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FIX installation and workflows #127

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Merged
NelleV merged 6 commits into from
May 21, 2025
Merged

FIX installation and workflows #127

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929c3cb
FIX test workflow
gesinecauer May 18, 2025
64fa9cf
update for PEP517
gesinecauer May 18, 2025
13277ac
newer setuptools, min python version 3.9
gesinecauer May 18, 2025
a0abec8
min python version 3.8
gesinecauer May 18, 2025
ec23730
FIX python version 3.9, add timeout-minutes
gesinecauer May 19, 2025
f64438c
Update pyproject.toml
NelleV May 21, 2025
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8 changes: 7 additions & 1 deletion .github/workflows/build-doc.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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}
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6 changes: 4 additions & 2 deletions .github/workflows/test.yml
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Expand Up @@ -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"

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48 changes: 47 additions & 1 deletion pyproject.toml
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@@ -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
49 changes: 3 additions & 46 deletions setup.py
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@@ -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',
]
}
)