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Merge pull request #10 from s-sajid-ali/cleanup_and_ci
refactor & CI with GithubActions
2 parents 1f334c9 + 821c966 commit af3bd95

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‎.github/dependabot.yml

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# Set update schedule for GitHub Actions
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version: 2
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updates:
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- package-ecosystem: "github-actions"
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directory: "/"
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schedule:
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# Check for updates to GitHub Actions every week
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interval: "weekly"
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‎.github/workflows/ci.yml

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name: Python package
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on: [push]
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jobs:
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build:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.10", "3.11", "3.12"]
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: python -m pip install .[test]
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- name: Test with pytest
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run: pytest
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‎.gitignore

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# setuptools
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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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share/python-wheels/
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*.egg-info/
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__pycache__
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*.pyc
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.installed.cfg
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*.egg
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MANIFEST
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# conda
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conda_recipe/linux-64/
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conda_recipe/linux-ppc64le/
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conda_recipe/osx-64/
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conda_recipe/win-64/
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.nox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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*.py,cover
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.hypothesis/
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.pytest_cache/
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cover/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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db.sqlite3
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db.sqlite3-journal
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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.pybuilder/
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# IPython
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profile_default/
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ipython_config.py
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# pyenv
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# For a library or package, you might want to ignore these files since the code is
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# intended to run in multiple environments; otherwise, check them in:
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# .python-version
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# pipenv
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# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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# However, in case of collaboration, if having platform-specific dependencies or dependencies
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# having no cross-platform support, pipenv may install dependencies that don't work, or not
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# install all needed dependencies.
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#Pipfile.lock
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# poetry
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# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
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# This is especially recommended for binary packages to ensure reproducibility, and is more
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# commonly ignored for libraries.
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# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
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#poetry.lock
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# pdm
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# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
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#pdm.lock
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# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
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# in version control.
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# https://pdm.fming.dev/#use-with-ide
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.pdm.toml
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
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__pypackages__/
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# Celery stuff
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celerybeat-schedule
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celerybeat.pid
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# SageMath parsed files
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*.sage.py
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# Environments
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.env
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.venv
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env/
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venv/
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ENV/
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env.bak/
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venv.bak/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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.dmypy.json
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dmypy.json
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# ruff Python linter
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.ruff_cache/
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# Pyre type checker
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.pyre/
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# pytype static type analyzer
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.pytype/
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# Cython debug symbols
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cython_debug/
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# PyCharm
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# JetBrains specific template is maintained in a separate JetBrains.gitignore that can
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# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
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# and can be added to the global gitignore or merged into this file. For a more nuclear
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# option (not recommended) you can uncomment the following to ignore the entire idea folder.
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#.idea/

‎README.md

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# openPMD Updater
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[![Build Status `master`](https://img.shields.io/travis/openPMD/openPMD-updater/master.svg?label=master)](https://travis-ci.com/openPMD/openPMD-updater/branches)
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[![CI:ubuntu](https://github.com/openPMD/openPMD-updater/actions/workflows/ci.yml/badge.svg)](https://github.com/openPMD/openPMD-updater/actions/workflows/ci.yml)
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![Supported Python Versions](https://img.shields.io/pypi/pyversions/openPMD-updater.svg)
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[![License](https://img.shields.io/badge/license-ISC-blue.svg)](https://opensource.org/licenses/ISC)
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cd openPMD-updater
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# install dependencies
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pip install -r requirements.txt
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pip install .
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# optional: append --user
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python setup.py install
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# with optional dependencies for testing
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pip install .[test]
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```
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## Usage
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### Testing
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Additional packages need to be installed for the tests. To install them do:
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```bash
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export PYTHONPATH=$(pwd):$PYTHONPATH
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pip install .[test]
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```
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Then one can run the tests as follows:
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```bash
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# all
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nosetests
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pytest
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# specific
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nosetests tests/test_backend_h5.py
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# manual
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python tests/test_backend_h5.py
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```
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*note*: this changes your `example_files/1_1_0/structure.h5` files in-place.
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`git checkout` it for a reset or do a comparison:
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```bash
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h5diff -c example_files/1_1_0/structure.h5.bak example_files/1_1_0/structure.h5
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attribute: <openPMD of </>> and <openPMD of </>>
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35 differences found
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Not comparable: <openPMDextension> is of class H5T_INTEGER and <openPMDextension> is of class H5T_STRING
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# ...
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pytest tests/test_backend_h5.py
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```

‎example_files/1_1_0/structure.h5

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‎openpmd_updater/Updater.py

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Authors: Axel Huebl
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License: ISC
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"""
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import packaging.version
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from openpmd_updater.backends.HDF5 import HDF5
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from openpmd_updater.transforms.v2_0_0 import \
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DataOrder, GridUnit, ParticleBoundary, ExtensionString, Version
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from .backends.HDF5 import HDF5
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from .transforms.v2_0_0 import (
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DataOrder,
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GridUnit,
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ParticleBoundary,
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ExtensionString,
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Version,
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)
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class Updater(object):
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(see: openpmd_updater.backend.IBackend) for a given file and applies a set
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of transformations (see: openpmd_updater.transforms.ITransform) on it.
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"""
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def __init__(self, filename, verbose=False):
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"""Open a file with suiteable file format backend.
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"""
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"""Open a file with suiteable file format backend."""
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# supported file format backends
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self.backends = [HDF5]
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# dict of updates with each a list of transforms
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# keys: "to_version" of targeted openPMD standard version
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# values: ordered list of transforms
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self.updates = {
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"2.0.0" : [
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"2.0.0": [
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DataOrder.DataOrder, # must be before move of particleBoundary
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GridUnit.GridUnit,
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ParticleBoundary.ParticleBoundary,
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ExtensionString.ExtensionString,
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Version.Version # must be last
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Version.Version, # must be last
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]
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}
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for b in self.backends:
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if self.verbose:
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print("[Updater] Trying file format {0}".format(type(b)))
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print("[Updater] Trying file format {0}".format(b.__name__))
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if b.can_handle(filename):
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self.fb = b(filename)
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break
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if self.fb is None:
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raise RuntimeError("No matching file format backend found for "
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"{0}!".format(filename))
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raise RuntimeError(
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"No matching file format backend found for " "{0}!".format(filename)
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)
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def update(self, new_version="2.0.0", in_place=True):
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"""Perform update to new version of the openPMD standard"""
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# check if new version is known by the updater
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if new_version not in self.updates.keys():
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raise RuntimeError("Only updates to openPMD standard(s) '{0}' are "
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"supported!".format(" ".join(self.updates.keys())))
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raise RuntimeError(
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"Only updates to openPMD standard(s) '{0}' are " "supported!".format(
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" ".join(self.updates.keys())
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)
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)
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if file_version == packaging.version.parse(new_version):
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print("[Updater] File is at already at the requested version!")
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return
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# note: multiple updates over intermediate openPMD standard releases are possible
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if self.verbose:
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print("[Updater] Performing update from {0} to "
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"{1}".format(file_version, new_version))
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print(
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"[Updater] Performing update from {0} to " "{1}".format(
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file_version, new_version
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)
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)
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for t in self.updates[new_version]:
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self.fb.cd(None)
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next_transform = t(self.fb)
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if self.verbose:
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name, desc = t.name
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print("[Updater] Transform {0}: "
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"{1}".format(name, desc))
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print("[Updater] Transform {0}: " "{1}".format(name, desc))
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next_transform.transform(in_place)
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file_version = packaging.version.parse(new_version)
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if not update_valid:
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raise RuntimeError("Unsupported openPMD standard '{0}' in file "
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"'{1}':".format(file_version, self.filename))
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raise RuntimeError(
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"Unsupported openPMD standard '{0}' in file " "'{1}':".format(
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file_version, self.filename
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)
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)

‎openpmd_updater/__init__.py

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"⏫ Update openPMD files to newer versions of the openPMD standard"
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from .Updater import *
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from .backends import *
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from .transforms import *

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