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Install Python packages​

Installing packages without internet

It's possible to install Python packages without internet by downloading the source code of a package compressed in tar.gz, copying it to the machine via scp/other methods, and running (having previously loaded a Python module):

$> tar xzf {package}.tar.gz
$> cd {package}
$> python setup.py install / pip install . (both methods usually work)

Requirements to install packages​

Requirements to install packages networked (must have Internet access)​

  • Connect to a login4 of MareNostrum5:

    mylaptop$> ssh {username}@glogin4.bsc.es
    mylaptop$> ssh {username}@alogin4.bsc.es
    IMPORTANT

    The MareNostrum5 login4 are restricted to BSC staff and are only accessible from the BSC internal network or the Virtual Private Network (VPN).

  • Check the Internet connectivity from glogin4/alogin4, for example:

    $> wget --tries=3 --timeout=5 -q --spider google.com && echo "Networked" || echo "Non-networked"
    Networked

Check the Python interpreter​

  • Load Python in the session, for example:

    $> module purge && module load oneapi hdf5 python

  • Ensure you can run Python from the command line:

    $> which python
    /apps/GPP/PYTHON/3.12.1/INTEL/bin/python
    $> python --version
    Python 3.12.1

Check the 'pip' package manager​

pip is the recommended package installer, allowing packages installation from PyPI (Python Package Index), local projects, or directly from distribution files. It also supports version control.

"python3 -m pip" executes pip using the Python interpreter you specified as python3.

  • Ensure you can run pip from the command line:

    $> python -m pip --version
    pip 24.0 from /apps/GPP/PYTHON/3.12.1/INTEL/lib/python3.12/site-packages/pip (python 3.12)

Install and manage packages​

Install packages​

  • Install a package from PyPI:

    $> python -m pip install SomePackage            # Latest version
    $> python -m pip install "SomePackage==1.0.4"   # Specific version
    $> python -m pip install "SomePackage>=1.0.4"   # Minimum version

  • Install a package locally (from PyPI):

    $> python3 -m pip install --user SomePackage    # At the user default location

    Or:

    $> export PYTHONUSERBASE=/path/to/my/python/local/project
    $> python3 -m pip install --user SomePackage

  • Install a list of packages specified in a requirements file:

    $> python3 -m pip install -r requirements.txt

    Maybe you want to do something like this:

    SomePythonEnv$> python3 -m pip freeze > requirements.txt

    MyPythonEnv$> python3 -m pip install -r requirements.txt

  • Install packages from a source file:

    $> python3 -m pip install SomePackage-1.0.4.tar.gz

Update packages​

  • Upgrade an already installed package to the latest from PyPI:

    $> python3 -m pip install --upgrade SomePackage

    # Dependencies are upgraded only when they don't meet
    # the requirements of the upgraded packages

    Or:

    $> python3 -m pip install SomePackage --upgrade --upgrade-strategy eager

    # Dependencies are upgraded regardless of whether the currently
    # the currently installed version meets the requirements
    # of the upgraded package

Uninstall packages​

  • Uninstall a package:

    $> python3 -m pip uninstall SomePackage
    $> python3 -m pip uninstall SomePackage --yes   # Don't ask for confirmation, also '-y'

  • Uninstall a list of packages from a requirements file:

    $> python3 -m pip uninstall -r requirements.txt [--yes, -y]

Verification of installed packages​

  • Show the list of existing packages:

    $> python3 -m pip list          # Packages that are globally installed
    $> python3 -m pip list --user   # Packages that are locally installed

    Or:

    $> python3 -m pip freeze
    $> python3 -m pip freeze --user

    It can also be helpful:

    $> python3 -m pip list [--user] | grep -i SomePackage
    $> python3 -m pip freeze [--user] | grep -i SomePackage

  • Show the list of outdated packages (and show the latest version available):

    $> python3 -m pip list --outdated

  • Show location of existing packages:

    $> python3 -m site              # Globally installed packages
    $> python3 -m site --user-site  # Locally installed packages

  • Show details of a specific package:

    $> python3 -m pip show SomePackage

  • Verify that installed packages have compatible dependencies:

    $> python3 -m pip check
    No broken requirements found.   # The desirable

Work with environments​