From ad52d54a997a12796fbcdb2d7225d32f5a9b6de0 Mon Sep 17 00:00:00 2001
From: WardDeb <ward@deboutte.be>
Date: Thu, 1 Aug 2024 11:07:52 +0200
Subject: [PATCH] makePairs as an entry point

---
 pyproject.toml                              | 41 +++++++++++++++++++++
 requirements.txt                            |  6 ---
 setup.py                                    | 28 --------------
 snakePipes/workflows/makePairs/makePairs.py |  2 +
 4 files changed, 43 insertions(+), 34 deletions(-)
 create mode 100644 pyproject.toml
 delete mode 100644 requirements.txt
 delete mode 100755 setup.py
 create mode 100644 snakePipes/workflows/makePairs/makePairs.py

diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 000000000..c81ec925a
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,41 @@
+[build-system]
+requires = ["setuptools >= 61.0", "setuptools_scm>=8"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "snakePipes"
+description = 'Snakemake workflows and wrappers for NGS data processing from the MPI-IE'
+readme = "README.rst"
+version = "3.9.1"
+keywords = [
+    "DNA-mapping",
+    "ChIP-Seq",
+    "mRNA-seq",
+    "noncoding-RNA-seq",
+    "ATAC-seq",
+    "scRNA-seq",
+    "WGBS / Bisulfite seq",
+    "epigenetics workflows",
+    "Illumina"
+]
+authors = [
+  {name = "Bioinfo-Core MPI-IE"}
+]
+requires-python = ">=3.9"
+dependencies = [
+    "snakemake >= 6.2.1, <7.19.0",
+    "psutil",
+    "pandas",
+    "thefuzz",
+    "pyyaml >= 5.1",
+    "tabulate < 0.9"
+]
+classifiers = [
+    "Intended Audience :: Bioinformaticians",
+    "Intended Audience :: Biologists",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",   
+]
+
+[project.scripts]
+makePairs = "snakePipes.workflows.makePairs.makePairs:main"
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index 2df31a410..000000000
--- a/requirements.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-snakemake >= 6.2.1, <7.19.0
-psutil
-pandas
-thefuzz
-pyyaml >= 5.1
-tabulate < 0.9
diff --git a/setup.py b/setup.py
deleted file mode 100755
index 9b83b8527..000000000
--- a/setup.py
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env python
-from setuptools import setup, find_packages
-from glob import glob
-import os.path
-
-# Set __version__
-exec(open('snakePipes/__init__.py').read())
-
-scripts = ['bin/snakePipes']
-for d in glob('snakePipes/workflows/*'):
-    scripts.append(os.path.join(d, os.path.split(d)[1]))
-
-requires = open("requirements.txt").read().strip().split("\n")
-
-setup(
-    name='snakePipes',
-    version=__version__,  # noqa: F821
-    scripts=scripts,
-    packages=find_packages(),
-    include_package_data=True,
-    python_requires='>=3.7',
-    install_requires=requires,
-    url='https://github.com/maxplanck-ie/snakepipes',
-    license='MIT',
-    description='Snakemake workflows and wrappers for NGS data processing from the MPI-IE',
-    zip_safe=False,
-    data_files=[("", ["LICENSE"])]
-)
diff --git a/snakePipes/workflows/makePairs/makePairs.py b/snakePipes/workflows/makePairs/makePairs.py
new file mode 100644
index 000000000..f51f47823
--- /dev/null
+++ b/snakePipes/workflows/makePairs/makePairs.py
@@ -0,0 +1,2 @@
+def main():
+    print("Bonjour from makePairs ! ")
\ No newline at end of file