Closed editorialbot closed 1 year ago
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Software report:
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Python 19 845 2157 2726
YAML 7 8 7 405
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reStructuredText 7 214 187 168
Markdown 2 58 0 111
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DOS Batch 1 8 1 26
make 1 4 7 9
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SUM: 40 1164 2367 3746
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gitinspector failed to run statistical information for the repository
Wordcount for paper.md
is 1030
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.34194/geusb.v15.5045 is OK
- 10.1038/s41558-022-01441-2 is OK
- 10.5194/essd-13-3819-2021 is OK
- 10.17897/E594-NV64 is OK
- 10.22008/FK2/IW73UU is OK
- 10.22008/FK2/GNYFUK is OK
- 10.22008/FK2/IPOHT5 is OK
- 10.5334/jors.148 is OK
- 10.1038/nclimate2899 is OK
- 10.3389/feart.2022.970026 is OK
- 10.25923/c430-hb50 is OK
- 10.1175/BAMS-D-22-0082.1 is OK
- 10.1038/s41467-022-34049-3 is OK
- 10.5281/zenodo.3509134 is OK
- 10.22008/FK2/VVXGUT 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:
I opened an issue regarding a documentation update which would need to be fixed.
Hi @jroettenbacher @simonrp84,
I just want to quickly touch base and see if there are any issues/questions you might have. It would be great if we could finish the review in the next two weeks.
Have a great start into the week, Hauke
Hi @observingClouds, thanks for getting back to us. I am done with my review. The code works as expected and the documentation is sufficient to guide first time users and potential contributors to a point where the package is working and one can interact with data.
There are a few tests included in the package but those are not documented. I opened an issue about this, but I don't see this as absolutely necessary for acceptance. Another nice to have feature in the documentation would be some example plots of the data, so one can get a rough idea of what the data can be used for and how it could be plotted. I opened another issue for that. Again, this is not absolutely necessary for acceptance.
Thus, I recommend the acceptance of the manuscript and package.
Best, Johannes
I've not yet had time to look through this, but hope to do so later this week. Apologies for the delay.
@simonrp84 , no worries, you informed me already when I asked you to review.
There are a few tests included in the package but those are not documented. I opened an https://github.com/GEUS-Glaciology-and-Climate/pypromice/issues/135 about this, but I don't see this as absolutely necessary for acceptance. Another nice to have feature in the documentation would be some example plots of the data, so one can get a rough idea of what the data can be used for and how it could be plotted. I opened another https://github.com/GEUS-Glaciology-and-Climate/pypromice/issues/136 for that. Again, this is not absolutely necessary for acceptance.
As these are fairly straightforward requests, I don't see any problem in addressing these comments as part of this review and will be happy to take a look at this shortly. They are both valid points and will help with the usability of pypromice and our weather station data.
These comments have now been addressed in https://github.com/GEUS-Glaciology-and-Climate/pypromice/pull/137
Thank you @PennyHow for addressing the comments and @jroettenbacher to approve the changes. I see that we are getting closer to the finish line. If there are any questions, please let me know.
I've now had a chance to look through this properly and overall it seems good! I raised one issue about the tests, and have a few minor comments below:
On github page: Add link to readthedocs as the website on the right hand upper side.
I think the index page for readthedocs could be improved. Can you add an additional sentence or two after "pypromice is designed for processing and handling PROMICE automated weather station (AWS) data." to describe what PROMICE data is and why a tool is needed to handle it? I know you mention this elsewhere, but it would be nice tohave that up-front in the docs.
It's not immediately clear in the readthedocs pages where the example .toml files are located, it owuld be good to directly specify where the example toml files are from within the user guide section.
This may be a lack of library knowledge on my part, but why does the 'developer install 'section of the docs say that netcdf, xarray, pandas and pathlib need to be installed via conda? All the other dependencies are installed via pip when running "pip install ."
In the user guide, the code given in the Level 0 to Level 3 processing section is incorrectly indented, the leading space at the beginning of the lines should be removed.
Thanks for the comments @simonrp84!
On github page: Add link to readthedocs as the website on the right hand upper side.
Would it be possible to create a conda version of the install to complement pip? Pip-only could be problematic for users as mixing pip and conda installs on the same environment can cause strange behaviour and issues.
I think the index page for readthedocs could be improved. Can you add an additional sentence or two after "pypromice is designed for processing and handling PROMICE automated weather station (AWS) data." to describe what PROMICE data is and why a tool is needed to handle it? I know you mention this elsewhere, but it would be nice tohave that up-front in the docs.
It's not immediately clear in the readthedocs pages where the example .toml files are located, it owuld be good to directly specify where the example toml files are from within the user guide section.
This may be a lack of library knowledge on my part, but why does the 'developer install 'section of the docs say that netcdf, xarray, pandas and pathlib need to be installed via conda? All the other dependencies are installed via pip when running "pip install ."
In the user guide, the code given in the Level 0 to Level 3 processing section is incorrectly indented, the leading space at the beginning of the lines should be removed.
Thanks for your changes, all look good to me. Let me know your thoughts about conda and whether that's something you can do in the near future - if not then that could be something for a future release instead.
Thanks @simonrp84 for reviewing the new changes. I agree that the packaging is not necessary for the publication in JOSS, but it would make the software package more complete and easier for users to keep track of versions. Installations from the master branch could lead to installations of broken/development versions instead of operational releases.
@PennyHow please let us know about your decision. @simonrp84, could you please check if your checklist is up to date and you ticked off all steps that you reviewed?
Oops, sorry I overlooked that @observingClouds. Done now.
@simonrp84, a distrbutable pip package is now set up here from our most recent release. This should update automatically when new repo releases are made, as defined by the new Action on this branch. Docs and readmes have also been updated on this branch.
I'll make a PR once we have come to an agreement about whether to include a conda package or not. I've been having a look at some way of making the conda package from the pip package using conda skeleton
or grayskull
and therefore would be able to do this under the same Action triggered on a repo release. However, if it is not necessary for this review then I personally think we could work towards this in the future after some more stringent testing. It is still a very good suggestion and I am happy to continue working on it beyond this review. Let me know what you think and if this is okay @observingClouds.
Hi again @observingClouds, I've been testing a conda build of pypromice and all is working okay. The only thing is that one of our dependencies, pydataverse
, is not available as a conda package and all dependencies must be conda builds in order for it to work.
So the options are to either
pydataverse
as an optional dependency in the conda build, so therefore users have to install it themselvespydataverse
This is quite an important dependency as it is how our users can access our datasets through the pypromice.get
module. Therefore I'm currently trying to implement the latter option and have opened an issue with pydataverse. I've successfully made a conda build for pydataverse
myself, so I am hoping they will see that it is relatively straightforward.
Again, I am happy to continue pursuing this outside this JOSS review and hope this demonstrates that we have the ball rolling on getting pypromice a conda distribution.
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.34194/geusb.v15.5045 is OK
- 10.1038/s41558-022-01441-2 is OK
- 10.5194/essd-13-3819-2021 is OK
- 10.17897/E594-NV64 is OK
- 10.22008/FK2/IW73UU is OK
- 10.22008/FK2/GNYFUK is OK
- 10.22008/FK2/IPOHT5 is OK
- 10.5334/jors.148 is OK
- 10.1038/nclimate2899 is OK
- 10.3389/feart.2022.970026 is OK
- 10.25923/c430-hb50 is OK
- 10.1175/BAMS-D-22-0082.1 is OK
- 10.1038/s41467-022-34049-3 is OK
- 10.5281/zenodo.3509134 is OK
- 10.22008/FK2/VVXGUT 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:
@simonrp84 @jroettenbacher thank you very much for your collaboration and time investment. I appreciate it a lot! 🏅 At this point the review process is complete.
Hi @PennyHow, Please excuse the delay. I totally agree that the dependency should not further delay the acceptance of this submission. A few items are left to do now before I can recommend the acceptance. Could you please:
Thank you!
My pleasure! Congrats, @PennyHow et al for a nice paper and a great new library.
Great! I'll make a start on those requests and let you know when it is all finalized. Thanks for a really nice review process, and some great comments and feedback!
@observingClouds, here is what you requested:
- [X] Make a tagged release of your software, and list the version tag of the archived version here. You might want to consider merging the pip-branch beforehand.
Done. The pip-branch has been merged and the new release is here. The release tag is v1.2.0
- [X] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
Done. Our institute uses Dataverse, which we have been using to store pypromice releases here
- [X] Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
Done. On the Dataverse entry, the title fits with the pypromice release and the authorship list corresponds to our JOSS paper submission (including ORCID ids)
- [X] Please list the DOI of the archived version here.
@editorialbot set 10.22008/FK2/3TSBF0 as archive
Done! archive is now 10.22008/FK2/3TSBF0
@editorialbot set v1.2.0 as version
Done! version is now v1.2.0
@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
- 10.34194/geusb.v15.5045 is OK
- 10.1038/s41558-022-01441-2 is OK
- 10.5194/essd-13-3819-2021 is OK
- 10.17897/E594-NV64 is OK
- 10.22008/FK2/IW73UU is OK
- 10.22008/FK2/GNYFUK is OK
- 10.22008/FK2/IPOHT5 is OK
- 10.5334/jors.148 is OK
- 10.1038/nclimate2899 is OK
- 10.3389/feart.2022.970026 is OK
- 10.25923/c430-hb50 is OK
- 10.1175/BAMS-D-22-0082.1 is OK
- 10.1038/s41467-022-34049-3 is OK
- 10.5281/zenodo.3509134 is OK
- 10.22008/FK2/VVXGUT is OK
MISSING DOIs
- None
INVALID DOIs
- None
Thanks @PennyHow for going through the checklist. It looks all good to me 🥳 I'll hand the manuscript now over to the EiC who will take a last look and do the actual publishing. This will happen rather quickly.
Many thanks again to @jroettenbacher and @simonrp84 to take the time to review this submission.
@editorialbot recommend-accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.34194/geusb.v15.5045 is OK
- 10.1038/s41558-022-01441-2 is OK
- 10.5194/essd-13-3819-2021 is OK
- 10.17897/E594-NV64 is OK
- 10.22008/FK2/IW73UU is OK
- 10.22008/FK2/GNYFUK is OK
- 10.22008/FK2/IPOHT5 is OK
- 10.5334/jors.148 is OK
- 10.1038/nclimate2899 is OK
- 10.3389/feart.2022.970026 is OK
- 10.25923/c430-hb50 is OK
- 10.1175/BAMS-D-22-0082.1 is OK
- 10.1038/s41467-022-34049-3 is OK
- 10.5281/zenodo.3509134 is OK
- 10.22008/FK2/VVXGUT is OK
MISSING DOIs
- None
INVALID DOIs
- None
:wave: @openjournals/ese-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/4253, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept
Thanks @PennyHow for going through the checklist. It looks all good to me partying_face I'll hand the manuscript now over to the EiC who will take a last look and do the actual publishing. This will happen rather quickly.
Many thanks again to @jroettenbacher and @simonrp84 to take the time to review this submission.
Thanks @observingClouds! And thanks again @simonrp84 and @jroettenbacher
Hi again @observingClouds, I've just been told that the DOIs for our weather station dataset are being merged into one, so they will have a different DOI to those cited in the JOSS paper. Would it be possible to edit the paper with this update?
Sorry for this (very) late edit. I was unaware that this plan was being put into action imminently by our organization.
Hi @PennyHow, As DOIs should be persistent identifiers they should continue to point to the same datasets, but if you like to cite a collection DOI or a newer version of the dataset, please go ahead and change the paper and references accordingly and we'll see what we can do.
@openjournals/ese-eics @kthyng please wait until https://github.com/openjournals/joss-reviews/issues/5298#issuecomment-1561082423 has been addressed. I remove the recommend-accept label for now.
Thanks so much @observingClouds! I've now made the change and the DOI has been updated to reflect the most recent changes. I'll run the editorial checks again. Then please feel free to continue with the acceptance and proofing.
Submitting author: !--author-handle-->@PennyHow<!--end-author-handle-- (Penelope How) Repository: https://github.com/GEUS-Glaciology-and-Climate/pypromice Branch with paper.md (empty if default branch): Version: v1.2.1 Editor: !--editor-->@observingClouds<!--end-editor-- Reviewers: @jroettenbacher, @simonrp84 Archive: 10.22008/FK2/3TSBF0
Status
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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
@jroettenbacher & @simonrp84, 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 @observingClouds know.
✨ 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 ✨
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