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

Ge dev to main #53

Merged
merged 5 commits into from
Dec 12, 2024
Merged
Show file tree
Hide file tree
Changes from all 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
Binary file added docs2/.installation.rst.kate-swp
Binary file not shown.
Binary file added docs2/.usage.rst.kate-swp
Binary file not shown.
50 changes: 6 additions & 44 deletions docs2/installation.rst
Original file line number Diff line number Diff line change
Expand Up @@ -2,54 +2,16 @@
Installation
############

There are many ways you can install our package, using pip to download our latest stable version,
Docker, Singularity/Apptainer or manual installation directly from the source code. We highly suggest to install
our latest PyPI wheel. Note that the Singularity/Apptainer versions are outdated.
To install **NiChart Project** with pip, just do: ::

$ pip install NiChart_Project

****************
Install with pip
****************

To install **NiChart DLMUSE** with pip, just do: ::

$ pip install NiChart_DLMUSE

We always have our latest stable version on PyPI, so we highly suggest you to install it this way, as this package is under
heavy development and building from source can lead to crashes and bugs.


.. _`Docker Container`:

****************
Docker Container
****************

The package comes already pre-built as a docker container that you can download at our `docker hub <https://hub.docker.com/r/cbica/nichart_dlmuse/tags>`_.
You can build the package by running the following command: ::

$ docker build -t cbica/nichart_dlmuse .

.. _`Singularity/Apptainer build`

Singularity and Apptainer images can be built for NiChart_DLMUSE, allowing for frozen versions of the pipeline and easier
installation for end-users. Note that the Singularity project recently underwent a rename to "Apptainer", with a commercial
fork still existing under the name "Singularity" (confusing!). Please note that while for now these two versions are largely identical,
future versions may diverge. It is recommended to use the AppTainer distribution. For now, these instructions apply to either.
After installing the container engine, run: ::

$ singularity build nichart_dlmuse.sif singularity.def

This will take some time, but will build a containerized version of your current repo. Be aware that this includes any local changes!
The nichart_dlmuse.sif file can be distributed via direct download, or pushed to a container registry that accepts SIF images.

.. _`Manual installation`
We always have our latest stable version on PyPI, so we highly suggest you to install it this way.

You can manually build the package from source by running: ::

$ git clone https://github.com/CBICA/NiChart_DLMUSE
$ git clone https://github.com/CBICA/NiChart_Project

$ cd NiChart_DLMUSE && python3 -m pip install -e .
$ cd NiChart_Project && python3 -m pip install -e .

We **do not** recomment installing the package directly from source as the repository above is under heavy development and can cause
crashes and bugs.
We **do not** recomment installing the package directly from source as the repository is under development and this can cause crashes and bugs.
Loading