Make conda_env_setup more verbose

Use verbose mode when sourcing conda_init and print other
messages. Use more robust method of finding repo directory.

src/conda/conda_env_setup.sh

@@ -7,10 +7,20 @@ set -Eeo pipefail
 # https://www.gnu.org/software/bash/manual/bashref.html#Pattern-Matching
 shopt -s extglob 
 
-# get directory this script is located in
-script_dir=$( cd "$(dirname "${BASH_SOURCE[0]}")" ; pwd -P )
+# paranoid code to get directory this script is located in, resolving any 
+# symlinks/aliases (https://stackoverflow.com/a/246128)
+_source="${BASH_SOURCE[0]}"
+while [ -h "$_source" ]; do # resolve $_source until the file is no longer a symlink
+    script_dir="$( cd -P "$( dirname "$_source" )" >/dev/null 2>&1 && pwd )"
+    _source="$( readlink "$_source" )"
+    # if $_source was a relative symlink, we need to resolve it relative to the 
+    # path where the symlink file was located
+    [[ $_source != /* ]] && _source="$script_dir/$_source" 
+done
+script_dir="$( cd -P "$( dirname "$_source" )" >/dev/null 2>&1 && pwd )"
+
 # relative paths resolved relative to repo directory, which is grandparent
-repo_dir=$( cd "${script_dir}/../.." ; pwd -P )
+repo_dir="$( cd -P "$script_dir" >/dev/null 2>&1 && cd ../../ && pwd )"
 
 pushd "$PWD" > /dev/null
 # parse aruments manually
@@ -27,7 +37,7 @@ while (( "$#" )); do
         -e|--env)
             # specify one env by name
             env_glob="env_${2}.yml" 
-            if [[ ! -f "${script_dir}/${env_glob}" ]]; then
+            if [ ! -f "${script_dir}/${env_glob}" ]; then
                 echo "ERROR: ${script_dir}/${env_glob} not found."
                 exit 1
             fi
@@ -46,7 +56,7 @@ while (( "$#" )); do
         -d|--env_dir)
             # specify install destination; resolve path first
             cd "$repo_dir"
-            if [[ ! -d "$2" ]]; then
+            if [ ! -d "$2" ]; then
                 echo "Creating directory $2"
                 mkdir -p "$2"
             fi
@@ -57,7 +67,7 @@ while (( "$#" )); do
         -c|--conda_root)
             # manually specify path to conda installation; resolve path first
             cd "$repo_dir"
-            if [[ ! -d "$2" ]]; then
+            if [ ! -d "$2" ]; then
                 echo "ERROR: can't find conda dir $2"
                 exit 1
             fi
@@ -76,53 +86,54 @@ done
 popd > /dev/null   # restore CWD
 
 # setup conda in non-interactive shell
-if [[ -z "$_MDTF_CONDA_ROOT" ]]; then
+if [ -z "$_MDTF_CONDA_ROOT" ]; then
     set -- # clear cmd line
-    source "${script_dir}/conda_init.sh"
+    . "${script_dir}/conda_init.sh" -v
 else
     # pass conda installation dir to setup script
-    source "${script_dir}/conda_init.sh" "$_MDTF_CONDA_ROOT"
+    . "${script_dir}/conda_init.sh" -v "$_MDTF_CONDA_ROOT"
 fi
-if [[ -z "$_CONDA_ENV_ROOT" ]]; then
+if [ -z "$_CONDA_ENV_ROOT" ]; then
     # not set, create conda env without --prefix
     echo "Installing envs into system Anaconda"
 else
     # set, create and change conda envs using --prefix
     echo "Installing envs into $_CONDA_ENV_ROOT"
-    echo "To use envs interactively, run conda config --append envs_dirs $_CONDA_ENV_ROOT"
+    echo "To use envs interactively, run \"conda config --append envs_dirs $_CONDA_ENV_ROOT\""
 fi
 
 # create all envs in a loop
 "$CONDA_EXE" clean -i
 for env_file in "${script_dir}/"${env_glob}; do
-    [[ -e "$env_file" ]] || continue # catch the case where nothing matches
+    [ -e "$env_file" ] || continue # catch the case where nothing matches
     # get env name from reading "name:" attribute of yaml file 
     env_name=$( sed -n "s/^[[:space:]]*name:[[:space:]]*\([[:alnum:]_\-]*\)[[:space:]]*/\1/p" "$env_file" )
-    if [[ -z "$_CONDA_ENV_ROOT" ]]; then
-        echo "Creating conda env ${env_name}"
+    if [ -z "$_CONDA_ENV_ROOT" ]; then
+        echo "Creating conda env ${env_name}..."
         "$CONDA_EXE" env create --force -q -f="$env_file"
     else
         conda_prefix="${_CONDA_ENV_ROOT}/${env_name}"
-        echo "Creating conda env ${env_name} in ${conda_prefix}"
+        echo "Creating conda env ${env_name} in ${conda_prefix}..."
         "$CONDA_EXE" env create --force -q -p="$conda_prefix" -f="$env_file"
     fi
+    echo "... conda env ${env_name} created."
 done
 "$CONDA_EXE" clean -ay
 
 # create script wrapper to activate base environment
 _CONDA_WRAPPER="${repo_dir}/mdtf"
-if [[ -f "$_CONDA_WRAPPER" ]]; then
+if [ -e "$_CONDA_WRAPPER" ]; then
     rm -f "$_CONDA_WRAPPER"
 fi
 echo '#!/usr/bin/env bash' > "$_CONDA_WRAPPER"
 echo "# This wrapper script is generated by conda_env_setup.sh." >> "$_CONDA_WRAPPER"
 echo "_mdtf_src=\"${repo_dir}/src\"" >> "$_CONDA_WRAPPER"
 echo "source \${_mdtf_src}/conda/conda_init.sh -q \"${_CONDA_ROOT}\"" >> "$_CONDA_WRAPPER"
-if [[ -z "$_CONDA_ENV_ROOT" ]]; then
+if [ -z "$_CONDA_ENV_ROOT" ]; then
     echo "conda activate _MDTF_base" >> "$_CONDA_WRAPPER"
 else
     echo "conda activate ${_CONDA_ENV_ROOT}/_MDTF_base" >> "$_CONDA_WRAPPER"
 fi
 echo "\${_mdtf_src}/mdtf.py \"\$@\"" >> "$_CONDA_WRAPPER"
 chmod +x "$_CONDA_WRAPPER"
-echo "Created wrapper script at env ${_CONDA_WRAPPER}"
+echo "Created MDTF wrapper script at ${_CONDA_WRAPPER}"