Merge pull request #127 from gesinecauer/fix_install_from_repo

FIX installation and workflows

Author: NelleV

.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}

.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"
 

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 = "[email protected]"}
+]
+maintainers = [
+  {name = "Nelle Varoquaux", email = "[email protected]"}
+]
+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

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 = '[email protected]'
-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',
-        ]
-    }
 )
-