From c94200f0d7a950e49310543e81b0b1f794aa48c6 Mon Sep 17 00:00:00 2001
From: Daniel Weindl <dweindl@users.noreply.github.com>
Date: Wed, 13 Dec 2023 10:14:27 +0100
Subject: [PATCH] setup.py -> pyproject.toml (#381)

Move python/swig/ to swig/ to not interfere with python packaging.
---
 CMakeLists.txt                         |  2 +-
 python/pyproject.toml                  | 43 ++++++++++++++++++++++++++
 python/setup.py                        | 30 ------------------
 {python/swig => swig}/CMakeLists.txt   |  0
 {python/swig => swig}/parpe.i          |  0
 {python/swig => swig}/std_unique_ptr.i |  0
 6 files changed, 44 insertions(+), 31 deletions(-)
 create mode 100644 python/pyproject.toml
 delete mode 100644 python/setup.py
 rename {python/swig => swig}/CMakeLists.txt (100%)
 rename {python/swig => swig}/parpe.i (100%)
 rename {python/swig => swig}/std_unique_ptr.i (100%)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 1bc8190b3..efad43293 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -199,7 +199,7 @@ endif()
 if(BUILD_PYTHON_MODULE AND CMAKE_BUILD_TYPE MATCHES Debug)
     # Only build swig/python module when we are in debug mode
     # This requires PIC, but we don't want PIC for release build at the moment
-    add_subdirectory(python/swig)
+    add_subdirectory(swig)
 endif()
 
 
diff --git a/python/pyproject.toml b/python/pyproject.toml
new file mode 100644
index 000000000..9cebdd8d6
--- /dev/null
+++ b/python/pyproject.toml
@@ -0,0 +1,43 @@
+[build-system]
+requires = ["setuptools", "setuptools-scm"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "parpe"
+version = "0.0.0"
+authors = [
+    {name = "Daniel Weindl", email = "sci@danielweindl.de"},
+]
+description = "parpe python package"
+requires-python = ">=3.9"
+license = {text = "MIT"}
+dependencies = [
+    'numpy>=1.18.1',
+    'termcolor>=1.1.0',
+    'colorama>=0.4.3',
+    'petab>=0.1.18',
+    'amici>=0.20.0',
+    'h5py>=3.0.0',
+    'python-libsbml>=5.17.0',
+    'snakemake>=5.10.0',
+    'coloredlogs>=15.0',
+    'scipy',
+    'matplotlib',
+]
+
+[project.optional-dependencies]
+test = ["pytest", "pre-commit"]
+
+[project.scripts]
+parpe_petab_to_hdf5 = "parpe.hdf5_pe_input:main"
+
+[project.urls]
+Documentation = "https://parpe.readthedocs.io/"
+Repository = "https://github.com/ICB-DCM/parPE/"
+
+[tool.black]
+line-length = 79
+
+[tool.semantic_release]
+version_toml = "pyproject.toml:project.version"
+
diff --git a/python/setup.py b/python/setup.py
deleted file mode 100644
index 23479437e..000000000
--- a/python/setup.py
+++ /dev/null
@@ -1,30 +0,0 @@
-from setuptools import setup, find_packages
-
-ENTRY_POINTS = {
-    'console_scripts': [
-        'parpe_petab_to_hdf5 = parpe.hdf5_pe_input:main',
-    ]
-}
-
-setup(
-    name='parpe',
-    version='0.0.0',
-    url='https://github.com/ICB-DCM/parPE/',
-    author='Daniel Weindl',
-    author_email='daniel.weindl@helmholtz-muenchen.de',
-    description='parpe python package',
-    packages=find_packages(),
-    install_requires=['numpy>=1.18.1',
-                      'termcolor>=1.1.0',
-                      'colorama>=0.4.3',
-                      'petab>=0.1.18',
-                      'amici>=0.11.15',
-                      'h5py>=3.0.0',
-                      'python-libsbml>=5.17.0',
-                      'snakemake>=5.10.0',
-                      'coloredlogs>=15.0',
-                      'scipy',
-                      'matplotlib',
-                      ],
-    entry_points=ENTRY_POINTS,
-)
diff --git a/python/swig/CMakeLists.txt b/swig/CMakeLists.txt
similarity index 100%
rename from python/swig/CMakeLists.txt
rename to swig/CMakeLists.txt
diff --git a/python/swig/parpe.i b/swig/parpe.i
similarity index 100%
rename from python/swig/parpe.i
rename to swig/parpe.i
diff --git a/python/swig/std_unique_ptr.i b/swig/std_unique_ptr.i
similarity index 100%
rename from python/swig/std_unique_ptr.i
rename to swig/std_unique_ptr.i