Documentation

Main Page -> Documentation

Mailing lists and collaborative tools

• Project web page: has to come
• General mailing list: pCT@uib.no
• Slack project

Software installation

• Software tutorial at IFT
• ROOT installation
• Geant 4 installation
• Gate installation
• FLUKA installation
• Insight Toolkit (ITK) installation

  https://itk.org/

  https://github.com/InsightSoftwareConsortium/ITK

• Reconstruction Toolkit (RTK) installation

  http://www.openrtk.org/

  https://github.com/SimonRit/RTK

• DTC Toolkit for reconstruction

  User guide and tutorial

  https://github.com/HelgeEgil/focal (to be merged into gitlab)

  Cluster convolution for GATE

• Visualization Toolkit (VTK) Installation and usage

  http://www.vtk.org/

  https://github.com/Kitware/VTK

Software repository

We use the gitlab server hosted by IT of University of Bergen.

Get access to the repositories - with UiB account

Open the UiB gitlab web interface.

Log in with your UiB account, then the administrators will give you access to the pCT group. Since authentication goes via Dataporten service, accounts from other Norwegian universities or institutions can be used in the same way.

Get access to the repositories - without UiB account

It is possible to use a github user account to login to the UiB gitlab, however such external users are not allowed to create forks in the gitlab domain. Since forks are mandatory for the development cycle, github logins can effectively only be used for read access. Again the repository administrators need to add you to the pCT group.

Guest accounts for external developers can be set up, get in contact with the group over the general channels

Further information:

• Gitlab basics
• Gitlab workflow

Development workflow

Every logged-in user can access the main repository, however only a small group of administrators has write access. To contribute, a user creates a fork (see here) from the repository. This is a repository copy in the Gitlab system where a single developer or a group of developers have full access.

A local copy of the repository is required on the working machine in order to work on the project. This copy is referred to be a clone (see here).

Making local working copy

A project is utilized through a local working copy referred to be a clone. The project can be cloned from either the main repository in the group space or the fork in the user space depending on the role.

In the examples replace user and wpn (e.g. wp7) appropriately.

Note: the gitlab offers two modes for the link to be cloned, you can choose ssh (default setting) or https. If you can not clone with the proposed default link, try option https://.

From the main repository

The main repository is cloned like

   git clone https://gitlab.uib.no/pct/wpn.git

The upstream link can be changed later to any other repository like e.g. a development fork as follows (given the clone directory is the current working directory)

   git remote set-url origin https://user@gitlab.uib.no/user/wpn.git

The originally cloned remote repository will get the identifier origin in your local clone.

From development fork

Clone directly from your development fork

   git clone https://user@gitlab.uib.no/user/wpn.git

This will create a local directory wpn, an optional argument after the link allows to change the directory name, e.g.

   git clone https://user@gitlab.uib.no/user/wpn.git mywork

Multiple upstream repositories

As a more advanced option, multiple remote repositories can be added to the clone. All remote repositories are referenced through their identifiers, e.g. origin pointing to the fork and pctgroup pointing to main repository (chosen as an example).

   git remote add pctgroup https://gitlab.uib.no/pct/wpn.git

Check configured upstream repositories

The configured upstream repositories can be checked with

   git remote -v

This will display the identifier and link to the configured upstream repositories.

Pushing to development fork

Once you have added commits to e.g. the dev branch, those commits can be pushed upstream to the fork (if origin refers to the fork)

   git push origin dev

Or using the direct link

   git push https://user@gitlab.uib.no/user/wpn.git dev

Importing an external package

The project will use a couple of external packages which are hosted in a different master repository. Copies of such external packages can be added to the gitlab server under our project group to provide a consistent package.

Here is a proposed workflow for importing a package which is already hosted in git.

1. Create new repository in the pCT group or ask for creation, lets call it newPackage
2. Fork the repository to your user space
3. Clone the package you want to import

    git clone <some_external_link> newPackage # we give it the new name

    cd newPackage

4. Redirect upstream URL to the fork in your gitlab user space

    git remote set-url origin https://user@gitlab.uib.no/user/newPackage.git

5. Now make a forced push (option -f) to import the repository to your fork

    git push -f origin

6. Create merge request to branch import (if not existing, master or any other appropriate branch) by following the instructions Pull/Merge request