virtualship 0.0.3.dev44__tar.gz

virtualship-0.0.3.dev44/.github/CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment include:
+
+- Using welcoming and inclusive language
+- Being respectful of differing viewpoints and experiences
+- Gracefully accepting constructive criticism
+- Focusing on what is best for the community
+- Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+- The use of sexualized language or imagery and unwelcome sexual attention or advances
+- Trolling, insulting/derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information, such as a physical or electronic address, without explicit permission
+- Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at E.vanSebille@uu.nl. The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/

virtualship-0.0.3.dev44/.github/CONTRIBUTING.md

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+See the following [contributing guide](../docs/contributing.md).

virtualship-0.0.3.dev44/.github/dependabot.yml

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+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    groups:
+      actions:
+        patterns:
+          - "*"

virtualship-0.0.3.dev44/.github/release.yml

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+changelog:
+  exclude:
+    authors:
+      - dependabot
+      - pre-commit-ci

virtualship-0.0.3.dev44/.github/workflows/cd.yml

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+name: CD
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+  release:
+    types:
+      - published
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  # Many color libraries just need this to be set to any value, but at least
+  # one distinguishes color depth, where "3" -> "256-bit color".
+  FORCE_COLOR: 3
+
+jobs:
+  dist:
+    name: Distribution build
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: hynek/build-and-inspect-python-package@v2
+
+  publish:
+    needs: [dist]
+    name: Publish to PyPI
+    environment: pypi
+    permissions:
+      id-token: write
+      attestations: write
+      contents: read
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release' && github.event.action == 'published'
+
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: Packages
+          path: dist
+
+      - name: Generate artifact attestation for sdist and wheel
+        uses: actions/attest-build-provenance@v1.4.1
+        with:
+          subject-path: "dist/*"
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          # Remember to tell (test-)pypi about this repo before publishing
+          # Remove this line to publish to PyPI
+          repository-url: https://test.pypi.org/legacy/

virtualship-0.0.3.dev44/.github/workflows/ci.yml

@@ -0,0 +1,55 @@
+name: CI
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  # Many color libraries just need this to be set to any value, but at least
+  # one distinguishes color depth, where "3" -> "256-bit color".
+  FORCE_COLOR: 3
+
+jobs:
+  # pylint:
+  #   name: Format
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - name: Run PyLint
+  #       run: pipx run nox -s pylint -- --output-format=github
+
+  tests:
+    name: tests (${{ matrix.runs-on }} | Python ${{ matrix.python-version }})
+    runs-on: ${{ matrix.runs-on }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.13"]
+        runs-on: [ubuntu-latest, windows-latest, macos-14]
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          environment-file: environment.yml
+          python-version: ${{ matrix.python-version }}}
+          channels: conda-forge
+
+      - name: Test package
+        run: >-
+          python -m pytest -ra --cov --cov-report=xml --cov-report=term
+          --durations=20
+
+      - name: Upload coverage report
+        uses: codecov/codecov-action@v4.5.0
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

virtualship-0.0.3.dev44/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Figures
+*.jpg
+*.gif
+
+# Data files created
+/results
+*.geojson
+*.zarr
+*.nc
+*.zip
+
+# 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/
+docs/api/
+
+# 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/#use-with-ide
+.pdm.toml
+
+# 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/
+
+# Auto generated by setuptools scm
+src/virtualship/_version_setup.py
+
+.vscode/

virtualship-0.0.3.dev44/.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+        exclude: .*\.zarr/
+      - id: check-yaml
+      - id: check-ast
+      - id: check-json
+        types: [text]
+        files: \.(json|ipynb)$
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.5
+    hooks:
+      - id: ruff
+        args: [--fix, --show-fixes]
+      - id: ruff
+        name: ruff (isort jupyter)
+        args: [--select, I, --fix]
+        types_or: [jupyter]
+      - id: ruff-format
+        types_or: [python, jupyter]
+  - repo: https://github.com/rbubley/mirrors-prettier # Update mirror as official mirror is deprecated
+    rev: v3.3.3
+    hooks:
+      - id: prettier

virtualship-0.0.3.dev44/.readthedocs.yaml

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+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: mambaforge-22.9
+  jobs:
+    pre_build:
+      - sphinx-build -b linkcheck docs/ _build/linkcheck
+      - sphinx-apidoc -o docs/api/ --module-first --no-toc --force src/virtualship
+
+conda:
+  environment: environment.yml

virtualship-0.0.3.dev44/LICENSE

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+MIT License
+
+Copyright (c) 2023 OceanParcels
+
+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.

virtualship-0.0.3.dev44/PKG-INFO

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+Metadata-Version: 2.1
+Name: virtualship
+Version: 0.0.3.dev44
+Summary: Code for the Virtual Ship Classroom, where Marine Scientists can combine Copernicus Marine Data with an OceanParcels ship to go on a virtual expedition.
+Author: oceanparcels.org team
+License: MIT License
+        
+        Copyright (c) 2023 OceanParcels
+        
+        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.
+        
+Project-URL: Homepage, https://oceanparcels.org/
+Project-URL: Repository, https://github.com/OceanParcels/virtualship
+Project-URL: Bug Tracker, https://github.com/OceanParcels/virtualship/issues
+Project-URL: Changelog, https://github.com/OceanParcels/virtualship/releases
+Classifier: Development Status :: 3 - Alpha
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Education
+Classifier: Intended Audience :: Education
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: click
+Requires-Dist: parcels<4,>=3
+Requires-Dist: pyproj<4,>=3
+Requires-Dist: sortedcontainers==2.4.0
+Requires-Dist: opensimplex==0.4.5
+Requires-Dist: numpy<2,>=1
+Requires-Dist: pydantic<3,>=2
+
+<p align="center">
+<picture>
+  <source media="(prefers-color-scheme: dark)" srcset="./docs/_static/virtual_ship_logo_inverted.png">
+  <img alt="VirtualShipParcels logo'" width="200" src="./docs/_static/virtual_ship_logo.png">
+</picture>
+</p>
+
+<!-- Badges -->
+
+---
+
+<!-- SPHINX-START -->
+<table>
+    <tr>
+        <th>Project Owner</th>
+        <td>Emma Daniels (e.e.daniels1@uu.nl)</td>
+    </tr>
+    <tr>
+        <!-- Should mirror pyproject.toml. Use one of the "Development status" flags from https://pypi.org/classifiers/-->
+        <th>Development status</th>
+        <td>Alpha</td>
+    </tr>
+</table>
+
+<!-- Insert catchy summary -->
+
+VirtualShipParcels is a command line simulator allowing students to plan and conduct a virtual research expedition, receiving measurements as if they were coming from actual oceanographic instruments including:
+
+- ADCP (for currents)
+- CTD (for conductivity, and temperature)
+- underwater measurements (salinity and temperature)
+- surface drifters
+- argo float deployments
+
+<!-- TODO: future. Along the way students will encounter difficulties such as: -->
+
+## Installation
+
+For a normal installation do:
+
+```bash
+conda create -n my_env python=3.12
+conda activate my_env
+conda install -c conda-forge virtualship
+```
+
+For a development installation, please follow the instructions detailed in the [contributing page](.github/CONTRIBUTING.md).
+
+## Usage
+
+```console
+$ virtualship --help
+Usage: virtualship [OPTIONS] COMMAND [ARGS]...
+
+Options:
+  --version  Show the version and exit.
+  --help  Show this message and exit.
+
+Commands:
+  fetch  Download the relevant data specified in an expedition directory...
+  init   Initialize a directory for a new expedition, with an example...
+  run    Do the expedition.
+```
+
+```console
+$ virtualship init --help
+Usage: virtualship init [OPTIONS] PATH
+
+  Initialize a directory for a new expedition, with an example configuration.
+
+Options:
+  --help  Show this message and exit.
+```
+
+```console
+
+$ virtualship fetch --help
+Usage: virtualship fetch [OPTIONS] PATH
+
+  Download the relevant data specified in an expedition directory (i.e., by
+  the expedition config).
+
+Options:
+  --help  Show this message and exit.
+```
+
+```console
+$ virtualship run --help
+Usage: virtualship run [OPTIONS] PATH
+
+  Do the expedition.
+
+Options:
+  --help  Show this message and exit.
+
+```
+
+For examples, see LINK_TO_TURORIALS.
+
+<!-- TODO: Link to tutorials -->
+
+## Input data
+
+The scripts are written to work with A-grid ocean data from CMEMS.

virtualship-0.0.3.dev44/README.md

@@ -0,0 +1,104 @@
+<p align="center">
+<picture>
+  <source media="(prefers-color-scheme: dark)" srcset="./docs/_static/virtual_ship_logo_inverted.png">
+  <img alt="VirtualShipParcels logo'" width="200" src="./docs/_static/virtual_ship_logo.png">
+</picture>
+</p>
+
+<!-- Badges -->
+
+---
+
+<!-- SPHINX-START -->
+<table>
+    <tr>
+        <th>Project Owner</th>
+        <td>Emma Daniels (e.e.daniels1@uu.nl)</td>
+    </tr>
+    <tr>
+        <!-- Should mirror pyproject.toml. Use one of the "Development status" flags from https://pypi.org/classifiers/-->
+        <th>Development status</th>
+        <td>Alpha</td>
+    </tr>
+</table>
+
+<!-- Insert catchy summary -->
+
+VirtualShipParcels is a command line simulator allowing students to plan and conduct a virtual research expedition, receiving measurements as if they were coming from actual oceanographic instruments including:
+
+- ADCP (for currents)
+- CTD (for conductivity, and temperature)
+- underwater measurements (salinity and temperature)
+- surface drifters
+- argo float deployments
+
+<!-- TODO: future. Along the way students will encounter difficulties such as: -->
+
+## Installation
+
+For a normal installation do:
+
+```bash
+conda create -n my_env python=3.12
+conda activate my_env
+conda install -c conda-forge virtualship
+```
+
+For a development installation, please follow the instructions detailed in the [contributing page](.github/CONTRIBUTING.md).
+
+## Usage
+
+```console
+$ virtualship --help
+Usage: virtualship [OPTIONS] COMMAND [ARGS]...
+
+Options:
+  --version  Show the version and exit.
+  --help  Show this message and exit.
+
+Commands:
+  fetch  Download the relevant data specified in an expedition directory...
+  init   Initialize a directory for a new expedition, with an example...
+  run    Do the expedition.
+```
+
+```console
+$ virtualship init --help
+Usage: virtualship init [OPTIONS] PATH
+
+  Initialize a directory for a new expedition, with an example configuration.
+
+Options:
+  --help  Show this message and exit.
+```
+
+```console
+
+$ virtualship fetch --help
+Usage: virtualship fetch [OPTIONS] PATH
+
+  Download the relevant data specified in an expedition directory (i.e., by
+  the expedition config).
+
+Options:
+  --help  Show this message and exit.
+```
+
+```console
+$ virtualship run --help
+Usage: virtualship run [OPTIONS] PATH
+
+  Do the expedition.
+
+Options:
+  --help  Show this message and exit.
+
+```
+
+For examples, see LINK_TO_TURORIALS.
+
+<!-- TODO: Link to tutorials -->
+
+## Input data
+
+The scripts are written to work with A-grid ocean data from CMEMS.