From ecc60eed22afadfb36ccf457f23b735246ca48e5 Mon Sep 17 00:00:00 2001
From: Anton Morgunov <morgunov@mit.edu>
Date: Tue, 24 Oct 2023 11:11:22 -0400
Subject: [PATCH] GIT: update the package requirements

---
 .github/workflows/main.yml   | 12 ++++++------
 ChemSpaceAL/README.md        |  8 ++++++++
 ChemSpaceAL/requirements.txt | 11 +++++++++++
 setup.py                     | 27 ++++++++++++++++++---------
 4 files changed, 43 insertions(+), 15 deletions(-)
 create mode 100644 ChemSpaceAL/requirements.txt

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 31fa12d..88e67d5 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -13,11 +13,6 @@ jobs:
     - name: Checkout code
       uses: actions/checkout@v2
 
-    - name: Upload coverage reports to Codecov
-      uses: codecov/codecov-action@v3
-      env:
-        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
-
     - name: Set up Python
       uses: actions/setup-python@v2
       with:
@@ -34,5 +29,10 @@ jobs:
 
     - name: Run pytest
       run: |
-        pytest tests/
+        pytest --cov tests/
+
+    - name: Upload coverage reports to Codecov
+      uses: codecov/codecov-action@v3
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
diff --git a/ChemSpaceAL/README.md b/ChemSpaceAL/README.md
index 99a815b..124dae9 100644
--- a/ChemSpaceAL/README.md
+++ b/ChemSpaceAL/README.md
@@ -6,3 +6,11 @@
 - [ ] cite the DiffDock repo and cite it's license
 - [ ] get rid of the `try/except` loop in `scoring/score_protein_ligand_pose.py`
 - [ ] we need to possibly change AL construction procedure s.t. if `n_replicate` is False, more molecules are sampled from the training set until `training_size` is satisfied
+
+## Misc
+
+The requirements.txt is generated using
+
+```bash
+pipreqs ./ChemSpaceAL --ignore ./ChemSpaceAL/Docking.py --force
+```
diff --git a/ChemSpaceAL/requirements.txt b/ChemSpaceAL/requirements.txt
new file mode 100644
index 0000000..56ca45a
--- /dev/null
+++ b/ChemSpaceAL/requirements.txt
@@ -0,0 +1,11 @@
+numpy==1.24.3
+pandas==1.5.3
+plotly==5.16.1
+prolif==2.0.1
+PyYAML==6.0
+rdkit==2023.3.1
+scikit_learn==1.3.2
+Sophia==0.1.1
+torch
+tqdm==4.64.1
+wandb==0.15.4
diff --git a/setup.py b/setup.py
index b0d7148..269ec78 100644
--- a/setup.py
+++ b/setup.py
@@ -1,19 +1,22 @@
-from distutils.core import setup
+from setuptools import setup
 
+# Reading long description from README.md file
+with open("README.md", "r", encoding="utf-8") as fh:
+    long_description = fh.read()
+
+with open("ChemSpaceAL/requirements.txt") as f:
+    required = f.read().splitlines()
 
 setup(
     name="ChemSpaceAL",
     packages=["ChemSpaceAL"],
-    version="1.0.3",
+    version="1.0.0",
     description="ChemSpaceAL Python package: an efficient active learning methodology applied to protein-specific molecular generation",
-    install_requires=[
-        # "prolif==2.0.0.post1",
-        # "rdkit==2023.3.3",
-        # "wandb==0.15.10",
-    ],
+    long_description=long_description,
+    long_description_content_type="text/markdown",
     author="Gregory W. Kyro, Anton Morgunov & Rafael I. Brent",
     author_email="gregory.kyro@yale.edu",
-    url="https://github.com/gregory-kyro/ChemSpaceAL/tree/main",
+    url="https://github.com/batistagroup/ChemSpaceAL",
     download_url="https://github.com/gregory-kyro/ChemSpaceAL/archive/refs/tags/v1.0.3.tar.gz",
     keywords=[
         "active learning",
@@ -23,5 +26,11 @@
         "molecular generation",
         "drug discovery",
     ],
-    classifiers=[],
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "License :: OSI Approved :: MIT License",
+        "Operating System :: OS Independent",
+    ],
+    install_requires=required,
+    python_requires=">=3.10",
 )