Added env file specification and bash script for env setup

environment.yml

-name: multiphase_chemistry_env
+name: PythonEnv5505v2
+prefix: ./envs/PythonEnv5505v2  # Custom output folder
 channels:
   - conda-forge
   - defaults
@@ -8,15 +9,11 @@ dependencies:
   - numpy
   - pandas
   - matplotlib
-  - plotly=5.18
-#  - openssl
+  - plotly=5.24
   - scipy
-# I installed openpyxl through anaconda manager from their default curated channels
-  - openpyxl=3.0.10
   - pip
   - pip:
-    - h5py==3.10
-    - pybis==1.35
-    - igor2
-    - ipykernel
-#    - openai
+      - h5py==3.10
+      - pybis==1.35
+      - igor2
+      - ipykernel

setup_env.sh

+#!/bin/bash
+
+# Define the name and location of the environment
+ENV_NAME="PythonEnv5505"
+ENV_PATH="./envs/$ENV_NAME"  # Define a custom output folder
+
+# Check if mamba is available and use it instead of conda for faster installation
+if command -v mamba &> /dev/null; then
+    CONDA_COMMAND="mamba"
+else
+    CONDA_COMMAND="conda"
+fi
+
+# Create the conda environment with all dependencies
+$CONDA_COMMAND create -y -p "$ENV_PATH" python=3.11 \
+    jupyter numpy pandas matplotlib plotly=5.24 scipy pip
+
+# Activate the new environment
+source activate "$ENV_PATH" || conda activate "$ENV_PATH"
+
+# Install pip packages in one go to avoid repeated initializations
+pip install h5py==3.10 pybis==1.35 igor2 ipykernel
+
+# Export the environment to a YAML file
+$CONDA_COMMAND env export --prefix "$ENV_PATH" > "$ENV_PATH/environment.yaml"
+
+# Print success message
+echo "Environment '$ENV_NAME' created successfully at '$ENV_PATH'."
+echo "Environment configuration saved to '$ENV_PATH/environment.yaml'."