Solved binary incompatibility issue of generated environment by conda installing h5py and numpy from conda-forge or default channels.

environment.yml

@@ -1,5 +1,5 @@
 name: pyenv5505
-prefix: ./envs/pyenv5505  # Custom output folder
+#prefix: ./envs/pyenv5505  # Custom output folder
 channels:
   - conda-forge
   - defaults
@@ -7,6 +7,7 @@ dependencies:
   - python=3.11
   - jupyter
   - numpy
+  - h5py
   - pandas
   - matplotlib
   - plotly=5.24
@@ -14,7 +15,7 @@ dependencies:
   - sphinx 
   - pip
   - pip:
-      - h5py==3.10
+#      - h5py==3.10
       - pybis==1.35
       - igor2
       - ipykernel

setup_env.sh

@@ -1,8 +1,7 @@
 #!/bin/bash
 
-# Define the name and location of the environment
+# Define the name of the environment
 ENV_NAME="pyenv5505"
-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
@@ -11,19 +10,38 @@ else
     CONDA_COMMAND="conda"
 fi
 
-# Create the conda environment with all dependencies
+# Create the conda environment with all dependencies, resolving from conda-forge and defaults
-$CONDA_COMMAND create -y -p "$ENV_PATH" python=3.11 \
+$CONDA_COMMAND create -y -n "$ENV_NAME" -c conda-forge -c defaults python=3.11 \
-    jupyter numpy pandas matplotlib plotly=5.24 scipy pip
+    jupyter numpy h5py pandas matplotlib plotly=5.24 scipy pip
+
+# Check if the environment was successfully created
+if [ $? -ne 0 ]; then
+    echo "Failed to create the environment '$ENV_NAME'. Please check the logs above for details."
+    exit 1
+fi
 
 # Activate the new environment
-source activate "$ENV_PATH" || conda activate "$ENV_PATH"
+if source activate "$ENV_NAME" 2>/dev/null || conda activate "$ENV_NAME" 2>/dev/null; then
+    echo "Environment '$ENV_NAME' activated successfully."
+else
+    echo "Failed to activate the environment '$ENV_NAME'. Please check your conda setup."
+    exit 1
+fi
 
-# Install pip packages in one go to avoid repeated initializations
+# Install additional pip packages only if the environment is activated
-pip install h5py==3.10 pybis==1.35 igor2 ipykernel sphinx
+echo "Installing additional pip packages..."
+pip install pybis==1.35 igor2 ipykernel sphinx
 
-# Export the environment to a YAML file
+# Check if pip installations were successful
-$CONDA_COMMAND env export --prefix "$ENV_PATH" > "$ENV_PATH/environment.yaml"
+if [ $? -ne 0 ]; then
+    echo "Failed to install pip packages. Please check the logs above for details."
+    exit 1
+fi
+
+# Optional: Export the environment to a YAML file (commented out)
+# $CONDA_COMMAND env export -n "$ENV_NAME" > "$ENV_NAME-environment.yaml"
 
 # Print success message
-echo "Environment '$ENV_NAME' created successfully at '$ENV_PATH'."
+echo "Environment '$ENV_NAME' created and configured successfully."
-echo "Environment configuration saved to '$ENV_PATH/environment.yaml'."
+# echo "Environment configuration saved to '$ENV_NAME-environment.yaml'."
+