Closed editorialbot closed 1 year ago
Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.
For a list of things I can do to help you, just type:
@editorialbot commands
For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
@editorialbot generate pdf
Software report:
github.com/AlDanial/cloc v 1.88 T=0.15 s (158.1 files/s, 43501.5 lines/s)
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Language files blank comment code
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Python 13 911 762 4053
Bourne Shell 3 73 40 327
TeX 1 16 0 168
Markdown 2 37 0 119
YAML 4 3 4 81
Dockerfile 1 2 2 5
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SUM: 24 1042 808 4753
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gitinspector failed to run statistical information for the repository
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1093/bioinformatics/btu153 is OK
- 10.1073/pnas.0506758102 is OK
- 10.1093/bioinformatics/btv421 is OK
- 10.1093/gigascience/giz119 is OK
- 10.1186/s13059-020-02090-4 is OK
- 10.1093/gigascience/giy015 is OK
- 10.1093/bioinformatics/bty744 is OK
- 10.1186/s13059-016-1108-8 is OK
- 10.1093/bioinformatics/bty539 is OK
- 10.1099/mgen.0.000338 is OK
- 10.1073/pnas.252529799 is OK
- 10.1007/978-3-030-38281-0_1 is OK
- 10.1186/s12864-022-08303-3 is OK
- 10.1371/journal.pcbi.1007732 is OK
- 10.1093/bioinformatics/btaa792 is OK
MISSING DOIs
- None
INVALID DOIs
- None
Wordcount for paper.md
is 539
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
ππΌ @milnus, @iferres, @asafpr - this is the review thread for the submission. All of our communications will happen here from now on.
Please check the post at the top of the issue for instructions on how to generate your own review checklist. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.
The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues directly in the software repository. If you do so, please mention this thread so that a link is created (and I can keep an eye on what is happening). Please also feel free to comment and ask questions in this thread. It is often easier to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.
Please feel free to ping me (@csoneson) if you have any questions or concerns. Thanks!
@milnus the workflow wiki page has a broken link to gff files dir, should be https://github.com/asafpr/Corekaburra/tree/main/Example_workflow/Input_Gff_files
@milnus after panaroo-generate-gffs
why should the file names be changed? Is there another use for that script with the original output file names? why not producing the correct file names in this script?
@milnus the file coreless_contig_accessory_gene_content.tsv is missing from output dir. Also the file core_gene_graph.gml has a typo in the wiki page (core_gene_grapgh.gml) and the last paragraph has some mixed singular/plural. In addition some of the output files are tsv while others are csv, I think they should all be the same. I didn't understand the definition of sub-segments, maybe you can explain it in more detail. The downstream analysis in my opinion should be wrapped in scripts, at least the most common questions, it will be more user-friendly this way and I think this is the main use-case of the tool.
@milnus in the paper line 24 "dispite" -> "despite"
@asafpr - Response to comments:
@milnus the workflow wiki page has a broken link to gff files dir, should be
Thanks! Very thorough reading and checking of links. The dead link has now been fixed.
@milnus after
panaroo-generate-gffs
why should the file names be changed? Is there another use for that script with the original output file names? why not producing the correct file names in this script?
The panaroo-generate-gffs
script is not part of Corekaburra, but Panaroo. The file names are changed so that Corekaburra can connect the Gff file name to a column in the gene_presence_absence.csv file. The Gff files produced from the panaroo-generate-gffs
are very unlikely to be used for any post-processing in Panaroo, as the pan-genome graph is preferred.
the file coreless_contig_accessory_gene_content.tsv is missing from output dir
This file is only produced when there are at least one contig with no core genes. This has been clarified in the documentation.
Also the file core_gene_graph.gml has a typo in the wiki page (core_gene_grapgh.gml) and the last paragraph has some mixed singular/plural
This has been corrected
In addition some of the output files are tsv while others are csv, I think they should all be the same.
Agreed, it was a bit silly. Now everything is converted to .tsv output.
I didn't understand the definition of sub-segments, maybe you can explain it in more detail.
The paragraphs core_segments.tsv
and no_accessory_core_segments.tsv
have both been reworded to hopefully give a cleaner explanation around segments and sub-segments.
The downstream analysis in my opinion should be wrapped in scripts, at least the most common questions, it will be more user-friendly this way and I think this is the main use-case of the tool.
I see the point, and it has been debated heavily in our group. We have produced some 'beta' scripts to do small tasks but always find it to be less flexible than using command-line tools to query output files. Currently our view is that the amount of time for implementation and maintenance is better spend on future feature implementations, likely to detect rearrangements. If we find a query that is not easily made with command-line tools, we will definitely look to make a script.
@milnus in the paper line 24 "dispite" -> "despite"
This has been corrected.
Hi @csoneson , all looks ok to me.
Thanks @iferres!
I think all the issues I raised were also covered so you've got my ok too.
That's great, thanks a lot @asafpr!
@milnus - I will also have a look through the submission and get back to you shortly with the next steps.
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1093/bioinformatics/btu153 is OK
- 10.1073/pnas.0506758102 is OK
- 10.1093/bioinformatics/btv421 is OK
- 10.1093/gigascience/giz119 is OK
- 10.1186/s13059-020-02090-4 is OK
- 10.1093/gigascience/giy015 is OK
- 10.1093/bioinformatics/bty744 is OK
- 10.1186/s13059-016-1108-8 is OK
- 10.1093/bioinformatics/bty539 is OK
- 10.1099/mgen.0.000338 is OK
- 10.1073/pnas.252529799 is OK
- 10.1007/978-3-030-38281-0_1 is OK
- 10.1186/s12864-022-08303-3 is OK
- 10.1371/journal.pcbi.1007732 is OK
- 10.1093/bioinformatics/btaa792 is OK
MISSING DOIs
- None
INVALID DOIs
- None
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
ππ» @milnus - I have gone through the submission, and made a PR with a couple of small fixes, mostly to the bibliography. Please have a look and merge if you agree. The next steps then are as follows:
I can then move forward with accepting the submission.
I have created a new tagged release (v0.0.5). Zenodo upload: doi.org/10.5281/zenodo.7344004
@editorialbot generate pdf
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1093/bioinformatics/btu153 is OK
- 10.1073/pnas.0506758102 is OK
- 10.1093/bioinformatics/btv421 is OK
- 10.1093/gigascience/giz119 is OK
- 10.1186/s13059-020-02090-4 is OK
- 10.1093/gigascience/giy015 is OK
- 10.1093/bioinformatics/bty744 is OK
- 10.1186/s13059-016-1108-8 is OK
- 10.1093/bioinformatics/bty539 is OK
- 10.1099/mgen.0.000338 is OK
- 10.1073/pnas.252529799 is OK
- 10.1007/978-3-030-38281-0_1 is OK
- 10.1186/s12864-022-08303-3 is OK
- 10.1371/journal.pcbi.1007732 is OK
- 10.1093/bioinformatics/btaa792 is OK
MISSING DOIs
- None
INVALID DOIs
- None
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@editorialbot set 0.0.5 as version
Done! version is now 0.0.5
@editorialbot set 10.5281/zenodo.7344004 as archive
Done! Archive is now 10.5281/zenodo.7344004
@milnus Great, thanks! All looks good to me, I will hand over to the track EiC for the final steps. Thanks for submitting to JOSS!
@editorialbot recommend-accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1093/bioinformatics/btu153 is OK
- 10.1073/pnas.0506758102 is OK
- 10.1093/bioinformatics/btv421 is OK
- 10.1093/gigascience/giz119 is OK
- 10.1186/s13059-020-02090-4 is OK
- 10.1093/gigascience/giy015 is OK
- 10.1093/bioinformatics/bty744 is OK
- 10.1186/s13059-016-1108-8 is OK
- 10.1093/bioinformatics/bty539 is OK
- 10.1099/mgen.0.000338 is OK
- 10.1073/pnas.252529799 is OK
- 10.1007/978-3-030-38281-0_1 is OK
- 10.1186/s12864-022-08303-3 is OK
- 10.1371/journal.pcbi.1007732 is OK
- 10.1093/bioinformatics/btaa792 is OK
MISSING DOIs
- None
INVALID DOIs
- None
:wave: @openjournals/bcm-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/3742, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept
@editorialbot set v0.0.5 as version
Done! version is now v0.0.5
@milnus as the AEiC of this track I am here to help process this submission for acceptance. I have just inspected the repository, the archive, this review, and reviewed the paper and all seems in order. I will now proceed to accept this submission.
@editorialbot accept
Doing it live! Attempting automated processing of paper acceptance...
@milnus Congratulations on this publiction in JOSS!
@csoneson thanks for editing this submission!
Special thanks also to @iferres and @asafpr for their review efforts!!!!!
π¦π¦π¦ π Tweet for this paper π π¦π¦π¦
πππ π Toot for this paper π πππ
π¨π¨π¨ THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! π¨π¨π¨
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The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:
Submitting author: !--author-handle-->@milnus<!--end-author-handle-- (Magnus Jespersen) Repository: https://github.com/milnus/Corekaburra Branch with paper.md (empty if default branch): main Version: v0.0.5 Editor: !--editor-->@csoneson<!--end-editor-- Reviewers: @iferres, @asafpr Archive: 10.5281/zenodo.7344004
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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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@iferres & @asafpr, 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:
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