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[[Main Page]] -> [[Documentation]]
[[Main Page]] -> [[Documentation | Software Documentation]]
 
This is the landing page for software documentation, installation instructions, the development workflow, etc.


== Mailing lists and collaborative tools ==
== Mailing lists and collaborative tools ==
* Project web page: has to come
* Project web page: [https://www.uib.no/en/ift/142356/medical-physics-bergen-pct-project https://www.uib.no/en/ift/142356/medical-physics-bergen-pct-project]
* General mailing list: pCT@uib.no
* General mailing list: pCT@uib.no
* [https://pctbergen.slack.com Slack project]
* [https://pctbergen.slack.com Slack project]
== [[Software structure]] ==


== Software installation ==
== Software installation ==
* [[Software tutorial at IFT]]
* [[ROOT installation]]
* [[ROOT installation]]
* [[Geant 4 installation]]
* [[Geant 4 installation]]
* [[Gate installation]]
* [[Gate installation]]
* [[FLUKA 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|DTC Toolkit for reconstruction]]
*: [[Software for design optimization|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
* [[Docker containers]]


== Software repository ==
== Software repositories ==
We use the '''gitlab''' server hosted by IT of University of Bergen. We start with a repository per ''work package (wp)''. As there is overlap in terms of software, this structure might change in the future. Log in with your UiB account, then the administrators will give you access to the pCT group. If you don't have an account yet, get in contact with the group over the general [[Documentation#Mailing lists and collaborative tools | channels]]. There might be an admin mailing list later.
We use the '''GitLab''' service hosted by IT of University of Bergen: [https://git.app.uib.no/ https://git.app.uib.no/]


* [https://gitlab.uib.no/pct UiB gitlab web interface].
=== Get access to the repositories - with UiB account ===
Open the [https://git.app.uib.no/pct UiB gitlab web interface].


Further information:
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.
* [https://docs.gitlab.com/ce/gitlab-basics/README.html Gitlab basics]
* [https://docs.gitlab.com/ee/workflow/README.html  Gitlab workflow]


==== [[Gitlab best practice]] ====
=== 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.


== Development workflow ==
Guest accounts for external developers can be set up, get in contact with the group over the general [[Documentation#Mailing lists and collaborative tools | channels]]
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''  from the repository. This is a copy where a single developer or a group of developers have full access.


The main repository has the following branches:
Further information on GitLab in general can by found on the following external webpages:
* '''production''': the latest production code, in this branch we have release tags
* [https://docs.gitlab.com/ce/gitlab-basics/README.html Gitlab basics]
* '''master''': the latest stable release
* [https://docs.gitlab.com/ee/workflow/README.html  Gitlab workflow]
* '''dev''': the development branch


In addition to those main branches there can be ''feature'' branches where development happens detached from the main branches. A ''feature'' branch is based on the ''dev'' branch and has a limited lifetime.
<br>
The specific instructions how to use the repositories within the pCT project are collected in the following pages:
==== [[GitLab best practice]] ====
==== [[GitLab Developer FAQ]] ====
==== [[Gitlab Master FAQ]] ====


=== Creating a project fork ===
== Getting the code ==
A ''project fork'' or ''repository fork'' is a copy of the original repository where a user or a group of users has/have full control. All development in our project is carried out in the individual forks. Branches of project forks are merged back into the main repository by '''merge requests''', preferably via '''fast forward''' merges. That requires developers to rebase project forks to the main repository and resolve all conflicts before requesting a merge.
If you simply need the code, you can download an archive from the GitLab web interface. However, if there is a tiny chance that you might start developing, the recommended way is to clone the repository. See [[GitLab best practice#Roles]].


[https://docs.gitlab.com/ce/gitlab-basics/fork-project.html How to fork a project]
== 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''' from the repository. This is a repository copy in the GitLab system where a single developer or a group of developers have full access, see [[GitLab Developer FAQ#Working with forks]].
Your repository fork is your sandbox, you can do whatever you want. Unless you have your own rules at hand right now you can apply the following:
* leave the ''master'' branch in sync with the main repository, do not make commits to it
* commit your changes to the ''dev'' branch
* if you start a new feature, and it's expected to take a while, make a ''feature'' branch, e.g. ''dev-feature'' and give the feature a name
* synchronize regularly to the main repository by rebasing (tutorial coming soon)
 
=== Making local development copy ===
==== From development fork ====
Clone directly from your development fork, 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://''.
    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
 
The remote repository will get the identifier ''origin'' in your local clone, check with
    git remote -v
 
==== 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
 
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.
    git remote add pctgroup https://gitlab.uib.no/pct/wpn.git
 
=== 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
 
=== Pull/Merge request ===
All updates to the main repository are made via ''merge requests'' (github refers to them as ''pull requests''). A merge request requires the code update to be in a mergable branch in a development fork.
 
Merge request are also used widely to share ''work-in-progress'' with your colleagues and for code reviews. Mark such Merge request with "'''WIP:'''".
 
==== Preparation ====
In order to avoid conflicts, first the fork has to be updated to the main repository. The idea behind this is that all potential conflicts can be resolved by the developer with the best knowledge about the matter, while the maintainer can simple merge ''fast-forward''.
 
This description expects ''origin'' pointing to the fork and ''pctgroup'' pointing to main repository (see [[Documentation#From_the_main_repository | here]]).
 
# Synchronize with main repository
#: <pre> git remote update</pre>
# Rebase your development to the main repository, ''rebase'' means that all the new commits are done with respect to the tip of the specified branch. There can be ''merge conflicts'' which need to be resolved with appropriate changes and commits.
#: <pre> git rebase remotes/pctgroup/dev dev</pre>
# Check your commits and commit messages, eventually ''squash'' (combine) or ''reword''. This advanced option is described later.
# Push to fork. As the commit history has most likely been changed, the option ''-f'' (force) has to be used
#: <pre> git push -f origin dev
 
The branch ''dev'' in the fork is now ready for a merge request. The branch name can be adjusted, there is nothing preventing other branch names.
 
==== Example workflow for a Merge request ====
# Go to your gitlab user space at [https://gitlab.uib.no/user https://gitlab.uib.no/user] (replace ''user'' appropriately.
# Find the project fork, e.g. in the list of projects associated with you from the upper main menu.
# In the line with the many columns regarding the repository, click on the "+"-symbol on the right hand side and choose "New merge request"
# Select project and branch for both source and target, and click "Compare branches and continue"
# Review the list of commits in this merge request, give it a descriptive title and description, pick an assignee
# Submit the merge request
 
=== 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.
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 [[GitLab Developer FAQ#How can I make a clone of a project in my fork]].
# Create new repository in the pCT group or ask for creation, lets call it ''newPackage''
# Fork the repository to your user space
# Clone the package you want to import
#:<pre> git clone <some_external_link> newPackage # we give it the new name</pre>
#:<pre> cd newPackage</pre>
# Redirect upstream URL to the fork in your gitlab user space
#:<pre> git remote set-url origin https://user@gitlab.uib.no/user/newPackage.git</pre>
# Now make a forced push (option ''-f'') to import the repository to your fork
#:<pre> git push -f origin</pre>
# Create merge request to branch ''import'' (if not existing, ''master'' or any other appropriate branch) by following the instructions [[Documentation#Pull/Merge request | Pull/Merge request]]


== User documentation ==
== User documentation ==

Latest revision as of 11:28, 17 March 2021

Main Page -> Software Documentation

This is the landing page for software documentation, installation instructions, the development workflow, etc.

Mailing lists and collaborative tools

Software structure

Software installation

Software repositories

We use the GitLab service hosted by IT of University of Bergen: https://git.app.uib.no/

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 on GitLab in general can by found on the following external webpages:


The specific instructions how to use the repositories within the pCT project are collected in the following pages:

GitLab best practice

GitLab Developer FAQ

Gitlab Master FAQ

Getting the code

If you simply need the code, you can download an archive from the GitLab web interface. However, if there is a tiny chance that you might start developing, the recommended way is to clone the repository. See GitLab best practice#Roles.

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 from the repository. This is a repository copy in the GitLab system where a single developer or a group of developers have full access, see GitLab Developer FAQ#Working with forks.

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 GitLab Developer FAQ#How can I make a clone of a project in my fork.

User documentation

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