update dockerfile with submodule

.github/workflows/ci.yaml

@@ -18,7 +18,8 @@ jobs:
         uses: actions/checkout@v4
         with:
           submodules: recursive
-          #token: ${{ secrets.GHCR_TOKEN }}
+          token: ${{ secrets.GHCR_TOKEN }}
+          fetch-depth: 1
       # See https://github.com/marketplace/actions/setup-micromamba
       - name: Install conda env
         uses: mamba-org/[email protected]

Dockerfile

@@ -12,15 +12,11 @@ USER root
 WORKDIR /lidro
 
 
-# Create directories
-RUN mkdir tmp data
+# # Create directories
+RUN mkdir tmp 
 
 COPY . .
 
-# Sync and update submodules (ensure they are configured in the repository)
-RUN git submodule sync && \
-    git submodule update --init --recursive
-
 RUN chown $MAMBA_USER:$MAMBA_USER environment.yml
 RUN micromamba install -y -n base -f environment.yml && \
     micromamba clean --all --yes
@@ -43,6 +39,12 @@ ENV ENV=base
 ARG MAMBA_DOCKERFILE_ACTIVATE=1
 
 
+# Sync and update submodules (ensure they are configured in the repository)
+RUN git submodule sync && \
+    git submodule update --init --recursive
+
+RUN mkdir tmp
+