[REVIEW]: teiphy: A Python Package for Converting TEI XML Collations to NEXUS and Other Formats

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@jjmccollum@majensen<!--end-editor-- Reviewers: @tresoldi, @SimonGreenhill Archive: 10.5281/zenodo.7455638

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Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@tresoldi & @SimonGreenhill, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @majensen know.

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Checklists

📝 Checklist for @SimonGreenhill

📝 Checklist for @tresoldi

jjmccollum commented 1 year ago

Agreed. But that should happen automatically once we update the release on GitHub, right?

majensen commented 1 year ago

(Here's an example that used a thing called Network, created when the Earth was young:

)

from https://pubmed.ncbi.nlm.nih.gov/11861556/)

jjmccollum commented 1 year ago

@majensen Oh yeah! I've seen median-joining networks before. They've actually been used in textual criticism, as well, for the very reasons you've described (the earliest example I can think of is https://link.springer.com/article/10.1023/B:CHUM.0000009290.14571.59).

I've also connected the latest release of teiphy to Zenodo. The assigned DOI for all versions of the software is 10.5281/zenodo.7455638.

@rbturnbull, it looks like the IQTREE workflow is now failing for some reason. I'm not sure why, as it was passing the last time I merged a pull request. Do you think it might be an issue with the version of IQTREE being installed in the workflow?

majensen commented 1 year ago

Great @jjmccollum - are you willing to name the archive with the exact name of the paper? If so, this is preferred by JOSS.

majensen commented 1 year ago

@editorialbot set 10.5281/zenodo.7455638 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.7455638

majensen commented 1 year ago

@editorialbot set v0.1.3 as version

editorialbot commented 1 year ago

Done! version is now v0.1.3

jjmccollum commented 1 year ago

@majensen All right, I've updated the archive name to match the paper name! Since Zenodo updates the archive every time I push a new release to the GitHub code, it will likely change the archive name to the name of the current release, but the archive corresponding to the publication release will at least match the paper name.

majensen commented 1 year ago

That's fine @jjmccollum, we have a stake in the ground. I'm going issue the command that is supposed to call the Associate Editor in Chief. After we will be in his or her hands. Sometimes there is a minor change requested.

rbturnbull commented 1 year ago

@jjmccollum I'll create a separate issue about the iqtree workflow. It's just that there's now iqtree executable in the path after it is installed with apt-get. I don't think it is related to our code.

majensen commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

:wave: @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3825, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

majensen commented 1 year ago

@editorialbot ping track-eic

editorialbot commented 1 year ago

:bellhop_bell::exclamation:Hey @openjournals/csism-eics, this submission requires your attention.

editorialbot commented 1 year ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1093/sysbio/46.4.590 is OK
- 10.1111/cla.12160 is OK
- 10.1093/molbev/msaa015 is OK
- 10.1093/bioinformatics/btu033 is OK
- 10.1093/sysbio/sys029 is OK
- 10.1371/journal.pcbi.1006650 is OK
- 10.16995/dscn.291 is OK
- 10.1007/978-94-011-0325-1_2 is OK
- 10.1038/29667 is OK
- 10.1023/B:CHUM.0000009290.14571.59 is OK
- 10.1628/978-3-16-153324-2 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.3509134 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.1080/106351501753462876 is OK

MISSING DOIs

- None

INVALID DOIs

- None

danielskatz commented 1 year ago

@majensen - this paper is far too long for a JOSS paper, which isn't worth fixing at this point, but is something we should look for in the future...

danielskatz commented 1 year ago

@jjmccollum - as the track editor here, I've proofread your paper, and have a bunch of small changes in https://github.com/jjmccollum/teiphy/pull/63 - please check the case changes in the bib file carefully, then merge this, or let me know what you disagree with, and we can then proceed to acceptance and publication.

jjmccollum commented 1 year ago

@danielskatz Thank you for the edits and recommendations! The small changes look good to me, and most of the case changes in the bib file look correct. (Apologies for messing around with the capitalization; I'm used to doing this with the standard LaTeX citation style to achieve American-style capitalization for things like titles, but I didn't think about whether this was the preference for JOSS.) I would only suggest the following additional changes:

In the bhbr_phylogeny_1998 entry, the book title The Canterbury Tales, which occurs within the article title, should be in italics. If this can be achieved by changing that part of the article title to \emph{{T}he {C}anterbury {T}ales}, then that would be ideal.
In the entries baldwin_fa_2010, swh_pathways_2004, and ubs5, the word "Greek" in the title field should be capitalized.
In the swh_vorlage_2002 entry, the words "Greek" and "Vorlage" (the latter being a German noun) in the title field should be capitalized.
In the carlson_text_2015 entry, the word "Galatians" in the title field should be capitalized (as it is a proper noun), and the word "Untersuchungen" in the series field should be capitalized (per the conventions of German capitalization).
In the edmondson_analysis_2019 entry, "Coherence-Based Genealogical Method" is a proper noun, and as such, it should be capitalized.

I have copied these comments into my review of your proposed changes, as well. If you have any further questions, feel free to let me know. Thanks again!

danielskatz commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

danielskatz commented 1 year ago

@jjmccollum - once this command finishes, can you check the generated pdf and let me know if you are ok with it? I will do the same, then hopefully we can finish this publication.

editorialbot commented 1 year ago

:wave: @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3827, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

editorialbot commented 1 year ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1093/sysbio/46.4.590 is OK
- 10.1111/cla.12160 is OK
- 10.1093/molbev/msaa015 is OK
- 10.1093/bioinformatics/btu033 is OK
- 10.1093/sysbio/sys029 is OK
- 10.1371/journal.pcbi.1006650 is OK
- 10.16995/dscn.291 is OK
- 10.1007/978-94-011-0325-1_2 is OK
- 10.1038/29667 is OK
- 10.1023/B:CHUM.0000009290.14571.59 is OK
- 10.1628/978-3-16-153324-2 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.3509134 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.1080/106351501753462876 is OK

MISSING DOIs

- None

INVALID DOIs

- None

danielskatz commented 1 year ago

I see line 275 of the bib should be title = {The Text of {G}alatians and Its History}, - I left some extra {}s

danielskatz commented 1 year ago

otherwise, this looks good to me, so if you can make that fix, please do

jjmccollum commented 1 year ago

All right, I've just pushed that change to line 275. Otherwise, everything in the paper and the bibliography looks good to me, as well!

danielskatz commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

majensen commented 1 year ago

@danielskatz thanks, I look forward to your guidance on that point. I appreciate your moving forward with this recommendation.

editorialbot commented 1 year ago

:wave: @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3828, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz commented 1 year ago

@editorialbot accept

editorialbot commented 1 year ago

Doing it live! Attempting automated processing of paper acceptance...

editorialbot commented 1 year ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1093/sysbio/46.4.590 is OK
- 10.1111/cla.12160 is OK
- 10.1093/molbev/msaa015 is OK
- 10.1093/bioinformatics/btu033 is OK
- 10.1093/sysbio/sys029 is OK
- 10.1371/journal.pcbi.1006650 is OK
- 10.16995/dscn.291 is OK
- 10.1007/978-94-011-0325-1_2 is OK
- 10.1038/29667 is OK
- 10.1023/B:CHUM.0000009290.14571.59 is OK
- 10.1628/978-3-16-153324-2 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.3509134 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.1080/106351501753462876 is OK

MISSING DOIs

- None

INVALID DOIs

- None

danielskatz commented 1 year ago

@danielskatz thanks, I look forward to your guidance on that point. I appreciate your moving forward with this recommendation.

I think it's just to check the paper's length when our process starts, and when it is over 1000 words, think about if parts of the paper don't match the typical JOSS paper (e.g., they include material that should be in the documentation, they include results that would better fit a science paper) and then ask the author to reduce it at that point, before the review starts

editorialbot commented 1 year ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 1 year ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 1 year ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/3829
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04879
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz commented 1 year ago

Congratulations to @jjmccollum (Joey McCollum) and co-author on your publication!!

And thanks to @tresoldi and @SimonGreenhill for reviewing, and to @majensen for editing! We couldn't do this without you

editorialbot commented 1 year ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04879">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04879/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04879/status.svg
   :target: https://doi.org/10.21105/joss.04879

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jjmccollum commented 1 year ago

@danielskatz It's been several minutes, but when I click on the DOI link, the JOSS page for the paper still displays an error 404 (file not found) message. Does this usually take a while to update, or did something go wrong?

danielskatz commented 1 year ago

It works fine for me - it's likely a DNS caching issue on your side. (I've learned to wait about 5 minutes after the message "Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04879" to avoid such issues... If you are still having problems after a while (~6 hours), please let us know.

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