roms-tools 1.2.0__tar.gz → 1.4.0__tar.gz

{roms_tools-1.2.0 → roms_tools-1.4.0}/.github/workflows/pypipublish.yaml

@@ -59,7 +59,6 @@ jobs:
         run: |
           ls -ltrh
           ls -ltrh dist
-
       - name: Verify the built dist/wheel is valid
         run: |
           python -m pip install --upgrade pip

{roms_tools-1.2.0 → roms_tools-1.4.0}/.github/workflows/sphinx.yaml

@@ -23,7 +23,7 @@ jobs:
         shell: micromamba-shell {0}
         run: |
            python - V
-           python -m pip install -e . --no-deps --force-reinstall
+           python -m pip install -e . --force-reinstall
       - name: Build Docs
         shell: bash -l {0}
         run: |

roms_tools-1.4.0/.github/workflows/tests.yaml

@@ -0,0 +1,106 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  test-without-dask:
+    name: ${{ matrix.python-version }}-build-without-dask
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Create conda environment
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          cache-downloads: true
+          cache-environment: true
+          micromamba-version: 'latest'
+          environment-file: ci/environment.yml
+          create-args: |
+            python=${{ 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: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          flags: unittests # optional
+
+  test-with-dask:
+    name: 3.12-build-with-dask
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.12"]  # Only Python 3.12
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Create conda environment
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          cache-downloads: true
+          cache-environment: true
+          micromamba-version: 'latest'
+          environment-file: ci/environment.yml
+          create-args: |
+            python=${{ 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-1.2.0 → roms_tools-1.4.0}/.pre-commit-config.yaml

@@ -1,6 +1,9 @@
+default_stages: [commit, push]
 ci:
   autoupdate_schedule: monthly
 
+exclude: roms_tools/tests/test_setup/test_data/
+
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.3.0

{roms_tools-1.2.0 → roms_tools-1.4.0}/.readthedocs.yaml

@@ -18,14 +18,8 @@ sphinx:
 conda:
     environment: ci/environment.yml
 
-# Optionally build your docs in additional formats such as PDF and ePub
-# formats:
-#    - pdf
-#    - epub
-
-# Optional but recommended, declare the Python requirements required
-# to build your documentation
-# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
-# python:
-#    install:
-#    - requirements: docs/requirements.txt
+# Python dependencies and install method
+python:
+  install:
+    - method: pip
+      path: .

{roms_tools-1.2.0 → roms_tools-1.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: roms-tools
-Version: 1.2.0
+Version: 1.4.0
 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
@@ -19,16 +19,19 @@ Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: xarray>=2022.6.0
-Requires-Dist: xarray-datatree
 Requires-Dist: numpy
-Requires-Dist: netcdf4
 Requires-Dist: pooch
 Requires-Dist: matplotlib
 Requires-Dist: cartopy
 Requires-Dist: packaging
 Requires-Dist: scipy
 Requires-Dist: gcm_filters
-Requires-Dist: numba
+Requires-Dist: netcdf4
+Requires-Dist: PyYAML
+Requires-Dist: pyamg
+Requires-Dist: bottleneck
+Provides-Extra: dask
+Requires-Dist: dask; extra == "dask"
 
 # ROMS-Tools
 [![PyPI version](https://img.shields.io/pypi/v/roms-tools.svg)](https://pypi.org/project/roms-tools/)
@@ -50,29 +53,54 @@ A suite of python tools for setting up a [ROMS](https://github.com/CESR-lab/ucla
 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, clone the source repository and install it:
+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
+```
+
+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 install and activate the following conda environment:
+Before running the tests, you can activate the conda environment created in the previous section:
 
 ```bash
-cd roms-tools
-conda env create -f ci/environment.yml
 conda activate romstools
 ```
 
 Check the installation of `ROMS-Tools` has worked by running the test suite
 ```bash
+cd roms-tools
 pytest
 ```
 

{roms_tools-1.2.0 → roms_tools-1.4.0}/README.md

@@ -18,29 +18,54 @@ A suite of python tools for setting up a [ROMS](https://github.com/CESR-lab/ucla
 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, clone the source repository and install it:
+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
+```
+
+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 install and activate the following conda environment:
+Before running the tests, you can activate the conda environment created in the previous section:
 
 ```bash
-cd roms-tools
-conda env create -f ci/environment.yml
 conda activate romstools
 ```
 
 Check the installation of `ROMS-Tools` has worked by running the test suite
 ```bash
+cd roms-tools
 pytest
 ```
 

{roms_tools-1.2.0 → roms_tools-1.4.0}/ci/environment.yml

@@ -3,20 +3,11 @@ channels:
   - conda-forge
   - nodefaults
 dependencies:
-  - python>=3.9
-  - numpy
-  - scipy
-  - matplotlib
-  - cartopy
-  - xarray
-  - xarray-datatree
-  - netcdf4
-  - pooch
-  - packaging
-  - numba
-  - gcm_filters
+  - python>=3.10
   # testing
+  - zarr
   - pytest
+  - pytest-xdist
   - flake8
   - black
   - pre-commit

roms_tools-1.4.0/conftest.py

@@ -0,0 +1,385 @@
+import pytest
+from datetime import datetime
+from roms_tools import (
+    Grid,
+    TidalForcing,
+    InitialConditions,
+    BoundaryForcing,
+    SurfaceForcing,
+)
+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},
+        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",
+        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,
+    )
+
+
+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()