From e63c1a32f9ec926e9d407bbf80e50d0679e74d76 Mon Sep 17 00:00:00 2001
From: akhanf <alik@robarts.ca>
Date: Thu, 12 Nov 2020 16:38:09 -0500
Subject: [PATCH] updates for packaging, and snakebids updates

---
 requirements.txt |  1 -
 run.py           | 13 ++++++++-----
 setup.py         | 31 +++++++++++++++++++++++++++++++
 3 files changed, 39 insertions(+), 6 deletions(-)
 delete mode 100644 requirements.txt
 create mode 100644 setup.py

diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index f5047d7..0000000
--- a/requirements.txt
+++ /dev/null
@@ -1 +0,0 @@
-snakebids==0.0.1
diff --git a/run.py b/run.py
index fc89480..8dc200e 100755
--- a/run.py
+++ b/run.py
@@ -1,10 +1,13 @@
 #!/usr/bin/env python3
 import os
-
 from snakebids.app import SnakeBidsApp
 
-pwd = os.path.abspath(os.path.dirname(__file__))
-app = SnakeBidsApp(snakebids_config=os.path.join(pwd,'config','snakebids.yml'),
-                    snakefile=os.path.join(pwd,'workflow','Snakefile'))
-app.run_snakemake()
 
+def main():
+
+    app = SnakeBidsApp(os.path.abspath(os.path.dirname(__file__)))
+    app.run_snakemake()
+
+
+if __name__ == "__main__":
+    main()
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000..64c6ad6
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,31 @@
+import setuptools
+
+with open("README.md", "r") as fh:
+    long_description = fh.read()
+
+setuptools.setup(
+    name="denoise-fmri", 
+    version="0.1.0",
+    author="Ali Khan",
+    author_email="alik@robarts.ca",
+    description="Snakemake BIDS app for denoising fmriprep, uses the snakebids package for running snakemake workflow as bids app",
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    url="https://github.com/akhanf/denoise-fmri",
+    packages=setuptools.find_packages(),
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "License :: OSI Approved :: MIT License",
+        "Operating System :: OS Independent",
+    ],
+    entry_points={'console_scripts': [
+        'denoise-fmri=run:main'
+    ]},
+    install_requires=[
+        "snakebids>=0.1.1",
+        "nilearn",
+        "pandas",
+        "numpy"
+    ],
+    python_requires='>=3.7'
+)