roms-tools 3.2.0__tar.gz → 3.3.0__tar.gz

roms_tools-3.3.0/.github/workflows/tests.yaml

@@ -0,0 +1,378 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  test-without-dask:
+    name: ${{ matrix.python-version }}-build-without-dask
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11", "3.12", "3.13"]
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Create conda environment
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          cache-downloads: true
+          cache-environment: true
+          micromamba-version: 'latest'
+          environment-file: ci/environment.yml
+          create-args: |
+            python=${{ 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 . --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 || 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-1:
+    name: 3.13-build-with-dask-1
+    runs-on: ubuntu-latest
+    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
+
+      - 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/ --ignore=roms_tools/tests/test_setup/test_boundary_forcing.py --ignore=roms_tools/tests/test_setup/test_initial_conditions.py --ignore=roms_tools/tests/test_setup/test_surface_forcing.py
+
+      - 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: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          flags: with-dask-1
+          name: with-dask-1-py${{ matrix.python-version }}
+          fail_ci_if_error: false
+
+  test-with-dask-2:
+    name: 3.13-build-with-dask-2
+    runs-on: ubuntu-latest
+    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
+
+      - 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/test_setup/test_boundary_forcing.py roms_tools/tests/test_setup/test_initial_conditions.py roms_tools/tests/test_setup/test_surface_forcing.py
+
+      - 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: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          flags: with-dask-2
+          name: with-dask-2-py${{ 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"]
+    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 .[stream]  --force-reinstall
+
+      - name: Running Tests with Streaming
+        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 -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: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          flags: with-streaming
+          name: with-streaming
+          fail_ci_if_error: false
+
+  test-with-dask-and-xesmf-1:
+    name: 3.13-build-with-dask-and-xesmf-1
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.13"]
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Create conda environment
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          cache-downloads: true
+          cache-environment: true
+          micromamba-version: 'latest'
+          environment-file: ci/environment-with-xesmf.yml
+          create-args: |
+            python=${{ 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
+
+      - name: Running Tests with Dask and Xesmf
+        shell: bash -l {0}
+        run: |
+           python -V
+           coverage run --rcfile=coverage.toml -m pytest --use_dask --verbose roms_tools/tests/ --ignore=roms_tools/tests/test_setup/test_boundary_forcing.py --ignore=roms_tools/tests/test_setup/test_initial_conditions.py --ignore=roms_tools/tests/test_setup/test_surface_forcing.py
+
+      - 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: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          flags: with-dask-and-xesmf-1
+          name: with-dask-and-xesmf-1
+          fail_ci_if_error: false
+
+  test-with-dask-and-xesmf-2:
+    name: 3.13-build-with-dask-and-xesmf-2
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.13"]
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Create conda environment
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          cache-downloads: true
+          cache-environment: true
+          micromamba-version: 'latest'
+          environment-file: ci/environment-with-xesmf.yml
+          create-args: |
+            python=${{ 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
+
+      - name: Running Tests with Dask and Xesmf
+        shell: bash -l {0}
+        run: |
+           python -V
+           coverage run --rcfile=coverage.toml -m pytest --use_dask --verbose roms_tools/tests/test_setup/test_boundary_forcing.py roms_tools/tests/test_setup/test_initial_conditions.py roms_tools/tests/test_setup/test_surface_forcing.py
+
+      - 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: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          flags: with-dask-and-xesmf-2
+          name: with-dask-and-xesmf-2
+          fail_ci_if_error: false
+
+  test-glorys-regional-invariance:
+    name: 3.13-build-glorys-regional-invariance
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push' || github.event.pull_request.head.repo.fork == false
+    strategy:
+      matrix:
+        python-version: ["3.13"]
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Create conda environment
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          cache-downloads: true
+          cache-environment: true
+          micromamba-version: 'latest'
+          environment-file: ci/environment.yml
+          create-args: |
+            python=${{ 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: glorys-regional-invariance
+          name: glorys-regional-invariance
+          fail_ci_if_error: false

roms_tools-3.3.0/PKG-INFO

@@ -0,0 +1,156 @@
+Metadata-Version: 2.4
+Name: roms-tools
+Version: 3.3.0
+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
+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 :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: xarray<2025.8.0,>=2022.6.0
+Requires-Dist: numpy<2.3,>2.0
+Requires-Dist: pooch
+Requires-Dist: matplotlib
+Requires-Dist: cartopy
+Requires-Dist: packaging
+Requires-Dist: scipy
+Requires-Dist: gcm_filters>=0.5.1
+Requires-Dist: netcdf4
+Requires-Dist: PyYAML
+Requires-Dist: pyamg
+Requires-Dist: bottleneck
+Requires-Dist: regionmask
+Requires-Dist: xgcm>=0.9.0
+Requires-Dist: numba>=0.61.2
+Requires-Dist: pydantic<3,>2
+Provides-Extra: dask
+Requires-Dist: dask[diagnostics]; extra == "dask"
+Requires-Dist: zarr; extra == "dask"
+Provides-Extra: stream
+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)
+![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
+
+A suite of Python tools for setting up and analyzing a [UCLA-ROMS](https://github.com/CESR-lab/ucla-roms) simulation with or without [MARBL biogeochemistry](https://marbl-ecosys.github.io/versions/latest_release/index.html).
+
+## Installation
+
+### ⚡️ **Installation from Conda-Forge**
+
+To install `ROMS-Tools` with all dependencies, including `xesmf`, `dask` and all packages required for streaming source data directly from the cloud, use:
+
+```bash
+conda install -c conda-forge roms-tools
+```
+
+> [!Note]
+>  Installation from Conda-Forge is the recommended installation method to ensure all features of `ROMS-Tools` are available.
+
+### 📦 **Installation from PyPI (pip)**
+
+You can also install `ROMS-Tools` from `pip`:
+
+```bash
+pip install roms-tools
+```
+
+If you want to use `ROMS-Tools` with `dask` (recommended for parallel and out-of-core computation), install it with the additional dependency:
+
+```bash
+pip install roms-tools[dask]
+```
+
+If you want to use `ROMS-Tools` with `dask` and all packages required for streaming source data directly from the cloud, install it with the additional dependencies:
+
+```bash
+pip install roms-tools[stream]
+```
+
+
+> [!Note]
+>  The PyPI versions of `ROMS-Tools` do not include `xesmf`, so some features will be unavailable.
+
+
+### 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-with-xesmf.yml
+conda activate romstools-test
+```
+
+Finally, install `ROMS-Tools` in the same environment:
+
+```bash
+pip install -e .
+```
+
+If you want to use `ROMS-Tools` with `dask` (recommended for parallel and out-of-core computation), you can
+install `ROMS-Tools` along with the additional dependency via:
+
+```bash
+pip install -e ".[dask]"
+```
+
+If you want to use `ROMS-Tools` with `dask` and all packages required for streaming source data directly from the cloud, you can
+install `ROMS-Tools` along with the additional dependencies via:
+
+```bash
+pip install -e ".[stream]"
+```
+
+## 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)