Reinvent: Dockerfile fixes

packages/Chem/dockerfiles/reinvent/Dockerfile

@@ -25,7 +25,10 @@ WORKDIR /app
 RUN git clone https://github.com/MolecularAI/REINVENT4.git && \
     git clone https://github.com/MolecularAI/DockStream.git
 
-RUN find /app/REINVENT4 -type f -exec sed -i 's/model_dump()/model_config/g' {} +
+# Fix issues by modifying specific scripts in the REINVENT repository
+# Replace calls to `model_dump()` with `model_config` due to compatibility problems
+RUN find /app/REINVENT4/reinvent -type f \( -name "Reinvent.py" -o -name "run_staged_learning.py" \) \
+    -exec sed -i 's/model_dump()/model_config/g' {} +
 
 COPY . /app
 
@@ -35,6 +38,7 @@ RUN python3.10 -m venv /app/venv && \
     cd /app/REINVENT4 && \
     /app/venv/bin/pip install --no-deps .
 
+# Install Miniforge for macOS compatibility (handles macOS-specific Python environment issues)
 RUN if [ "$(uname -m)" = "aarch64" ]; then \
         curl -fsSL https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-aarch64.sh -o /tmp/miniforge.sh; \
     else \
@@ -51,7 +55,13 @@ RUN conda update -n base -c defaults conda -y
 
 WORKDIR /app/DockStream
 
-RUN sed -i 's/python = 3.7/python = 3.10/' environment.yml
+# Update DockStream environment file:
+# - Change Python version to 3.10
+# - Remove incompatible `pydantic` version and manually specify compatible version
+RUN sed -i 's/python = 3.7/python = 3.10/' environment.yml && \
+    sed -i '/pydantic/d' environment.yml && \
+    sed -i '/dependencies:/a \  - pip' environment.yml && \
+    sed -i '/- pip/a \  - pip:\n    - pydantic==1.10.19' environment.yml
 
 RUN conda env create -f environment.yml && \
     conda clean --all --yes

packages/Chem/dockerfiles/reinvent/reinvent.py

@@ -9,12 +9,11 @@
 
 app = Flask(__name__)
 
-# Configure logging
 logging.basicConfig(
     level=logging.DEBUG,
     format="%(asctime)s [%(levelname)s] %(message)s",
     handlers=[
-        logging.StreamHandler(sys.stdout)  # Output logs to stdout for Docker compatibility
+        logging.StreamHandler(sys.stdout)
     ]
 )
 
@@ -78,7 +77,7 @@ def run_reinvent():
         device = "cpu"
         """
 
-        prior_filename = "/Users/aleksashka/REINVENT4/priors/mol2mol_similarity.prior"
+        prior_filename = f"/{current_directory}/REINVENT4/priors/mol2mol_similarity.prior"
         parameters = f"""
         [parameters]
         prior_file = "{prior_filename}"
@@ -87,7 +86,7 @@ def run_reinvent():
         sample_strategy = "multinomial"
         smiles_file = "/{current_directory}/{smiles_filename}"
 
-        batch_size = 5
+        batch_size = 1
 
         use_checkpoint = false
         use_cuda = false
@@ -106,7 +105,7 @@ def run_reinvent():
         [[stage]]
         
         max_score = 1.0
-        max_steps = 25
+        max_steps = 1
         chkpt_file = 'stage1.chkpt'
         
         [stage.scoring]
@@ -117,9 +116,9 @@ def run_reinvent():
         [[stage.scoring.component.DockStream.endpoint]]
         name = "Docking with Dockstream"
         weight = 1
-        params.configuration_path = "/Users/aleksashka/Desktop/AutoDock_Vina_demo/kras_docking.json"
-        params.docker_script_path = "/Users/aleksashka/DockStream/docker.py"
-        params.docker_python_path =   "/opt/anaconda3/envs/DockStream/bin/python"
+        params.configuration_path = "/{current_directory}/kras_docking.json"
+        params.docker_script_path = "/{current_directory}/DockStream/docker.py"
+        params.docker_python_path =   "/opt/conda/envs/DockStream/bin/python"
         transform.type = "reverse_sigmoid"
         transform.high = 0
         transform.low = -10