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Fix bash script, previous version created an env with incopatible binaries.

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florez_j
2025-01-29 14:51:08 +01:00
parent 11d53e4bc4
commit d1514cf423
1 changed files with 32 additions and 13 deletions
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45
env_setup.sh
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@ -1,8 +1,7 @@
#!/bin/bash #!/bin/bash
# Define the name and location of the environment # Define the name of the environment
ENV_NAME="multiphase_chem_env" ENV_NAME="multiphase_chemistry_env"
ENV_PATH="./envs/$ENV_NAME" # Define a custom output folder
# Check if mamba is available and use it instead of conda for faster installation # Check if mamba is available and use it instead of conda for faster installation
if command -v mamba &> /dev/null; then if command -v mamba &> /dev/null; then
@ -11,19 +10,39 @@ else
CONDA_COMMAND="conda" CONDA_COMMAND="conda"
fi 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 # 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 dash dash-bootstrap-components echo "Installing additional pip packages..."
pip install pybis==1.35 igor2 ipykernel sphinx
pip install dash dash-bootstrap-components
# 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" > "$ENV_NAME-environment.yaml"
# Print success message # Print success message
echo "Environment '$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'."