README.md

# FSL conda package infrastructure


_This documentation is a work in progress_


This repository hosts information and documentation regarding the FSL conda
package infrastructure.


This `README` file contains a general overview. More detailed information on
different topics can be found in the folowing files:


 - [`development_workflow.md`](development_workflow.md): Details on
   development and release workflows and processes.
 - [`official_fsl_installations.md`](official_fsl_installations.md): Details
   on official/full conda-based FSL installations.
 - [`local_development.md`](local_development.md): Setting up an FSL
   development environment on your own machine.
 - [`building_fsl_conda_packages.md`](building_fsl_conda_packages.md): Details
   on how to build a FSL conda package locally.
 - [`creating_fsl_conda_recipes.md`](creating_fsl_conda_recipes.md): Details
   on how to create a FSL conda recipe.


## Quick summary


FSL is organised into a number of repositories hosted at
https://git.fmrib.ox.ac.uk.

 - fsl/conda/docs> (this repository): High level documentation
 - fsl/conda/manifest>: Metadata for managing public and internal FSL
   releases
 - fsl/conda/manifest-rules>: CI configuration used by the
   fsl/conda/manifest> repository
 - fsl/conda/installer>: Home of the `fslinstaller.py` script, for
   installing FSL
 - fsl/conda/fsl-ci-rules>: CI rules for automated building and publishing
   of FSL conda packages
 - `fsl/<project>`: Source code repository for FSL project `<project>`
   (e.g. fsl/avwutils>)
 - `fsl/conda/fsl-<project>`: Conda recipe repository for FSL project
   `<project>` (e.g. fsl/conda/fsl-avwutils>)


## Overview

FSL is installed using the [**conda**](https://conda.io/) package and
environment management system. Each FSL project is built as a conda package,
and published to an internally hosted conda channel.


Prior to FSL 6.0.6, FSL was released and installed as a monolithic archive
file, containing most FSL tools, and a separate conda environment called
`fslpython`, configured after the archive file was installed. Some of the
reasons for transitioning to a purely conda-based release model are as
follows:

 - Simplify FSL installation procedure
 - Reduce the size of `$FSLDIR`
 - Allow "minimal" FSL installations, with only the utilities that are
   required
 - Improve build reproducibility
 - Improve support for container-based FSL installations
 - Simplify cross-platform management of external dependencies (e.g. VTK,
   OpenBLAS)


## FSL releases


Public and internal FSL release are defined by a set of conda
[`environment.yml`
files](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#create-env-file-manually),
one for each supported platform and CUDA version.  Each `environment.yml` file
contains a list of the packages which are included in the FSL release.


FSL releases are described by a `manifest.json` file, which is an index of all
available `environment.yml` files, and which contains all of the information
needed to install a particular FSL release.


The fsl/conda/manifest> repository is where new FSL releases, both public and
internal, are created. The `environment.yml` and `manifest.json` files for a
new release are automatically generated from information stored in the
`fsl-release.yml` file in that repository.


The `manifest.json` and `environment.yml` files for public and internal
release are currently published to
https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/.


## The `fslinstaller.py` script

FSL releases are installed via a script called `fslinstaller.py`, which is
maintained at the fsl/conda/installer> repository.

The `fslinstaller.py` script performs the following tasks:

1. Downloads the FSL release `manifest.json` file, and the appropriate
   `environment.yml` file for the platform.
2. Downloads a `miniconda` installer.
3. Installs a base `miniconda` environment into `$FSLDIR` (where `$FSLDIR`
   defaults to `/usr/local/fsl/`, or is explicitly specified by the user).
4. Installs all FSL packages into the `$FSLDIR` base conda environment.
5. Sets up the user shell profile so that FSL is configured in their shell
   environment by default.


## Partial FSL installations


Users may choose to install specific FSL packages by installing the desired
FSL packages directly from the FSL conda channel into their own conda
environment.


> **Note:** All FSL conda packages list the dependencies required for their
> execution, so when a particular package is installed, all of its run-time
> dependencies will also be installed. However, as we transition away from
> monolithic installations and towards conda-based installations, there are
> likely to be omissions and errors in the dependency hierarchy. These issues
> will be resolved on a case-by-case basis.


## FSL conda packages


All FSL projects and their dependencies are published as conda packages. Most
FSL conda packages are published to an internally maintained channel, but some
packages are published to the `conda-forge` channel at https://anaconda.org.


All FSL projects, and any dependencies which are not available on
https://anaconda.org, are built according to a conda *recipe*, which describes
how the project can be built as a conda package. All FSL conda recipes are
hosted as git repositories on the FMRIB gitlab server, under the `fsl/conda/`
group.


To clarify, each FSL project, and internally managed dependency, comprises
**two** git repositories<sup>*</sup>:

* The **project** repository contains the project source code/resources, and
  is typically hosted at `https://git.fmrib.ox.ac.uk/fsl/<project>`
* The **recipe** repository contains a conda recipe for the project, and is
  hosted at `https://git.fmrib.ox.ac.uk/fsl/conda/fsl-<project>`.


FSL conda packages are built automatically using Gitlab CI - the CI
infrastructure for automatically building conda packages is hosted in the
fsl/fsl-ci-rules> repository.


> <sup>*</sup>A small number of FSL projects have more than one recipe
> repository associated with them - for example, the
> [`fsl/fdt`](https://git.fmrib.ox.ac.uk/fsl/fdt) project has two recipes -
> the [`fsl/conda/fsl-fdt`](https://git.fmrib.ox.ac.uk/fsl/conda/fsl-fdt)
> recipe provides CPU executables, and the
> [`fsl/conda/fsl-fdt-cuda`](https://git.fmrib.ox.ac.uk/fsl/conda/fsl-fdt-cuda)
> recipe provides GPU/CUDA executables.


## Public and internal channels


FSL projects are published to one of two conda internally managed conda
channels:

  - The **public** channel contains stable and development packages for most
    FSL projects.  Every time a new tag is added to a project repository, a
    stable conda package is built and published to the public channel. Every
    time commits are merged into the master branch of a repository, a
    development conda package is built and published to the public channel.

  - The **internal** channel contains stable and development packages for FSL
    projects which are not part of official FSL releases, and are only part of
    internal release.

These channels are currently hosted online at the following URLs:

 - https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/
 - https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/internal/