From d18a355957878ebdde1d9c42e4a49f1a72519fa7 Mon Sep 17 00:00:00 2001 From: Alex Mestiashvili Date: Thu, 16 Oct 2025 15:32:30 +0200 Subject: [PATCH 1/4] Add pyproject.toml, courtesy Nikitas Rontsis, nrontsis@gmail.com --- pyproject.toml | 53 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 pyproject.toml diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..25e8298 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,53 @@ +[project] +name = "plip" +dynamic = ["version"] +description = "PLIP - Fully automated protein-ligand interaction profiler" +readme = "README.md" +requires-python = ">=3.6" +license = {file = "LICENSE.txt"} + +authors = [ + {name = "PharmAI GmbH", email = "hello@pharm.ai"} +] +maintainers = [ + {name = "PharmAI GmbH", email = "hello@pharm.ai"} +] + +keywords = ["bioinformatics", "protein-ligand", "interactions", "molecular-modeling"] + +classifiers = [ + "Development Status :: 5 - Production/Stable", + "Intended Audience :: Science/Research", + "Natural Language :: English", + "License :: OSI Approved :: GNU General Public License v2 (GPLv2)", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.6", + "Programming Language :: Python :: 3.7", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Topic :: Scientific/Engineering :: Bio-Informatics" +] + +dependencies = [ + "numpy>=1.13.3", + "lxml>=4.2.1" +] + +[project.optional-dependencies] +openbabel = ["openbabel>=3.0.0"] + +[project.urls] +Homepage = "https://github.com/pharmai/plip" +Repository = "https://github.com/pharmai/plip" + +[project.scripts] +plip = "plip.plipcmd:main" + +[tool.setuptools] +packages = ["plip"] + +[tool.setuptools.dynamic] +version = {attr = "plip.basic.config.__version__"} From 9bdf35dcf5f5b4751caf68791819ab33ba3e3cbc Mon Sep 17 00:00:00 2001 From: Alex Mestiashvili Date: Thu, 16 Oct 2025 15:35:29 +0200 Subject: [PATCH 2/4] Drop requirements.txt --- requirements.txt | 4 ---- 1 file changed, 4 deletions(-) delete mode 100644 requirements.txt diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 6d4d07c..0000000 --- a/requirements.txt +++ /dev/null @@ -1,4 +0,0 @@ -lxml~=4.2.1 -numpy~=1.13.3 -pymol~=2.3.0 -openbabel~=3.0.0 \ No newline at end of file From 871ef565a69765dcbf91fa0af4bdac66fe19316c Mon Sep 17 00:00:00 2001 From: Alex Mestiashvili Date: Thu, 16 Oct 2025 15:38:13 +0200 Subject: [PATCH 3/4] Update pyproject.toml, adjust build system to use setup.py --- pyproject.toml | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 25e8298..a910db7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,10 +1,14 @@ +[build-system] +build-backend = "setuptools.build_meta" +requires = ["setuptools","pip","requests"] + [project] name = "plip" +license = "GPL-2.0-only" dynamic = ["version"] description = "PLIP - Fully automated protein-ligand interaction profiler" readme = "README.md" requires-python = ">=3.6" -license = {file = "LICENSE.txt"} authors = [ {name = "PharmAI GmbH", email = "hello@pharm.ai"} @@ -19,7 +23,6 @@ classifiers = [ "Development Status :: 5 - Production/Stable", "Intended Audience :: Science/Research", "Natural Language :: English", - "License :: OSI Approved :: GNU General Public License v2 (GPLv2)", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", @@ -33,12 +36,10 @@ classifiers = [ dependencies = [ "numpy>=1.13.3", - "lxml>=4.2.1" + "lxml>=4.2.1", + "openbabel>=3.1.1", ] -[project.optional-dependencies] -openbabel = ["openbabel>=3.0.0"] - [project.urls] Homepage = "https://github.com/pharmai/plip" Repository = "https://github.com/pharmai/plip" @@ -46,8 +47,8 @@ Repository = "https://github.com/pharmai/plip" [project.scripts] plip = "plip.plipcmd:main" -[tool.setuptools] -packages = ["plip"] +[tool.setuptools.packages.find] +include = ["plip*"] [tool.setuptools.dynamic] version = {attr = "plip.basic.config.__version__"} From 6d5f7188eb801aaf5ba34e2d44938f96c785452d Mon Sep 17 00:00:00 2001 From: Alex Mestiashvili Date: Thu, 16 Oct 2025 15:50:23 +0200 Subject: [PATCH 4/4] hardocde verion, since ./plip is not available while building module --- setup.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/setup.py b/setup.py index fb2404b..5d80ca3 100644 --- a/setup.py +++ b/setup.py @@ -3,8 +3,6 @@ from setuptools.command.install import install from distutils.command.build import build -from plip.basic import config - def install_pkg_via_pip(package): import sys import subprocess @@ -74,7 +72,7 @@ def run(self): return setup(name='plip', - version=config.__version__, + version='2.4.0', description='PLIP - Fully automated protein-ligand interaction profiler', classifiers=[ 'Development Status :: 5 - Production/Stable',