Merge pull request #171 from nmfs-opensci/eeholmes-patch-2

Update Dockerfile

Dockerfile

@@ -105,17 +105,17 @@ RUN mkdir -p /pyrocket_scripts && \
 RUN usermod -a -G staff "${NB_USER}"
 
 # Install R, RStudio via Rocker scripts
-ENV R_DOCKERFILE="verse_${R_VERSION}"
-RUN PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin && \
-  chmod +x ${REPO_DIR}/rocker.sh && \
-  ${REPO_DIR}/rocker.sh
+# ENV R_DOCKERFILE="verse_${R_VERSION}"
+# RUN PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin && \
+#  chmod +x ${REPO_DIR}/rocker.sh && \
+#  ${REPO_DIR}/rocker.sh
 
 # Install extra conda packages
 RUN /pyrocket_scripts/install-conda-packages.sh ${REPO_DIR}/environment.yml
 
 # Install extra apt packages
 # Install linux packages after R installation since the R install scripts get rid of packages
-RUN /pyrocket_scripts/install-apt-packages.sh ${REPO_DIR}/apt.txt
+# RUN /pyrocket_scripts/install-apt-packages.sh ${REPO_DIR}/apt.txt
 
 # Re-enable man pages disabled in Ubuntu 18 minimal image
 # https://wiki.ubuntu.com/Minimal

scripts/install-conda-packages.sh

@@ -40,7 +40,7 @@ if ! ${CONDA_DIR}/condabin/conda env list | grep -q "^${CONDA_ENV} "; then
         INSTALLATION_HAPPENED=true
     elif grep -q "name:" "$ENV_FILE"; then
         echo "  Detected environment.yml file."
-        ${CONDA_DIR}/condabin/mamba env create -f "$ENV_FILE"
+        ${CONDA_DIR}/condabin/mamba env create --name ${CONDA_ENV} -f "$ENV_FILE"
         INSTALLATION_HAPPENED=true
     else
         echo "Error: Unrecognized file format in '${ENV_FILE}'."
@@ -61,7 +61,7 @@ else
         ${CONDA_DIR}/condabin/mamba env update --name ${CONDA_ENV} -f "$ENV_FILE"
         INSTALLATION_HAPPENED=true
     else
-        echo "Error: Unrecognized file format in '${ENV_FILE}'."
+        echo "  Error: Unrecognized file format in '${ENV_FILE}'."
         echo "  - For an environment.yml file, ensure it includes a 'name:' entry. Any name is acceptable."
         echo "  - For a conda-lock.yml file, ensure it includes a 'lock_set:' entry."
         exit 1
@@ -70,6 +70,7 @@ fi
 
 # Run cleanup if installation occurred
 if [ "$INSTALLATION_HAPPENED" = true ]; then
+    echo "Installation clean-up."
     ${CONDA_DIR}/condabin/mamba clean -yaf
     find ${CONDA_DIR} -follow -type f -name '*.a' -delete
     find ${CONDA_DIR} -follow -type f -name '*.js.map' -delete