytest.fixture(scope="session")
+def surface_forcing(request, use_dask):
+    """Fixture for creating a SurfaceForcing object."""
+
+    grid = Grid(
+        nx=5,
+        ny=5,
+        size_x=1800,
+        size_y=2400,
+        center_lon=180,
+        center_lat=61,
+        rot=20,
+    )
+
+    start_time = datetime(2020, 1, 31)
+    end_time = datetime(2020, 2, 2)
+
+    fname = download_test_data("ERA5_global_test_data.nc")
+
+    return SurfaceForcing(
+        grid=grid,
+        start_time=start_time,
+        end_time=end_time,
+        source={"name": "ERA5", "path": fname},
+        use_dask=use_dask,
+    )
+
+
+@pytest.fixture(scope="session")
+def coarse_surface_forcing(request, use_dask):
+    """Fixture for creating a SurfaceForcing object."""
+
+    grid = Grid(
+        nx=5,
+        ny=5,
+        size_x=1800,
+        size_y=2400,
+        center_lon=180,
+        center_lat=61,
+        rot=20,
+    )
+
+    start_time = datetime(2020, 1, 31)
+    end_time = datetime(2020, 2, 2)
+
+    fname = download_test_data("ERA5_global_test_data.nc")
+
+    return SurfaceForcing(
+        grid=grid,
+        start_time=start_time,
+        end_time=end_time,
+        use_coarse_grid=True,
+        source={"name": "ERA5", "path": fname},
+        use_dask=use_dask,
+    )
+
+
+@pytest.fixture(scope="session")
+def corrected_surface_forcing(request, use_dask):
+    """Fixture for creating a SurfaceForcing object with shortwave radiation
+    correction."""
+
+    grid = Grid(
+        nx=5,
+        ny=5,
+        size_x=1800,
+        size_y=2400,
+        center_lon=180,
+        center_lat=61,
+        rot=20,
+    )
+
+    start_time = datetime(2020, 1, 31)
+    end_time = datetime(2020, 2, 2)
+
+    fname = download_test_data("ERA5_global_test_data.nc")
+
+    return SurfaceForcing(
+        grid=grid,
+        start_time=start_time,
+        end_time=end_time,
+        source={"name": "ERA5", "path": fname},
+        correct_radiation=True,
+        use_dask=use_dask,
+    )
+
+
+@pytest.fixture(scope="session")
+def bgc_surface_forcing(request, use_dask):
+    """Fixture for creating a SurfaceForcing object with BGC."""
+    grid = Grid(
+        nx=5,
+        ny=5,
+        size_x=1800,
+        size_y=2400,
+        center_lon=180,
+        center_lat=61,
+        rot=20,
+    )
+
+    start_time = datetime(2020, 2, 1)
+    end_time = datetime(2020, 2, 1)
+
+    fname_bgc = download_test_data("CESM_surface_global_test_data.nc")
+
+    return SurfaceForcing(
+        grid=grid,
+        start_time=start_time,
+        end_time=end_time,
+        source={"name": "CESM_REGRIDDED", "path": fname_bgc},
+        type="bgc",
+        use_dask=use_dask,
+    )
+
+
+@pytest.fixture(scope="session")
+def bgc_surface_forcing_from_climatology(request, use_dask):
+    """Fixture for creating a SurfaceForcing object with BGC from climatology."""
+    grid = Grid(
+        nx=5,
+        ny=5,
+        size_x=1800,
+        size_y=2400,
+        center_lon=180,
+        center_lat=61,
+        rot=20,
+    )
+
+    start_time = datetime(2020, 2, 1)
+    end_time = datetime(2020, 2, 1)
+
+    fname_bgc = download_test_data("CESM_surface_global_test_data_climatology.nc")
+
+    return SurfaceForcing(
+        grid=grid,
+        start_time=start_time,
+        end_time=end_time,
+        source={"name": "CESM_REGRIDDED", "path": fname_bgc, "climatology": True},
+        type="bgc",
+        use_dask=use_dask,
+    )
+
+
+@pytest.fixture(scope="session")
+def era5_data(request, use_dask):
+    fname = download_test_data("ERA5_regional_test_data.nc")
+    data = ERA5Dataset(
+        filename=fname,
+        start_time=datetime(2020, 1, 31),
+        end_time=datetime(2020, 2, 2),
+        use_dask=use_dask,
+    )
+
+    return data
+
+
+@pytest.fixture(scope="session")
+def glorys_data(request, use_dask):
+    # the following GLORYS data has a wide enough domain
+    # to have different masks for tracers vs. velocities
+    fname = download_test_data("GLORYS_test_data.nc")
+
+    data = GLORYSDataset(
+        filename=fname,
+        start_time=datetime(2012, 1, 1),
+        end_time=datetime(2013, 1, 1),
+        use_dask=use_dask,
+    )
+
+    ds = data.ds.isel(depth=[0, 10, 30])
+    object.__setattr__(data, "ds", ds)
+
+    data.extrapolate_deepest_to_bottom()
+
+    return data
+
+
+@pytest.fixture(scope="session")
+def tpxo_data(request, use_dask):
+    fname = download_test_data("TPXO_regional_test_data.nc")
+
+    data = TPXODataset(
+        filename=fname,
+        use_dask=use_dask,
+    )
+
+    return data
+
+
+@pytest.fixture(scope="session")
+def cesm_bgc_data(request, use_dask):
+    fname = download_test_data("CESM_regional_test_data_one_time_slice.nc")
+
+    data = CESMBGCDataset(
+        filename=fname,
+        start_time=datetime(2012, 1, 1),
+        end_time=datetime(2013, 1, 1),
+        climatology=False,
+        use_dask=use_dask,
+    )
+
+    return data
+
+
+@pytest.fixture(scope="session")
+def coarsened_cesm_bgc_data(request, use_dask):
+    fname = download_test_data("CESM_BGC_2012.nc")
+
+    data = CESMBGCDataset(
+        filename=fname,
+        start_time=datetime(2012, 1, 1),
+        end_time=datetime(2013, 1, 1),
+        climatology=False,
+        use_dask=use_dask,
+    )
+
+    data.extrapolate_deepest_to_bottom()
+
+    return data
+
+
+@pytest.fixture(scope="session")
+def cesm_surface_bgc_data(request, use_dask):
+    fname = download_test_data("CESM_BGC_SURFACE_2012.nc")
+
+    data = CESMBGCSurfaceForcingDataset(
+        filename=fname,
+        start_time=datetime(2012, 1, 1),
+        end_time=datetime(2013, 1, 1),
+        climatology=False,
+        use_dask=use_dask,
+    )
+    data.post_process()
+
+    return data
+
+
+def calculate_file_hash(filepath, hash_algorithm="sha256"):
+    """Calculate the hash of a file using the specified hash algorithm."""
+    hash_func = hashlib.new(hash_algorithm)
+    with open(filepath, "rb") as f:
+        for chunk in iter(lambda: f.read(4096), b""):
+            hash_func.update(chunk)
+    return hash_func.hexdigest()