cruiseplan 0.1.0__tar.gz

cruiseplan-0.1.0/.github/ISSUE_TEMPLATE.md

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+---
+name: "🐛 Bug Report / 💡 Feature Request"
+about: "Report a bug or suggest an improvement for the amocarray project"
+title: "[Bug] <brief description>" or "[Feature] <brief description>"
+labels: []
+assignees: []
+---
+
+## Description
+
+Please describe the bug or feature request clearly and concisely.
+
+**For bugs:**
+- What did you expect to happen?
+- What actually happened?
+- If applicable, include error messages or stack traces.
+
+**For features:**
+- What problem does this feature solve?
+- How would this feature improve the project?
+
+
+## Reproduction (for bugs)
+
+Please provide steps to reproduce the issue, if possible:
+
+1. Go to '...'
+2. Run '...'
+3. Observe '...'
+
+If you can, include a minimal, reproducible example or link to a failing test.
+
+
+## Environment
+
+- OS: [e.g., macOS 13.3, Ubuntu 22.04, etc.]
+- Python version: [e.g., 3.11]
+- amocarray version: [if applicable]
+- Virtualenv / Conda / System Python?: [env type]
+
+
+## Checklist
+
+- [ ] I have checked the existing [issues](https://github.com/AMOCcommunity/amocarray/issues) to avoid duplicates.
+- [ ] I have included steps to reproduce the issue, if it's a bug.
+- [ ] I have described the motivation clearly, if it's a feature request.
+
+
+## Additional context
+
+Add any other context or screenshots about the problem or feature request here.
+
+---
+
+*This issue template was prepared with assistance from ChatGPT to support clear and collaborative development.*
+

cruiseplan-0.1.0/.github/PULL_REQUEST_TEMPLATE.md

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+You can delete unused sections.
+
+## PR Title Convention
+
+Please prefix your pull request title with one of the following tags for clarity:
+
+- `[DOC]` for documentation updates
+- `[FIX]` for bug fixes
+- `[FEAT]` for new features
+- `[REFACTOR]` for code improvements
+- `[TEST]` for tests
+- `[CI]` for CI/CD or automation updates
+- `[CLEANUP]` for general maintenance
+
+Example:
+> `[FIX] Correct dimension handling in OSNAP reader`
+
+**Description:**
+
+Please describe your changes clearly and concisely.
+
+- What is the purpose of this pull request?
+- What issue(s) does it address? Please link them (e.g., closes #12).
+- Briefly explain the approach taken.
+
+**Checklist:**
+
+- [ ] I have followed the [coding conventions](https://amoccommunity.github.io/amocarray/conventions.html).
+- [ ] I have updated or added tests to cover my changes.
+- [ ] I have updated the documentation if needed.
+- [ ] I have run `pytest` to check that all tests pass.
+- [ ] I have run `pre-commit run --all-files` to lint and format the code.
+
+**Related Issues / Pull Requests:**
+
+Link any related issues, pull requests, or discussions:
+- Fixes #
+- Related to #
+
+**Additional Notes:**
+
+Include any additional information reviewers might need:
+
+- Screenshots (if UI/outputs are affected)
+- Design decisions or trade-offs
+- Anything reviewers should look at closely
+

cruiseplan-0.1.0/.github/workflows/docs.yml

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+name: Test documentation build
+
+on:
+  pull_request:
+    paths:
+      - '**.py'
+      - '**.ipynb'
+      - '**.rst'
+      - '**.md'
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        # Critical: "bash -l {0}" is required for Micromamba environments to activate
+        shell: bash -l {0}
+    permissions:
+      contents: read
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: "3.9"
+
+    - name: Setup Micromamba
+      uses: mamba-org/setup-micromamba@v1
+      with:
+        environment-file: environment.yml
+        cache-environment: true
+
+    - name: Install package
+      run: |
+        python -m pip install -e . --force-reinstall
+
+    - name: Build documentation
+      run: |
+        set -e
+        jupyter nbconvert --to notebook --execute notebooks/demo.ipynb --output=demo-output.ipynb --ExecutePreprocessor.allow_errors=True
+        mv notebooks/*output.ipynb docs/source/
+        pushd docs
+        make clean html
+        popd

cruiseplan-0.1.0/.github/workflows/docs_deploy.yml

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+name: Deploy Documentation
+
+on:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  deploy-docs:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        # Critical: "bash -l {0}" is required for Micromamba environments to activate
+        shell: bash -l {0}
+    permissions:
+      contents: write
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: "3.9"
+
+    - name: Setup Micromamba
+      uses: mamba-org/setup-micromamba@v1
+      with:
+        environment-file: environment.yml
+        cache-environment: true
+
+    - name: Install package
+      run: |
+        python -m pip install -e . --force-reinstall
+
+    - name: Build documentation
+      run: |
+        set -e
+        jupyter nbconvert --to notebook --execute notebooks/demo.ipynb --output=demo-output.ipynb --ExecutePreprocessor.allow_errors=True
+        mv notebooks/*output.ipynb docs/source/
+        pushd docs
+        make clean html
+        popd
+
+    - name: Deploy to GitHub Pages
+      uses: peaceiris/actions-gh-pages@v4
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: docs/build/html

cruiseplan-0.1.0/.github/workflows/tests.yml

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+name: Run tests
+
+on:
+  push:
+    branches: [ "main" ]
+    paths:
+      - '**.py'
+      - 'cruiseplan/**'
+      - 'tests/**'
+      - 'pyproject.toml'
+      - 'requirements*.txt'
+      - '.pre-commit-config.yaml'
+  pull_request:
+    branches: [ "main" ]
+    paths:
+      - '**.py'
+      - 'cruiseplan/**'
+      - 'tests/**'
+      - 'pyproject.toml'
+      - 'requirements*.txt'
+      - '.pre-commit-config.yaml'
+
+jobs:
+  test:
+    name: ${{ matrix.os }} / Py ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        # Critical: "bash -l {0}" is required for Micromamba environments to activate
+        shell: bash -l {0}
+    strategy:
+      fail-fast: true
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        # Testing across all selected supported versions from your spec
+        python-version: ["3.9", "3.12"]
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+
+      - name: Install package
+        run: |
+          python -m pip install -e .[dev] --force-reinstall
+
+      - name: Test with pytest
+        run: |
+          pytest

cruiseplan-0.1.0/.gitignore

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+setup.sh
+*/_version.py
+data/temp.nc
+tests_output/*
+data/bathymetry/ETOPO_2022_v1_60s_N90W180_bed.nc
+
+logs/*log
+
+# VSCode settings
+.vscode/*
+
+# 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
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# 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/
+
+# 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/
+test_output/test_map_VA176.html

cruiseplan-0.1.0/.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/psf/black
+    rev: 24.3.0
+    hooks:
+      - id: black
+        language_version: python3
+        files: \.(py|ipynb)$
+        exclude: ^data/
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6  # Check for the latest version
+    hooks:
+      - id: codespell
+        args: ["--ignore-words-list", "nd"]  # Optional: ignore some false positives
+
+#  - repo: https://github.com/pycqa/isort
+#    rev: 5.13.2
+#    hooks:
+#      - id: isort
+#        language_version: python3
+#        files: \.(py|ipynb)$
+#        exclude: ^data/
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: end-of-file-fixer
+        files: \.(py|yaml|yml|ipynb)$
+        exclude: ^data/
+      - id: trailing-whitespace
+        files: \.(py|yaml|yml|ipynb)$
+        exclude: ^data/
+      - id: check-yaml
+        files: \.(yaml|yml)$
+        exclude: ^data/
+      - id: check-added-large-files
+
+  - repo: local
+    hooks:
+      - id: pytest
+        name: pytest
+        entry: pytest -q
+        language: system
+        types: [python]
+        exclude: ^data/
+
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.3.0
+    hooks:
+      - id: ruff
+        args: [
+          "--fix",
+          "--exit-zero",
+          "--select",
+          "E,F,W,C90,ANN,B,BLE,TRY,ARG,SLF",
+        ]
+        exclude: ^data/

cruiseplan-0.1.0/CITATION.cff

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+cff-version: 1.2.0
+title: "CruisePlan: A Tool for Oceanographic Cruise Planning"
+message: "If you use this software, please cite it as below."
+type: software
+authors:
+  - family-names: Frajka-Williams
+    given-names: Eleanor
+    orcid: "https://orcid.org/0000-0001-8773-7838"
+    affiliation: "University of Hamburg, Institute of Oceanography"
+  - family-names: Sorge
+    given-names: Yves
+    orcid: https://orcid.org/0009-0007-0043-9207
+  - family-names: Trace-Kleeberg
+    given-names: Sunke
+    orcid: https://orcid.org/0000-0002-5980-2492
+repository-code: "https://github.com/ocean-uhh/cruiseplan"
+url: "https://ocean-uhh.github.io/cruiseplan"
+abstract: >-
+  CruisePlan is a Python package for planning and scheduling oceanographic
+  research cruises. It provides tools for station distribution calculation,
+  CTD profile timing estimation, mooring operation planning, travel time
+  calculations, and multi-format output generation including HTML schedules,
+  CSV data, KML visualization files, and NetCDF scientific data formats.
+  The package includes interactive station selection tools with PANGAEA
+  database integration for historical oceanographic data analysis.
+keywords:
+  - oceanography
+  - cruise planning
+  - research vessels
+  - CTD
+  - moorings
+  - bathymetry
+  - station planning
+license: MIT
+version: "0.1.0"
+date-released: "2025-01-02"

cruiseplan-0.1.0/CONTRIBUTING.md

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+# Contributing to CruisePlan
+
+Thank you for your interest in contributing to CruisePlan! This document provides guidelines and information for contributors.
+
+## Development Setup
+
+### Prerequisites
+- Python 3.9 or later
+- Git
+
+### Installation for Development
+
+1. Fork and clone the repository:
+   ```bash
+   git clone https://github.com/ocean-uhh/cruiseplan.git
+   cd cruiseplan
+   ```
+
+2. Create a virtual environment:
+   ```bash
+   python -m venv .venv
+   source .venv/bin/activate  # On Windows: .venv\Scripts\activate
+   ```
+
+3. Install the package in development mode with all dependencies:
+   ```bash
+   pip install -e .[dev]
+   ```
+
+4. Install pre-commit hooks:
+   ```bash
+   pre-commit install
+   ```
+
+## Development Workflow
+
+### Code Style
+- We use [Ruff](https://github.com/astral-sh/ruff) for linting and formatting
+- Follow [PEP 8](https://pep8.org/) style guidelines
+- Use type hints where possible
+- Write docstrings following [NumPy style](https://numpydoc.readthedocs.io/en/latest/format.html)
+
+### Testing
+- Write tests for new functionality
+- Ensure all tests pass before submitting a PR
+- Run tests with: `pytest`
+- Check code coverage: `pytest --cov=cruiseplan`
+
+### Documentation
+- Update docstrings for any modified functions
+- Add examples for new features in the demo notebook
+- Build documentation locally: `cd docs && make html`
+
+### Pull Requests
+1. Create a feature branch from `main`
+2. Make your changes
+3. Run tests and linting: `pytest && ruff check .`
+4. Update documentation if needed
+5. Submit a pull request with a clear description
+
+## Project Structure
+
+```
+cruiseplan/
+├── cli/           # Command-line interface
+├── core/          # Core cruise planning logic
+├── calculators/   # Distance, duration, routing calculations
+├── data/          # Data loading and caching
+├── interactive/   # Interactive widgets and tools
+├── output/        # Report generation (HTML, LaTeX, KML, NetCDF)
+└── utils/         # Utilities and helpers
+```
+
+## Reporting Issues
+
+When reporting bugs or requesting features:
+- Use GitHub Issues
+- Provide a clear description and steps to reproduce
+- Include relevant error messages and system information
+- For bugs, include a minimal reproducible example
+
+## Code of Conduct
+
+This project follows a code of conduct to ensure a welcoming environment for all contributors. Please be respectful and constructive in all interactions.
+
+## License
+
+By contributing to CruisePlan, you agree that your contributions will be licensed under the same license as the project (MIT License).

cruiseplan-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2024 Eleanor Frajka-Williams
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.