fix: open babel installation issues

Dockerfile

@@ -18,7 +18,7 @@ RUN mv surge /usr/bin
 
 RUN conda install -c conda-forge python=${PYTHON_VERSION} sqlite --force-reinstall
 #RUN conda install -c conda-forge rdkit==RDKIT_VERSION
-RUN conda install -c conda-forge openbabel>=OPENBABEL_VERSION
+#RUN conda install -c conda-forge openbabel
 
 RUN python3 -m pip install -U pip
 
@@ -32,7 +32,7 @@ RUN pip3 install --upgrade setuptools pip
 RUN pip3 install --no-cache-dir -r /code/requirements.txt
 RUN python3 -m pip uninstall -y imantics
 RUN pip3 install imantics==0.1.12
-RUN pip3 install rdkit
+RUN pip3 install rdkit openbabel-wheel
 RUN pip3 install --no-deps decimer-segmentation==1.1.3
 RUN pip3 install --no-deps decimer==2.3.0
 RUN pip3 install --no-deps STOUT-pypi==2.0.5

Dockerfile.lite

@@ -2,7 +2,6 @@ FROM continuumio/miniconda3:24.1.2-0 AS cheminf-python-ms
 
 ENV PYTHON_VERSION=3.11
 ENV RDKIT_VERSION=2023.09.4
-ENV OPENBABEL_VERSION=v3.1.1
 ENV INCLUDE_OCSR=false
 # Install runtime dependencies
 RUN apt-get update && \
@@ -17,22 +16,19 @@ RUN chmod +x surge
 RUN mv surge /usr/bin
 
 RUN conda install -c conda-forge python=${PYTHON_VERSION} sqlite --force-reinstall
-#RUN conda install -c conda-forge rdkit==RDKIT_VERSION
-RUN conda install -c conda-forge openbabel>=OPENBABEL_VERSION
-
 RUN python3 -m pip install -U pip
 
 ENV JAVA_HOME /usr/lib/jvm/java-11-openjdk-amd64/
 RUN export JAVA_HOME
 
 WORKDIR /code
-COPY ./requirements.txt /code/requirements.txt
+COPY ./requirements_lite.txt /code/requirements_lite.txt
 
 RUN pip3 install --upgrade setuptools pip
 RUN pip3 install --no-cache-dir -r /code/requirements_lite.txt
 RUN python3 -m pip uninstall -y imantics
 RUN pip3 install imantics==0.1.12
-RUN pip3 install rdkit
+RUN pip3 install rdkit openbabel-wheel
 RUN pip3 install --no-deps STOUT-pypi==2.0.5
 RUN python3 -m pip install uvicorn[standard]