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[REVIEW]: Bam-readcount - rapid generation of basepair-resolution sequence metrics #3722

Closed whedon closed 2 years ago

whedon commented 3 years ago

Submitting author: @chrisamiller (Christopher A. Miller) Repository: https://github.com/genome/bam-readcount Version: v1.0.1 Editor: @lpantano Reviewers: @friedue, @bebatut Archive: 10.5281/zenodo.5879149

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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.)

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@friedue, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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Review checklist for @friedue

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @bebatut

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

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General checks

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Software paper

whedon commented 3 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @friedue it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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whedon commented 3 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.06 s (870.7 files/s, 81442.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
CMake                           20            210            404            960
Python                           5            112            223            914
C++                              8            140            111            846
Markdown                         5            100              0            169
C/C++ Header                     5             29              0            128
XSLT                             1              5              0            112
Perl                             2             24              0             96
Dockerfile                       1              9              6             27
YAML                             1              0              0             21
diff                             1              4             16             10
Bourne Shell                     1              0              0              1
-------------------------------------------------------------------------------
SUM:                            50            633            760           3284
-------------------------------------------------------------------------------

Statistical information for the repository '04f8f3c9ee7bd25d0aa32333' was
gathered on 2021/09/13.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Ajay Khanna                      9           110             47            2.84
Chris Miller                     2             9              1            0.18
Dave Larson                     57          1358            866           40.30
Morgan Taschuk                   1             1              1            0.04
Sam Brightman                    1             4              4            0.14
Travis Abbott                   16          1133            986           38.39
dlarson                          7           973             26           18.10

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Ajay Khanna                  92           83.6         13.3               16.30
Chris Miller                  7           77.8         78.8                0.00
Dave Larson                 865           63.7         83.8                6.47
Morgan Taschuk                1          100.0         72.7                0.00
Sam Brightman                 4          100.0         58.8                0.00
Travis Abbott               546           48.2        102.9                9.89
whedon commented 3 years ago

PDF failed to compile for issue #3722 with the following error: 

 Can't find any papers to compile :-(
apldx commented 3 years ago

@whedon generate pdf from branch joss-paper

whedon commented 3 years ago 
Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...
whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

friedue commented 3 years ago

I've opened a couple of issues in the repo, most of them dealing with relatively minor issues. The main issue IMO is the installation/docker use and the lack of a proper use-case.

https://github.com/genome/bam-readcount/issues/79, https://github.com/genome/bam-readcount/issues/80, https://github.com/genome/bam-readcount/issues/81, https://github.com/genome/bam-readcount/issues/82

lpantano commented 3 years ago

@whedon add @bebatut as reviewer

whedon commented 3 years ago

OK, @bebatut is now a reviewer

bebatut commented 3 years ago

I agree with @friedue about the major issues. I added some comments in the already existing issues and also create new ones:

A last comment: is the data used to generate the graphs in the paper available somewhere?

chrisamiller commented 3 years ago

Thanks, both of you, for the feedback. We'll get cracking on this and report back soon!

whedon commented 3 years ago

:wave: @friedue, please update us on how your review is going (this is an automated reminder).

friedue commented 3 years ago

Feedback has been given; @chrisamiller et al are working on it

lpantano commented 3 years ago

@chrisamiller, do you have a timeline for the updates? thanks!

chrisamiller commented 3 years ago

Almost done merging them all - should finish up this week - thanks!

chrisamiller commented 2 years ago

This got delayed by a variety of other projects on our end - appreciate your patience! At this point we believe that we've addressed all of the the reviewer concerns. They were really useful comments, and I think the package and the paper are stronger as a result - much appreciated! (@bebatut @friedue)

chrisamiller commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

PDF failed to compile for issue #3722 with the following error: 

 Can't find any papers to compile :-(
chrisamiller commented 2 years ago

@whedon generate pdf from branch joss-paper

whedon commented 2 years ago 
Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...
whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

chrisamiller commented 2 years ago

@whedon generate pdf from branch joss-paper

whedon commented 2 years ago 
Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...
whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

friedue commented 2 years ago

@lpantano My suggestions have been addressed; I'll wait for @bebatut's verdict, but I have no hesitation to recommend this for publication now.

lpantano commented 2 years ago

Thank you, @friedue. @bebatut, let me know if you think this is ready according to you. Thanks!

lpantano commented 2 years ago

Hi @bebatut! Any chance you can finish this soon? You can go over the checklist in the issue description and see if all of them are now checked. Thanks!

bebatut commented 2 years ago

Sorry for the delay (some health issues). Everything looks good now on my side. It seems ready to go :rocket:

chrisamiller commented 2 years ago

Appreciated, all! Just let us know what the next steps are from our side!

lpantano commented 2 years ago

@chrisamiller, At this point could you:

I can then move forward with accepting the submission.

chrisamiller commented 2 years ago

Thanks!

lpantano commented 2 years ago

@whedon set v1.0.1 as version

whedon commented 2 years ago

OK. v1.0.1 is the version.

chrisamiller commented 2 years ago

Just checking in - is there anything else we need to do here? @lpantano Thanks!

lpantano commented 2 years ago

sorry, got into some other tasks. I asked, and it seems it is ok not to have the title match.

lpantano commented 2 years ago

@whedon set 10.5281/zenodo.5879149 as archive

whedon commented 2 years ago

OK. 10.5281/zenodo.5879149 is the archive.

lpantano commented 2 years ago

@whedon recommend-accept t

whedon commented 2 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 2 years ago

PDF failed to compile for issue #3722 with the following error: 

 Can't find any papers to compile :-(
chrisamiller commented 2 years ago

Thanks! Think it'll need to be pointed to branch joss-paper

arfon commented 2 years ago

@whedon recommend-accept from branch joss-paper

whedon commented 2 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1093/gigascience/giab007 is OK
- 10.1038/nm.3733 is OK
- 10.1111/gcb.15291 is OK
- 10.1186/s12920-019-0508-5 is OK
- 10.1371/journal.pcbi.1004274 is OK
- 10.1093/bioinformatics/btw536 is OK
- 10.1038/s41375-018-0193-y is OK
- 10.1001/jamaoncol.2016.0494 is OK
- 10.1016/j.cels.2015.08.015 is OK
- 10.1182/blood-2017-03-735654 is OK
- 10.1093/infdis/jiy358 is OK
- 10.1002/0471250953.bi1504s44 is OK
- 10.3390/v12121414 is OK
- 10.1101/2021.05.06.21256753 is OK
- 10.1056/NEJMoa1301689 is OK
- 10.1038/s41598-020-64708-8 is OK
- 10.1093/bioinformatics/bty518 is OK
- 10.1101/mcs.a002444 is OK
- 10.1038/s41588-018-0257-y is OK
- 10.1093/bioinformatics/bty316 is OK
- 10.1093/bioinformatics/bty316 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 2 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2914

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2914, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch joss-paper
arfon commented 2 years ago

@whedon accept deposit=true from branch joss-paper

whedon commented 2 years ago 
Doing it live! Attempting automated processing of paper acceptance...
whedon commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 2 years ago

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/2915
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03722
  3. If everything looks good, then close this review issue.

  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

    Any issues? Notify your editorial technical team...

arfon commented 2 years ago

@friedue, @bebatut – many thanks for your reviews here and to @lpantano for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@chrisamiller – your paper is now accepted and published in JOSS :zap::rocket::boom: