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datalad / datalad-installer

Installation script for Datalad and related components
MIT License
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GitHub <https://github.com/datalad/datalad-installer> | PyPI <https://pypi.org/project/datalad-installer/> | Anaconda <https://anaconda.org/conda-forge/datalad-installer> | Issues <https://github.com/datalad/datalad-installer/issues> | Changelog <https://github.com/datalad/datalad-installer/blob/master/CHANGELOG.md>_

datalad-installer is a script for installing Datalad, git-annex, and related components all in a single invocation. It requires no third-party Python libraries, though it does make heavy use of external packaging commands.

.. _Datalad: https://www.datalad.org .. _git-annex: https://git-annex.branchable.com

Installation

datalad-installer requires Python 3.7 or higher. Just use pip <https://pip.pypa.io>_ for Python 3 (You have pip, right?) to install it::

python3 -m pip install datalad-installer

datalad-installer is also available for conda! To install, run::

conda install -c conda-forge datalad-installer

Alternatively, download the latest version directly from https://raw.githubusercontent.com/datalad/datalad-installer/master/src/datalad_installer.py.

Usage

::

datalad-installer [<global options>] <component>[=<version>] [<options>] <component>[=<version>] [<options>] ...

datalad-installer provisions one or more components listed on the command line. Each component is either a software package (e.g., Datalad or git-annex) or an environment in which software packages can be installed. If no components are specified on the command line, the script defaults to installing the datalad component.

Global Options

-E FILE, --env-write-file FILE Append any PATH modifications or other shell commands needed to use the new components to the given file. This option can be specified multiple times. If this option is not given, the data is written to a temporary file whose location is logged at the beginning of the program.

-l LEVEL, --log-level LEVEL Set the log level to the given value. Possible values are "CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG" (all case-insensitive) and their Python integer equivalents. [default value: INFO]

--sudo <ask|error|ok> What to do when the script needs to run a command with sudo or privilege escalation: ask for confirmation (default), error, or run without confirmation. This is always "ok" on Windows, where the system always asks for confirmation.

-V, --version Display the script version and exit

-h, --help Display usage information and exit

Components

venv


Creates a Python virtual environment using ``python -m venv``.  Subsequent
``datalad`` components on the command line will be installed into this virtual
environment by default if not overridden by an intervening component.

Options
'''''''

-e ARGS, --extra-args ARGS      Specify extra command-line arguments to pass to
                                ``python -m venv``

--path PATH                     Create the virtual environment at ``PATH``.  If
                                not specified, the environment will be created
                                in a directory in ``$TMPDIR``.

``miniconda``

Installs the latest version of Miniconda. Subsequent conda-env components on the command line will use this installation, and subsequent datalad, git-annex, rclone, and git-annex-remote-rclone components will be installed using this conda by default if not overridden by an intervening component.

A specific version to install can be specified by suffixing "miniconda" with "=" and the version on the command line, where the version is the version component of a file at $ANACONDA_URL or https://repo.anaconda.com/miniconda/, e.g., py37_23.1.0-1. Run datalad-installer miniconda --help-versions to see a list of available versions for your platform.

If not specified, the version defaults to latest.

The Miniconda installation script is downloaded from $ANACONDA_URL/Miniconda3-$VERSION-$OS-$ARCH.{sh,exe}, where $ANACONDA_URL is taken from the environment, defaulting to https://repo.anaconda.com/miniconda.

Options '''''''

--batch Run the Miniconda installation script in batch (noninteractive) mode. This is always done when installing on Windows.

                            In addition, if a spec is given (see below),
                            this option causes ``--yes`` to be passed to
                            ``conda install``.

-c CHANNEL, --channel CHANNEL Specify additional Conda channels to use when installing the packages listed in the spec (see below). This option can be specified multiple times.

-e ARGS, --extra-args ARGS Specify extra command-line arguments to pass to the Miniconda installation script.

--path PATH Install Miniconda at PATH. If not specified, it will be installed in a directory in $TMPDIR.

--python-match <major|minor|micro> Include python=V in the --spec, where V is the Python version used to run datalad-installer to the given version level (e.g., under Python 3.9.13, --python-match major will install python=3, minor will install python=3.9, and micro will install python=3.9.13)

--spec SPEC Space-separated specifiers for packages to install in the Conda base environment after provisioning.

--help-versions Show a list of available Miniconda versions for this platform and exit

conda-env


Creates a Conda environment.  If there is no preceding ``miniconda`` component
on the command line, Conda must already be installed on the system, and this
installation will be used to create the environment.

Subsequent ``datalad``, ``git-annex``, ``rclone``, and
``git-annex-remote-rclone`` components will be installed into this environment
by default if not overridden by an intervening component.

Options
'''''''

-e ARGS, --extra-args ARGS      Specify extra command-line arguments to pass to
                                the ``conda create`` command.

-n NAME, --name NAME            The name for the new environment.  If not
                                specified, a random name will be generated.

--spec SPEC                     Space-separated specifiers for packages to
                                install in the new environment.

``neurodebian``

Installs & configures NeuroDebian <https://neuro.debian.net>_.

Options '''''''

-e ARGS, --extra-args ARGS Specify extra command-line arguments to pass to the nd-configurerepo command.

git-annex


Installs git-annex_.  The component takes an ``-m``, ``--method`` option
specifying the installation method to use; the supported methods are:

- ``apt``
- ``autobuild``
- ``brew``
- ``conda`` (only supported on Linux)
- ``datalad/git-annex``
- ``datalad/git-annex:release``
- ``datalad/git-annex:tested``
- ``datalad/packages``
- ``deb-url``
- ``dmg``
- ``neurodebian``
- ``snapshot``

If no method is specified, or if the method is set to "``auto``", then the most
recent component on the command line that provides a compatible installation
method will be used.  If there is no such component, the first supported
installation method from the following list will be used:

- ``conda``
- ``apt``
- ``neurodebian``
- ``brew``
- ``autobuild``
- ``datalad/packages``

A specific version to install can be specified for those methods that support
it by suffixing "``git-annex``" with "``=``" and the version number on the
command line.

The ``git-annex`` component also accepts all options for the supported
installation methods; options not belonging to whichever method ends up used
will be ignored.

``datalad``

Installs Datalad_. The component takes an -m, --method option specifying the installation method to use; the supported methods are:

If no method is specified, or if the method is set to "auto", then the most recent component on the command line that provides a compatible installation method will be used. If there is no such component, the first supported installation method from the following list will be used:

A specific version to install can be specified for those methods that support it by suffixing "datalad" with "=" and the version number on the command line.

The datalad component also accepts all options for the supported installation methods; options not belonging to whichever method ends up used will be ignored.

rclone


Installs rclone_.  The component takes an ``-m``, ``--method`` option
specifying the installation method to use; the supported methods are:

.. _rclone: https://rclone.org

- ``apt``
- ``brew``
- ``conda``
- ``deb-url``
- ``downloads.rclone.org``

If no method is specified, or if the method is set to "``auto``", then the most
recent component on the command line that provides a compatible installation
method will be used.  If there is no such component, the first supported
installation method from the following list will be used:

- ``conda``
- ``apt``
- ``brew``
- ``downloads.rclone.org``

A specific version to install can be specified for those methods that support
it by suffixing "``rclone``" with "``=``" and the version number on the
command line.

The ``rclone`` component also accepts all options for the supported
installation methods; options not belonging to whichever method ends up used
will be ignored.

``git-annex-remote-rclone``

Installs git-annex-remote-rclone_. The component takes an -m, --method option specifying the installation method to use; the supported methods are:

.. _git-annex-remote-rclone: https://github.com/DanielDent/git-annex-remote-rclone

If no method is specified, or if the method is set to "auto", then the most recent component on the command line that provides a compatible installation method will be used. If there is no such component, the first supported installation method from the following list will be used:

A specific version to install can be specified for those methods that support it by suffixing "git-annex-remote-rclone" with "=" and the version number on the command line.

The git-annex-remote-rclone component also accepts all options for the supported installation methods; options not belonging to whichever method ends up used will be ignored.

Installation Methods

apt


Installs with ``sudo apt-get install``.  Supports installing specific versions.

Options
'''''''

--build-dep                     Run ``sudo apt-get build-dep`` instead of
                                ``sudo apt-get install``.

-e ARGS, --extra-args ARGS      Specify extra command-line arguments to pass to
                                the installation command.

``autobuild``

Downloads & installs the latest official build of git-annex from kitenet.net. Does not support installing specific versions.

This installation method is only supported on Linux and macOS.

brew


Installs with ``brew`` (`Homebrew <https://brew.sh>`_).  Does not support
installing specific versions.

Options
'''''''

-e ARGS, --extra-args ARGS      Specify extra command-line arguments to pass to
                                the installation command.

``conda``

Installs with conda install. Supports installing specific versions.

Options '''''''

-e ARGS, --extra-args ARGS Specify extra command-line arguments to pass to the installation command.

DanielDent/git-annex-remote-rclone


Downloads & installs ``git-annex-remote-rclone`` from a release of its GitHub
project.

This installation method is only supported on Linux and macOS.

Options
'''''''

--bin-dir DIR                   Directory in which to install the ``rclone``
                                executable.  Defaults to ``/usr/local/bin``.
                                If this contains the string ``{tmpdir}``, it
                                will be replaced with the path to a directory
                                in ``$TMPDIR``.

``datalad/git-annex``

Downloads & installs git-annex from the latest build of datalad/git-annex <https://github.com/datalad/git-annex>_ that produced artifacts for the running OS. Does not support installing specific versions.

This installation method requires a GitHub OAuth token with appropriate permissions. It must be specified either via the GITHUB_TOKEN environment variable or as the value of the hub.oauthtoken Git config option.

Options '''''''

--install-dir DIR Directory in which to unpack the *.deb package instead of installing it system-wide. If this contains the string {tmpdir}, it will be replaced with the path to a directory in $TMPDIR. (Linux only)

datalad/git-annex:release


Downloads & installs ``git-annex`` for the running OS from the latest release
(or the specified version) of `datalad/git-annex
<https://github.com/datalad/git-annex>`_.  If no explicit version is specified
and the latest release lacks an asset for the running OS, the most recent
release with a matching asset is used.

Options
'''''''

--install-dir DIR               Directory in which to unpack the ``*.deb``
                                package instead of installing it system-wide.
                                If this contains the string ``{tmpdir}``, it
                                will be replaced with the path to a directory
                                in ``$TMPDIR``. (Linux only)

``datalad/git-annex:tested``

Downloads & installs git-annex from the latest successful build of datalad/git-annex <https://github.com/datalad/git-annex>_ for the running OS. Does not support installing specific versions.

This installation method requires a GitHub OAuth token with appropriate permissions. It must be specified either via the GITHUB_TOKEN environment variable or as the value of the hub.oauthtoken Git config option.

Options '''''''

--install-dir DIR Directory in which to unpack the *.deb package instead of installing it system-wide. If this contains the string {tmpdir}, it will be replaced with the path to a directory in $TMPDIR. (Linux only)

datalad/packages


Downloads & installs ``git-annex`` from
<https://datasets.datalad.org/?dir=/datalad/packages> for the running OS.
Supports installing specific versions (though note that the version strings for
this method tend to include Git commit information, e.g.,
"``8.20210127+git111-gbe5a0e4b8``").

Options
'''''''

--install-dir DIR               Directory in which to unpack the ``*.deb``
                                package instead of installing it system-wide.
                                If this contains the string ``{tmpdir}``, it
                                will be replaced with the path to a directory
                                in ``$TMPDIR``. (Linux only)

``deb-url``

Download & install a given *.deb package. Does not support installing specific versions.

Options '''''''

-e ARGS, --extra-args ARGS Specify extra command-line arguments to pass to the installation command.

--install-dir DIR Directory in which to unpack the *.deb package instead of installing it system-wide. If this contains the string {tmpdir}, it will be replaced with the path to a directory in $TMPDIR. If this contains the string {version}, it will be replaced with the package's version. (git-annex only)

--url URL Specify the URL of the *.deb package. This option is required for this installation method.

dmg


Installs ``git-annex`` to the ``/Applications`` directory from a properly-built
``*.dmg`` image.  Does not support installing specific versions.

This installation method is only supported on macOS.

Options
'''''''

--path PATH                     Specify the path to the ``*.dmg`` image.  This
                                option is required for this installation
                                method.

``downloads.rclone.org``

Downloads & installs rclone from https://downloads.rclone.org.

Options '''''''

--bin-dir DIR Directory in which to install the rclone executable. This option is required on Windows. On Linux & macOS, the directory defaults to /usr/local/bin. If the path contains the string {tmpdir}, it will be replaced with the path to a directory in $TMPDIR.

--man-dir DIR Directory under which to install the rclone manpage; specifically, the file rclone.1 will be placed in the man1/ subdirectory of the given directory. If this option is not specified, the manpage is not installed. If the path contains the string {tmpdir}, it will be replaced with the path to a directory in $TMPDIR (the same one as used for --bin-dir, if applicable).

neurodebian


Installs from NeuroDebian repositories with ``sudo apt-get install``.  Supports
installing specific versions.

Options
'''''''

--build-dep                     Run ``sudo apt-get build-dep`` instead of
                                ``sudo apt-get install``.

-e ARGS, --extra-args ARGS      Specify extra command-line arguments to pass to
                                the installation command.

``pip``

Installs with python -m pip. Supports installing specific versions.

If a venv component is previously given on the command line, the installation will be performed in that virtual environment; otherwise, it will be performed using the same Python used to run datalad-installer.

Options '''''''

--devel Install the given component from its GitHub repository instead of from PyPI.

-e ARGS, --extra-args ARGS Specify extra command-line arguments to pass to the installation command.

-E EXTRAS, --extras EXTRAS Specify (comma-separated) package extras to install.

snapshot



Downloads & installs the latest official snapshot build of ``git-annex`` from
kitenet.net.  Does not support installing specific versions.

This installation method is only supported on Linux and macOS.