Update Dockerfile

Dockerfile

@@ -100,8 +100,19 @@ RUN wget -q https://github.com/conda-forge/miniforge/releases/latest/download/Mi
  && bash /tmp/m.sh -b -p /opt/conda \
  && rm /tmp/m.sh \
  && /opt/conda/bin/conda clean -afy
-ENV PATH=/opt/conda/bin:$PATH
-# Create env and try pip wheels; if that fails, fall back to conda-forge.
+
+# After installing Miniforge, add proper conda initialization
+RUN /opt/conda/bin/conda init bash && \
+    echo "conda activate base" >> ~/.bashrc
+
+# Set more comprehensive conda environment variables
+ENV CONDA_DEFAULT_ENV=LinkOrgs_env \
+    CONDA_PREFIX=/opt/conda/envs/LinkOrgs_env \
+    CONDA_PYTHON_EXE=/opt/conda/bin/python \
+    CONDA_EXE=/opt/conda/bin/conda \
+    PATH=/opt/conda/envs/LinkOrgs_env/bin:/opt/conda/bin:$PATH
+
+# After creating the environment, ensure it's properly registered
 RUN mamba create -y -n LinkOrgs_env python=3.11 pip && \
     /opt/conda/envs/LinkOrgs_env/bin/pip install --only-binary=:all: \
         tensorflow==2.15 \
@@ -117,8 +128,13 @@ RUN mamba create -y -n LinkOrgs_env python=3.11 pip && \
             tensorflow=2.15 numpy=1.26.4 tensorflow-probability=0.23 \
             jax=0.4.26 jaxlib=0.4.26 optax=0.2.2 equinox=0.11.4 && \
         /opt/conda/envs/LinkOrgs_env/bin/pip install jmp==0.0.4 && \
-        /opt/conda/bin/conda clean -afy)
-ENV RETICULATE_PYTHON=/opt/conda/envs/LinkOrgs_env/bin/python
+        /opt/conda/bin/conda clean -afy) && \
+    # Important: Create a conda env config file for reticulate
+    echo "/opt/conda/envs/LinkOrgs_env/bin/python" > /opt/conda/envs/LinkOrgs_env/.conda_prefix
+
+# Keep RETICULATE_PYTHON but also add RETICULATE_CONDA
+ENV RETICULATE_PYTHON=/opt/conda/envs/LinkOrgs_env/bin/python \
+    RETICULATE_CONDA=/opt/conda/bin/conda
 
 # ------------------------------------------------------------------------------
 # App code