From e10ec2acbdf2598e79ff4b1d8ff55f3636ad0844 Mon Sep 17 00:00:00 2001 From: Eleftherios Zisis Date: Wed, 15 May 2024 09:38:29 +0200 Subject: [PATCH] OSS updates (#1) --- .github/workflows/sdist.yml | 48 +++++++++ .github/workflows/tox.yml | 42 ++++++++ .gitlab-ci.yml | 3 - AUTHORS.txt | 8 ++ LICENSE.txt | 202 ++++++++++++++++++++++++++++++++++++ MANIFEST.in | 7 -- README.rst | 28 +++-- pyproject.toml | 66 ++++++++++-- setup.py | 63 ----------- src/blue_cwl/__init__.py | 7 +- src/blue_cwl/cli.py | 2 +- src/blue_cwl/version.py | 4 - tox.ini | 28 ++--- 13 files changed, 399 insertions(+), 109 deletions(-) create mode 100644 .github/workflows/sdist.yml create mode 100644 .github/workflows/tox.yml delete mode 100644 .gitlab-ci.yml create mode 100644 AUTHORS.txt create mode 100644 LICENSE.txt delete mode 100644 MANIFEST.in delete mode 100644 setup.py delete mode 100644 src/blue_cwl/version.py diff --git a/.github/workflows/sdist.yml b/.github/workflows/sdist.yml new file mode 100644 index 0000000..ec2117f --- /dev/null +++ b/.github/workflows/sdist.yml @@ -0,0 +1,48 @@ +name: sdist + +on: + workflow_dispatch: + pull_request: + push: + branches: + - main + release: + types: + - published + +jobs: + + build_sdist: + name: Build sdist + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + + - name: Build SDist + run: pipx run build --sdist + + - name: Check metadata + run: pipx run twine check dist/* + + - uses: actions/upload-artifact@v4 + with: + name: build + path: dist + + upload_sdist: + name: Upload sdist + needs: [build_sdist] + runs-on: ubuntu-latest + permissions: + # IMPORTANT: this permission is mandatory for trusted publishing + id-token: write + if: github.event_name == 'release' && github.event.action == 'published' + + steps: + - uses: actions/download-artifact@v4 + with: + name: build + path: dist + + - name: Publish package distributions to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 diff --git a/.github/workflows/tox.yml b/.github/workflows/tox.yml new file mode 100644 index 0000000..8df5d92 --- /dev/null +++ b/.github/workflows/tox.yml @@ -0,0 +1,42 @@ +name: tox + +on: + workflow_dispatch: + pull_request: + push: + branches: + - main + release: + types: + - published + +jobs: + checks: + + runs-on: ubuntu-latest + strategy: + matrix: + tox-env: ['py310', 'py311', 'py312'] + + steps: + + - uses: actions/checkout@v4 + + - name: Set up Python 3.10 + uses: actions/setup-python@v4 + with: + python-version: '3.10' + + - name: Install dependencies + run: | + python -m pip install --upgrade pip + python -m pip install tox tox-gh-actions + + - name: Run tox + run: tox + + - name: Upload coverage reports to Codecov + uses: codecov/codecov-action@v4.0.1 + with: + token: ${{ secrets.CODECOV_TOKEN }} + slug: BlueBrain/blue-cwl diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml deleted file mode 100644 index e2f4ae8..0000000 --- a/.gitlab-ci.yml +++ /dev/null @@ -1,3 +0,0 @@ -include: - - project: nse/ci - file: /ci/pipelines/nse.cwl-registry.yml diff --git a/AUTHORS.txt b/AUTHORS.txt new file mode 100644 index 0000000..9d3474a --- /dev/null +++ b/AUTHORS.txt @@ -0,0 +1,8 @@ +Maintainer +---------- +* BBP/NSE + +Authors +------- +Eleftherios Zisis +Mike Gevaert diff --git a/LICENSE.txt b/LICENSE.txt new file mode 100644 index 0000000..d645695 --- /dev/null +++ b/LICENSE.txt @@ -0,0 +1,202 @@ + + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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Replace this text by proper installation instructions. +Acknowledgements +================ +The development of this software was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology. -Examples --------- +For license and authors, see LICENSE.txt and AUTHORS.txt respectively. -.. Provide here some examples on how this software can be used. \ No newline at end of file +Copyright (c) 2022-2024 Blue Brain Project/EPFL diff --git a/pyproject.toml b/pyproject.toml index 631715b..1c389e8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,15 +1,61 @@ -[tool.black] -line-length = 100 -target-version = [ - 'py37', - 'py38', - 'py39', +[build-system] +requires = [ + "setuptools>=64", + "setuptools_scm>=8" +] +build-backend = "setuptools.build_meta" + +[project] +name = "blue-cwl" +description = "Common Workflow Language inspired workflow definitions." +readme = { file = "README.rst", content-type = "text/x-rst" } +requires-python = ">=3.10" +license = { file = "LICENSE.txt" } +authors = [ + { name = "Blue Brain Project, EPFL" }, +] +dependencies = [ + "click>=8.0", + "libsonata", + "numpy", + "pandas", + "voxcell", + "joblib", + "entity_management>=1.2.45", # latest emodel definitions + "pyarrow>=3.0.0", + "fz_td_recipe>=0.2.0", # support for json recipe + "pydantic", + "morph-tool", + "jsonschema", + "luigi", +] +classifiers = [ + "Development Status :: 2 - Pre-Alpha", + "Intended Audience :: Education", + "Intended Audience :: Science/Research", + "Programming Language :: Python", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Topic :: Scientific/Engineering :: Bio-Informatics", ] -include = 'src/blue_cwl\/.*\.py$|tests\/.*\.py$|doc\/source\/conf\.py$|setup\.py$' +dynamic = ["version"] + +[project.optional-dependencies] +docs = [ + "sphinx-bluebrain-theme", +] + +[project.urls] +Homepage = "https://github.com/BlueBrain/blue-cwl" +Repository = "https://github.com/BlueBrain/blue-cwl" +Issues = "https://github.com/BlueBrain/blue-cwl/issues" + +[project.scripts] +blue-cwl = "blue_cwl.cli:main" -[tool.isort] -profile = "black" -line_length = 100 +[tool.setuptools.packages.find] +where = ["src"] [tool.ruff] line-length = 100 diff --git a/setup.py b/setup.py deleted file mode 100644 index 8c26cf9..0000000 --- a/setup.py +++ /dev/null @@ -1,63 +0,0 @@ -#!/usr/bin/env python -import importlib.util -from pathlib import Path - -from setuptools import setup, find_packages - -spec = importlib.util.spec_from_file_location( - "blue_cwl.version", - "src/blue_cwl/version.py", -) -module = importlib.util.module_from_spec(spec) -spec.loader.exec_module(module) -VERSION = module.__version__ - - -setup( - name="blue-cwl", - author="bbp-ou-nse", - author_email="bbp-ou-nse@groupes.epfl.ch", - version=VERSION, - description="Common Workflow Language tool definitions", - long_description=Path("README.rst").read_text(encoding="utf-8"), - long_description_content_type="text/x-rst", - url="https://bbpteam.epfl.ch/documentation/projects/blue-cwl", - project_urls={ - "Tracker": "https://bbpteam.epfl.ch/project/issues/projects/NSETM/issues", - "Source": "git@bbpgitlab.epfl.ch:nse/blue-cwl.git", - }, - license="BBP-internal-confidential", - entry_points={"console_scripts": ["blue-cwl=blue_cwl.cli:main"]}, - install_requires=[ - "click>=8.0", - "libsonata", - "numpy", - "pandas", - "voxcell", - "joblib", - "entity_management>=1.2.45", # latest emodel definitions - "blue-cwl>=1.0.0", - "pyarrow>=3.0.0", - "fz_td_recipe>=0.2.0", # support for json recipe - "pydantic", - "morph-tool", - "jsonschema", - "luigi" - ], - packages=find_packages(where="src"), - package_dir={"": "src"}, - include_package_data=True, - python_requires=">=3.10", - extras_require={ - "docs": ["sphinx", "sphinx-bluebrain-theme"], - }, - classifiers=[ - "Development Status :: 2 - Pre-Alpha", - "Intended Audience :: Education", - "Intended Audience :: Science/Research", - "Programming Language :: Python", - "Programming Language :: Python :: 3.9", - "Programming Language :: Python :: 3.10", - "Topic :: Scientific/Engineering :: Bio-Informatics", - ], -) diff --git a/src/blue_cwl/__init__.py b/src/blue_cwl/__init__.py index 0f02ce7..ef29c81 100644 --- a/src/blue_cwl/__init__.py +++ b/src/blue_cwl/__init__.py @@ -1,6 +1,9 @@ """blue_cwl.""" -__all__ = ["Variant", "__version__"] +from importlib.metadata import version + +__version__ = version(__package__) from blue_cwl.variant import Variant -from blue_cwl.version import __version__ + +__all__ = ["Variant", "__version__"] diff --git a/src/blue_cwl/cli.py b/src/blue_cwl/cli.py index 60f2404..cbdb07f 100644 --- a/src/blue_cwl/cli.py +++ b/src/blue_cwl/cli.py @@ -5,7 +5,7 @@ import click -from blue_cwl.version import VERSION +from blue_cwl import __version__ as VERSION from blue_cwl.wrappers import ( cell_composition_manipulation, cell_composition_summary, diff --git a/src/blue_cwl/version.py b/src/blue_cwl/version.py deleted file mode 100644 index ecccf09..0000000 --- a/src/blue_cwl/version.py +++ /dev/null @@ -1,4 +0,0 @@ -"""Package version.""" - -VERSION = "2.0.0" -__version__ = VERSION diff --git a/tox.ini b/tox.ini index 08a367d..7e2ea10 100644 --- a/tox.ini +++ b/tox.ini @@ -10,13 +10,15 @@ basetemp=tmptestdir/{envname} minversion = 3.18 -# ignore basepython for envs that already specify a version -ignore_basepython_conflict = true +[tox] +envlist = + lint + docs + coverage + check-packaging + py{310,311,312} [testenv] -basepython=python3.10 -setenv = - PIP_INDEX_URL = https://bbpteam.epfl.ch/repository/devpi/simple deps = {[base]testdeps} commands_pre = /bin/mkdir -p {[base]basetemp} commands = python -m pytest --basetemp=tmptestdir/{envname} tests/unit {posargs} @@ -79,17 +81,13 @@ commands = connectome_placeholder: python -m pytest --basetemp=tmptestdir/{envname} tests/functional/test_connectome_generation_placeholder.py connectome_filtering: python -m pytest --basetemp=tmptestdir/{envname} tests/functional/test_connectome_filtering_synapses.py -[testenv:check-version] -skip_install = true -deps = bbp-nse-ci>=0.4.2 -commands = do_release.py -p . check-version - [testenv:check-packaging] +skip_install = true deps = - wheel + build twine commands = - python setup.py sdist bdist_wheel -d {envtmpdir}/dist + python -m build -o {envtmpdir}/dist twine check {envtmpdir}/dist/* [testenv:lint] @@ -148,3 +146,9 @@ ignore = E731,W503,W504,E501,E203 # D417: Missing argument description add-ignore = D413, D415, D417 convention = google + +[gh-actions] +python = + 3.10: py310, lint + 3.11: py311, docs + 3.12: py312, check-packaging