roms-tools 3.1.2__tar.gz → 3.2.0__tar.gz

roms_tools-3.2.0/.github/workflows/draft-pdf.yaml

@@ -0,0 +1,31 @@
+name: JOSS paper
+on:
+  pull_request:
+    paths:
+      - 'paper.md'
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.head_ref }}
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          paper-path: paper.md
+
+      - name: Upload
+        uses: actions/upload-artifact@v4
+        with:
+          name: paper
+          path: paper.pdf
+      - name: Commit PDF to repository
+        uses: EndBug/add-and-commit@v9
+        with:
+          message: '(auto) Paper PDF Draft'
+          add: 'paper.pdf'

{roms_tools-3.1.2 → roms_tools-3.2.0}/.github/workflows/tests.yaml

@@ -44,6 +44,22 @@ jobs:
            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 || true
+          coverage xml || true
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v4.0.1
+        continue-on-error: true
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          flags: without-dask
+          name: without-dask-py${{ matrix.python-version }}
+          fail_ci_if_error: false
+
   test-with-dask:
     name: 3.13-build-with-dask
     runs-on: ubuntu-latest
@@ -79,9 +95,26 @@ jobs:
            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 || true
+          coverage xml || true
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v4.0.1
+        continue-on-error: true
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          flags: with-dask
+          name: with-dask-py${{ matrix.python-version }}
+          fail_ci_if_error: false
+
   test-with-streaming:
     name: 3.13-build-with-streaming
     runs-on: ubuntu-latest
+    if: github.event_name == 'push' || github.event.pull_request.head.repo.fork == false
     strategy:
       matrix:
         python-version: ["3.13"]
@@ -118,6 +151,22 @@ jobs:
            copernicusmarine login
            coverage run --rcfile=coverage.toml -m pytest -m stream --stream --use_dask --use_gcsfs --use_copernicus --verbose roms_tools/tests/*
 
+      - name: Get coverage report
+        shell: bash -l {0}
+        run: |
+          coverage report -m || true
+          coverage xml || true
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v4.0.1
+        continue-on-error: true
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          flags: with-streaming
+          name: with-streaming
+          fail_ci_if_error: false
+
   test-with-dask-and-xesmf:
     name: 3.13-build-with-dask-and-xesmf
     runs-on: ubuntu-latest
@@ -156,12 +205,73 @@ jobs:
       - name: Get coverage report
         shell: bash -l {0}
         run: |
-          coverage report -m
-          coverage xml
+          coverage report -m || true
+          coverage xml || true
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v4.0.1
+        continue-on-error: true
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          flags: with-dask-and-xesmf
+          name: with-dask-and-xesmf
+          fail_ci_if_error: false
+
+
+  test-glorys-regional-invariance:
+    name: 3.13-build-glorys-regional-invariance
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push' || github.event.pull_request.head.repo.fork == false
+    strategy:
+      matrix:
+        python-version: ["3.13"]
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Create conda environment
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          cache-downloads: true
+          cache-environment: true
+          micromamba-version: 'latest'
+          environment-file: ci/environment.yml
+          create-args: |
+            python=${{ matrix.python-version }}
+          cache-environment-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
+           python -m pip install copernicusmarine
+
+      - name: Running Tests without Dask
+        shell: bash -l {0}
+        env:
+          COPERNICUSMARINE_SERVICE_USERNAME: ${{ secrets.COPERNICUSMARINE_SERVICE_USERNAME }}
+          COPERNICUSMARINE_SERVICE_PASSWORD: ${{ secrets.COPERNICUSMARINE_SERVICE_PASSWORD }}
+        run: |
+           python -V
+           copernicusmarine login
+           coverage run --rcfile=coverage.toml -m pytest --use_copernicus --use_dask --verbose -k "test_invariance_to_get_glorys_bounds" roms_tools/tests/
+
+      - name: Get coverage report
+        shell: bash -l {0}
+        run: |
+          coverage report -m || true
+          coverage xml || true
 
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v4.0.1
+        continue-on-error: true
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           files: ./coverage.xml
-          flags: unittests # optional
+          flags: glorys-regional-invariance
+          name: glorys-regional-invariance
+          fail_ci_if_error: false

{roms_tools-3.1.2 → roms_tools-3.2.0}/.pre-commit-config.yaml

@@ -30,3 +30,14 @@ repos:
       - id: ruff-check
         args: ["--fix"]
       - id: ruff-format
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.16.1
+    hooks:
+      - id: mypy
+        additional_dependencies: [
+          "types-requests",
+          "types-python-dateutil",
+          "types-PyYAML",
+          "types-pytz",
+        ]

{roms_tools-3.1.2 → roms_tools-3.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: roms-tools
-Version: 3.1.2
+Version: 3.2.0
 Summary: Tools for running and analysing UCLA-ROMS simulations
 Author-email: Nora Loose <nora.loose@gmail.com>, Thomas Nicholas <tom@cworthy.org>, Scott Eilerman <scott.eilerman@cworthy.org>
 License: Apache-2
@@ -42,15 +42,25 @@ Requires-Dist: dask[diagnostics]; extra == "stream"
 Requires-Dist: gcsfs; extra == "stream"
 Requires-Dist: zarr; extra == "stream"
 Requires-Dist: copernicusmarine; extra == "stream"
+Provides-Extra: notebooks
+Requires-Dist: dask[diagnostics]; extra == "notebooks"
+Requires-Dist: gcsfs; extra == "notebooks"
+Requires-Dist: zarr; extra == "notebooks"
+Requires-Dist: copernicusmarine; extra == "notebooks"
+Requires-Dist: gdown; extra == "notebooks"
+Requires-Dist: ipykernel; extra == "notebooks"
+Requires-Dist: jupyter; extra == "notebooks"
 Dynamic: license-file
 
 # 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/)
+[![Run Tests](https://github.com/CWorthy-ocean/roms-tools/actions/workflows/tests.yaml/badge.svg)](https://github.com/CWorthy-ocean/roms-tools/actions/workflows/tests.yaml?query=branch%3Amain)
 [![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)
+[![PyPI Downloads](https://static.pepy.tech/personalized-badge/roms-tools?period=total&units=INTERNATIONAL_SYSTEM&left_color=BLACK&right_color=GREEN&left_text=downloads)](https://pepy.tech/projects/roms-tools)
 
 ## Overview
 

{roms_tools-3.1.2 → roms_tools-3.2.0}/README.md

@@ -1,10 +1,12 @@
 # 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/)
+[![Run Tests](https://github.com/CWorthy-ocean/roms-tools/actions/workflows/tests.yaml/badge.svg)](https://github.com/CWorthy-ocean/roms-tools/actions/workflows/tests.yaml?query=branch%3Amain)
 [![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)
+[![PyPI Downloads](https://static.pepy.tech/personalized-badge/roms-tools?period=total&units=INTERNATIONAL_SYSTEM&left_color=BLACK&right_color=GREEN&left_text=downloads)](https://pepy.tech/projects/roms-tools)
 
 ## Overview
 

{roms_tools-3.1.2 → roms_tools-3.2.0}/conftest.py

@@ -126,6 +126,24 @@ def grid() -> Grid:
     return grid
 
 
+@pytest.fixture(scope="session")
+def large_grid():
+    grid = Grid(
+        nx=24,
+        ny=48,
+        size_x=500,
+        size_y=1000,
+        center_lon=0,
+        center_lat=55,
+        rot=10,
+        N=3,
+        theta_s=5.0,
+        theta_b=2.0,
+        hc=250.0,
+    )
+    return grid
+
+
 @pytest.fixture(scope="session")
 def grid_that_straddles_dateline() -> Grid:
     grid = Grid(
@@ -135,6 +153,21 @@ def grid_that_straddles_dateline() -> Grid:
     return grid
 
 
+@pytest.fixture(scope="session")
+def tiny_grid_that_straddles_dateline() -> Grid:
+    grid = Grid(
+        nx=5,
+        ny=5,
+        size_x=10,
+        size_y=10,
+        center_lon=0,
+        center_lat=61,
+        rot=20,
+    )
+
+    return grid
+
+
 @pytest.fixture(scope="session")
 def grid_that_straddles_180_degree_meridian() -> Grid:
     """Fixture for creating a domain that straddles 180 degree meridian.
@@ -155,6 +188,21 @@ def grid_that_straddles_180_degree_meridian() -> Grid:
     return grid
 
 
+@pytest.fixture(scope="session")
+def tiny_grid_that_straddles_180_degree_meridian() -> Grid:
+    grid = Grid(
+        nx=5,
+        ny=5,
+        size_x=10,
+        size_y=10,
+        center_lon=180,
+        center_lat=61,
+        rot=20,
+    )
+
+    return grid
+
+
 @pytest.fixture(scope="session")
 def small_grid() -> Grid:
     """Create a grid that covers a small surface area."""
@@ -191,6 +239,24 @@ def tiny_grid() -> Grid:
     )
 
 
+@pytest.fixture(scope="session")
+def tiny_rotated_grid() -> Grid:
+    """Create a grid that covers a small surface area."""
+    return Grid(
+        nx=3,
+        ny=3,
+        size_x=10,
+        size_y=10,
+        center_lon=-17,
+        center_lat=60,
+        rot=20,
+        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
+    )
+
+
 @pytest.fixture(scope="session")
 def tidal_forcing(use_dask: bool) -> TidalForcing:
     grid = Grid(
@@ -203,7 +269,7 @@ def tidal_forcing(use_dask: bool) -> TidalForcing:
 
     return TidalForcing(
         grid=grid,
-        source={"name": "TPXO", "path": fname_dict},
+        source={"name": "TPXO", "path": fname_dict},  # type: ignore[dict-item]
         ntides=1,
         use_dask=use_dask,
     )
@@ -236,6 +302,19 @@ def initial_conditions(use_dask: bool) -> InitialConditions:
     )
 
 
+@pytest.fixture(scope="session")
+def initial_conditions_on_large_grid(large_grid, use_dask):
+    """Fixture for creating an InitialConditions object."""
+    fname = Path(download_test_data("GLORYS_coarse_test_data.nc"))
+
+    return InitialConditions(
+        grid=large_grid,
+        ini_time=datetime(2021, 6, 29),
+        source={"path": fname, "name": "GLORYS"},
+        use_dask=use_dask,
+    )
+
+
 @pytest.fixture(scope="session")
 def initial_conditions_adjusted_for_zeta(use_dask: bool) -> InitialConditions:
     """Fixture for creating an InitialConditions object."""
@@ -350,7 +429,7 @@ def initial_conditions_with_bgc_from_climatology(use_dask: bool) -> InitialCondi
         bgc_source={
             "path": fname_bgc,
             "name": "CESM_REGRIDDED",
-            "climatology": True,
+            "climatology": True,  # type: ignore[dict-item]
         },
         use_dask=use_dask,
     )
@@ -381,7 +460,7 @@ def initial_conditions_with_unified_bgc_from_climatology(
         grid=grid,
         ini_time=datetime(2021, 6, 29),
         source={"path": fname, "name": "GLORYS"},
-        bgc_source={"path": fname_bgc, "name": "UNIFIED", "climatology": True},
+        bgc_source={"path": fname_bgc, "name": "UNIFIED", "climatology": True},  # type: ignore[dict-item]
         use_dask=use_dask,
     )
 
@@ -477,7 +556,7 @@ def bgc_boundary_forcing_from_climatology(use_dask: bool) -> BoundaryForcing:
         grid=grid,
         start_time=datetime(2021, 6, 29),
         end_time=datetime(2021, 6, 30),
-        source={"path": fname_bgc, "name": "CESM_REGRIDDED", "climatology": True},
+        source={"path": fname_bgc, "name": "CESM_REGRIDDED", "climatology": True},  # type: ignore[dict-item]
         type="bgc",
         apply_2d_horizontal_fill=True,
         use_dask=use_dask,
@@ -507,7 +586,7 @@ def bgc_boundary_forcing_from_unified_climatology(use_dask: bool) -> BoundaryFor
         grid=grid,
         start_time=datetime(2021, 6, 29),
         end_time=datetime(2021, 6, 30),
-        source={"path": fname_bgc, "name": "UNIFIED", "climatology": True},
+        source={"path": fname_bgc, "name": "UNIFIED", "climatology": True},  # type: ignore[dict-item]
         type="bgc",
         apply_2d_horizontal_fill=True,
         use_dask=use_dask,
@@ -713,7 +792,7 @@ def bgc_surface_forcing_from_climatology(use_dask: bool) -> SurfaceForcing:
         grid=grid,
         start_time=start_time,
         end_time=end_time,
-        source={"name": "CESM_REGRIDDED", "path": fname_bgc, "climatology": True},
+        source={"name": "CESM_REGRIDDED", "path": fname_bgc, "climatology": True},  # type: ignore[dict-item]
         type="bgc",
         coarse_grid_mode="never",
         use_dask=use_dask,
@@ -742,7 +821,7 @@ def bgc_surface_forcing_from_unified_climatology(use_dask: bool) -> SurfaceForci
         grid=grid,
         start_time=start_time,
         end_time=end_time,
-        source={"name": "UNIFIED", "path": fname_bgc, "climatology": True},
+        source={"name": "UNIFIED", "path": fname_bgc, "climatology": True},  # type: ignore[dict-item]
         type="bgc",
         coarse_grid_mode="never",
         use_dask=use_dask,

roms_tools-3.2.0/coverage.toml

@@ -0,0 +1,14 @@
+[tool.coverage.run]
+source = ["roms_tools"]
+omit = [
+    "roms_tools/tests/*",
+    "**/__init__.py",
+]
+branch = true
+
+[tool.coverage.report]
+skip_covered = true
+show_missing = true
+
+[tool.coverage.xml]
+relative_files = true

{roms_tools-3.1.2 → roms_tools-3.2.0}/docs/api.rst

@@ -75,6 +75,7 @@ Analyzing ROMS output
    :toctree: generated/
 
    roms_tools.ROMSOutput
+   roms_tools.Ensemble
 
 =======
 
@@ -85,4 +86,6 @@ Utilities
    :toctree: generated/
 
    roms_tools.tiling.partition.partition_netcdf
+   roms_tools.tiling.join.join_netcdf
    roms_tools.plot.plot
+   roms_tools.setup.datasets.get_glorys_bounds