Blackbird

[iimog]

This pull-request will add the following features from Blackbird (related to #63):

• Add support for BIOM version 2.x
• Add automatic conversion from dense to sparse (Fix Unable to import dense biom files #64)
• Export as svg (Fix Need option for Hi-Res graphic export #43, taxonomy bar charts exporting with low res and bad font, also can't re-order bars #35)
• Allow all Browsers (Fix Why is Phinch limited to Chrome Browser? #57)
• Correct License file (Fix Ambiguous licensing #56)

Further the pull requests by @bgruening and @blankenberg are included:

• Resolves Fix variable name #49
• Resolves Enable URL BIOM file import and fix bugs. #54

The pull request by @colinbrislawn will be obsolete:

• Closes add JSON conversion to README.md #60

All possibly conflicting changes (e.g. switch to SQLite) are not included in this pull request. Instead of Blackbird a preview version of Phinch after merging this pull request is running on https://blackbird.iimog.org. I will shut it down as soon as this pull request is merged.

To deploy the new version of Phinch on your server make sure that the python biom tool is installed. Otherwise upload of hdf5 files will result in an error. Please refer to these instructions: http://biom-format.org/#installing-the-biom-format-python-package

If there are any further questions I'm happy to assist.

[bgruening]

@iimog thanks for assembling this all together!

[iimog]

Added a fix for bug #69 (hiding of wrong OTUs)

[colinbrislawn]

Good afternoon @shujianbu, @hollybik, @nthitz

Could you tell me more about the status of Phinch? Given that this repo has not been touched in 2+ years, should we continue to submit PRs to this repo, or continue development in another fork?

Thanks for making this software! 🐦 🛫

[bgruening]

@hollybik since this is an organisation, would it be possible to give someone else commit access so that we can maintain this repo?

[hollybik]

Hi @bgruening @colinbrislawn - the tentative plan is for Phinch to re-enter active development on July 1, 2017 (pending our funding renewal being approved through the Sloan foundation). Can you wait two months, or do we need to merge these commits now?

We're going to come up with a better plan for community contributions and repo maintenance once we re-enter development - I agree this situation has not been ideal the past two years. Currently @nthitz has the primary repo oversight at Pitch Interactive, and I'm not sure what their capacity is to merge these pull requests. This repo feeds directly back to http://phinch.org, so any changes here will affect the live website (hence why only select people have commit access at the moment.

[colinbrislawn]

This sounds very reasonable. I wish you good luck for funding, and I really appreciate your communication to this small developer community.

Having a commercial sponsor leading development is very worthwhile. I'm willing to wait and see about funding, before we do independant development on a fork.