[REVIEW]: CAZy-parser a way to extract information from the Carbohydrate-Active enZYmes Database about joss-reviews HOT 37 CLOSED

I can review this, @pjotrp

from joss-reviews.

from joss-reviews.

I'll do it this weekend.

On 09/27, Pjotr Prins wrote:

Hi @luizirber, any idea when you can do the review? Thanks.

You are receiving this because you were mentioned.
Reply to this email directly or view it on GitHub:
#53 (comment)

from joss-reviews.

Great. @luizirber can you take another look?

from joss-reviews.

Sorry for the delay @arfon I'll look into it asap.

from joss-reviews.

@luizirber many thanks for the review here and @pjotrp many thanks for editing this submission ⚡

@rodrigovrgs - your paper is now accepted into JOSS and your DOI is http://dx.doi.org/10.21105/joss.00053 ⚡️ 🚀 💥

from joss-reviews.

/ cc @openjournals/joss-reviewers - would anyone be willing to review this submission?

If you would like to review this submission then please comment on this thread so that others know you're doing a review (so as not to duplicate effort). Something as simple as :hand: I am reviewing this will suffice.

Reviewer instructions

• Please work through the checklist at the start of this issue.
• If you need any further guidance/clarification take a look at the reviewer guidelines here http://joss.theoj.org/about#reviewer_guidelines
• Please make a publication recommendation at the end of your review

Any questions, please ask for help by commenting on this issue! 🚀

from joss-reviews.

I'm not @rodrigovrgs

from joss-reviews.

I'm not @rodrigovrgs

Thanks @rvargas. Seems like @rodrigovrgs gave us the wrong GitHub handle :-|

from joss-reviews.

That's strange—the "Submitting author" looks correct

from joss-reviews.

That's strange—the "Submitting author" looks correct

Yeah but the submitting author also just enters their GitHub handle manually which it looks like @rodrigovrgs did incorrectly.

from joss-reviews.

That's strange—the "Submitting author" looks correct

Yeah but the submitting author also just enters their GitHub handle manually which it looks like @rodrigovrgs did incorrectly.

Sorry for that, I'm the @rodrigovrgs you are looking for. @arfon, is there a way for me to fix handle?

from joss-reviews.

@rodrigovrgs - I've updated this thread with the correct GitHub handle. You can just change your GitHub username on JOSS here: http://joss.theoj.org/profile

from joss-reviews.

I am not in a position to review this paper, but I would like to note this software consists of about 400 lines of code. I would like to ask the author to confirm here that he thinks this software is a valuable contribution to research. I want to point out that once this work has been published it will be visible forever. Adding an example of having used this tool in research would be strongly recommended.

from joss-reviews.

Hi @rodrigovrgs - I am looking for a reviewer for your submission. Do you know anyone who may be interested in reviewing and who is independent?

from joss-reviews.

@whedon commands

from joss-reviews.

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the reviewer of this submission
@whedon assign @username as reviewer

# List the GitHub usernames of the JOSS editors
@whedon list editors

# List of JOSS reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Change editorial assignment
@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Open the review issue
@whedon start review

🚧 Important 🚧

This is all quite new. Please make sure you check the top of the issue after running a @whedon command (you might also need to refresh the page to see the issue update).

from joss-reviews.

@whedon assign @pjotrp as editor

from joss-reviews.

OK, the editor is @pjotrp

from joss-reviews.

@whedon assign @luizirber as reviewer

from joss-reviews.

OK, the reviewer is @luizirber

from joss-reviews.

Hi @luizirber, any idea when you can do the review? Thanks.

from joss-reviews.

@luizirber ping. When do you have time to review?

from joss-reviews.

The software is useful and I think it should be accepted, but some points need to be addressed:

• Installation instruction can be clearer: it only talks about dependencies,
  but doesn't say that the repository needs to be downloaded or where to get the
  released version. Can you add a setup.py and publish the package to
  PyPI? pip is the standard way of installing Python packages, this also
  increases the reach of your software. I see @jkhan already added an issue for this: rvhonorato/cazy-parser#2
• Functionality documentation: there is no exposed API besides the two scripts,
  for using from a shell. One of them doesn't have options, and the other one uses argparse for options.
  Even if there are no options create-cazy-db.py could have a --help option to at least explain what the command does.
• Automated tests: not available.
• Community guidelines: Kind of. There is an email for contact, but no guidelines
  on how to collaborate. A CONTRIBUTING.md file in the repo goes a long way on
  addressing this.

from joss-reviews.

Sorry for the delay @pjotrp. @rodrigovrgs, I can help with more details on how to address these points if you want, should I open some issues in the cazy-parser repo?

from joss-reviews.

@luizirber thanks for your review! No need to take extra action on your part.

from joss-reviews.

@pjotrp @luizirber I'll address the issues as soon as I can, thank you very much!

from joss-reviews.

@luizirber thanks for your review, I've made some changes to the code and the documentation to fit your feedback and make the code compliant to joss.

Installation instruction can be clearer: it only talks about dependencies,
but doesn't say that the repository needs to be downloaded or where to get the
released version. Can you add a setup.py and publish the package to
PyPI? pip is the standard way of installing Python packages, this also
increases the reach of your software. I see @jkhan already added an issue for this: rvhonorato/cazy-parser#2

I've added the functionality and the issue has been closed.

Functionality documentation: there is no exposed API besides the two scripts,
for using from a shell. One of them doesn't have options, and the other one uses argparse for options.
Even if there are no options create-cazy-db.py could have a --help option to at least explain what the command does.

The recently implement setup.py installation method makes it so that the scripts can be run from the command line. Also, --help arg has been implemented in the code as well as a means to display the user what argument is missing if that is the case.

Automated tests: not available.

I'm not quite sure how to produce this, could you please give me one example?

Community guidelines: Kind of. There is an email for contact, but no guidelines
on how to collaborate. A CONTRIBUTING.md file in the repo goes a long way on
addressing this.

I've added a CONTRIBUTING.md stating which features would be a great addiditon to the cazy-parser.

from joss-reviews.

@luizirber when could you take another look at this?

from joss-reviews.

Great work @rodrigovrgs!

About the tests: it is one of the journal requirements, but it is not so easy to test your scripts (because it depends on a big DB generated with one of them). You could set up a subset of the DB and execute the extract_cazy_ids.py on it, and check the outputs. Another alternative would be refactoring your scripts into functions to make it easier to test, but I think this gets out of the scope of the submission.

@pjotrp, what would be the recommendation in this case?

from joss-reviews.

Thank you @luizirber .

@arfon I think we can accept this paper. @rodrigovrgs can look into improving the tests - but I think we are good to go.

from joss-reviews.

@arfon I think we can accept this paper. @rodrigovrgs can look into improving the tests - but I think we are good to go.

👍 ok thanks.

@rodrigovrgs - At this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

from joss-reviews.

@rodrigovrgs - At this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

Bump @rodrigovrgs - we're ready to accept this submission but need you to complete this last step before we can proceed.

from joss-reviews.

I've created an archive with the reviewed software at Zenodo, updated the doi and the master's branch README.md.

Is that everything?

from joss-reviews.

@whedon set 10.5281/zenodo.200893 as archive

from joss-reviews.

OK. 10.5281/zenodo.200893 is the archive.

from joss-reviews.

Is that everything?

👍 yes. I'm finishing up the submission now.

from joss-reviews.