eo-tides 0.6.1__tar.gz → 0.6.2.dev7__tar.gz

eo_tides-0.6.2.dev7/.editorconfig

@@ -0,0 +1,5 @@
+max_line_length = 120
+
+[*.json]
+indent_style = space
+indent_size = 4

eo_tides-0.6.2.dev7/.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,31 @@
+---
+name: Bug report
+about: Report a bug or problem
+title: "Bug report: "
+labels: bug
+assignees: ""
+---
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Describe the problem**
+A clear and concise description of the bug or problem (i.e. what actually happens).
+
+**To reproduce**
+Steps to reproduce the behavior:
+
+1. Run function/notebook '....'
+2. See error '....'
+3. A minimum reproducible code example is greatly appreciated!
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Environment:**
+
+- OS: [e.g. Linux, Windows]
+- `eo-tides` version: [e.g. `v0.1.0`]
+
+**Additional context**
+Add any other context about the problem here.

eo_tides-0.6.2.dev7/.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,13 @@
+---
+name: Feature suggestion
+about: Suggest an idea for this project
+title: "Feature suggestion: "
+labels: enhancement
+assignees: ""
+---
+
+**Describe your idea or suggestion**
+A clear and concise description of your idea or suggestion.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

eo_tides-0.6.2.dev7/.github/actions/setup-python-env/action.yml

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+name: "Setup Python Environment"
+description: "Set up Python environment for the given Python version"
+
+inputs:
+  python-version:
+    description: "Python version to use"
+    required: true
+    default: "3.10"
+  resolution:
+    description: "Resolution strategy"
+    required: true
+    default: "frozen"
+  uv-version:
+    description: "uv version to use"
+    required: true
+    default: "0.6.2"
+
+runs:
+  using: "composite"
+  steps:
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ inputs.python-version }}
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v2
+      with:
+        version: ${{ inputs.uv-version }}
+        enable-cache: "true"
+        cache-suffix: ${{ inputs.python-version }}-${{ inputs.resolution }}
+
+      # Install eo-tides and all required dependencies.
+      # --all-extras installs all optional dependencies.
+      # If resolution method is "frozen", then use existing lockfile.
+      # Otherwise, pass resolution method to specify "highest"
+      # dependencies or "lowest-direct" dependencies
+    - name: Install Python dependencies
+      run: |
+        if [ "${{ inputs.resolution }}" == "frozen" ]; then
+        uv sync --frozen --all-extras
+        else
+        uv sync --all-extras --resolution ${{ inputs.resolution }}
+        fi
+      shell: bash

eo_tides-0.6.2.dev7/.github/workflows/check-links.yml

@@ -0,0 +1,33 @@
+name: Check for broken links
+
+on:
+  workflow_dispatch: # Triggered manually
+
+jobs:
+  link-checker:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          submodules: true
+
+      - name: Check links
+        id: check-links
+        uses: lycheeverse/lychee-action@v2
+        with:
+          fail: false
+          output: /tmp/broken-links-report.md
+          args: >
+            --exclude-path ./tests/testing.ipynb
+            **/*.md **/*.ipynb **/*.yaml **/*.yml
+
+      - name: Create issue
+        if: steps.check-links.outputs.exit_code != 0
+        uses: peter-evans/create-issue-from-file@v5
+        with:
+          title: Fix broken links
+          content-filepath: /tmp/broken-links-report.md
+          labels: link-checker

eo_tides-0.6.2.dev7/.github/workflows/main.yml

@@ -0,0 +1,108 @@
+name: Main
+
+on:
+  push:
+    branches:
+      - main
+    paths-ignore:
+      - "paper/**"
+      - "README.md"
+  pull_request:
+    types: [opened, synchronize, reopened]
+    paths-ignore:
+      - "paper/**"
+      - "README.md"
+
+env:
+  EO_TIDES_TIDE_MODELS: ./tests/data/tide_models
+
+jobs:
+  quality:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out
+        uses: actions/checkout@v4
+
+      - uses: actions/cache@v4
+        with:
+          path: ~/.cache/pre-commit
+          key: pre-commit-${{ hashFiles('.pre-commit-config.yaml') }}
+
+      - name: Set up the environment
+        uses: ./.github/actions/setup-python-env
+
+      - name: Run checks
+        run: make check
+
+  run-tests:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        resolution: ["highest", "lowest-direct"]
+        exclude: # Temporarily excluded due to 3.13 only supported by Numpy >=2.0
+          - python-version: "3.13"
+            resolution: "lowest-direct"
+      fail-fast: false
+      max-parallel: 10
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - name: Check out
+        uses: actions/checkout@v4
+
+      - name: Extract model data
+        run: |
+          # Extract tide modelling test files
+          tar -xvzf ./tests/data/tide_models.tar.gz -C ./tests/data
+
+      - name: Set up the environment
+        uses: ./.github/actions/setup-python-env
+        with:
+          python-version: ${{ matrix.python-version }}
+          resolution: ${{ matrix.resolution }}
+
+      - name: Run Python unit tests
+        timeout-minutes: 10
+        run: uv run python -m pytest tests --cov --cov-config=pyproject.toml --cov-report=xml --verbose
+
+      - name: Run Jupyter Notebook integration tests
+        timeout-minutes: 10
+        run: uv run python -m pytest --nbval-lax docs/notebooks/
+
+      - name: Check typing
+        run: uv run mypy
+
+      - name: Upload coverage reports to Codecov with GitHub Action on Python 3.10
+        uses: codecov/codecov-action@v4
+        if: ${{ matrix.python-version == '3.10' && matrix.resolution == 'highest' }}
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+  check-docs:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out
+        uses: actions/checkout@v4
+
+      - name: Set up the environment
+        uses: ./.github/actions/setup-python-env
+
+      - name: Check if documentation can be built
+        run: uv run mkdocs build -s
+
+  # Only deploy docs if on push and if all tests pass
+  deploy-docs:
+    if: github.event_name == 'push'
+    needs: [quality, check-docs, run-tests]
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out
+        uses: actions/checkout@v4
+
+      - name: Set up the environment
+        uses: ./.github/actions/setup-python-env
+
+      - name: Deploy documentation
+        run: uv run mkdocs gh-deploy --force

eo_tides-0.6.2.dev7/.github/workflows/on-release-main.yml

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+name: release-main
+
+on:
+  release:
+    types: [published]
+  push:
+    branches: [main]
+
+jobs:
+  set-version:
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # Need full history for tags
+
+      - name: Export tag
+        id: vars
+        run: echo tag=${GITHUB_REF#refs/*/} >> $GITHUB_OUTPUT
+        if: ${{ github.event_name == 'release' }}
+
+      # For full releases, use tag for version name
+      - name: Set release version
+        run: |
+          sed -i "s/^version = \".*\"/version = \"$RELEASE_VERSION\"/" pyproject.toml
+        env:
+          RELEASE_VERSION: ${{ steps.vars.outputs.tag }}
+        if: ${{ github.event_name == 'release' }}
+
+      # For merges to main, incremement patch version by one
+      # and use ".devN" suffix based on commits since tag
+      - name: Set dev version
+        run: |
+          LATEST_TAG=$(git describe --tags --abbrev=0)
+          IFS='.' read -r MAJOR MINOR PATCH <<< "$LATEST_TAG"
+          PATCH=$((PATCH + 1))
+          DEV_NUM=$(git rev-list $LATEST_TAG..HEAD --count)
+          DEV_VERSION="$MAJOR.$MINOR.$PATCH.dev$DEV_NUM"
+          sed -i "s/^version = \".*\"/version = \"$DEV_VERSION\"/" pyproject.toml
+        if: ${{ github.event_name == 'push' }}
+
+      - name: Upload updated pyproject.toml
+        uses: actions/upload-artifact@v4
+        with:
+          name: pyproject-toml
+          path: pyproject.toml
+
+  publish:
+    runs-on: ubuntu-latest
+    needs: [set-version]
+    steps:
+      - name: Check out
+        uses: actions/checkout@v4
+
+      - name: Set up the environment
+        uses: ./.github/actions/setup-python-env
+
+      - name: Download updated pyproject.toml
+        uses: actions/download-artifact@v4
+        with:
+          name: pyproject-toml
+
+      - name: Build package
+        run: uv build
+
+      - name: Publish package
+        run: uv publish
+        env:
+          UV_PUBLISH_TOKEN: ${{ secrets.PYPI_TOKEN }}
+
+  deploy-docs:
+    needs: publish
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out
+        uses: actions/checkout@v4
+
+      - name: Set up the environment
+        uses: ./.github/actions/setup-python-env
+
+      - name: Deploy documentation
+        run: uv run mkdocs gh-deploy --force

eo_tides-0.6.2.dev7/.github/workflows/paper.yml

@@ -0,0 +1,47 @@
+name: Draft paper PDF
+on:
+  push:
+    branches:
+      - main
+      - JOSS_paper
+    paths:
+      - paper/**
+      - .github/workflows/paper.yml
+  pull_request:
+    branches:
+      - main
+      - JOSS_paper
+    paths:
+      - paper/**
+      - .github/workflows/paper.yml
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Generate paper draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          paper-path: paper/paper.md
+
+      - name: Upload
+        uses: actions/upload-artifact@v4
+        with:
+          name: paper
+          # Output path where Pandoc will write the compiled PDF.
+          # Note, this should be the same directory as the input
+          # paper.md
+          path: paper/paper.pdf
+
+      - name: Commit updated PDF
+        uses: stefanzweifel/git-auto-commit-action@v4
+        if: github.event_name == 'pull_request'
+        continue-on-error: true
+        with:
+          commit_message: Update generated PDF
+          file_pattern: "paper/paper.pdf"

eo_tides-0.6.2.dev7/.gitignore

@@ -0,0 +1,143 @@
+# Ignore project-specific directories
+tests/data/tide_models
+tests/data/tide_models_clipped
+docs/source
+
+# From https://raw.githubusercontent.com/github/gitignore/main/Python.gitignore
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# Vscode config files
+.vscode/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

eo_tides-0.6.2.dev7/.pre-commit-config.yaml

@@ -0,0 +1,27 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v4.4.0"
+    hooks:
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-toml
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.6.4
+    hooks:
+      # Run the linter.
+      - id: ruff
+        types_or: [python, pyi]
+        args: [--fix, --select=I] # --select=ALL, I
+      # Run the formatter.
+      - id: ruff-format
+        types_or: [python, pyi]
+
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v3.0.3"
+    hooks:
+      - id: prettier

eo_tides-0.6.2.dev7/CITATION.cff

@@ -0,0 +1,30 @@
+# YAML 1.2
+---
+abstract: ""
+authors:
+  - affiliation: "Geoscience Australia"
+    family-names: "Bishop-Taylor"
+    given-names: Robbi
+    orcid: "https://orcid.org/0000-0002-1533-2599"
+  - affiliation: "Geoscience Australia"
+    family-names: Sagar
+    given-names: Stephen
+  - affiliation: "Geoscience Australia"
+    family-names: Phillips
+    given-names: Claire
+  - affiliation: "Geoscience Australia"
+    family-names: Newey
+    given-names: Vanessa
+    orcid: "https://orcid.org/0000-0003-3705-5665"
+cff-version: "1.1.0"
+date-released: 2024-10-30
+doi: ""
+keywords:
+  - "Tide modelling"
+  - "Earth Observation"
+  - "Remote sensing"
+license: "Apache-2.0"
+message: "Please cite `eo-tides` using the citation below:"
+repository-code: "https://github.com/GeoscienceAustralia/eo-tides"
+title: "eo-tides: Tide modelling tools for large-scale satellite earth observation analysis"
+# version: "1.0.0"

eo_tides-0.6.2.dev7/CONTRIBUTING.md

@@ -0,0 +1,102 @@
+# Contributing to `eo-tides`
+
+Contributions are welcome, and they are greatly appreciated!
+
+You can contribute in many ways:
+
+# Types of Contributions
+
+## Report Bugs
+
+Report bugs at https://github.com/GeoscienceAustralia/eo-tides/issues
+
+If you are reporting a bug, please include:
+
+- Your operating system name and version.
+- Any details about your local setup that might be helpful in troubleshooting.
+- Detailed steps to reproduce the bug.
+
+## Fix Bugs
+
+Look through the GitHub issues for bugs.
+Anything tagged with "bug" and "help wanted" is open to whoever wants to implement a fix for it.
+
+## Implement Features
+
+Look through the GitHub issues for features.
+Anything tagged with "enhancement" and "help wanted" is open to whoever wants to implement it.
+
+## Submit Feedback
+
+The best way to send feedback is to file an issue at https://github.com/GeoscienceAustralia/eo-tides/issues.
+
+If you are proposing a new feature:
+
+- Explain in detail how it would work.
+- Keep the scope as narrow as possible, to make it easier to implement.
+- Remember that this is a volunteer-driven project, and that contributions
+  are welcome :)
+
+# Get Started!
+
+Ready to contribute? Here's how to set up `eo-tides` for local development.
+Please note this documentation assumes you already have `uv` and `Git` installed and ready to go.
+
+1. Fork the `eo-tides` repo on GitHub.
+
+2. Clone your fork locally:
+
+```bash
+cd <directory_in_which_repo_should_be_created>
+git clone git@github.com:YOUR_NAME/eo-tides.git
+```
+
+3. Now we need to install the environment. Navigate into the directory
+
+```bash
+cd eo-tides
+```
+
+Then, install and activate the environment with:
+
+```bash
+uv sync
+```
+
+4. Install pre-commit to run linters/formatters at commit time:
+
+```bash
+uv run pre-commit install
+```
+
+5. Create a branch for local development:
+
+```bash
+git checkout -b name-of-your-bugfix-or-feature
+```
+
+Now you can make your changes locally.
+
+6. Don't forget to add test cases for your added functionality to the `tests` directory.
+
+7. When you're done making changes, check that your changes pass the formatting tests.
+
+```bash
+make check
+```
+
+Now, validate that all unit tests are passing:
+
+```bash
+make test
+```
+
+9. Commit your changes and push your branch to GitHub:
+
+```bash
+git add .
+git commit -m "Your detailed description of your changes."
+git push origin name-of-your-bugfix-or-feature
+```
+
+11. Submit a pull request through the GitHub website.

eo_tides-0.6.2.dev7/Dockerfile

@@ -0,0 +1,21 @@
+# Install uv
+FROM python:3.12-slim
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /bin/uv
+
+# Change the working directory to the `app` directory
+WORKDIR /app
+
+# Copy the lockfile and `pyproject.toml` into the image
+ADD uv.lock /app/uv.lock
+ADD pyproject.toml /app/pyproject.toml
+
+# Install dependencies
+RUN uv sync --frozen --no-install-project
+
+# Copy the project into the image
+ADD . /app
+
+# Sync the project
+RUN uv sync --frozen
+
+CMD [ "python", "eo_tides/foo.py"]