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Move conda environment activation to own script
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-62
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2 files changed

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‎scripts/activateCondaEnvironment.sh‎

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#!/usr/bin/env bash
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# Activates the Conda (Python package manager) environment "codegraph" with all packages needed to execute the Jupyter Notebooks.
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# Note: This script uses the conda environment defined in CODEGRAPH_CONDA_ENVIRONMENT (defaults to "codegraph").
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# If the environment hadn't been created yet it will use "environment.yml"
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# in the same directory as the given jupyter notebook ipynb file
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# to create the environment.
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# Requires operatingSystemFunctions.sh
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# Fail on any error ("-e" = exit on first error, "-o pipefail" exist on errors within piped commands)
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set -eo pipefail
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## Get this "scripts" directory if not already set
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# Even if $BASH_SOURCE is made for Bourne-like shells it is also supported by others and therefore here the preferred solution.
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# CDPATH reduces the scope of the cd command to potentially prevent unintended directory changes.
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# This way non-standard tools like readlink aren't needed.
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SCRIPTS_DIR=${SCRIPTS_DIR:-$( CDPATH=. cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd -P )} # Repository directory containing the shell scripts
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echo "activateCondaEnvironment: SCRIPTS_DIR=$SCRIPTS_DIR"
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# Get the "jupyter" directory by taking the path of this script and going two directory up and then to "jupyter".
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JUPYTER_NOTEBOOK_DIRECTORY=${JUPYTER_NOTEBOOK_DIRECTORY:-"${SCRIPTS_DIR}/../jupyter"} # Repository directory containing the Jupyter Notebooks
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echo "activateCondaEnvironment: JUPYTER_NOTEBOOK_DIRECTORY=$JUPYTER_NOTEBOOK_DIRECTORY"
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# Define conda environment to use for code structure analysis. Default "codegraph"
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CODEGRAPH_CONDA_ENVIRONMENT=${CODEGRAPH_CONDA_ENVIRONMENT:-"codegraph"} # Name of the conda environment to use for code graph analysis
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echo "activateCondaEnvironment: CONDA_PREFIX=${CONDA_PREFIX}"
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echo "activateCondaEnvironment: Current conda environment=${CONDA_DEFAULT_ENV}"
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echo "activateCondaEnvironment: Target conda environment=${CODEGRAPH_CONDA_ENVIRONMENT}"
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if [ "${CONDA_DEFAULT_ENV}" = "${CODEGRAPH_CONDA_ENVIRONMENT}" ] ; then
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echo "activateCondaEnvironment: Skipping activation. Target conda environment ${CODEGRAPH_CONDA_ENVIRONMENT} is already activated."
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exit 0
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fi
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# Include operation system function to for example detect Windows.
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source "${SCRIPTS_DIR}/operatingSystemFunctions.sh"
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# Determine the path to "conda"
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if [ -n "${CONDA}" ]; then
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if isWindows; then
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pathToConda="${CONDA}\\Scripts\\" # the trailing backslash character is required
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else
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pathToConda="${CONDA}/bin/" # the trailing slash character is required
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fi
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else
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pathToConda=""
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fi
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echo "activateCondaEnvironment: pathToConda=${pathToConda}"
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scriptExtension=$(ifWindows ".bat" "")
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echo "activateCondaEnvironment: scriptExtension=${scriptExtension}"
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# Activate conda shell hook. Also resets CONDA_DEFAULT_ENV to base.
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# Thats why CONDA_DEFAULT_ENV (base) is never equal to CODEGRAPH_CONDA_ENVIRONMENT (codegraph).
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eval "$(${pathToConda}conda${scriptExtension} shell.bash hook)"
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echo "activateCondaEnvironment: Current conda environment after shell hook=${CONDA_DEFAULT_ENV}"
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# Create (if missing) and activate Conda environment for code structure graph analysis
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if { "${pathToConda}conda" env list | grep "$CODEGRAPH_CONDA_ENVIRONMENT "; } >/dev/null 2>&1; then
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echo "activateCondaEnvironment: Conda environment $CODEGRAPH_CONDA_ENVIRONMENT already created"
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else
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if [ ! -f "${JUPYTER_NOTEBOOK_DIRECTORY}/environment.yml" ] ; then
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echo "activateCondaEnvironment: Couldn't find environment file ${jupyter_notebook_file_path}/environment.yml."
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exit 2
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fi
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echo "activateCondaEnvironment: Creating Conda environment ${CODEGRAPH_CONDA_ENVIRONMENT}"
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"${pathToConda}conda" env create --file "${jupyter_notebook_file_path}/environment.yml" --name "${CODEGRAPH_CONDA_ENVIRONMENT}"
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fi
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echo "activateCondaEnvironment: Activating Conda environment ${CODEGRAPH_CONDA_ENVIRONMENT}"
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"${pathToConda}conda" activate ${CODEGRAPH_CONDA_ENVIRONMENT}
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if [ "${CONDA_DEFAULT_ENV}" != "${CODEGRAPH_CONDA_ENVIRONMENT}" ] ; then
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echo "activateCondaEnvironment: Retry activating Conda environment ${CODEGRAPH_CONDA_ENVIRONMENT} with plain 'conda' command"
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conda activate ${CODEGRAPH_CONDA_ENVIRONMENT}
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fi
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if [ "${CONDA_DEFAULT_ENV}" = "${CODEGRAPH_CONDA_ENVIRONMENT}" ] ; then
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echo "activateCondaEnvironment: Activated Conda environment: ${CONDA_DEFAULT_ENV}"
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else
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echo "activateCondaEnvironment: Error: Failed to activate Conda environment ${CODEGRAPH_CONDA_ENVIRONMENT}. ${CONDA_DEFAULT_ENV} still active."
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exit 1
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fi

‎scripts/executeJupyterNotebook.sh‎

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Original file line numberDiff line numberDiff line change
@@ -82,62 +82,8 @@ if [ ! -f "${jupyter_notebook_file_path}/.env" ] ; then
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echo "NEO4J_INITIAL_PASSWORD=${NEO4J_INITIAL_PASSWORD}" > "${jupyter_notebook_file_path}/.env"
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fi
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# Define conda environment to use for code structure analysis. Default "codegraph"
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CODEGRAPH_CONDA_ENVIRONMENT=${CODEGRAPH_CONDA_ENVIRONMENT:-"codegraph"} # Name of the conda environment to use for code graph analysis
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backupCondaEnvironment=$CONDA_DEFAULT_ENV
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echo "executeJupyterNotebook: CODEGRAPH_CONDA_ENVIRONMENT=${CODEGRAPH_CONDA_ENVIRONMENT}"
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echo "executeJupyterNotebook: CONDA_PREFIX=${CONDA_PREFIX}"
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echo "executeJupyterNotebook: Current conda environment=${CONDA_DEFAULT_ENV}"
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# Include operation system function to for example detect Windows.
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source "${SCRIPTS_DIR}/operatingSystemFunctions.sh"
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# Determine the path to "conda"
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if [ -n "${CONDA}" ]; then
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if isWindows; then
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pathToConda="${CONDA}\\Scripts\\" # the trailing backslash character is required
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else
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pathToConda="${CONDA}/bin/" # the trailing slash character is required
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fi
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else
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pathToConda=""
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fi
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echo "executeJupyterNotebook: pathToConda=${pathToConda}"
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scriptExtension=$(ifWindows ".bat" "")
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echo "executeJupyterNotebook: scriptExtension=${scriptExtension}"
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# Activate conda shell hook. Also resets CONDA_DEFAULT_ENV to base.
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# Thats why CONDA_DEFAULT_ENV (base) is never equal to CODEGRAPH_CONDA_ENVIRONMENT (codegraph).
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eval "$(${pathToConda}conda${scriptExtension} shell.bash hook)"
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echo "executeJupyterNotebook: Current conda environment after shell hook=${CONDA_DEFAULT_ENV}"
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# Create (if missing) and activate Conda environment for code structure graph analysis
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if { "${pathToConda}conda" env list | grep "$CODEGRAPH_CONDA_ENVIRONMENT "; } >/dev/null 2>&1; then
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echo "executeJupyterNotebook: Conda environment $CODEGRAPH_CONDA_ENVIRONMENT already created"
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else
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if [ ! -f "${jupyter_notebook_file_path}/environment.yml" ] ; then
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echo "executeJupyterNotebook: Couldn't find environment file ${jupyter_notebook_file_path}/environment.yml."
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exit 2
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fi
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echo "executeJupyterNotebook: Creating Conda environment ${CODEGRAPH_CONDA_ENVIRONMENT}"
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"${pathToConda}conda" env create --file "${jupyter_notebook_file_path}/environment.yml" --name "${CODEGRAPH_CONDA_ENVIRONMENT}"
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fi
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echo "executeJupyterNotebook: Activating Conda environment ${CODEGRAPH_CONDA_ENVIRONMENT}"
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if isWindows; then
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"${pathToConda}conda" activate ${CODEGRAPH_CONDA_ENVIRONMENT}
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else
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conda activate "${CODEGRAPH_CONDA_ENVIRONMENT}"
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fi
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if [ "${CONDA_DEFAULT_ENV}" = "${CODEGRAPH_CONDA_ENVIRONMENT}" ] ; then
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echo "executeJupyterNotebook: Activated Conda environment: ${CONDA_DEFAULT_ENV}"
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else
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echo "executeJupyterNotebook: Error: Failed to activate Conda environment ${CODEGRAPH_CONDA_ENVIRONMENT}. ${CONDA_DEFAULT_ENV} still active."
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exit 1
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fi
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# Create and activate (if necessary) Conda environment as defined in environment variable CODEGRAPH_CONDA_ENVIRONMENT (default "codegraph")
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source "${SCRIPTS_DIR}/activateCondaEnvironment.sh"
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# Execute the Jupyter Notebook and write it to the output file name
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jupyter nbconvert --to notebook \
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# Convert the Jupyter Notebook to PDF
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if [ -n "${ENABLE_JUPYTER_NOTEBOOK_PDF_GENERATION}" ]; then
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jupyter nbconvert --to webpdf --no-input --allow-chromium-download --disable-chromium-sandbox "$jupyter_notebook_output_file"
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fi
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# Restore Conda environment
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if [ ! "${backupCondaEnvironment}" = "${CODEGRAPH_CONDA_ENVIRONMENT}" ] ; then
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"${pathToConda}conda" activate "${backupCondaEnvironment}"
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echo "executeJupyterNotebook: Restored Conda Environment to ${backupCondaEnvironment}: ${CONDA_DEFAULT_ENV}"
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fi

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