pelagos-py 0.0.0__tar.gz

pelagos_py-0.0.0/.github/workflows/buildDocs.yml

@@ -0,0 +1,55 @@
+name: Build Documentation
+
+on:
+  push:
+    branches:
+      - main
+      - dev
+
+permissions:
+  contents: write
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+
+      - name: Set Up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+
+      - name: Install Dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r docs/requirements.txt
+
+      - name: Clean Python Cache and Docs Artifacts
+        run: |
+          find . -name '__pycache__' -type d -exec rm -r {} +
+          find . -name '*.pyc' -delete
+          rm -rf docs/_build/
+          rm -rf docs/api/
+          ls . 
+
+      - name: Build Documentation
+        run: |
+          sphinx-build -b html docs/ docs/_build/html/
+
+      - name: Ensure Static Files Are Present
+        run: |
+          ls -p docs/_build/html/
+
+      - name: Disable Jekyll Processing
+        run: touch docs/_build/html/.nojekyll
+
+      - name: Deploy to GitHub Pages
+        if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/dev'
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          branch: gh-pages  # Deploy to the root of gh-pages
+          folder: docs/_build/html  # Ensure this points to the html folder
+          clean: true  # Deletes old files before deployment

pelagos_py-0.0.0/.github/workflows/bump-patch.yml

@@ -0,0 +1,43 @@
+name: Auto patch tag
+
+# On every merge to main, create the next patch tag (vX.Y.Z+1). These tags
+# are NOT releases, so they never trigger publish.yml — they just advance the
+# version reported by setuptools-scm between PyPI releases. Tags pushed with
+# GITHUB_TOKEN do not trigger other workflows, so there is no publish risk.
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  tag:
+    # Never runs on forks.
+    if: github.repository == 'NOC-OBG-Autonomy/pelagos-py'
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write  # required to push the new tag
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Create next patch tag
+        run: |
+          git fetch --tags --force
+          LATEST=$(git tag --list 'v[0-9]*.[0-9]*.[0-9]*' --sort=-v:refname | head -n1)
+          if [ -z "$LATEST" ]; then
+            echo "::notice::No version tag found. Create the initial release (v0.0.0) before auto-bumping."
+            exit 0
+          fi
+          VER="${LATEST#v}"
+          MAJOR="${VER%%.*}"
+          REST="${VER#*.}"
+          MINOR="${REST%%.*}"
+          PATCH="${REST#*.}"
+          NEXT="v${MAJOR}.${MINOR}.$((PATCH + 1))"
+          echo "Latest tag $LATEST -> new tag $NEXT"
+          git tag "$NEXT"
+          git push origin "$NEXT"

pelagos_py-0.0.0/.github/workflows/publish.yml

@@ -0,0 +1,59 @@
+name: Publish to PyPI
+
+# Publishing is INTENTIONAL: it only happens when a maintainer creates a
+# GitHub Release on the canonical repo. setuptools-scm turns the release tag
+# (e.g. v0.1.0) into the package version. By convention only minor/major
+# releases (patch == 0, i.e. vX.Y.0) are published; patch tags created
+# automatically on merge are ignored.
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  publish:
+    # Never runs on forks — only the canonical repo can publish.
+    if: github.repository == 'NOC-OBG-Autonomy/pelagos-py'
+    runs-on: ubuntu-latest
+
+    # GitHub environment: add required reviewers / tag restrictions here for
+    # an extra human gate before anything reaches PyPI.
+    environment:
+      name: pypi
+      url: https://pypi.org/p/pelagos_py
+
+    permissions:
+      id-token: write  # required for PyPI Trusted Publishing (OIDC)
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # setuptools-scm needs full history + tags
+
+      - name: Gate on release version (publish only vX.Y.0)
+        id: gate
+        run: |
+          TAG="${GITHUB_REF_NAME#v}"
+          PATCH="${TAG##*.}"
+          if [ "$PATCH" = "0" ]; then
+            echo "publish=true" >> "$GITHUB_OUTPUT"
+            echo "Release $GITHUB_REF_NAME is a minor/major release -> publishing."
+          else
+            echo "publish=false" >> "$GITHUB_OUTPUT"
+            echo "::notice::Release $GITHUB_REF_NAME has patch != 0 -> skipping PyPI publish by convention."
+          fi
+
+      - uses: actions/setup-python@v5
+        if: steps.gate.outputs.publish == 'true'
+        with:
+          python-version: "3.12"
+
+      - name: Build sdist and wheel
+        if: steps.gate.outputs.publish == 'true'
+        run: |
+          python -m pip install --upgrade build
+          python -m build
+
+      - name: Publish to PyPI
+        if: steps.gate.outputs.publish == 'true'
+        uses: pypa/gh-action-pypi-publish@release/v1

pelagos_py-0.0.0/.github/workflows/runPytest.yml

@@ -0,0 +1,43 @@
+name: Run Pytest
+
+on:
+  push:
+    branches:
+      - "**"
+  pull_request:
+    branches:
+      - "**"
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+        # python-version: ["3.11", "3.12", "3.13", "3.14"]
+        python-version: ["3.14"]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        pip install -e .[test]
+
+    - name: Run tests
+      run: |
+        pytest tests/ -v
+
+# pytest tests/ -v --cov-report xml --cov=NOCAT
+    # - name: Upload coverage to Codecov
+    #   uses: codecov/codecov-action@v4
+    #   with:
+    #     fail_ci_if_error: false
+    #     flags: pytest
+    #     files: ./coverage.xml
+    #     token: ${{ secrets.CODECOV_TOKEN }} # required

pelagos_py-0.0.0/.gitignore

@@ -0,0 +1,110 @@
+# OS Generated Files
+.DS_Store
+
+# Project Specific
+*.nc
+data/
+/data/
+testing/
+/testing/
+
+# Keep test data (these are reduced size .nc files for unit testing)
+!tests/test_data/*.nc 
+
+# Python Core & Compilation
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+
+# Environments & Dependency Management
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+.pdm.toml
+.pdm-python
+.pdm-build/
+__pypackages__/
+
+# Distribution & Packaging
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+*.manifest
+*.spec
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Testing & Coverage
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Jupyter & Notebooks
+.ipynb_checkpoints
+profile_default/
+ipython_config.py
+*.sage.py
+
+# Databases & Logs
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Web Frameworks & Background Tasks
+instance/
+.webassets-cache
+.scrapy
+docs/_build/
+celerybeat-schedule
+celerybeat.pid
+
+# Editors, IDEs & Tooling
+.spyderproject
+.spyproject
+.ropeproject
+.idea/
+.pybuilder/
+target/
+/site
+.mypy_cache/
+.dmypy.json
+dmypy.json
+.pyre/
+.pytype/
+cython_debug/
+.pypirc
+*.mo
+*.pot
+src/pelagos_py/_version.py
+.vscode/

pelagos_py-0.0.0/.vscode/launch.json

@@ -0,0 +1,15 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python Debugger: main.py File",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "${workspaceFolder}/src/pelagos_py/main.py",
+            "console": "integratedTerminal"
+        }
+    ]
+}

pelagos_py-0.0.0/.vscode/settings.json

@@ -0,0 +1,4 @@
+{
+    "python-envs.defaultEnvManager": "ms-python.python:conda",
+    "python-envs.defaultPackageManager": "ms-python.python:conda"
+}

pelagos_py-0.0.0/CITATION.cff

@@ -0,0 +1,51 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: Pelagos_py
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: Adam
+    family-names: Ward
+    affiliation: National Oceanography Centre
+    orcid: 'https://orcid.org/0009-0008-3463-2694'
+  - given-names: Daniel
+    family-names: Bangay
+    affiliation: National Oceanography Centre
+    orcid: 'https://orcid.org/0009-0000-4285-1952'
+  - given-names: Louis
+    family-names: Clement
+    orcid: 'https://orcid.org/0000-0002-6935-9455'
+    affiliation: National Oceanography Centre
+  - given-names: Colin
+    family-names: Sauze
+    affiliation: National Oceanography Centre
+    orcid: 'https://orcid.org/0000-0001-5368-9217'
+  - given-names: Filipa
+    family-names: Carvalho
+    orcid: 'https://orcid.org/0000-0002-8355-4329'
+    affiliation: National Oceanography Centre
+  - given-names: Flavien
+    family-names: Petit
+    orcid: 'https://orcid.org/0000-0002-2068-7933'
+    affiliation: National Oceanography Centre
+  - given-names: Hans
+    family-names: Hilder
+    orcid: 'https://orcid.org/0009-0008-8882-0754'
+    affiliation: National Oceanography Centre
+  - given-names: Nathan
+    family-names: Briggs
+    orcid: 'https://orcid.org/0000-0003-1549-1386'
+    affiliation: National Oceanography Centre
+  - given-names: Callum
+    family-names: Rollo
+    affiliation: ' Voice of the Ocean Foundation'
+    orcid: 'https://orcid.org/0000-0002-5134-7886'
+  - given-names: Aaron
+    family-names: Mau
+    affiliation: Voice of the Ocean Foundation
+repository-code: 'https://github.com/NOC-OBG-Autonomy/pelagos_py'
+license: Apache-2.0

pelagos_py-0.0.0/CONTRIBUTING.md

@@ -0,0 +1,66 @@
+<!-- omit in toc -->
+# Contributing to pelagos_py
+
+First off, thanks for taking the time to contribute!
+
+All types of contributions are encouraged and valued. Please make sure to read the relevant section of this document before making your contribution. It will make it a lot easier for us maintainers and smooth out the experience for all involved.
+
+<!-- omit in toc -->
+## Table of Contents
+
+- [I Have a Question](#i-have-a-question)
+- [I Want To Contribute](#i-want-to-contribute)
+- [Reporting Bugs](#reporting-bugs)
+
+## I Have a Question
+
+Before you ask a question, it is best to search for existing [Issues](https://github.com/NOC-OBG-Autonomy/pelagos_py/issues) that might help you. In case you have found a suitable issue and still need clarification, you can write your question in this issue. It is also advisable to search the internet for answers first.
+
+If you then still feel the need to ask a question and need clarification, we recommend the following:
+
+- Open an [Issue](https://github.com/NOC-OBG-Autonomy/pelagos_py/issues/new).
+- Provide as much context as you can about what you're running into.
+- Provide project, Python version and details of your Python environment (pip/conda and versions of dependencies).
+
+We will then take care of the issue as soon as possible.
+
+## I Want To Contribute
+
+> ### Legal Notice <!-- omit in toc -->
+> When contributing to this project, you must agree that you have authored 100% of the content, that you have the necessary rights to the content and that the content you contribute will be provided under the project's Apache2 license.
+
+### Reporting Bugs
+
+<!-- omit in toc -->
+#### Before Submitting a Bug Report
+
+A good bug report shouldn't leave others needing to chase you up for more information. Therefore, we ask you to investigate carefully, collect information and describe the issue in detail in your report. Please complete the following steps in advance to help us fix any potential bug as fast as possible.
+
+- Make sure that you are using the latest version.
+- Determine if your bug is really a bug and not an error on your side e.g. using incompatible environment components/versions.
+- To see if other users have experienced (and potentially already solved) the same issue you are having, check if there is not already a bug report existing for your bug or error in the [bug tracker](https://github.com/NOC-OBG-Autonomy/pelagos_py/issues?q=label%3Abug).
+- Collect information about the bug:
+- Stack trace (Traceback)
+- OS, Platform and Version (Windows, Linux, macOS, x86, ARM)
+- Version of Python, package manager (conda/pip etc), depending on what seems relevant.
+- Possibly your input, the output any error messages you are seeing.
+- Can you reliably reproduce the issue?
+
+<!-- omit in toc -->
+#### How Do I Submit a Good Bug Report?
+
+We use GitHub issues to track bugs and errors. If you run into an issue with the project:
+
+- Open an [Issue](https://github.com/NOC-OBG-Autonomy/pelagos_py/issues/new). (Since we can't be sure at this point whether it is a bug or not, we ask you not to talk about a bug yet and not to label the issue.)
+- Explain the behavior you would expect and the actual behavior.
+- Please provide as much context as possible and describe the *reproduction steps* that someone else can follow to recreate the issue on their own. This usually includes your code. For good bug reports you should isolate the problem and create a reduced test case.
+- Provide the information you collected in the previous section.
+
+Once it's filed:
+
+- The project team will label the issue accordingly.
+- A team member will try to reproduce the issue with your provided steps. If there are no reproduction steps or no obvious way to reproduce the issue, the team will ask you for those steps. Bugs will not be addressed until they are reproducible.
+
+<!-- omit in toc -->
+## Attribution
+This guide is based on the [contributing.md](https://contributing.md/generator)!

pelagos_py-0.0.0/LICENSE

@@ -0,0 +1,201 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to Licensor for inclusion in the Work by the copyright owner
+      or by an individual or Legal Entity authorized to submit on behalf of
+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
+
+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      copyright license to reproduce, prepare Derivative Works of,
+      publicly display, publicly perform, sublicense, and distribute the
+      Work and such Derivative Works in Source or Object form.
+
+   3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
+          excluding those notices that do not pertain to any part of
+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
+      the brackets!)  The text should be enclosed in the appropriate
+      comment syntax for the file format. We also recommend that a
+      file or class name and description of purpose be included on the
+      same "printed page" as the copyright notice for easier
+      identification within third-party archives.
+
+   Copyright 2025-2026 The National Oceanography Centre and The Contributors
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.