My Blog

Dedication to the late Professor Ian Bryden

My life would not be the same today if it were not for Prof. Ian Bryden. I would not be doing the work I am doing, in Ian’s beloved field of ocean renewable energy, and I may not even have the family I love if it were not for Ian.

Initially, Ian started as somewhat of a mythical figure to me. While I was searching for a masters project at the University of Southampton, I was fortunate enough to get an email from Prof. Bakr Bahaj, who would later hand me one of Ian’s articles regarding the exciting new technology of tidal current energy conversion. This would set me on the road to becoming an ocean energy researcher, and it would not be long before I would meet Ian again, while being interviewed to become a PhD student under the Supergen Marine programme.

I began my PhD in Robert Gordon’s University in Aberdeen, with Ian as my first supervisor, which would soon become a PhD in the University of Edinburgh, following Ian’s return to the home of his PhD (Ian would later be drawn back to the north to join the University of Highlands and Islands in Inverness). It was at the University of Edinburgh that I met Lucy, my amazing long-term partner and mother to my son.

Completing my PhD was not easy. There were many moments when I considered quitting and it took substantially longer to finish than it should have done. Nonetheless, Ian always supported me, and he was always willing to trust in my ability to meet my potential.

Ian was also a good laugh. I fondly remember being regaled with tales of Subarus and Wankel engines, and it was always fun to spot Ian’s leather jacket being sported in his (numerous) television interviews. It was always a pleasure to be in his company and I am sad that I will not have the chance to speak with him again.

Ian and I also shared another geeky interest, that of Star Trek. I must admit to a tinge of jealousy at Ian’s collection of Star Trek models, proudly displayed in his office – I wish I had the courage to be so openly Trekkie! The overarching theme of Star Trek is exploration, which is the same reason that we do science. I’m proud to have published an article (alongside my co-authors) in Ian’s special Issue in Renewable and Sustainable Energy Reviews, and I hope, Ian, that you would be proud of our achievements (and maybe enjoy the content, too!). Thank you for your faith in me and for making all this possible, and for teaching me to boldly go where no one has gone before…

Latex PhD Thesis Template Update

New Lay Summary Section

The unofficial University of Edinburgh latex PhD thesis template, edengths, has been updated to include the new requirement of a “Lay Summary” section. This follows changes to the thesis regulations at The University of Edinburgh. The summary section is added by using the latex command \summary within the precntnt.tex file. This is included by default in both the standard and nomenclature versions of the template.

Migration to Github

To provide a more friendly environment for collaborative development of edengths I have moved the code from Bitbucket to Github. The repository can now be found here. Contributors should follow similar rules to those laid out for DTOcean. The main difference with edengths is that two branches are supported - the master branch which contains the standard template and the nomencl branch which contains the version including a nomenclature.

DTOcean Development: Change Management

Github Repository Structures

In the interest of external engagement and maintaining a fairly simple management structure for handling updates through pull requests, a process similar to many mature python packages that are developed through Github, such as IPython or Pandas, will be used.

The basic concept is that each repository will have just two branches as follows:

  1. Master: This is the default branch of Github repositories and will carry the development version of each package. This branch should be stable and should work with upstream packages but it is not guaranteed.
  2. Release(s): This branch will hold the latest stable version of the code. The branch itself will be labelled following the “major.minor” version number of the package and then tags will be used to indicate micro version changes. It may be that multiple release branches need maintained while upstream packages “catch-up” to the release, but the older releases should have no further commits made to them.

Package Version Numbers

The version numbering of the DTOcean packages generally relates to the amount of effort required for upstream repositories as a result of changes made downstream. Some typical examples of changes for the three level version hierarchy is as follows:

  • Micro version: Small bug fixes that make no API changes
  • Minor version: Minor API changes that require small changes upstream; More significant code changes for new features, performance or accuracy improvements but which do not significantly alter the results
  • Major version: Major API changes that significant affect other components of DTOcean or the data model; Changes that significantly alter the results of the code from new features or changes to existing features.

Some judgement may be necessary as to define the appropriate level to be incremented for a particular change, but the idea is that the hierarchy considers the level of impact on upstream packages. Indeed, beyond micro version changes (which should require no action from upstream) the developers of upstream packages should be consulted to discuss the likely level of impact.

The updating of a version number in a package should “automatically” trigger an update of the matching hierarchy version in upstream packages. Although this can not really happen automatically for changes other than micro versions, the process should be instigated once the upstream package developer has been made aware of the change through the DTOcean Mailing List.

Development Stack

In order to allow developers of modules to evaluate the impact of their changes, outside of any automated tests, it is necessary to provide a development stack that can be used to create a “local” version of DTOcean.

To facilitate this the stable (release) version of all the DTOcean packages will be made available through Anaconda Cloud, which can then be installed through the “conda” package management system.

Details of how to install and develop the complete DTOcean system can be found on the dtocean-app Github repository page.

Updating Process

All updates to the dtocean repositories shall be handled through pull requests and apart from micro version bug fixes, they should be made against the master branch. In the case of micro version changes these should be submitted to the current release branch.

In order to cleanly maintain the two public branches, other branches must not be part of any pull request. Private branches are not discouraged, but when submitting to the public server they must either be “fast-forward” merged or “rebased”. This way all changes are maintained in the master branch.

The same process should be followed for changes submitted to the release branch but those changes may or may not be incorporated into the master branch depending on its level of development.

This process is detailed in the following subsections which is adapted from the descriptions in Nicola Paolucci’s blog post.

Creating a Fork and Cloning

The developer should use a personal fork of the DTOcean repository, rather than working directly on the official repositories themselves. The process is started as follows:

  1. “Fork” the DTOcean repository into a personal repository on Github. This can be done using the “Fork” button in the top right of the Github page.
  2. “Clone” the personal fork onto your computer to produce a local working copy.

Syncing the Fork

It is desirable to keep the fork in sync with the official repository, both for submitting work and reusing the fork in the future (rather than deleting and cloning again).

A summary of the syncing process is as follows:

  1. Add the DTOcean repository as the “upstream” remote.
  2. “Fetch” changed from upstream.
  3. Apply those changes to your local master branch.
  4. Push the updates to Github

In code:

git remote add upstream*.git
git fetch upstream
git checkout master
git rebase upstream/master
git push origin

Steps 2, 3 & 4 can be repeated as required. Note that we never merge branches in this approach to repository management.

Creating a branch and working on it

In your personal fork, create a new branch to create your new code and test it. DO NOT WORK ON THE MASTER OR RELEASE BRANCHES. If you submit a pull request on either of these branches your local fork will become irrecoverably out of sync with the DTOcean organisation version.

Do your work on the new branch in your personal fork. You can commit and push this branch without worry. When the code is ready and tested the branch can then be prepared for a pull request.

Rebase the branch

Before submitting your branch as a pull request, it is useful to rebase the branch with the current upstream repository. Assuming that the feature is being developed on branch “feature-x” the rebasing process is as follows.

git checkout feature-x
git fetch upstream
git rebase upstream/master
git push origin

Assuming there are no conflicting changes on the official repository this should happen smoothly. Otherwise you may need to resolve a merge conflict, see Resolving merge conflicts after a Git rebase for a description about how to resolve these. Its possible you may also need the “-f” flag for the push, if the rebase has changed the history of your personal fork.

Once the rebase is done, a pull request can be made on the GitHub website.

Pull Request

Use the interface to make a pull request for your branch. Switch to the feature branch and push the “New pull request” button. Make sure that the base fork points to the official DTOcean repository and that the base branch is either “master” or a release branch.

Add a short message about the purpose of the pull request and ensure that the “allow edits from maintainers” box is ticked so that the official repository maintainer can help. Then click “Create pull request”.

Modification, Acceptance and Tidy-Up

Once the pull request has been submitted the repository maintainer will review it and maybe make suggestions as to how it can be improved. They may also work on the branch itself. If you add commits to the branch, these will automatically be included in the pull request.

Once the maintainer is happy, the request will be accepted and the branch will be rebased into the requested official branch. The feature branch will then no longer exist in the history of the official repository and should be deleted in your personal copy. This can be started by pressing the “Delete branch” button at the bottom of the pull request.

Following the branch delete in your person Github repository, the local repository should be synced to the updated official repository so that you can see your changes and continue working. The process is as follows:

git checkout master
git fetch upstream
git rebase upstream/master
git fetch origin --prune
git branch -D feature-x
git push origin

This process will align your master (or release) branch with the official repository and then prune and delete your feature branch. Note that “feature-x” should be replaced with the name of your feature branch.

Returning to your personal Github repository of the package should now show the message:

This branch is even with DTOcean:master.

Impact on other DTOcean Packages

The act of making a pull request allows time for both review of the new code itself, but also the impact on upstream packages. If it is deemed in the pull request that some work is required upstream, this work can be scheduled. In terms of minor changes, and assuming the code passes review, scheduling upstream changes may be sufficient to allow the pull request to be merged. However, for major changes, the pull request may be delayed until the upstream packages are ready or (in extreme circumstance) may be moved to another branch or repository.

Collaborative Working

Although the above process would seem to suggest that either working alone to create stable code or submitting unstable code in order to facilitate collaboration are the only options available. However, this is not the case, it’s just that collaboration on a fix or feature should be carried out on a forked repository rather than the official repository itself. In the forked repositories any number of collaborators and branches can be utilised.


The project will also endeavour to maintain useful change logs, as described at, in order to provide a user friendly description of changes between versions. An official approach for maintaining these changelogs is yet to be decided, however.

Further Reading

Further reading about the mechanism for this “Trunk” style updating process can be found in the following references:


The techniques presented in this blog post represent a new paradigm for the development of DTOcean. Previously it followed a multi-branch approach with each team maintaining their own branch before integration. Some mistakes will certainly be made along the way while we learn to effectively implement these new processes, but aligning with common practice in open source development will allow the developer base to grow beyond the original project development team.