ocstrack 0.1.4.post0__tar.gz → 0.2.2.dev0__tar.gz

ocstrack-0.2.2.dev0/.github/workflows/docs.yml

@@ -0,0 +1,55 @@
+# GitHub Actions workflow for building and deploying the MkDocs site
+
+name: Deploy Documentation
+
+on:
+  push:
+    branches:
+      - main
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    env:
+      FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
+    steps:
+      - name: Check out code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install mkdocs-material "mkdocstrings[python]"
+          pip install .
+
+      - name: Build MkDocs site
+        run: mkdocs build
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: ./site
+
+  deploy:
+    needs: build
+    runs-on: ubuntu-latest
+    permissions:
+      pages: write
+      id-token: write
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

ocstrack-0.2.2.dev0/.github/workflows/lint.yml

@@ -0,0 +1,44 @@
+# GitHub Actions workflow for Continuous Integration (CI)
+
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    env:
+      FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
+    steps:
+      - name: Check out code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.9'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install pylint pytest pytest-cov
+
+      - name: Run Pylint
+        run: |
+          python -m pylint ocstrack
+          
+      - name: Run Pytest and Generate Coverage Report
+        run: |
+          python -m pytest --cov=ocstrack --cov-report=xml
+          
+      - name: Upload Coverage to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }} # Optional for public repos

{ocstrack-0.1.4.post0 → ocstrack-0.2.2.dev0}/.github/workflows/publish-to-pypi.yml

@@ -1,17 +1,20 @@
 # .github/workflows/publish-to-pypi.yml
 #
 # This workflow builds and publishes the package to PyPI
-# every time you create a new release on GitHub.
+# every time you push a new tag that starts with 'v'.
 #
 name: Publish Python - PyPI
 
 on:
-  release:
-    types: [created]  # This is the trigger
+  push:
+    tags:
+      - 'v*'
 
 jobs:
   deploy:
     runs-on: ubuntu-latest
+    env:
+      FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
 
     steps:
     - uses: actions/checkout@v4

{ocstrack-0.1.4.post0 → ocstrack-0.2.2.dev0}/.github/workflows/run-tests.yml

@@ -9,6 +9,8 @@ jobs:
   # --- JOB 1: RUN PYLINT --- #
   lint:
     runs-on: ubuntu-latest  # No need to run on all OSs
+    env:
+      FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
     steps:
     - name: Check out code
       uses: actions/checkout@v4
@@ -33,6 +35,8 @@ jobs:
   # --- JOB 2: RUN TESTS --- #
   test:
     runs-on: ${{ matrix.os }}
+    env:
+      FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]

ocstrack-0.2.2.dev0/.pylintrc

@@ -0,0 +1,26 @@
+# .pylintrc - Configuration for Pylint
+
+[MAIN]
+# A comma-separated list of plugin modules to load.
+load-plugins=
+
+[MESSAGES CONTROL]
+# Disable specific messages by their symbolic name.
+# docstring-first-line: Good practice, but can be noisy initially.
+# missing-module-docstring: Disabling for now to focus on code logic.
+# missing-class-docstring: Your classes have good docstrings.
+# missing-function-docstring: Your functions have good docstrings.
+# trailing-whitespace: This is better handled by a code formatter like black or ruff.
+disable=
+    missing-module-docstring,
+    trailing-whitespace
+
+[REPORTS]
+# Set the failure threshold for the score.
+# If the score is below this value, Pylint will exit with an error code.
+# This is what CI systems use to fail a build.
+fail-under=7.5
+
+[FORMAT]
+# Set the expected maximum line length.
+max-line-length=100

ocstrack-0.2.2.dev0/PKG-INFO

@@ -0,0 +1,230 @@
+Metadata-Version: 2.4
+Name: ocstrack
+Version: 0.2.2.dev0
+Summary: Satellite data download, crop, and collocation with model outputs
+Author-email: Felicio Cassalho <felicio.cassalho@noaa.gov>
+License: Creative Commons Legal Code
+        
+        CC0 1.0 Universal
+        
+            CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE
+            LEGAL SERVICES. DISTRIBUTION OF THIS DOCUMENT DOES NOT CREATE AN
+            ATTORNEY-CLIENT RELATIONSHIP. CREATIVE COMMONS PROVIDES THIS
+            INFORMATION ON AN "AS-IS" BASIS. CREATIVE COMMONS MAKES NO WARRANTIES
+            REGARDING THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS
+            PROVIDED HEREUNDER, AND DISCLAIMS LIABILITY FOR DAMAGES RESULTING FROM
+            THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED
+            HEREUNDER.
+        
+        Statement of Purpose
+        
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+        2. Waiver. To the greatest extent permitted by, but not in contravention
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+         a. No trademark or patent rights held by Affirmer are waived, abandoned,
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+            warranties of any kind concerning the Work, express, implied,
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+            Further, Affirmer disclaims responsibility for obtaining any necessary
+            consents, permissions or other rights required for any use of the
+            Work.
+         d. Affirmer understands and acknowledges that Creative Commons is not a
+            party to this document and has no duty or obligation with respect to
+            this CC0 or use of the Work.
+        
+Project-URL: Homepage, https://github.com/noaa-ocs-modeling/OCSTrack
+Project-URL: Repository, https://github.com/noaa-ocs-modeling/OCSTrack
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: numpy
+Requires-Dist: xarray
+Requires-Dist: scipy
+Requires-Dist: tqdm
+Requires-Dist: requests
+Requires-Dist: netcdf4
+Requires-Dist: h5netcdf
+Requires-Dist: dask
+Provides-Extra: dev
+Requires-Dist: pytest>=6.0; extra == "dev"
+Requires-Dist: pylint; extra == "dev"
+Dynamic: license-file
+
+# OCSTrack: Ocean-Model-Data Collocation Tools
+
+[![CI/CD](https://github.com/noaa-ocs-modeling/OCSTrack/actions/workflows/lint.yml/badge.svg)](https://github.com/noaa-ocs-modeling/OCSTrack/actions/workflows/lint.yml)
+[![PyPI version](https://badge.fury.io/py/ocstrack.svg)](https://badge.fury.io/py/ocstrack)
+[![codecov](https://codecov.io/gh/noaa-ocs-modeling/OCSTrack/graph/badge.svg?token=YOUR_CODECOV_TOKEN_IF_PRIVATE)](https://codecov.io/gh/noaa-ocs-modeling/OCSTrack)
+[![Pylint Score](https://img.shields.io/badge/pylint-8.11-blue)](https://github.com/noaa-ocs-modeling/OCSTrack/actions/workflows/lint.yml)
+[![License: CC0-1.0](https://img.shields.io/badge/License-CC0%201.0-lightgrey.svg)](http://creativecommons.org/publicdomain/zero/1.0/)
+
+**OCSTrack** is an object-oriented Python package for the along-track collocation of satellite (2D) and Argo Float (3D) data with ocean circulation and wave model outputs. It simplifies the process of aligning diverse datasets, making it easier to compare and validate model simulations against observational data.
+
+---
+
+## Key Features
+
+- **Automated Data Fetching**: Downloads satellite altimetry and Argo float data from public repositories.
+- **Model Support**: Natively handles outputs from SCHISM, ADCIRC, and SWAN models.
+- **Flexible Collocation**: Performs temporal and spatial collocation for both 2D surface tracks and 3D profiles.
+- **Efficient & Scalable**: Uses `xarray` and `dask` for efficient, out-of-core computations on large datasets.
+- **Customizable**: Object-oriented design makes it easy to extend support for new models or observational data types.
+
+## Installation
+
+You can install OCSTrack directly from PyPI:
+
+```bash
+pip install ocstrack
+```
+
+To install the latest development version directly from this repository:
+
+```bash
+pip install git+https://github.com/noaa-ocs-modeling/OCSTrack.git
+```
+
+## Quick Start
+
+Here is a minimal example of how to collocate satellite altimetry data with a SCHISM model run.
+
+```python
+from ocstrack import Collocate
+from ocstrack.Model import SCHISM
+from ocstrack.Observation import Satellite
+
+# 1. Define time range and region of interest
+start_date = '2021-05-01'
+end_date = '2021-05-05'
+bbox = [-76, 34, -72, 38]  # [lon_min, lat_min, lon_max, lat_max]
+
+# 2. Initialize the Model object
+# This assumes a SCHISM run directory with standard outputs
+schism_run_dir = '/path/to/your/schism/run/'
+model = SCHISM(schism_run_dir, start_date=start_date, end_date=end_date)
+
+# 3. Initialize the Observation object
+sat_name = 'sentinel-3a' # Example satellite
+observation = Satellite(sat_name, start_date=start_date, end_date=end_date, bbox=bbox)
+
+# 4. Create a Collocation object and run the analysis
+collocator = Collocate(model, observation)
+collocated_dataset = collocator.run(output_path='collocated_data.nc')
+
+print("Collocation complete!")
+print(collocated_dataset)
+```
+
+## Documentation
+
+For more detailed examples and the full API reference, please see our documentation website:
+
+[**https://noaa-ocs-modeling.github.io/OCSTrack/**](https://noaa-ocs-modeling.github.io/OCSTrack/)
+
+## Contributing
+
+We welcome contributions! If you have ideas for new features, find a bug, or would like to improve the documentation, please open an issue or submit a pull request.
+
+## License
+
+This project is licensed under the terms of the CC0 1.0 Universal license. See the `LICENSE.txt` file for details.
+
+
+---
+  
+#### Disclaimer
+This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an "as is" basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.
+

ocstrack-0.2.2.dev0/README.md

@@ -0,0 +1,85 @@
+# OCSTrack: Ocean-Model-Data Collocation Tools
+
+[![CI/CD](https://github.com/noaa-ocs-modeling/OCSTrack/actions/workflows/lint.yml/badge.svg)](https://github.com/noaa-ocs-modeling/OCSTrack/actions/workflows/lint.yml)
+[![PyPI version](https://badge.fury.io/py/ocstrack.svg)](https://badge.fury.io/py/ocstrack)
+[![codecov](https://codecov.io/gh/noaa-ocs-modeling/OCSTrack/graph/badge.svg?token=YOUR_CODECOV_TOKEN_IF_PRIVATE)](https://codecov.io/gh/noaa-ocs-modeling/OCSTrack)
+[![Pylint Score](https://img.shields.io/badge/pylint-8.11-blue)](https://github.com/noaa-ocs-modeling/OCSTrack/actions/workflows/lint.yml)
+[![License: CC0-1.0](https://img.shields.io/badge/License-CC0%201.0-lightgrey.svg)](http://creativecommons.org/publicdomain/zero/1.0/)
+
+**OCSTrack** is an object-oriented Python package for the along-track collocation of satellite (2D) and Argo Float (3D) data with ocean circulation and wave model outputs. It simplifies the process of aligning diverse datasets, making it easier to compare and validate model simulations against observational data.
+
+---
+
+## Key Features
+
+- **Automated Data Fetching**: Downloads satellite altimetry and Argo float data from public repositories.
+- **Model Support**: Natively handles outputs from SCHISM, ADCIRC, and SWAN models.
+- **Flexible Collocation**: Performs temporal and spatial collocation for both 2D surface tracks and 3D profiles.
+- **Efficient & Scalable**: Uses `xarray` and `dask` for efficient, out-of-core computations on large datasets.
+- **Customizable**: Object-oriented design makes it easy to extend support for new models or observational data types.
+
+## Installation
+
+You can install OCSTrack directly from PyPI:
+
+```bash
+pip install ocstrack
+```
+
+To install the latest development version directly from this repository:
+
+```bash
+pip install git+https://github.com/noaa-ocs-modeling/OCSTrack.git
+```
+
+## Quick Start
+
+Here is a minimal example of how to collocate satellite altimetry data with a SCHISM model run.
+
+```python
+from ocstrack import Collocate
+from ocstrack.Model import SCHISM
+from ocstrack.Observation import Satellite
+
+# 1. Define time range and region of interest
+start_date = '2021-05-01'
+end_date = '2021-05-05'
+bbox = [-76, 34, -72, 38]  # [lon_min, lat_min, lon_max, lat_max]
+
+# 2. Initialize the Model object
+# This assumes a SCHISM run directory with standard outputs
+schism_run_dir = '/path/to/your/schism/run/'
+model = SCHISM(schism_run_dir, start_date=start_date, end_date=end_date)
+
+# 3. Initialize the Observation object
+sat_name = 'sentinel-3a' # Example satellite
+observation = Satellite(sat_name, start_date=start_date, end_date=end_date, bbox=bbox)
+
+# 4. Create a Collocation object and run the analysis
+collocator = Collocate(model, observation)
+collocated_dataset = collocator.run(output_path='collocated_data.nc')
+
+print("Collocation complete!")
+print(collocated_dataset)
+```
+
+## Documentation
+
+For more detailed examples and the full API reference, please see our documentation website:
+
+[**https://noaa-ocs-modeling.github.io/OCSTrack/**](https://noaa-ocs-modeling.github.io/OCSTrack/)
+
+## Contributing
+
+We welcome contributions! If you have ideas for new features, find a bug, or would like to improve the documentation, please open an issue or submit a pull request.
+
+## License
+
+This project is licensed under the terms of the CC0 1.0 Universal license. See the `LICENSE.txt` file for details.
+
+
+---
+  
+#### Disclaimer
+This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an "as is" basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.
+

ocstrack-0.2.2.dev0/docs/collocation.md

@@ -0,0 +1,28 @@
+# Collocation
+
+This section provides the core tools for collocating model and observational data.
+
+## Core Collocation
+
+The main `Collocate` class is the primary entry point for running the collocation analysis.
+
+!!! note
+    The `Collocate` class is designed to be used with a `Model` object and an `Observation` object as inputs.
+
+::: ocstrack.Collocation.collocate
+
+## Output & Spatial/Temporal Helpers
+
+These modules provide helper functions for handling the output of the collocation, as well as for spatial and temporal operations.
+
+### Output
+
+::: ocstrack.Collocation.output
+
+### Spatial
+
+::: ocstrack.Collocation.spatial
+
+### Temporal
+
+::: ocstrack.Collocation.temporal

ocstrack-0.2.2.dev0/docs/index.md

@@ -0,0 +1,85 @@
+# OCSTrack: Ocean-Model-Data Collocation Tools
+
+[![CI/CD](https://github.com/noaa-ocs-modeling/OCSTrack/actions/workflows/lint.yml/badge.svg)](https://github.com/noaa-ocs-modeling/OCSTrack/actions/workflows/lint.yml)
+[![PyPI version](https://badge.fury.io/py/ocstrack.svg)](https://badge.fury.io/py/ocstrack)
+[![codecov](https://codecov.io/gh/noaa-ocs-modeling/OCSTrack/graph/badge.svg?token=YOUR_CODECOV_TOKEN_IF_PRIVATE)](https://codecov.io/gh/noaa-ocs-modeling/OCSTrack)
+[![Pylint Score](https://img.shields.io/badge/pylint-8.11-blue)](https://github.com/noaa-ocs-modeling/OCSTrack/actions/workflows/lint.yml)
+[![License: CC0-1.0](https://img.shields.io/badge/License-CC0%201.0-lightgrey.svg)](http://creativecommons.org/publicdomain/zero/1.0/)
+
+**OCSTrack** is an object-oriented Python package for the along-track collocation of satellite (2D) and Argo Float (3D) data with ocean circulation and wave model outputs. It simplifies the process of aligning diverse datasets, making it easier to compare and validate model simulations against observational data.
+
+---
+
+## Key Features
+
+- **Automated Data Fetching**: Downloads satellite altimetry and Argo float data from public repositories.
+- **Model Support**: Natively handles outputs from SCHISM, ADCIRC, and SWAN models.
+- **Flexible Collocation**: Performs temporal and spatial collocation for both 2D surface tracks and 3D profiles.
+- **Efficient & Scalable**: Uses `xarray` and `dask` for efficient, out-of-core computations on large datasets.
+- **Customizable**: Object-oriented design makes it easy to extend support for new models or observational data types.
+
+## Installation
+
+You can install OCSTrack directly from PyPI:
+
+```bash
+pip install ocstrack
+```
+
+To install the latest development version directly from this repository:
+
+```bash
+pip install git+https://github.com/noaa-ocs-modeling/OCSTrack.git
+```
+
+## Quick Start
+
+Here is a minimal example of how to collocate satellite altimetry data with a SCHISM model run.
+
+```python
+from ocstrack import Collocate
+from ocstrack.Model import SCHISM
+from ocstrack.Observation import Satellite
+
+# 1. Define time range and region of interest
+start_date = '2021-05-01'
+end_date = '2021-05-05'
+bbox = [-76, 34, -72, 38]  # [lon_min, lat_min, lon_max, lat_max]
+
+# 2. Initialize the Model object
+# This assumes a SCHISM run directory with standard outputs
+schism_run_dir = '/path/to/your/schism/run/'
+model = SCHISM(schism_run_dir, start_date=start_date, end_date=end_date)
+
+# 3. Initialize the Observation object
+sat_name = 'sentinel-3a' # Example satellite
+observation = Satellite(sat_name, start_date=start_date, end_date=end_date, bbox=bbox)
+
+# 4. Create a Collocation object and run the analysis
+collocator = Collocate(model, observation)
+collocated_dataset = collocator.run(output_path='collocated_data.nc')
+
+print("Collocation complete!")
+print(collocated_dataset)
+```
+
+## Documentation
+
+For more detailed examples and the full API reference, please see our documentation website:
+
+[**https://noaa-ocs-modeling.github.io/OCSTrack/**](https://noaa-ocs-modeling.github.io/OCSTrack/)
+
+## Contributing
+
+We welcome contributions! If you have ideas for new features, find a bug, or would like to improve the documentation, please open an issue or submit a pull request.
+
+## License
+
+This project is licensed under the terms of the CC0 1.0 Universal license. See the `LICENSE.txt` file for details.
+
+
+---
+  
+#### Disclaimer
+This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an "as is" basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.
+

ocstrack-0.2.2.dev0/docs/model.md

@@ -0,0 +1,22 @@
+# Model Interfaces
+
+This section provides interfaces for different ocean models.
+
+## SCHISM Model
+
+The `SCHISM` class provides an interface for handling SCHISM model outputs.
+
+::: ocstrack.Model.model.SCHISM
+
+## ADCSWAN Model
+
+The `ADCSWAN` class provides an interface for handling ADCIRC+SWAN model outputs.
+
+::: ocstrack.Model.model.ADCSWAN
+
+## Utility Functions
+
+These are helper functions used by the model interfaces.
+
+::: ocstrack.Model.model.natural_sort_key
+::: ocstrack.Model.model._parse_gr3_mesh