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[PRE REVIEW]: bio-go: A flexible tools Bioinformatics library #1645
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Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. For a list of things I can do to help you, just type:
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What happens now? This submission is currently in a You can help the editor by looking at this list of potential reviewers to identify individuals who might be able to review your submission (please start at the bottom of the list). Also, feel free to suggest individuals who are not on this list by mentioning their GitHub handles here. |
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👋 @rhagenson - please add to your paper an explantation of what research problems your software can help with (which is another way of saying who will cite your software). Perhaps add a little about how they would use your software. When you have done so, please enter |
@whedon generate pdf |
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👋 @lpantano - would you be willing to edit this? |
OK, the editor is @lpantano |
Hi @rhagenson, thanks for submitting to JOSS. I look around but I couldn't find any documentation of the tool. One of the mandatory requirement is to have full documentation with examples. If it is already done, can you put the link in the readme of the repo? Cheers |
@lpantano Documentation can be built through I have been using property tests to serve as both tests and examples. These can be run and seen from the repo root through I will add all the above directive information on viewing documentation and running tests to the README later today. In your opinion, are there other additions I need to make? |
Thank you for the detailed explanation, I think that would help a lot to show potential users how they can use your tool, and then the goDoc can get into details. Thanks for making the changes. |
@lpantano I added the documentation and testing sections to the README. However, due to my immediate schedule I will not be able to add |
@adavidzh, would you be interested in reviewing this tool? |
@lpantano Not done with the examples (they are being developed on
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@krother, do you think you would have time to review this new tool? Thanks |
@mskwark, would you be interested in reviewing this tool? |
I was asked (by email) to review, but declined: Sadly I know nothing about Go, and the project's current state of documentation leaves too steep a learning curve for me or any other bioinformatician curious to try it. It needs a quick start, I would think even a trivial example like loading a given DNA sequence (be it with IUPAC ambiguity codes or just A, C, G, T bases) from a FASTA file, translating it into an amino acid sequence, and then writing out this protein sequence as a new FASTA file would be useful. Looking at the module names I think this functionality would be covered already. |
@peterjc Thank you for the advice on a helpful and explanatory aggregate example of usage reading in a given DNA FASTA, translating it to protein, and writing it out as a new FASTA. In your opinion, are there any other rough edges about the project in its current state that need smoothing? |
@rhagenson the beginner documentation was the main thing lacking - beyond that it was hard to say more, sorry. |
@peterjc Thank you for the help you provided. I will add more documentation at the beginner level. |
@kortschak, would you like to review this tool? |
Sure. |
Happy to review this too if needed |
@whedon assign @kortschak as reviewer |
OK, the reviewer is @kortschak |
@whedon add @will-rowe as reviewer |
OK, @will-rowe is now a reviewer |
Thank you both to agree on reviewing this tool. I will wait until docs are updated to start the review. |
@lpantano, I finished writing the beginner documentation (available at https://bio-ext.github.io/bio-go/) and the updated version number is v1.1.3. |
@whedon start review |
OK, I've started the review over in #1741. Feel free to close this issue now! |
Submitting author: @rhagenson (Ryan Hagenson)
Repository: https://github.com/bio-ext/bio-go
Version: v1.0.0
Editor: @lpantano
Reviewers: @kortschak, @will-rowe
Author instructions
Thanks for submitting your paper to JOSS @rhagenson. Currently, there isn't an JOSS editor assigned to your paper.
@rhagenson if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.
Editor instructions
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