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jungarettijoshspicer
jungaretti
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joshspicer
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Fix installation of common Python packages (#1424)
* Fix package installation * Update comment * Move python to front of PATH * Add PYTHON parameter * Move ML packages to new script * Remove invalid docs * Check for PYTHON * Install packages from argument * Resolve comments * Add tests for new packages * Copy JupyterLab script * Use generic package install script * Add new script to README * Add missing $ * Try to fix smoke test * Revert changes to jupyterlab-debian.sh * Fix directory of Python * Remove busted sudos * Update test.sh Co-authored-by: Josh Spicer <[email protected]>
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‎containers/codespaces-linux/.devcontainer/base.Dockerfile‎

Lines changed: 15 additions & 4 deletions
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@@ -34,7 +34,7 @@ ENV SHELL=/bin/bash \
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JUPYTERLAB_PATH="${HOMEDIR}/.local/bin" \
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DOCKER_BUILDKIT=1
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ENV PATH="${NVM_DIR}/current/bin:${NPM_GLOBAL}/bin:${ORIGINAL_PATH}:${DOTNET_ROOT}:${DOTNET_ROOT}/tools:${SDKMAN_DIR}/bin:${SDKMAN_DIR}/candidates/gradle/current/bin:${SDKMAN_DIR}/candidates/java/current/bin:/opt/maven/lts:${GOROOT}/bin:${GOPATH}/bin:${PIPX_BIN_DIR}:/opt/conda/condabin:${JAVA_ROOT}/current/bin:${NODE_ROOT}/current/bin:${PHP_ROOT}/current/bin:${PYTHON_ROOT}/current/bin:${RUBY_ROOT}/current/bin:${MAVEN_ROOT}/current/bin:${HUGO_ROOT}/current/bin:${JUPYTERLAB_PATH}:${ORYX_PATHS}"
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ENV PATH="${NVM_DIR}/current/bin:${NPM_GLOBAL}/bin:${PYTHON_ROOT}/current/bin:${ORIGINAL_PATH}:${DOTNET_ROOT}:${DOTNET_ROOT}/tools:${SDKMAN_DIR}/bin:${SDKMAN_DIR}/candidates/gradle/current/bin:${SDKMAN_DIR}/candidates/java/current/bin:/opt/maven/lts:${GOROOT}/bin:${GOPATH}/bin:${PIPX_BIN_DIR}:/opt/conda/condabin:${JAVA_ROOT}/current/bin:${NODE_ROOT}/current/bin:${PHP_ROOT}/current/bin:${RUBY_ROOT}/current/bin:${MAVEN_ROOT}/current/bin:${HUGO_ROOT}/current/bin:${JUPYTERLAB_PATH}:${ORYX_PATHS}"
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# Install needed utilities and setup non-root user. Use a separate RUN statement to add your own dependencies.
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COPY library-scripts/* setup-user.sh first-run-notice.txt /tmp/scripts/
@@ -68,10 +68,21 @@ RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
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&& mkdir -p /usr/local/etc/vscode-dev-containers/ \
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&& mv -f /tmp/scripts/first-run-notice.txt /usr/local/etc/vscode-dev-containers/
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# Install Python, PHP, Ruby utilities, and JupyterLab
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# Install Python, JupyterLab, common machine learning packages, and Ruby utilities
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RUN bash /tmp/scripts/python-debian.sh "none" "/opt/python/latest" "${PIPX_HOME}" "${USERNAME}" "true" \
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&& bash /tmp/scripts/jupyterlab-debian.sh \
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&& pip install --user numpy pandas scipy matplotlib seaborn scikit-learn tensorflow keras torch requests \
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# Install JupyterLab and common machine learning packages
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&& PYTHON_BINARY="${PYTHON_ROOT}/current/bin/python" \
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&& bash /tmp/scripts/python-package-debian.sh "jupyterlab" "latest" $PYTHON_BINARY \
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&& bash /tmp/scripts/python-package-debian.sh "numpy" "latest" $PYTHON_BINARY \
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&& bash /tmp/scripts/python-package-debian.sh "pandas" "latest" $PYTHON_BINARY \
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&& bash /tmp/scripts/python-package-debian.sh "scipy" "latest" $PYTHON_BINARY \
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&& bash /tmp/scripts/python-package-debian.sh "matplotlib" "latest" $PYTHON_BINARY \
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&& bash /tmp/scripts/python-package-debian.sh "seaborn" "latest" $PYTHON_BINARY \
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&& bash /tmp/scripts/python-package-debian.sh "scikit-learn" "latest" $PYTHON_BINARY \
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&& bash /tmp/scripts/python-package-debian.sh "tensorflow" "latest" $PYTHON_BINARY \
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&& bash /tmp/scripts/python-package-debian.sh "keras" "latest" $PYTHON_BINARY \
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&& bash /tmp/scripts/python-package-debian.sh "torch" "latest" $PYTHON_BINARY \
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&& bash /tmp/scripts/python-package-debian.sh "requests" "latest" $PYTHON_BINARY \
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# Install rvm, rbenv, any missing base gems
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&& chown -R ${USERNAME} /opt/ruby/* \
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&& bash /tmp/scripts/ruby-debian.sh "none" "${USERNAME}" "true" "true" \

‎containers/codespaces-linux/.devcontainer/library-scripts/python-package-debian.sh‎

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@@ -0,0 +1,59 @@
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#!/usr/bin/env bash
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#-------------------------------------------------------------------------------------------------------------
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# Copyright (c) Microsoft Corporation. All rights reserved.
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# Licensed under the MIT License. See https://go.microsoft.com/fwlink/?linkid=2090316 for license information.
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#-------------------------------------------------------------------------------------------------------------
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#
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# Docs: https://github.com/microsoft/vscode-dev-containers/blob/main/script-library/docs/python-package-debian.md
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# Maintainer: The VS Code and Codespaces Teams
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#
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# Syntax: ./python-package-debian.sh
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set -e
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PACKAGE=${1:-""}
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VERSION=${2:-"latest"}
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PYTHON=${3:-"python"}
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USERNAME=${4-"automatic"}
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# If in automatic mode, determine if a user already exists, if not use vscode
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if [ "${USERNAME}" = "auto" ] || [ "${USERNAME}" = "automatic" ]; then
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USERNAME=""
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POSSIBLE_USERS=("vscode" "node" "codespace" "$(awk -v val=1000 -F ":" '$3==val{print $1}' /etc/passwd)")
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for CURRENT_USER in ${POSSIBLE_USERS[@]}; do
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if id -u ${CURRENT_USER} > /dev/null 2>&1; then
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USERNAME=${CURRENT_USER}
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break
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fi
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done
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if [ "${USERNAME}" = "" ]; then
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USERNAME=vscode
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fi
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elif [ "${USERNAME}" = "none" ]; then
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USERNAME=root
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USER_UID=0
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USER_GID=0
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fi
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# Use sudo to run as non-root user is not already running
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sudoUserIf()
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{
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if [ "$(id -u)" -eq 0 ] && [ "${USERNAME}" != "root" ]; then
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sudo -u ${USERNAME} "$@"
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else
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"$@"
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fi
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}
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# Make sure that Python is installed correctly
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if ! ${PYTHON} --version > /dev/null ; then
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echo "Python command not found: ${PYTHON}"
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exit 1
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fi
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# pip skips installation when a requirement is already satisfied
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if [ ${VERSION} = "latest" ]; then
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sudoUserIf ${PYTHON} -m pip install ${PACKAGE} --no-cache-dir
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else
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sudoUserIf ${PYTHON} -m pip install ${PACKAGE}==${VERSION} --no-cache-dir
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fi

‎containers/codespaces-linux/test-project/test.sh‎

Lines changed: 15 additions & 1 deletion
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@@ -20,7 +20,9 @@ check "dotnet-6-installed-by-oryx" dotnet --info | grep "/opt/dotnet/6\.0\.[0-9]
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# Check Python
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check "python" python --version
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check "pip" pip3 --version
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check "python3" python3 --version
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check "pip" pip --version
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check "pip3" pip3 --version
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check "pipx" pipx --version
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check "pylint" pylint --version
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check "flake8" flake8 --version
@@ -31,6 +33,18 @@ check "pydocstyle" pydocstyle --version
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check "bandit" bandit --version
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check "virtualenv" virtualenv --version
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# # Check Python packages
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# check "numpy" python -c 'import numpy'
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# check "pandas" python -c 'import pandas'
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# check "scipy" python -c 'import scipy'
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# check "matplotlib" python -c 'import matplotlib'
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# check "seaborn" python -c 'import seaborn'
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# check "scikit-learn" python -c 'import sklearn'
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# check "tensorflow" python -c 'import tensorflow'
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# check "keras" python -c 'import keras'
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# check "torch" python -c 'import torch'
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# check "requests" python -c 'import requests'
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# Check JupyterLab
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check "jupyter-lab" jupyter-lab --version
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‎script-library/README.md‎

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@@ -35,6 +35,7 @@ Some scripts have special installation instructions (like `desktop-lite-debian.s
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| [Node.js Install Script](docs/node.md) | `node-debian.sh` | VS Code and GitHub Codespaces teams|
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| [PowerShell Install Script](docs/powershell.md) | `powershell-debian.sh` | VS Code and GitHub Codespaces teams|
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| [Python Install Script](docs/python.md) | `python-debian.sh` | VS Code and GitHub Codespaces teams|
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| [Python Package Install Script](docs/python-package.md) | `python-package-debian.sh` | VS Code and GitHub Codespaces teams|
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| [Ruby Install Script](docs/ruby.md) | `ruby-debian.sh` | VS Code and GitHub Codespaces teams|
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| [Rust (rustlang) Install Script](docs/rust.md) | `rust-debian.sh` | VS Code and GitHub Codespaces teams|
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| [SSH Server Install Script](docs/sshd.md) | `sshd-debian.sh` | VS Code and GitHub Codespaces teams|

‎script-library/docs/python-package.md‎

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# Python Package Install Script
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*Installs a Python package.*
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**Script status**: Stable
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**OS support**: Debian 9+, Ubuntu 18.04+, and downstream distros.
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**Maintainer**: GitHub Codespaces team
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## Syntax
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```text
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./python-package-debian.sh PACKAGE [VERSION] [PYTHON_BINARY] [USERNAME]
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```
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## Usage
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### Script use
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1. Add [`python-package-debian.sh`](../python-package-debian.sh) to `.devcontainer/library-scripts`
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2. Add the following to your `.devcontainer/Dockerfile`:
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```Dockerfile
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COPY library-scripts/python-package-debian.sh /tmp/library-scripts/
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RUN bash /tmp/library-scripts/python-package-debian.sh PACKAGE
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```
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That's it!

‎script-library/python-package-debian.sh‎

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#!/usr/bin/env bash
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#-------------------------------------------------------------------------------------------------------------
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# Copyright (c) Microsoft Corporation. All rights reserved.
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# Licensed under the MIT License. See https://go.microsoft.com/fwlink/?linkid=2090316 for license information.
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#-------------------------------------------------------------------------------------------------------------
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#
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# Docs: https://github.com/microsoft/vscode-dev-containers/blob/main/script-library/docs/python-package-debian.md
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# Maintainer: The VS Code and Codespaces Teams
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#
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# Syntax: ./python-package-debian.sh
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set -e
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PACKAGE=${1:-""}
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VERSION=${2:-"latest"}
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PYTHON=${3:-"python"}
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USERNAME=${4-"automatic"}
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# If in automatic mode, determine if a user already exists, if not use vscode
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if [ "${USERNAME}" = "auto" ] || [ "${USERNAME}" = "automatic" ]; then
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USERNAME=""
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POSSIBLE_USERS=("vscode" "node" "codespace" "$(awk -v val=1000 -F ":" '$3==val{print $1}' /etc/passwd)")
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for CURRENT_USER in ${POSSIBLE_USERS[@]}; do
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if id -u ${CURRENT_USER} > /dev/null 2>&1; then
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USERNAME=${CURRENT_USER}
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break
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fi
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done
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if [ "${USERNAME}" = "" ]; then
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USERNAME=vscode
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fi
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elif [ "${USERNAME}" = "none" ]; then
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USERNAME=root
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USER_UID=0
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USER_GID=0
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fi
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# Use sudo to run as non-root user is not already running
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sudoUserIf()
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{
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if [ "$(id -u)" -eq 0 ] && [ "${USERNAME}" != "root" ]; then
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sudo -u ${USERNAME} "$@"
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else
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"$@"
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fi
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}
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# Make sure that Python is installed correctly
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if ! ${PYTHON} --version > /dev/null ; then
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echo "Python command not found: ${PYTHON}"
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exit 1
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fi
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# pip skips installation when a requirement is already satisfied
55+
if [ ${VERSION} = "latest" ]; then
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sudoUserIf ${PYTHON} -m pip install ${PACKAGE} --no-cache-dir
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else
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sudoUserIf ${PYTHON} -m pip install ${PACKAGE}==${VERSION} --no-cache-dir
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fi

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