new custom install

custom_install.sh

@@ -1,15 +1,17 @@
 #!/bin/bash
-#Script executes these commands with safeguards in place:
-# - Clones the main repository.
-# - Installs the main repository package.
-# - Updates the `cdiff_fbi` submodule to the latest tag.
+#Script executes these commands with some safeguards in place in case it fails:
+# git clone https://github.com/ssi-dk/serum_readfilter
+# cd serum_readfilter
+# pip install .
+
+#ENV_NAME=$1
 
 GIT_REPO=https://github.com/ssi-dk/serum_readfilter
 REPO_FOLDER=serum_readfilter
 SUBMODULE_PATH="bifrost_sp_cdiff/cdiff_fbi"  # Path to the submodule
 
 SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
-cd $SCRIPT_DIR || exit 1  # Avoid small edge case where bashrc sourcing changes your directory
+cd $SCRIPT_DIR # avoiding small edge case where bashrc sourcing changes your directory
 
 function exit_function() {
   echo "To rerun use the command:"
@@ -28,28 +30,41 @@ source $CONDA_BASE/etc/profile.d/conda.sh
 #   conda activate $ENV_NAME
 # fi
 
-# Check for git availability
-if ! command -v git &>/dev/null; then
-  echo "git is not installed."
-  echo "You can try installing git and rerunning the script."
-  exit_function
-fi
-
-# Clone the main repository if it does not exist
-if test -d "$SCRIPT_DIR/$REPO_FOLDER"; then
-  echo "$SCRIPT_DIR/$REPO_FOLDER already exists. If you want to overwrite, please remove the old repository folder:"
+if test -d "$SCRIPT_DIR/$REPO_FOLDER"
+then
+  echo "$SCRIPT_DIR/$REPO_FOLDER already exists, if you want to overwrite, please remove the old repository folder"
+  echo "You can use:"
   echo "rm -rf $SCRIPT_DIR/$REPO_FOLDER"
   exit_function
 else
-  echo "################# Cloning repository from $GIT_REPO"
-  if ! git clone $GIT_REPO; then
-    echo >&2 "git clone command failed."
+  git --version
+  GIT_IS_AVAILABLE=$?
+  if [ $GIT_IS_AVAILABLE -eq 0 ]
+  then
+    echo "#################Cloning repository from $GIT_REPO"
+    if ! git clone $GIT_REPO
+    then
+      echo >&2 "git clone command failed"
+      exit_function
+    else
+      cd $REPO_FOLDER
+      echo "#################Installing package using pip"
+      if ! pip install .
+      then
+        echo >&2 "pip install command failed"
+        exit_function
+      else
+        echo "Package successfully installed"
+      fi
+    fi
+  else
+    echo "git is not installed"
+    echo "You can try installing git and rerunning the script"
     exit_function
   fi
 fi
 
-# Navigate into the main repository
-cd $REPO_FOLDER || { echo "Failed to enter repository directory"; exit_function; }
+cd $SCRIPT_DIR
 
 # Initialize and update submodules
 echo "################# Initializing and updating submodules..."
@@ -58,13 +73,8 @@ if ! git submodule update --init --recursive; then
   exit_function
 fi
 
-# Navigate to the submodule directory
-if ! test -d "$SUBMODULE_PATH"; then
-  echo "Submodule path $SUBMODULE_PATH does not exist. Exiting."
-  exit_function
-fi
+cd $SUBMODULE_PATH || { echo "Failed to enter submodule cdiff_fbi repository directory"; exit_function; }
 
-cd $SUBMODULE_PATH || { echo "Failed to enter submodule directory $SUBMODULE_PATH"; exit_function; }
 
 # Fetch the latest tags
 echo "################# Fetching the latest tags for the submodule..."
@@ -111,16 +121,16 @@ if ! git checkout "$LATEST_TAG_COMMIT"; then
   exit_function
 fi
 
-# Navigate back to the main repository directory
-cd "$SCRIPT_DIR/$REPO_FOLDER" || exit_function
+# Determine the latest tag
+#LATEST_TAG=$(git rev-parse HEAD)
+#echo "TAG $LATEST_TAG"
 
-# Install the main package using pip
-echo "################# Installing package using pip..."
-if ! pip install .; then
-  echo >&2 "pip install command failed."
-  exit_function
-else
-  echo "Package successfully installed."
-fi
+# Identify the latest tag
+#LATEST_TAG_COMMIT=$(git for-each-ref --sort=-creatordate refs/tags | head -1 | cut -f1 -d ' ')
+#LATEST_TAG=$(git for-each-ref --sort=-creatordate refs/tags | head -1 | cut -f3 -d '/')
+
+#echo "TEST2 $LATEST_TAG: $LATEST_COMMIT"
+
+cd $SCRIPT_DIR
 
-echo "################# Installation complete."
+echo "Installation complete"