From 929c3cb8ba86947ef27c685014835a47dd567892 Mon Sep 17 00:00:00 2001 From: Gesine Cauer Date: Sat, 17 May 2025 19:46:53 -0700 Subject: [PATCH 1/6] FIX test workflow --- .github/workflows/test.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 28e43d3..30cf807 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: 3.8 MINIMUM_REQUIREMENTS: 1 OPTIONS_NAME: "min" From 64fa9cf5b846eec936c7988442ea7dc4e55fd3a1 Mon Sep 17 00:00:00 2001 From: Gesine Cauer Date: Sat, 17 May 2025 19:50:09 -0700 Subject: [PATCH 2/6] update for PEP517 --- pyproject.toml | 48 +++++++++++++++++++++++++++++++++++++++++++++++- setup.py | 49 +++---------------------------------------------- 2 files changed, 50 insertions(+), 47 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index d6f2015..500f29a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,2 +1,48 @@ [build-system] -requires=['setuptools', 'wheel', 'numpy', 'scipy'] +requires = ["setuptools", "wheel", "numpy", "scipy", "cython"] +build-backend = "setuptools.build_meta" + +[project] +name = "iced" +requires-python = ">= 3.8" +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@ensmp.fr"} +] +maintainers = [ + {name = "Nelle Varoquaux", email = "nelle.varoquaux@ensmp.fr"} +] +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', - ] - } ) - From 13277ac3c416fa3adc220f83f0affa9493b3031f Mon Sep 17 00:00:00 2001 From: Gesine Date: Sat, 17 May 2025 20:30:34 -0700 Subject: [PATCH 3/6] newer setuptools, min python version 3.9 --- pyproject.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 500f29a..796a15c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,10 +1,10 @@ [build-system] -requires = ["setuptools", "wheel", "numpy", "scipy", "cython"] +requires = ["setuptools>=77", "wheel", "numpy", "scipy", "cython"] build-backend = "setuptools.build_meta" [project] name = "iced" -requires-python = ">= 3.8" +requires-python = ">= 3.9" version = "0.6.0a0.dev0" dependencies = [ "numpy>=1.16.0", From a0abec8bb0185387ad69b20d4e8744631fd24ec1 Mon Sep 17 00:00:00 2001 From: Gesine Date: Sat, 17 May 2025 20:31:10 -0700 Subject: [PATCH 4/6] min python version 3.8 --- .github/workflows/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 30cf807..6283572 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -16,7 +16,7 @@ jobs: MINIMUM_REQUIREMENTS: [0] include: - platform_id: manylinux_x86_64 - python-version: 3.8 + python-version: 3.9 MINIMUM_REQUIREMENTS: 1 OPTIONS_NAME: "min" From ec23730228292b5f6cbe14b6f9c14d645555c42b Mon Sep 17 00:00:00 2001 From: Gesine Date: Sun, 18 May 2025 18:53:06 -0700 Subject: [PATCH 5/6] FIX python version 3.9, add timeout-minutes --- .github/workflows/build-doc.yml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) 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} From f64438c4200299a7d8c8bbb2bc1b3e058032122d Mon Sep 17 00:00:00 2001 From: Nelle Varoquaux Date: Wed, 21 May 2025 13:52:05 +0200 Subject: [PATCH 6/6] Update pyproject.toml --- pyproject.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 796a15c..d993328 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -16,10 +16,10 @@ license = "BSD-3-Clause" license-files = ["LICENSE"] keywords = ["iced", "hi-c", "chromatin"] authors = [ - {name = "Nelle Varoquaux", email = "nelle.varoquaux@ensmp.fr"} + {name = "Nelle Varoquaux", email = "nelle.varoquaux@gmail.com"} ] maintainers = [ - {name = "Nelle Varoquaux", email = "nelle.varoquaux@ensmp.fr"} + {name = "Nelle Varoquaux", email = "nelle.varoquaux@gmail.com"} ] classifiers=[ 'Development Status :: 3 - Alpha',