README.md

# FSL release manifest


This repository is used to manage FSL releases. The `fsl-release.yml` file
defines the packages that are installed as part of a FSL release.

FSL release `manifest.json` and `environment.yml` files are automatically
generated from information stored in this repository, using CI rules and
scripts in the fsl/conda/manifest-rules> repository.


This repository contains two branches, `master` and `external`. These two
branches are used to create three different types of FSL release:

 - Public FSL releases (e.g. FSL 6.0.6) are created from **tags** on the
   `external` branch.
 - Development releases (development versions of public releases) are created
   from **commits** on the `external` branch.
 - Internal FSL releases (for internal use only) are created from **commits**
   on the `master` branch


## The `fslinstaller.py` script


FSL is installed using a Python 2/3 script called
[fslinstaller.py](https://git.fmrib.ox.ac.uk/fsl/conda/installer).


The `fslinstaller` script starts by downloading a _manifest_ file (referred
to as `manifest.json`), a JSON file which contains information about:

  - available FSL releases (past and present)
  - miniconda installer releases, upon which FSL installations are based
  - The latest available version of the fslinstaller script itself (used
    for self-updating)


Once the appropriate FSL release has been determined, the `fslinstaller`
downloads a FSL release file - A FSL release is defined by a conda
environment specification file (referred to as `environment.yml`), which
is a YAML file that contains a list of the individual packages and their
respective versions that comprise a specific FSL release. Separate
`environment.yml` files exist for each supported platform and CUDA version.


## Generating the `manifest.json` and `environment.yml` files


The `manifest.json` and `environment.yml` files are automatically generated
from information stored in this repository:

 - The `fsl-release.yml` file contains information about the `fslinstaller`,
   miniconda installers, and packages for the latest FSL release.
 - Information about past FSL releases is obtained from the most recently
   generated `manifest.json` file.


The `fsl-release.yml` file is a YAML file with the following structure:

```yaml
# URL to FSL release information. The fslinstaller.py
# script, and previously generated manifest.json
# file is assumed to be downloadable from this URL.
# URLs for newly generated environment files are
# constructed using this URL.
release-url: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/

# Latest fslinstaller version
installer: 1.2.3

# URLs to miniconda installers to
# use for all supported platforms
miniconda:
  linux-64: https://github.com/conda-forge/miniforge/releases/download/4.10.3-1/Miniforge3-4.10.3-1-Linux-x86_64.sh
  macos-64: https://github.com/conda-forge/miniforge/releases/download/4.10.3-1/Miniforge3-4.10.3-1-MacOSX-x86_64.sh
  macos-M1: https://github.com/conda-forge/miniforge/releases/download/4.10.3-1/Miniforge3-4.10.3-1-MacOSX-arm64.sh

# Versions of CUDA for which FSL packages are
# built (currently only available on Linux).
cuda:
 - 9.2
 - 10.2
 - 11.0

# Conda channels to source packages from
channels:
 - https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/
 - conda-forge
 - defaults

# Private channel containing packages that are
# only released internally. This is prepended
# to the channels list for internal releases.
internal-channel: http://${FSLCONDA_USERNAME}:${FSLCONDA_PASSWORD}@https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/internal/

# The FSL installation is created in two stages.
# First of all, the base_packages are installed.
# Versions of these packages are specified in
# the packages list below
base-packages:
 - fsl-base
 - fslpy
 - fsl-sub
 - libopenblas
 ...

# List of all packages that comprise a FSL
# installation. All packages not installed
# in the first stage (see base_packages
# above) are installed in the second stage.
packages:
 - ciftilib 1.5.3
 - fsleyes 1.3.0
 - fslpy 3.7.0
 - fsl-avwutils 2007.0
 - fsl-base 2109.1
 - fsl-eddy 2106.0
 - fsl-sub 2.5.8
 - libopenblas 0.3.18 *openmp*
 ...

# List of additional platform-specific
# packages to be installed.
linux-64-packages: []
macos-64-packages: []
macos-M1-packages: []
```


When changes are made to the `fsl-release.yml` file, new versions of the
`manifest.json` and `environment.yml` files are generated and made available
for download.


Note that there are two types of manifest file:

  - The official release manifest, containing information about past and
    present public FSL releases - this is always called `manifest.json`, and
    may be re-generated on new public releases, and on updates to e.g. the
    fslinstaller script.

  - Development manifests, containing information about one internal or
    development FSL release. Development manifests are generated for every
    internal or development release. Development manifests are named according
    to a standard convention described in the **Internal/development FSL
    releases** section, below.


Manifest and environment files can only be published when they are generated
from a new tag, or when they are generated from specific branches (currently
`master` or `external`). However, manifest and environment files can be
downloaded as GitLab artifacts from any branch.


## New FSL releases


_Summary:_
 - New public FSL release are created by adding a tag to the `external` branch
   of this repository
 - The `deploy-release-manifest` and `deploy-environment-files` jobs, on the
   CI pipeline for the new tag, must be manually started in order to publish
   the new release.


New public FSL releases are denoted by adding a tag to the `external` branch
of this repository. The tag is used as the FSL version identifier, which must
be of the form `X.Y.Z[.W]`, where X, Y, Z, and W are integers.

When a new tag is added to this repository, the `manifest.json` and
`environment.yml` files are generated from the contents of `fsl-release.yml`,
and the contents of the previous `manifest.json` (used for obtaining
information about past FSL releases). These files are named according to these
conventions:

  - `manifest.json` - the release manifest
  - `fsl-<tag>_<platform>.yml` - FSL version `<tag>` for platform `<platform>`
    (e.g. `fsl-6.1.0_macos-64.yml`).
  - `fsl-<tag>_<platform>_cuda<cudaver>.yml` - FSL version `<tag>` for
    platform `<platform>` and CUDA version `<cudaver>`
    (e.g. `fsl-6.1.0_linux-64_cuda11.0.yml`).


After they have been generated, a test installation of the new release on each
supported platform is performed using the `fslinstaller.py` script, and then
the manifest and environment files are published to the FSL release web
server.  This publishing step must be manually triggered through the GitLab
web interface, via the `deploy-environment-files` and
`deploy-release-manifest` jobs.


## Internal/development FSL releases


_Summary:_
 - New internal FSL release may be created by adding commits to the `master`
   branch of this repository
 - New development releases may be created by adding commits to the `external`
   branch of this repository
 - In both cases, the `deploy-environment-files` and
   `deploy-development-manifest` jobs on the associated CI pipelines must be
   started manually.


When commits are added to the `master` or `external` branch of this
repository, separate `manifest.json` and `environment.yml` files are generated
from the contents of `fsl-release.yml` and made available for download.  These
files are assigned a version identifier of the form
`<tag>.<date>.<commit>.<branch>`, where:


where:
  - `<tag>` is the _most recent_ public FSL release version identifier (e.g
    `6.1.0`).
  - `<date>` is the date of the commit that the files are generated from,
    in the form `YYYYMMDD`.
  - `<commit>` is the short hash of the git commit that the files are
    generated from.
  - `<branchname>` is the name of the branch on this repository.


The released files are then named as follows, where:

  - `manifest-<tag>.<date>.<commit>.<branch>.json` - the development release
    manifest file
  - `fsl-<tag>.<date>.<commit>.<branch>_<platform>.yml` - FSL environment file
    for platform `<platform>`.
  - `fsl-<tag>.<date>.<commit>.<branch>_<platform>_cuda<cudaver>.yml` - FSL
    environment file for platform `<platform>` (e.g. `linux-64`) and CUDA
    version `<cudaver>` (e.g. `11.0`).

After they have been generated, the manifest and environment files may be
published. As with public releases, the process of publishing the manifest and
environment files must be manually triggered through the GitLab web interface,
via the `deploy-environment-files` and `deploy-development-manifest` jobs.


## Updates to `manifest.json`


_Summary:_
 - The public release `manifest.json` file can be updated by adding commits to
   the `master` or `external` branches of this repository
 - The `deploy-release-manifest` job on the associated CI pipeline must be
   started manually.


Sometimes the contents of the official release `manifest.json` file may need
to be changed independently of a public FSL release - for example, a new
version of the `fslinstaller.py` script may be released, or the `miniconda`
installer may need to be changed.


Normally, `manifest.json` files that are not associated with a tag are named
`manifest-<tag>.<date>.<commit>.<branch>.json` as outlined above. However, a
new release `manifest.json` file is always re-generated, and can be deployed
through the Gitlab web interface, via the `deploy-release-manifest` job (with
the caveat that only files generated from the `master` or `external` branches
may be published).


Release `manifest.json` files which are generated from branches will only
contain information about past official FSL releases. Release `manifest.json`
files which are generated from new tags will contain information about past
official FSL release, and also about the new FSL release.


## Development workflow


The `fsl-release.yml` file on the `master` branch should be updated as new
versions of FSL projects are released. This will result in new manifest and
environment files for internal installations to be created.


In order to create manifest and environment files for a new public FSL
release, the `fsl-release.yml` file on the `external` branch must be updated.
This can be accomplished using the following process:

1. Clone the `fsl/conda/manifest` repository locally:
   ```
   git clone git@git.fmrib.ox.ac.uk:fsl/conda/manifest.git
   cd manifest
   ```
2. Create a new branch off the `external` branch:
   ```
   git checkout -b rel/6.0.7 origin/external
   ```
3. Merge all changes from the `master` branch onto this branch:
   ```
   git merge origin/master
   ```
4. Resolve any conflicts that arise, making sure that internal-only FSL
   packages are not included in the package lists. A good idea is to compare
   your branch with the `master` branch - usually the only difference should
   be that your branch does not contain any internal-only packages:
   ```
   git diff origin/master HEAD
   ```
5. Merge your branch into the `external` branch on the `fsl/conda/manifest`
   GitLab repository via a merge request. This will result in new manifest
   and environment files for a new development release to be created.

6. If this is a public FSL release, create a new tag on the `external` branch.
   This will result in a new `manifest.json`, and environment files for the
   new FSL release to be created.