Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Cleaning up installation instructions #1113

Merged
Merged
Changes from 2 commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
52 changes: 34 additions & 18 deletions docs/installation.rst
Original file line number Diff line number Diff line change
Expand Up @@ -2,35 +2,51 @@
Installation
############

You'll need to set up a working development environment to use ``tedana``.
To set up a local environment, you will need Python >=3.8 and the following
packages will need to be installed:
You'll need to install ``tedana`` in your python environment.
If you already have a python environment and you want to add tedana, type:

- nilearn
- nibabel
- numpy
- scikit-learn
- scipy
- mapca
.. code-block:: bash

pip install tedana

After installing relevant dependencies, you can then install ``tedana`` with:
As long as your python environment contains a compatible version of python, this should work.

If you want more control over your environment to ensure that every python dependency
is optimized for tedana,
you can use a program like `conda`_ to create an environment specifically for ``tedana`` with:

.. code-block:: bash

conda create -n tedenv python=3.12 pip
conda activate tedenv
pip install tedana

In addition to the Python package, installing ``tedana`` will add the ``tedana``
and ``t2smap`` workflow CLIs to your path.
You can confirm that ``tedana`` has successfully installed by launching a Python instance and running:
The above will create a python environment for tedana called ``tedenv``,
and you can enter that environment with ``conda activate tedenv``.

.. code-block:: python
With either of the above methods, `pip` will install python and all its dependencies.
handwerkerd marked this conversation as resolved.
Show resolved Hide resolved
tedana's `dependencies are listed here`_.

import tedana

You can check that it is available through the command line interface (CLI) with:
Once ``tedana`` is installed, there are two ways to run it.
You can run ``tedana``, ``ica_reclassify``, and ``t2smap`` from the command line interface (CLI).
You can see the options for any of these commands using ``--help`` (i.e. ``tedana --help``).

.. code-block:: bash
You can also import these commands to run within python using:

tedana --help
.. code-block:: python

from tedana.workflows import ica_reclassify_workflow, t2smap_workflow, tedana_workflow

API instructions for running these `commands in python are here`_.

If no error occurs, ``tedana`` has correctly installed in your environment!

If you are having trouble solving errors,
`here are places the tedana community monitors`_ to offer support.


.. _commands in python are here: https://tedana.readthedocs.io/en/stable/api.html#module-tedana.workflows
.. _conda: https://www.anaconda.com/download
.. _dependencies are listed here: https://github.com/ME-ICA/tedana/blob/main/pyproject.toml
.. _here are places the tedana community monitors: https://tedana.readthedocs.io/en/stable/support.html