From 08bd5091a9590aeb4add2d0bb4391f5e056700c3 Mon Sep 17 00:00:00 2001
From: In-Ho Yi <in-ho@anagenex.com>
Date: Tue, 27 Sep 2022 20:43:31 -0400
Subject: [PATCH 1/3] Add top-level setup.py

With this, we can now pip install directly from the repo dir.
---
 setup.py | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 setup.py

diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000..1dced98
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,30 @@
+import io
+import os
+import re
+
+from setuptools import setup
+
+# Get the version from src/huggingmolecules/__init__.py
+# Adapted from https://stackoverflow.com/a/39671214
+this_directory = os.path.dirname(os.path.realpath(__file__))
+init_path = os.path.join(this_directory, 'src', 'huggingmolecules', '__init__.py')
+version_matches = re.search(
+    r'__version__\s*=\s*[\'"]([^\'"]*)[\'"]',
+    io.open(init_path, encoding='utf_8_sig').read(),
+)
+if version_matches is None:
+    raise Exception('Could not determine huggingmolecules version from __init__.py')
+__version__ = version_matches.group(1)
+
+setup(
+    name='huggingmolecules',
+    version=__version__,
+    packages=['huggingmolecules'],
+    package_dir={'':'src'},
+    install_requires=[
+        'torch>=1.7.0',
+        'scikit-learn>=0.23.2',
+        'filelock>=3.0.12',
+        'gdown>=3.12.2'
+    ]
+)

From d1c4755fca541797d09337d7aa9535d296ca61d1 Mon Sep 17 00:00:00 2001
From: In-Ho Yi <in-ho@anagenex.com>
Date: Tue, 27 Sep 2022 20:58:41 -0400
Subject: [PATCH 2/3] Use find_package to list all packages

---
 setup.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/setup.py b/setup.py
index 1dced98..d80e2cd 100644
--- a/setup.py
+++ b/setup.py
@@ -2,7 +2,7 @@
 import os
 import re
 
-from setuptools import setup
+from setuptools import setup, find_packages
 
 # Get the version from src/huggingmolecules/__init__.py
 # Adapted from https://stackoverflow.com/a/39671214
@@ -19,7 +19,7 @@
 setup(
     name='huggingmolecules',
     version=__version__,
-    packages=['huggingmolecules'],
+    packages=find_packages('src', include=['huggingmolecules*']),
     package_dir={'':'src'},
     install_requires=[
         'torch>=1.7.0',

From ebe0c9b7fe78b65136169f4dd123605d92d0a6aa Mon Sep 17 00:00:00 2001
From: In-Ho Yi <in-ho@anagenex.com>
Date: Tue, 27 Sep 2022 21:14:48 -0400
Subject: [PATCH 3/3] Add rdkit and setuptools as requirements

---
 setup.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index d80e2cd..df6b913 100644
--- a/setup.py
+++ b/setup.py
@@ -25,6 +25,8 @@
         'torch>=1.7.0',
         'scikit-learn>=0.23.2',
         'filelock>=3.0.12',
-        'gdown>=3.12.2'
+        'gdown>=3.12.2',
+        'rdkit',
+        'setuptools',
     ]
 )