diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml index 0409c388..e77a93dc 100644 --- a/.github/workflows/run-tests.yml +++ b/.github/workflows/run-tests.yml @@ -18,7 +18,7 @@ jobs: strategy: matrix: os: [windows-latest, ubuntu-latest, macos-latest] - python-version: [3.6, 3.7, 3.8] + python-version: ["3.7", "3.8", "3.9"] steps: - uses: actions/checkout@v2 - name: Set up Python ${{ matrix.python-version }} @@ -27,11 +27,12 @@ jobs: python-version: ${{ matrix.python-version }} - name: Install dependencies run: | - python -m pip install --upgrade pip - pip install -r requirements.txt - - name: Run nosetests - run: | - nosetests + python -m pip install --upgrade pip poetry + pip install ".[dev]" + - name: Run tests + run: nosetests + - name: Validate poetry file + run: poetry check test-deb10-i386: runs-on: ubuntu-latest @@ -55,6 +56,6 @@ jobs: # https://github.com/actions/checkout/issues/334 - uses: actions/checkout@v1 - - name: Run nosetests + - name: Run tests run: | nosetests3 diff --git a/.gitignore b/.gitignore index 84200fc5..ebdd3e46 100644 --- a/.gitignore +++ b/.gitignore @@ -69,3 +69,6 @@ target/ # OSX .DS_Store .DS_Store + +# pyenv +.python-version diff --git a/MANIFEST.in b/MANIFEST.in deleted file mode 100644 index 2f5dfb98..00000000 --- a/MANIFEST.in +++ /dev/null @@ -1,12 +0,0 @@ -# Include the license file -include LICENSE - -# Include readme file -include README.md - -# Include the data files -# recursive-include data * - -# If using Python 2.6 or less, then have to include package data, even though -# it's already declared in setup.py -# include sample/*.dat diff --git a/README.md b/README.md index 1c6e45cf..42d83e03 100644 --- a/README.md +++ b/README.md @@ -21,23 +21,28 @@ See the [demo.ipynb](https://github.com/MIT-LCP/wfdb-python/blob/master/demo.ipy ## Installation -The distribution is hosted on pypi at: . To directly install the package from pypi, run from your terminal:: +The distribution is hosted on PyPI at: . The package can be directly installed from PyPI using either pip or poetry: ```sh pip install wfdb +poetry add wfdb ``` The development version is hosted at: . This repository also contains demo scripts and example data. To install the development version, clone or download the repository, navigate to the base directory, and run: ```sh +# Without dev dependencies pip install . -``` +poetry install -## Development +# With dev dependencies +pip install ".[dev]" +poetry install -E dev +``` -The package is to be expanded with physiological signal-processing tools, and general improvements. Development is made for Python 3.6+ only. +See the [note](#package-management) below about dev dependencies. -## Contributing +## Developing We welcome community contributions in the form of pull requests. When contributing code, please ensure: @@ -45,6 +50,27 @@ We welcome community contributions in the form of pull requests. When contributi - Documentation is provided. New functions and classes should have numpy/scipy style [docstrings](https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt). - Unit tests are written for new features that are not covered by [existing tests](https://github.com/MIT-LCP/wfdb-python/tree/master/tests). +### Package Management + +This project uses [poetry](https://python-poetry.org/docs/) for package management and distribution. + +Development dependencies are specified as optional dependencies, and then added to the "dev" extra group in the [pyproject.toml](./pyproject.toml) file. + +```sh +# Do NOT use: poetry add --dev +poetry add --optional +``` + +The `[tool.poetry.dev-dependencies]` attribute is NOT used because of a [limitation](https://github.com/python-poetry/poetry/issues/3514) that prevents these dependencies from being pip installable. Therefore, dev dependencies are not installed when purely running `poetry install`, and the `--no-dev` flag has no meaning in this project. + +Make sure the versions in [version.py](./wfdb/version.py) and [pyproject.toml](./pyproject.toml) are kept in sync. + +To upload a new distribution to PyPI: + +```sh +poetry publish +``` + ## Citing When using this resource, please cite the software [publication](https://physionet.org/content/wfdb-python/) oh PhysioNet. diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 00000000..706379ee --- /dev/null +++ b/poetry.lock @@ -0,0 +1,526 @@ +[[package]] +name = "certifi" +version = "2021.10.8" +description = "Python package for providing Mozilla's CA Bundle." +category = "main" +optional = false +python-versions = "*" + +[[package]] +name = "charset-normalizer" +version = "2.0.12" +description = "The Real First Universal Charset Detector. 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+] diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 00000000..db065e97 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,24 @@ +[tool.poetry] +name = "wfdb" +version = "4.0.0a0" +description = "The WFDB Python package: tools for reading, writing, and processing physiologic signals and annotations." +authors = ["The Laboratory for Computational Physiology "] +license = "MIT" + +[tool.poetry.dependencies] +python = "^3.7" +numpy = "^1.10.1" +scipy = "^1.0.0" +pandas = "^1.0.0" +matplotlib = "^3.3.4" +requests = "^2.8.1" +nose = {version = "^1.3.7", optional = true} + +[tool.poetry.extras] +dev = ["nose"] + +# Do NOT use [tool.poetry.dev-dependencies]. See: https://github.com/python-poetry/poetry/issues/3514 + +[build-system] +requires = ["poetry-core>=1.0.0"] +build-backend = "poetry.core.masonry.api" diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index f9bb9b08..00000000 --- a/requirements.txt +++ /dev/null @@ -1,6 +0,0 @@ -matplotlib==3.3.4 -nose==1.3.7 -numpy==1.18.5 -pandas==1.0.3 -requests==2.23.0 -scipy==1.4.1 diff --git a/setup.py b/setup.py deleted file mode 100644 index 2549bc8f..00000000 --- a/setup.py +++ /dev/null @@ -1,106 +0,0 @@ -"""The WFDB Python Toolbox. -See: https://www.physionet.org/physiotools/wfdb.shtml -""" - -# Always prefer setuptools over distutils -from setuptools import setup, find_packages -# To use a consistent encoding -from codecs import open -from os import path - -here = path.abspath(path.dirname(__file__)) - -# Get the long description from the README file -with open(path.join(here, 'README.md'), encoding='utf-8') as f: - long_description = f.read() - -# Get the version number from the version.py file -with open('wfdb/version.py') as f: - __version__ = f.read().split()[-1].strip("'") - -setup( - name='wfdb', - - # Versions should comply with PEP440. For a discussion on single-sourcing - # the version across setup.py and the project code, see - # https://packaging.python.org/en/latest/single_source_version.html - version=__version__, - - description='The WFDB Python Toolbox', - long_description=long_description, - long_description_content_type="text/markdown", - - # The project's main homepage. - url='https://github.com/MIT-LCP/wfdb-python', - - # Author details - author='The Laboratory for Computational Physiology', - author_email='support@physionet.org', - - # Choose your license - license='MIT', - - # What does your project relate to? - keywords='WFDB clinical waveform', - - # You can just specify the packages manually here if your project is - # simple. Or you can use find_packages(). - # packages=find_packages(exclude=['contrib', 'docs', 'tests']), - packages=find_packages(), - - # Alternatively, if you want to distribute just a my_module.py, uncomment - # this: - # py_modules=["my_module"], - - # List run-time dependencies here. These will be installed by pip when - # your project is installed. For an analysis of "install_requires" vs pip's - # requirements files see: - # https://packaging.python.org/en/latest/discussions/install-requires-vs-requirements/?highlight=requirements - install_requires=[ - 'matplotlib>=3.3.4', - 'numpy>=1.10.1', - 'pandas>=0.17.0', - 'requests>=2.8.1', - 'scipy>=0.17.0', - ], - - # List additional groups of dependencies here (e.g. development - # dependencies). You can install these using the following syntax, - # for example: - # $ pip install -e .[dev,test] - extras_require={ - 'test': ['nose>=1.3.7'] - }, - - # If there are data files included in your packages that need to be - # installed, specify them here. If using Python 2.6 or less, then these - # have to be included in MANIFEST.in as well. - # package_data={'wfdb': ['wfdb.config'], - # }, - - # Although 'package_data' is the preferred approach, in some case you may - # need to place data files outside of your packages. See: - # http://docs.python.org/3.4/distutils/setupscript.html#installing-additional-files # noqa - # In this case, 'data_file' will be installed into '/my_data' - # data_files=[('my_data', ['data/data_file'])], - # data_files=[('config', ['wfdb.config'])], - - # To provide executable scripts, use entry points in preference to the - # "scripts" keyword. Entry points provide cross-platform support and allow - # pip to create the appropriate form of executable for the target platform. - # entry_points={ - # 'console_scripts': [ - # 'sample=sample:main', - # ], - # }, - - # Add ways to quickly filter project - classifiers=[ - "Programming Language :: Python", - "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.6", - "Programming Language :: Python :: 3.7", - "Programming Language :: Python :: 3.8", - "License :: OSI Approved :: MIT License" - ], -) diff --git a/wfdb/version.py b/wfdb/version.py index da4564dd..79fb7745 100644 --- a/wfdb/version.py +++ b/wfdb/version.py @@ -1 +1 @@ -__version__ = '3.4.1' +__version__ = '4.0.0a0'