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ddecrulleavouacr
ddecrulle
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avouacr
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fix(python): use prefix to install Python in separate location from ubuntu's system version (#295)
* use prefix for python installation and add `LD_LIBRARY_PATH` env * update * add symlink * add registry * add symplink for retrocompatibility * remove registry * fix test * trim * retro-compat * install in opt/python * fix tests --------- Co-authored-by: avouacr <avouacr@pm.me>
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‎base/scripts/fix-user-permissions.sh‎

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@@ -3,9 +3,8 @@ set -e
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# Chown only if needed to avoid duplicate files in Docker layers
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# Give user permission on all files in HOME
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find "${HOME}" -not -user "${USERNAME}" -execdir chown --no-dereference "${USERNAME}:${GROUPNAME}" {} \+
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find "/opt/" -not -user "${USERNAME}" -execdir chown --no-dereference "${USERNAME}:${GROUPNAME}" {} \+
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# Give user permissions on all files in /usr/local except cuda folders
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find /usr/local/ \( -path "/usr/local/cuda*" -prune \) -o \
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\( -not -user "${USERNAME}" -execdir chown --no-dereference "${USERNAME}:${GROUPNAME}" {} + \)

‎base/tests.yaml‎

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path: "/opt/onyxia-init.sh"
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shouldExist: true
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permissions: "-rwxr-xr-x"
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uid: 0
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gid: 0
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uid: 1000
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gid: 100
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commandTests:
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- name: "Does the binary exists?"
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command: "which"

‎jupyter/tests.yaml‎

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path: "/opt/onyxia-init.sh"
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shouldExist: true
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permissions: "-rwxr-xr-x"
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uid: 0
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gid: 0
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uid: 1000
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gid: 100
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commandTests:
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- name: "Does the binary exists?"
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command: "which"
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command: "which"
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args: ["mc"]
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expectedOutput: ["/usr/local/bin/mc"]
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- name: "Does the binary exists?"
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command: "which"
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args: ["python"]
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expectedOutput: ['/opt/python/bin/python']
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- name: "Does the binary exists?"
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command: "which"
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args: ["pip"]
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expectedOutput: ['/opt/python/bin/pip']
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- name: "Does the binary exists?"
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command: "which"
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args: ["jupyter-lab"]
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expectedOutput: ["/usr/local/bin/jupyter-lab"]
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expectedOutput: ["/opt/python/bin/jupyter-lab"]
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- name: "Does the binary exists?"
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command: "which"
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args: ["duckdb"]

‎python-datascience/tests.yaml‎

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path: "/opt/onyxia-init.sh"
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shouldExist: true
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permissions: "-rwxr-xr-x"
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uid: 0
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gid: 0
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uid: 1000
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gid: 100
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commandTests:
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- name: "Does the binary exists?"
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command: "which"
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- name: "Does the binary exists?"
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command: "which"
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args: ["python"]
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expectedOutput: ["/usr/local/bin/python"]
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expectedOutput: ['/opt/python/bin/python']
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- name: "Does the binary exists?"
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command: "which"
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args: ["pip"]
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expectedOutput: ["/usr/local/bin/pip"]
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expectedOutput: ['/opt/python/bin/pip']
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- name: "Does the binary exists?"
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command: "which"
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args: ["quarto"]

‎python-minimal/Dockerfile‎

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@@ -6,8 +6,9 @@ LABEL maintainer="InseeFrLab <innovation@insee.fr>"
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ARG PYTHON_VERSION="3.13.5"
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ENV PYTHON_VERSION=${PYTHON_VERSION}
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# Ensure local Python is preferred over system version
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ENV PATH="/usr/local/bin:${PATH}"
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# Install Python separately from system installation to avoid conflicts
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ARG PYTHON_DIR="/opt/python"
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ENV PATH="${PYTHON_DIR}/bin:${PATH}"
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USER root
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‎python-minimal/scripts/install-python.sh‎

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xz-utils \
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zlib1g-dev
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# Install Python
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# Build Python from sources
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wget -q https://www.python.org/ftp/python/${PYTHON_VERSION}/Python-${PYTHON_VERSION}.tgz
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tar xzvf Python-${PYTHON_VERSION}.tgz
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cd Python-${PYTHON_VERSION}
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./configure \
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--enable-loadable-sqlite-extensions \
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--enable-optimizations \
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--enable-shared \
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--with-lto
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make -j4
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--prefix="${PYTHON_DIR}" \
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--enable-loadable-sqlite-extensions \
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--enable-optimizations \
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--enable-shared \
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--with-lto \
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LDFLAGS="-Wl,-rpath ${PYTHON_DIR}/lib"
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make -j"$(nproc)"
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make install
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ldconfig
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# Useful symlinks
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ln -s /usr/local/bin/python3 /usr/local/bin/python
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ln -s /usr/local/bin/pip3 /usr/local/bin/pip
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# Checks
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python --version
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# Clean install files
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cd ..
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apt-mark manual $savedAptMark
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apt-get purge -y --auto-remove -o APT::AutoRemove::RecommendsImportant=false
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# Upgrade pip & install uv for further Python packages installation
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# Useful symlinks
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ln -sf "${PYTHON_DIR}/bin/python3" "${PYTHON_DIR}/bin/python"
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ln -sf "${PYTHON_DIR}/bin/pip3" "${PYTHON_DIR}/bin/pip"
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# Checks
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python --version
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which python
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# Upgrade pip & install uv
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pip install --no-cache-dir --upgrade pip
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pip install --no-cache-dir uv

‎python-minimal/tests.yaml‎

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path: "/opt/onyxia-init.sh"
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shouldExist: true
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permissions: "-rwxr-xr-x"
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uid: 0
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gid: 0
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uid: 1000
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gid: 100
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commandTests:
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- name: "Does the binary exists?"
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command: "which"
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- name: "Does the binary exists?"
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command: "which"
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args: ["python"]
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expectedOutput: ["/usr/local/bin/python"]
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expectedOutput: ['/opt/python/bin/python']
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- name: "Does the binary exists?"
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command: "which"
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args: ["pip"]
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expectedOutput: ["/usr/local/bin/pip"]
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expectedOutput: ['/opt/python/bin/pip']
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- name: "Does the binary exists?"
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command: "which"
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args: ["duckdb"]

‎python-pytorch/tests.yaml‎

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path: "/opt/onyxia-init.sh"
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shouldExist: true
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permissions: "-rwxr-xr-x"
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uid: 0
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gid: 0
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uid: 1000
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gid: 100
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commandTests:
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- name: "Does the binary exists?"
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command: "which"
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- name: "Does the binary exists?"
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command: "which"
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args: ["python"]
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expectedOutput: ["/usr/local/bin/python"]
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expectedOutput: ['/opt/python/bin/python']
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- name: "Does the binary exists?"
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command: "which"
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args: ["pip"]
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expectedOutput: ["/usr/local/bin/pip"]
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expectedOutput: ['/opt/python/bin/pip']
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- name: "Does the binary exists?"
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command: "which"
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args: ["duckdb"]

‎python-tensorflow/tests.yaml‎

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path: "/opt/onyxia-init.sh"
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shouldExist: true
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permissions: "-rwxr-xr-x"
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uid: 0
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gid: 0
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uid: 1000
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gid: 100
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commandTests:
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- name: "Does the binary exists?"
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command: "which"
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- name: "Does the binary exists?"
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command: "which"
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args: ["python"]
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expectedOutput: ["/usr/local/bin/python"]
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expectedOutput: ['/opt/python/bin/python']
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- name: "Does the binary exists?"
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command: "which"
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args: ["pip"]
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expectedOutput: ["/usr/local/bin/pip"]
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expectedOutput: ['/opt/python/bin/pip']
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- name: "Does the binary exists?"
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command: "which"
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args: ["duckdb"]

‎r-datascience/tests.yaml‎

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@@ -13,8 +13,8 @@ fileExistenceTests:
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path: "/opt/onyxia-init.sh"
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shouldExist: true
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permissions: "-rwxr-xr-x"
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uid: 0
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gid: 0
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uid: 1000
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gid: 100
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commandTests:
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- name: "Does the binary exists?"
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command: "which"

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