Blackbird: A fork of Phinch

[iimog]

Dear developers of Phinch,

I forked your project to https://github.com/iimog/Phinch
By now quite some changes have accumulated:

• All browsers are allowed (original project only allows Chrome)
• BIOM format version 2 is supported (in addition to version 1) by integrating biom-conversion-server and biojs-io-biom
• A few typos and bugs are fixed (e.g. Fix variable name #49)
• Share links are no longer sent via email
• SQL backend switched to sqlite and schema adapted
• A docker image is provided for self hosting

As some of these introduce quite fundamental changes I did not open a pull request, yet.
I plan on hosting a publicly available version of this fork, so my question is:

Is it sufficient to clearly mark this version of Phinch as a fork while keeping the original name and logo (something like Phinch - Fork by iimog) or should I use a completely new name and logo?

Thanks in advance,
Markus

PS: I'm also willing to help integrate my changes into the main project if you are interested.

[iimog]

I wanted to announce that I did a clean fork of Phinch which is called Blackbird.
The repository is at: https://github.com/molbiodiv/Blackbird
A public instance of the server is at: https://blackbird.iimog.org

In case you want to back-port some changes I made into Phinch I'm happy to assist.
It is a great pleasure building on your wonderful work.

[iimog]

@hollybik I need your help with a really tricky situation:
I'm automatically minting DOIs for Blackbird with Zenodo to properly cite specific versions, for example:
https://zenodo.org/record/61721
Zenodo automatically determines the contributors to a repository and lists them as authors.
As fork of Phinch author contributions are preserved in Blackbird and so Zenodo (correctly) lists contributors to Blackbird as:

Shujian Bu ; Markus Ankenbrand ; Nick Yahnke ; hollybik

I think this is the right thing to do as you deserve credit for this derived product. However a proper reference in a journal article might look like:

[1] Shujian Bu, Markus Ankenbrand, Nick Yahnke, and Holly Bik. Blackbird: Version 1.2.0. doi:10.5281/zenodo.61721, September 2016

This would imply however that we worked together on this project. An honor I can not claim. I do not even know if you approve of this project. So citing Blackbird this way is not an option without your consent.
As this entry is automatically generated I can not change the list of authors (and I think this would also not be the right thing to do).
So I'm stuck here. I'm eager to hear your opinion about this.
If you disapprove of using the Zenodo doi for citation I will drop the integration and go back to citing the project by url.

[iimog]

I solved the Zenodo citation problem as described here:
https://openscience.uni-bielefeld.de/985/how-to-properly-use-zenodo-dois-for-derived-software
Let me know if you are not okay with that.

[hollybik]

Hi Markus, Apologies for the delay in responding to you - I started a faculty position on Aug 1 (involving a cross-country relocation on top of setting up a new lab), and I'm only just getting through my backlog of emails. I submitted a review for your F1000 paper this morning, but I wanted to paste it here to get your feedback too - I think the "Blackbird" rebranding is not a good idea. I know you had to make a choice about this given my absence/silence, but I suggest we revert back to Phinch branding - you can submit a pull request and we will integrate your biom conversion tools into the live implementation of Phinch at http://phinch.org - what do you think?

Thanks for your bug fixes to the Phinch codebase, they all look great! And the conversion tools are an exciting (and much needed) new feature for people working with QIIME 1.9 onwards, since that is the main FAQ we are currently getting from users.

Here is an excerpt from my reviewer report explaining this rationale:

Since this project is based on the Phinch framework, I find the "Blackbird" rebranding of the fork to be very problematic. The "Blackbird" instance is really just an updated release of the Phinch framework, with some bug fixes, added features, and implementation of the new BIOM conversion server. The rebranding/renaming is confusing for the end user (see comment by other peer reviewer below), and mistakenly implies a number of scenarios that are not accurate: 1) that the authors were involved in the original development of data visualization tools, 2) that the Blackbird rebranding and design changes were approved from by the original developers, and 3) the "Blackbird" project represents a significant expansion or retooling of the current Phinch framework. I’m fully aware that this is open source software and the authors are free to reuse and share the Phinch codebase, but I don't really see the utility of the "Blackbird" rebranding, and creating an additional web instance that mostly replicates the functionality of http://phinch.org will confuse end users.

Since the authors here are really community contributors to the original Phinch project, I would recommend eliminating the "Blackbird" rebranding of the project, and reverting back to Phinch branding (citing the framework release as Phinch v2.0). We will then initiate a pull request to update the bug fixes and integrate the new biojs-io-biom source code to be live on http://phinch.org The visual layout for Phinch (name, logo and visualization layout) was thoughtfully constructed, and the new Blackbird logo and visual modifications will likely interfere with “brand recognition” that should be attributed to the original Phinch framework.

Once this pull request is initiated and completed, the “Application” manuscript text should be updated to reflect the live implementation of the conversion library on a v2.0 Phinch framework at phinch.org.

[iimog]

Hi Holly,

thanks for your reply. I hope you had a good start into your new position. Also many thanks for taking the time to submit a review for our F1000 paper. I'm absolutely happy with reverting all Blackbird branding and using Phinch in the fork as well. It was a solution we were not happy with either. But we felt that we can not (without permission) keep the name Phinch - because that would imply all of your three points (involvement in original development, approval by original developers, significant contribution) even more than the renaming. I will gladly submit my changes as a pull request to the Phinch repository. I will also shut down the public blackbird.iimog.org instance as soon as phinch.org is updated - it was meant mainly as proof that the changes we made are actually working.

Some questions:

1. Would you like to get a single pull request with all the changes or rather one pull request per feature/bug fix?
2. There are some changes (e.g. allowing browsers, other than Chrome, switching from MySQL to SQLite) that you might not want to integrate into the official Phinch instance. If so, tell me which ones I should leave out.
3. Integrating the biom-conversion-server also requires to have the official biom python command line tool installed on the server. If this is no problem you can skip the rest of this point. We built a docker container with biom and all dependencies installed. Also the web server parameters (like maximum allowed file size for upload) are optimized. Feel free to use this docker container. Alternatively just the biom-conversion-server can be hosted as a docker container or the conversion of biom version 2 can be delegated to biomcs.iimog.org - whatever you prefer.
4. I'd like to keep a fork of Phinch for further development as I plan to add some other features (e.g. donut partition plots for other observation metadata than taxonomy). I will suggest all features and future bug fixes as pull requests to the main Phinch project as well. Is it okay to keep the fork of Phinch under the name Phinch under this conditions?

Thanks again for your kind and comprehensive reply.

[iimog]

I opened the pull request (see #67). It contains all changes in a single pull request but with modular commits. Both biojs-io-biom and biom-conversion-server are included. So only the biom python package has to be installed on the server in order for the conversion to work. I also replaced the public Blackbird server with a preview instance of Phinch (with the functionality it will have after merging the pull request) https://blackbird.iimog.org. (Only sending mails when sharing is disabled on my server). I also added a note in the README of the Blackbird repo that it will retire after this pull request is merged.
If there is anything else I can do, please let me know.

[iimog]

Dear Holly,

we are currently working on the revision of our f1000 manuscript.
The plan is to submit the revised manuscript before Christmas.
We would like to remove all references to Blackbird which requires the merge of our pull request (#67).
I hope you find the time to do that in the next couple of days.
Let me know if there is anything I can do to assist.

Best regards,
Markus

[hollybik]

Hi Markus,

Apologies for the very belated response here - going through all the GitHub issues and realize I never responded. In case you didn't see, we're (hopefully) re-entering active development in July, so once we start work on Phinch 2.0 we will merge your pull request ASAP. Sorry we can't take action sooner, we have to wait until futher funding comes through for the developers to resume work.

Thanks,
Holly

[iimog]

Hi Holly,

thanks for your answer. I'll keep my fingers crossed for the funding to be approved.
In my opinion Phinch is already a great tool with the potential to be even better.
I'm looking forward to the next stage of development.

Best regards,
Markus