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Install: Add *nix shell scripts to install conda and mhkit-python
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‎mhkit/package/shell_script_templates/_header.sh.j2‎

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#!/bin/bash
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# MHKiT-MATLAB {{ script_title }}
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# Generated from template - DO NOT EDIT DIRECTLY
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# Report issues: {{ support.github_issues }}
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set -e # Exit on any error
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# Script configuration
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CONDA_ENV_NAME="{{ conda.environment_name }}"
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PYTHON_VERSION="{{ python.install_version }}"
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MHKIT_VERSION="{{ mhkit_python.version }}"
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GITHUB_ISSUES="{{ support.github_issues }}"
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# Logging functions
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log_info() {
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echo "[INFO] $1"
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}
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log_success() {
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echo "[SUCCESS] $1"
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}
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log_warning() {
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echo "[WARNING] $1"
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}
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log_error() {
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echo "[ERROR] $1"
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echo "[ERROR] Please report this issue: $GITHUB_ISSUES"
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}
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# Function to expand path with environment variables and ~
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expand_path() {
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local path="$1"
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# Expand ~ to $HOME
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path="${path/#\~/$HOME}"
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# Expand environment variables
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path=$(eval echo "$path")
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echo "$path"
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}
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# Function to test if a conda installation works
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test_conda_installation() {
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local conda_path="$1"
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log_info "Testing conda at: $conda_path"
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# Test if the conda executable exists and is executable
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if [[ -x "$conda_path" ]]; then
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# Test if conda info works (this is the most reliable test)
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if "$conda_path" info >/dev/null 2>&1; then
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local conda_version=$("$conda_path" --version 2>/dev/null || echo "unknown")
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local conda_location=$("$conda_path" info --base 2>/dev/null || echo "unknown")
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log_success "Working conda found!"
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log_info " Version: $conda_version"
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log_info " Location: $conda_location"
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return 0
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else
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log_warning "Conda executable found but 'conda info' failed"
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return 1
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fi
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else
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return 1
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fi
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}
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# OS Detection
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OS_TYPE=$(uname)
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ARCH_TYPE=$(uname -m)

‎mhkit/package/shell_script_templates/step1_detect_conda.sh.j2‎

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{% set script_title = "Step 1: Conda Detection" %}
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{% include "_header.sh.j2" %}
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# Function to check if conda is available
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detect_conda() {
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log_info "Starting comprehensive conda detection..."
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# Step 1: Check if conda is already in PATH and working
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if command -v conda >/dev/null 2>&1; then
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log_info "Found conda in PATH"
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if test_conda_installation "$(command -v conda)"; then
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echo "CONDA_DETECTED=true"
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echo "CONDA_PATH=$(command -v conda)"
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return 0
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else
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log_warning "Conda in PATH is not working properly"
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fi
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fi
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# Step 2: Check environment variables
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{% for env_var in conda.detection.environment_variables %}
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if [[ -n "${{ '${' }}{{ env_var }}:-}" ]]; then
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log_info "Checking environment variable {{ env_var }}: ${{ '${' }}{{ env_var }}}"
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local conda_from_env=""
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if [[ "{{ env_var }}" == "CONDA_EXE" ]]; then
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conda_from_env="${{ '${' }}{{ env_var }}}"
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elif [[ "{{ env_var }}" == "CONDA_PREFIX" ]]; then
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conda_from_env="${{ '${' }}{{ env_var }}}/bin/conda"
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fi
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if [[ -n "$conda_from_env" ]]; then
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conda_from_env=$(expand_path "$conda_from_env")
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if test_conda_installation "$conda_from_env"; then
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echo "CONDA_DETECTED=true"
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echo "CONDA_PATH=$conda_from_env"
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return 0
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fi
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fi
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fi
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{% endfor %}
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# Step 3: Check all common installation paths systematically
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log_info "Checking common conda installation paths..."
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local paths_to_check=(
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{% for path in conda.detection.common_paths.unix %}
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"{{ path }}"
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{% endfor %}
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)
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for path in "${paths_to_check[@]}"; do
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local expanded_path=$(expand_path "$path")
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if test_conda_installation "$expanded_path"; then
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echo "CONDA_DETECTED=true"
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echo "CONDA_PATH=$expanded_path"
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return 0
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fi
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done
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log_info "No working conda installation found"
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echo "CONDA_DETECTED=false"
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return 1
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}
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main() {
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log_info "Step 1: Detecting conda installation..."
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detect_conda
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}
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main "$@"

‎mhkit/package/shell_script_templates/step2_install_conda.sh.j2‎

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{% set script_title = "Step 2: Install Miniconda" %}
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{% include "_header.sh.j2" %}
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# Function to install miniconda
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install_conda() {
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log_info "Installing miniconda..."
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if [[ "$OS_TYPE" == "Darwin" ]]; then
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if [[ "$ARCH_TYPE" == "arm64" ]]; then
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MINICONDA_URL="{{ conda.miniconda_urls.mac_arm }}"
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else
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MINICONDA_URL="{{ conda.miniconda_urls.mac_intel }}"
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fi
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elif [[ "$OS_TYPE" == "Linux" ]]; then
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MINICONDA_URL="{{ conda.miniconda_urls.linux }}"
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else
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log_error "Unsupported operating system: $OS_TYPE"
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exit 1
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fi
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# Create miniconda directory
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mkdir -p ~/miniconda3
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# Download miniconda installer
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log_info "Downloading miniconda installer..."
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if command -v curl >/dev/null 2>&1; then
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curl -L "$MINICONDA_URL" -o ~/miniconda3/miniconda.sh
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elif command -v wget >/dev/null 2>&1; then
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wget "$MINICONDA_URL" -O ~/miniconda3/miniconda.sh
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else
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log_error "Neither curl nor wget found. Please install one of them first."
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exit 1
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fi
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# Install miniconda
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log_info "Installing miniconda to ~/miniconda3..."
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bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3
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# Remove installer
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rm ~/miniconda3/miniconda.sh
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# Initialize conda for future shells
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~/miniconda3/bin/conda init bash >/dev/null 2>&1 || true
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log_success "Miniconda installed successfully"
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# Output conda path for next steps
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echo "CONDA_PATH=$HOME/miniconda3/bin/conda"
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}
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main() {
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log_info "Step 2: Installing miniconda..."
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install_conda
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}
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main "$@"

‎mhkit/package/shell_script_templates/step3_create_env.sh.j2‎

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{% set script_title = "Step 3: Create Conda Environment" %}
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{% include "_header.sh.j2" %}
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# Function to check if conda environment exists
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check_conda_env() {
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local conda_path="$1"
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if "$conda_path" env list | grep -q "^$CONDA_ENV_NAME "; then
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log_success "Found existing conda environment: $CONDA_ENV_NAME"
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echo "ENV_EXISTS=true"
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return 0
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else
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log_info "Conda environment '$CONDA_ENV_NAME' not found, will create it"
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echo "ENV_EXISTS=false"
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return 1
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fi
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}
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# Function to create conda environment
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create_conda_env() {
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local conda_path="$1"
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log_info "Creating conda environment '$CONDA_ENV_NAME' with Python $PYTHON_VERSION..."
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# Accept conda Terms of Service to avoid interactive prompts
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log_info "Accepting conda Terms of Service..."
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"$conda_path" config --set solver libmamba 2>/dev/null || true
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# Try to accept TOS (may fail on older conda versions, that's OK)
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"$conda_path" tos accept --override-channels --channel https://repo.anaconda.com/pkgs/main 2>/dev/null || true
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"$conda_path" tos accept --override-channels --channel https://repo.anaconda.com/pkgs/r 2>/dev/null || true
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# Create environment using conda-forge to minimize TOS issues
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"$conda_path" create -n "$CONDA_ENV_NAME" python="$PYTHON_VERSION" -c conda-forge -y
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if [ $? -eq 0 ]; then
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log_success "Conda environment created successfully"
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echo "ENV_CREATED=true"
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else
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log_error "Failed to create conda environment"
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echo "ENV_CREATED=false"
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exit 1
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fi
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}
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# Function to verify Python version in environment
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verify_python_version() {
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local conda_path="$1"
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log_info "Verifying Python version in environment..."
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local py_version=$("$conda_path" run -n "$CONDA_ENV_NAME" python --version 2>&1 | cut -d' ' -f2)
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local major_minor=$(echo "$py_version" | cut -d'.' -f1,2)
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local expected_major_minor=$(echo "$PYTHON_VERSION" | cut -d'.' -f1,2)
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if [[ "$major_minor" == "$expected_major_minor" ]]; then
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log_success "Python version verified: $py_version"
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echo "PYTHON_VERSION_OK=true"
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return 0
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else
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log_warning "Python version mismatch. Expected: $PYTHON_VERSION, Got: $py_version"
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log_info "Environment will need to be recreated..."
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echo "PYTHON_VERSION_OK=false"
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return 1
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fi
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}
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main() {
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local conda_path="$1"
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if [[ -z "$conda_path" ]]; then
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log_error "No conda path provided. Usage: $0 <conda_path>"
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exit 1
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fi
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log_info "Step 3: Managing conda environment..."
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log_info "Using conda at: $conda_path"
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# Add conda to PATH for this session
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local conda_dir=$(dirname "$conda_path")
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export PATH="$conda_dir:$PATH"
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if ! check_conda_env "$conda_path"; then
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create_conda_env "$conda_path"
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fi
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if ! verify_python_version "$conda_path"; then
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log_info "Recreating environment with correct Python version..."
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"$conda_path" remove -n "$CONDA_ENV_NAME" --all -y >/dev/null 2>&1 || true
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create_conda_env "$conda_path"
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verify_python_version "$conda_path"
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fi
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}
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main "$@"

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