Closed editorialbot closed 8 months 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=0.02 s (1347.5 files/s, 233394.3 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
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R 10 103 574 1154
Markdown 4 210 0 796
Rmd 6 199 600 320
TeX 1 6 0 105
YAML 3 13 6 71
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SUM: 24 531 1180 2446
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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
- 10.1364/JOSA.60.000542 is OK
- 10.1016/j.rse.2008.02.012 is OK
- 10.1016/j.rse.2017.03.004 is OK
- 10.1016/j.rse.2018.11.002 is OK
- 10.1016/j.rse.2020.112173 is OK
- 10.1016/0034-4257(90)90100-Z is OK
- 10.1016/j.rse.2020.112176 is OK
MISSING DOIs
- None
INVALID DOIs
- None
Wordcount for paper.md
is 1983
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Dear @earth-chris, @nehakn and @ashiklom, thank you again for accepting review this submission for JOSS. The reviewing process is checklist based, and instructions were already posted above by the editorial bot - but let me know if you need any assistance, ok? Also, you can tag @jbferet if you have specific questions about the manuscript.
@jbferet, you can tag your co-author GitHub accounts if you want, so they will be able to follow this issue and answer to questions as well.
Suggests
, not Imports
, to simplify the installation.examples
folder, but these have to be run manually.@jbferet I have completed my review. Overall, a very solid piece of work!
The most important things that are missing for JOSS are automated tests and community guidelines. Everything else is fine as is, though I made some minor recommendations in various GitHub issues (all linked above).
@ashiklom thanks a lot for your review and insightful comments. I will work on addressing these suggestions in the coming days. best regards, Jean-Baptiste
@ashiklom and @jbferet A note β automated testing is not required by JOSS, but some means of testing that the code is running correctly is.
With that in mind, @jbferet how are your edits coming along?
@earth-chris, @nehakn How are your reviews coming?
hi @jbferet, I've concluded my review. Here's my recommended manuscript input. I have left a couple of boxes unchecked but I think there is a short pathway to resolving my current issues.
First is that the install instructions are incomplete. There are external dependencies that need to be installed (V8) that are not documented, which I had to debug. I've chimed in with an additional comment on ashiklom's issue.
Second is that the examples provided in the web documentation don't all run as-is. Primarily, the very first code block doesn't run. There's also an opportunity to port the more recent code blocks from the manuscript to the web docs, which would provide more comprehensive documentation. I've described that in more detail in this issue.
I would like to +1 ashiklom's review, and believe this software will be much improved after addressing those key issues. Many of them are nice-to-haves (like automated testing), and the only blockers to me are the install issues and the broken code in the web docs.
@jbferet I have completed my review. Automated tests are not described and the software is not compared with the state of the art.
@jbferet I haven't seen you for awhile. Are you still here?
@kthyng yes I am! Sorry for the poor communication, I have been working on corrections and updates of my package, following reviews from @ashiklom , @earth-chris and @nehakn . I just pushed an updated version of the package and paper. I will now exchange with @ashiklom and @earth-chris for specific suggestions they made in their detailed review listed in the issues of the package. thanks!
@editorialbot commands
Hello @jbferet, here are the things you can ask me to do:
# List all available commands
@editorialbot commands
# Get a list of all editors's GitHub handles
@editorialbot list editors
# Check the references of the paper for missing DOIs
@editorialbot check references
# Perform checks on the repository
@editorialbot check repository
# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist
# Set a value for branch
@editorialbot set joss-paper as branch
# Generates the pdf paper
@editorialbot generate pdf
# Generates a LaTeX preprint file
@editorialbot generate preprint
# Get a link to the complete list of reviewers
@editorialbot list reviewers
@editorialbot check repository
Software report:
github.com/AlDanial/cloc v 1.88 T=0.03 s (1020.7 files/s, 130930.9 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
R 16 111 705 1157
Markdown 6 187 0 576
Rmd 6 216 682 255
TeX 1 14 0 190
YAML 4 21 9 110
-------------------------------------------------------------------------------
SUM: 33 549 1396 2288
-------------------------------------------------------------------------------
gitinspector failed to run statistical information for the repository
Wordcount for paper.md
is 1946
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1364/JOSA.60.000542 is OK
- 10.1016/j.rse.2007.09.005 is OK
- 10.1016/j.rse.2008.02.012 is OK
- 10.1016/j.rse.2017.03.004 is OK
- 10.1016/j.rse.2018.11.002 is OK
- 10.1016/j.rse.2020.112173 is OK
- 10.1016/0034-4257(90)90100-Z is OK
- 10.1016/j.rse.2016.02.029 is OK
- 10.1109/TGRS.2011.2109390 is OK
- 10.1016/j.rse.2020.112176 is OK
- 10.1016/j.rse.2006.12.013 is OK
- 10.1109/TGRS.2007.895844 is OK
MISSING DOIs
- None
INVALID DOIs
- doi:10.1016/j.rse.2008.01.026 is INVALID (failed connection)
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1364/JOSA.60.000542 is OK
- 10.1016/j.rse.2007.09.005 is OK
- 10.1016/j.rse.2008.02.012 is OK
- 10.1016/j.rse.2017.03.004 is OK
- 10.1016/j.rse.2018.11.002 is OK
- 10.1016/j.rse.2020.112173 is OK
- 10.1016/0034-4257(90)90100-Z is OK
- 10.1016/j.rse.2016.02.029 is OK
- 10.1109/TGRS.2011.2109390 is OK
- 10.1016/j.rse.2020.112176 is OK
- 10.1016/j.rse.2006.12.013 is OK
- 10.1109/TGRS.2007.895844 is OK
MISSING DOIs
- None
INVALID DOIs
- doi:10.1016/j.rse.2008.01.026 is INVALID (failed connection)
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1364/JOSA.60.000542 is OK
- 10.1016/j.rse.2007.09.005 is OK
- 10.1016/j.rse.2008.02.012 is OK
- 10.1016/j.rse.2017.03.004 is OK
- 10.1016/j.rse.2018.11.002 is OK
- 10.1016/j.rse.2020.112173 is OK
- 10.1016/0034-4257(90)90100-Z is OK
- 10.1016/j.rse.2008.01.026 is OK
- 10.1016/j.rse.2016.02.029 is OK
- 10.1109/TGRS.2011.2109390 is OK
- 10.1016/j.rse.2020.112176 is OK
- 10.1016/j.rse.2006.12.013 is OK
- 10.1109/TGRS.2007.895844 is OK
MISSING DOIs
- None
INVALID DOIs
- None
Dear @kthyng, @ashiklom , @earth-chris and @nehakn , After a few commits and new versions 1.5.0 and 1.5.1 of the package, all issues are now solved and missing elements or modifications suggested in your reviews have been implemented. The latest version of the package is functional. I went through the online documentation, and tried my best to improve the manuscript. Automated tests were also added to the package.
Thank you for all these excellent suggestions. Let us know if you are ok with our answers to the issues opened in the github repository, and we will close them if ok for you, or work more on it if needed!
best regards
@jbferet I have concluded my review of the updated material and all the outstanding issues have been addressed from my perspective π
@jbferet Seconded! All my comments have been addressed, and I think this is ready to be published. Great work!
@earth-chris and @ashiklom Wonderful! Would you please make sure all the issues you opened have been addressed adequately and check off remaining boxes (unless there is something to bring up)?
yes, my checklist is complete and all issues are resolved in the prospect repository
Likewise -- checklist completed and all my issues closed.
Ok great! Next steps.
@editorialbot set <DOI here> as archive
@editorialbot set <version here> as version
@editorialbot generate pdf
@editorialbot check references
and ask author(s) to update as needed@editorialbot recommend-accept
@jbferet please go through the "additional author tasks..." above and do those steps (copy-paste the list as needed).
DOI for release on zenodo: https://doi.org/10.5281/zenodo.10480410
@kthyng all items from the list are checked, everything should be ok on my side. The DOI for the zenodo release is in the previous message. Thank you!
@jbferet and what version did you want associated with this JOSS review?
@editorialbot set 10.5281/zenodo.10480410 as archive
Done! archive is now 10.5281/zenodo.10480410
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@jbferet and what version did you want associated with this JOSS review?
@kthyng prospect version 1.6.0 is the version including all changes related to the JOSS review. Is there an action on my side in addition to specify it?
@jbferet paper comments:
Please correct all these items and given the number of mistakes found at this point, please go through and do a thorough reading to check for more.
@editorialbot set 1.6.0 as version
Done! version is now 1.6.0
@editorialbot check references
Submitting author: !--author-handle-->@jbferet<!--end-author-handle-- (Jean-Baptiste Feret) Repository: https://github.com/jbferet/prospect Branch with paper.md (empty if default branch): Version: 1.6.0 Editor: !--editor-->@marcosvital<!--end-editor-- Reviewers: @earth-chris, @nehakn, @ashiklom Archive: 10.5281/zenodo.10480410
Status
Status badge code:
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
@earth-chris & @nehakn & @ashiklom, 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:
The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @marcosvital know.
β¨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest β¨
Checklists
π Checklist for @earth-chris
π Checklist for @nehakn
π Checklist for @ashiklom