diff --git a/.github/workflows/build-doc.yml b/.github/workflows/build-doc.yml index f9d6500..9897b98 100644 --- a/.github/workflows/build-doc.yml +++ b/.github/workflows/build-doc.yml @@ -9,6 +9,12 @@ jobs: build: name: Build docs runs-on: ubuntu-latest + + timeout-minutes: 10 + + strategy: + fail-fast: false + steps: - name: Checkout 🛎️ uses: actions/checkout@v2 @@ -18,7 +24,7 @@ jobs: - name: Setup Python uses: actions/setup-python@v2 with: - python-version: 3.8 + python-version: 3.9 - name: Installation of the package shell: bash -l {0} diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 28e43d3..6283572 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -6,15 +6,17 @@ jobs: name: linux-cp${{ matrix.python-version }}-${{ matrix.OPTIONS_NAME }} runs-on: ubuntu-latest + timeout-minutes: 10 + strategy: - fail-fast: true + fail-fast: false matrix: python-version: ["3.9", "3.10", "3.11", "3.12"] PIP_FLAGS: [""] MINIMUM_REQUIREMENTS: [0] include: - platform_id: manylinux_x86_64 - python-version: 3.7 + python-version: 3.9 MINIMUM_REQUIREMENTS: 1 OPTIONS_NAME: "min" diff --git a/pyproject.toml b/pyproject.toml index d6f2015..d993328 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,2 +1,48 @@ [build-system] -requires=['setuptools', 'wheel', 'numpy', 'scipy'] +requires = ["setuptools>=77", "wheel", "numpy", "scipy", "cython"] +build-backend = "setuptools.build_meta" + +[project] +name = "iced" +requires-python = ">= 3.9" +version = "0.6.0a0.dev0" +dependencies = [ + "numpy>=1.16.0", + "scipy>=0.19.0", +] +readme = "README.rst" +description = "ICE normalization" +license = "BSD-3-Clause" +license-files = ["LICENSE"] +keywords = ["iced", "hi-c", "chromatin"] +authors = [ + {name = "Nelle Varoquaux", email = "nelle.varoquaux@gmail.com"} +] +maintainers = [ + {name = "Nelle Varoquaux", email = "nelle.varoquaux@gmail.com"} +] +classifiers=[ + 'Development Status :: 3 - Alpha', + 'Intended Audience :: Science/Research', + 'Intended Audience :: Developers', + 'Programming Language :: Python', + 'Topic :: Utilities', + 'Topic :: Software Development', + 'Topic :: Scientific/Engineering', + 'Operating System :: Microsoft :: Windows', + 'Operating System :: POSIX', + 'Operating System :: Unix', + 'Operating System :: MacOS'] + +[project.scripts] +ice = "iced.scripts.ice:main" + +[project.urls] +Homepage = "https://hiclib.github.io/iced/" +Documentation = "https://hiclib.github.io/iced/documentation.html" +Repository = "https://github.com/hiclib/iced.git" +Issues = "https://github.com/hiclib/iced/issues" +Download = "https://github.com/hiclib/iced/releases" + +[tool.setuptools] +include-package-data = true diff --git a/setup.py b/setup.py index 0bc1164..65df86c 100644 --- a/setup.py +++ b/setup.py @@ -1,57 +1,14 @@ -import os -import sys -from setuptools import Extension, setup, find_packages +from setuptools import Extension, setup import numpy as np -DISTNAME = 'iced' -DESCRIPTION = 'ICE normalization' -MAINTAINER = 'Nelle Varoquaux' -MAINTAINER_EMAIL = 'nelle.varoquaux@gmail.com' -VERSION = "0.6.0a0.dev0" -LICENSE = "BSD" - - -SCIPY_MIN_VERSION = '0.19.0' -NUMPY_MIN_VERSION = '1.16.0' - -extension_config = { - "_filter": [ - {"sources": ["_filter.pyx"]} - ], - "normalization": [ - {"sources": ["_normalization.pyx"]} - ] -} - - setup( - name=DISTNAME, - version=VERSION, - author=MAINTAINER, - author_email=MAINTAINER_EMAIL, - description=DESCRIPTION, - license=LICENSE, - classifiers=[ - "Development Status :: 3 - Alpha", - "Topic :: Utilities", - "License :: OSI Approved :: BSD License", - ], - packages=find_packages(where="."), ext_modules=[ Extension(name="iced._filter_", sources=["iced/_filter_.pyx"], - include_dirs=[np.get_include()] - ), - Extension(name="iced.normalization/_normalization_", + include_dirs=[np.get_include()]), + Extension(name="iced.normalization._normalization_", sources=["iced/normalization/_normalization_.pyx"], include_dirs=[np.get_include()] )], - include_package_data=True, - entry_points={ - 'console_scripts': [ - 'ice = iced.scripts.ice:main', - ] - } ) -