From 9ae3ba7f3f8ae25de9c28a7a3c2772ec1a8dfca9 Mon Sep 17 00:00:00 2001 From: Nikitas Rontsis Date: Thu, 30 Jan 2025 19:45:46 +0000 Subject: [PATCH 1/3] Update to numpy>2 --- pyproject.toml | 6 +++--- run_test.sh | 0 setup.cfg | 2 +- src/DockQ/operations.pyx | 1 + 4 files changed, 5 insertions(+), 4 deletions(-) mode change 100644 => 100755 run_test.sh diff --git a/pyproject.toml b/pyproject.toml index ea3684f..d467069 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,5 +1,5 @@ [build-system] -requires = ["setuptools>=68", "cython", "numpy < 2.0"] +requires = ["setuptools>=68", "cython", "numpy > 2.0"] build-backend = "setuptools.build_meta" [project] @@ -11,13 +11,13 @@ authors = [ ] description = "A Quality Measure for Protein, Nucleic Acids and Small Ligand Docking Models" readme = "README.md" -requires-python = ">=3.8" +requires-python = ">=3.10" classifiers = [ "Programming Language :: Python :: 3", "License :: OSI Approved :: MIT License", "Operating System :: OS Independent", ] -dependencies = ["numpy < 2.0", "biopython >= 1.79", "networkx", "parallelbar"] +dependencies = ["numpy > 2.0", "biopython >= 1.79", "networkx", "parallelbar"] [project.urls] Homepage = "https://github.com/bjornwallner/DockQ" diff --git a/run_test.sh b/run_test.sh old mode 100644 new mode 100755 diff --git a/setup.cfg b/setup.cfg index 7955081..ec766c7 100644 --- a/setup.cfg +++ b/setup.cfg @@ -10,7 +10,7 @@ install_requires = setuptools cython parallelbar - numpy<2.0 + numpy>2.0 biopython>=1.79 networkx diff --git a/src/DockQ/operations.pyx b/src/DockQ/operations.pyx index 282d8a9..e39ca08 100644 --- a/src/DockQ/operations.pyx +++ b/src/DockQ/operations.pyx @@ -1,6 +1,7 @@ #cython: language_level=3 import numpy as np cimport numpy as np +np.import_array() import cython @cython.boundscheck(False) From 65d65cedfe486e6c63aa665c7c2dfd3d4f900c73 Mon Sep 17 00:00:00 2001 From: Nikitas Rontsis Date: Thu, 30 Jan 2025 19:47:21 +0000 Subject: [PATCH 2/3] Less strict --- pyproject.toml | 4 ++-- setup.cfg | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index d467069..db6ea22 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,5 +1,5 @@ [build-system] -requires = ["setuptools>=68", "cython", "numpy > 2.0"] +requires = ["setuptools>=68", "cython", "numpy>=2.0"] build-backend = "setuptools.build_meta" [project] @@ -17,7 +17,7 @@ classifiers = [ "License :: OSI Approved :: MIT License", "Operating System :: OS Independent", ] -dependencies = ["numpy > 2.0", "biopython >= 1.79", "networkx", "parallelbar"] +dependencies = ["numpy >= 2.0", "biopython >= 1.79", "networkx", "parallelbar"] [project.urls] Homepage = "https://github.com/bjornwallner/DockQ" diff --git a/setup.cfg b/setup.cfg index ec766c7..bfe009d 100644 --- a/setup.cfg +++ b/setup.cfg @@ -10,7 +10,7 @@ install_requires = setuptools cython parallelbar - numpy>2.0 + numpy>=2.0 biopython>=1.79 networkx From ba4df5adaad7c77fd60851d0b7b05f2b77061ba2 Mon Sep 17 00:00:00 2001 From: nrontsis Date: Wed, 4 Jun 2025 16:36:39 +0000 Subject: [PATCH 3/3] Fix --- setup.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/setup.py b/setup.py index 460126e..0f06982 100644 --- a/setup.py +++ b/setup.py @@ -11,9 +11,10 @@ ] setup( - name="dockq", ext_modules=cythonize(extensions), package_data={ - "src/DockQ": ["operations.pyx"], + "DockQ": ["operations.pyx"], }, + packages=["DockQ"], + package_dir={"": "src"}, )