From 4b20ebe8eeb53b420efdc0b62c404a66b0b93d32 Mon Sep 17 00:00:00 2001
From: Calvin Pieters <calvinpieters@gmail.com>
Date: Tue, 14 Nov 2023 08:27:43 +0000
Subject: [PATCH 1/2] Changed install_sella.sh

Updated the bash script
---
 devtools/install_sella.sh | 26 ++++++++++++++++++--------
 1 file changed, 18 insertions(+), 8 deletions(-)

diff --git a/devtools/install_sella.sh b/devtools/install_sella.sh
index bc5356283f..94f39768c1 100644
--- a/devtools/install_sella.sh
+++ b/devtools/install_sella.sh
@@ -17,24 +17,34 @@ else
     exit 1
 fi
 
-# Set up Conda/Micromamba environment
-if [ "$COMMAND_PKG" == "micromamba" ]; then
+if [ "$COMMAND_PKG" = "micromamba" ]; then
     eval "$(micromamba shell hook --shell=bash)"
     micromamba activate base
     BASE=$MAMBA_ROOT_PREFIX
-    # shellcheck source=/dev/null
-    source "$BASE/etc/profile.d/micromamba.sh"
+    # Verify if the micromamba profile script exists
+    if [ -f "$BASE/etc/profile.d/micromamba.sh" ]; then
+        . "$BASE/etc/profile.d/micromamba.sh"
+    else
+        echo "File not found: $BASE/etc/profile.d/micromamba.sh"
+        exit 1
+    fi
 else
     BASE=$(conda info --base)
-    # shellcheck source=/dev/null
-    source "$BASE/etc/profile.d/conda.sh"
+    echo "Conda base directory: $BASE"
+    # Verify if the conda profile script exists
+    if [ -f "$BASE/etc/profile.d/conda.sh" ]; then
+        . "$BASE/etc/profile.d/conda.sh"
+    else
+        echo "File not found: $BASE/etc/profile.d/conda.sh"
+        exit 1
+    fi
 fi
 
 # clone the repo in the parent directory
 echo "Creating the Sella environment..."
 $COMMAND_PKG env create -f devtools/sella_environment.yml
 # Activate the environment
-if [ "$COMMAND_PKG" == "micromamba" ]; then
+if [ "$COMMAND_PKG" = "micromamba" ]; then
     micromamba activate sella_env
 else
     conda activate sella_env
@@ -53,5 +63,5 @@ echo 'export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:'"$BASE"'/envs/sella_env/lib' >>
 echo 'export LD_LIBRARY_PATH=${OLD_LD_LIBRARY_PATH}' >> $BASE/envs/sella_env/etc/conda/deactivate.d/env_vars.sh
 echo 'unset OLD_LD_LIBRARY_PATH' >> $BASE/envs/sella_env/etc/conda/deactivate.d/env_vars.sh
 
-source ~/.bashrc
+. ~/.bashrc
 echo "Done installing Sella."

From d9c2e659441787dc836dae5ddf4db8cbc7e7d9b6 Mon Sep 17 00:00:00 2001
From: Calvin Pieters <calvinpieters@gmail.com>
Date: Tue, 14 Nov 2023 08:28:24 +0000
Subject: [PATCH 2/2] Updated sella env

Added python version - now 3.8 minimum
added typing extensions as a packaged
---
 devtools/sella_environment.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/devtools/sella_environment.yml b/devtools/sella_environment.yml
index 720b7310ba..8c84f67fb7 100644
--- a/devtools/sella_environment.yml
+++ b/devtools/sella_environment.yml
@@ -2,11 +2,11 @@ name: sella_env
 channels:
   - conda-forge
 dependencies:
-  - python=3.7
+  - python>=3.8
   - xtb-python
   - pyyaml
   - pandas
   - ncurses
   - pip:
-    - sella==2.2.1
-  
\ No newline at end of file
+    - sella
+    - typing-extensions