Closed editorialbot closed 4 months ago
@abigailsnyder as you can see from the second round of reviews the clarity and reproducibility of the package would strongly benefit from a better description of the input data processing and its format. Please extend the current explanation.
While not necessary, I encourage you to make the package pip installable as znicholls suggests.
@Zeitsperre do you have anything to add?
@observingClouds @znicholls yes, thank you! I was just waiting for the second reviewer's feedback before responding.
re pip installable - normally this is the standard for our group. Unfortunately for us, there is already a package named stitches on PyPi. See https://pypi.org/project/stitches/. So we can't technically publish stitches to PyPi using the stitches name. It's a good reminder for us to check PyPi before naming packages in the future. I am checking with one of my co-authors who knows more about this to see if we can maybe publish the package on PyPi using a name like jgcri_stitches
for pip installation without have to change much in the package (you can tell this is not my expertise, so I appreciate the help from reviewers and editor!)
I will happily add additional description of input data processing - I agree with Zeb's issue text that it's a tricky thing to do and a critical part of the package.
a script or docs or something that shows how CMIP data is pre-processed, particularly details that are easy to get wrong e.g. area weighting, would be very useful still I think. Yes, this pre-processing is not necessarily part of stitches but it is important to get right in order to use stitches correctly so I think more discussion of this pre-processing step would be worthwhile to give users a better chance of using stitches correctly.
Just a few follow up questions so we can do it in a way that is satisfying:
The pre-processing functions are included in the package already so good news is it sounds like this is just a question of us referring to and describing them in the right place so users are aware. Thank you for flagging this! The functions doing the steps referred primarily in the make_tas_archive.py script. (https://github.com/JGCRI/stitches/blob/main/stitches/make_tas_archive.py) and then they get called simply with generate_package_data()
(https://github.com/JGCRI/stitches/blob/main/stitches/generate_package_data.py) as one of the steps. What would be the best way to document these so users are aware of them? I will add some brief text to the Install the package data from Zenodo
section of the quickstart, and I'm checking on getting it added to github.io page (https://jgcri.github.io/stitches/reference/api.html) as well. Is there anything else that would be preferable instead of these changes?
RE the other two items in the issue:
install_package_data seems to download all the data every time, even if data is already downloaded. Is that intended?
I would put a link to the ESD paper in the notebook where it is mentioned (at the moment it is just referred to but no link is included)
I will get on both of those today! The package data is installed every time the function is called, so I will add some text to that section of the quickstart to let users know that, and that they can comment it out if they have already run it once.
if we can maybe publish the package on PyPi using a name like
jgcri_stitches
for pip installation without have to change much in the package
Yep you can do this without issue, see e.g. pyam https://github.com/IAMconsortium/pyam which is under pyam-iamc on PyPI
What would be the best way to document these so users are aware of them?
Yes that would help. Also just having a notebook called, 'Preparing input data' or something that shows the steps would be very helpful.
The package data is installed every time the function is called, so I will add some text to that section of the quickstart to let users know that, and that they can comment it out if they have already run it once.
This is a solution. It would be slightly nicer if the downloader just checked if the data was already there before doing the download (trivial using packages like pooch https://www.fatiando.org/pooch/latest/index.html) but it's not a huge issue
Otherwise thanks for your efforts, I know it is mucking around sorting all this out.
@znicholls thanks for the suggestions! I'll be working on the Preparing input data notebook and hopefully while I do that, my colleague will have a few free moments to push things to PyPi (thank you for the example!)
@znicholls @observingClouds: We have addressed these items and all changes have been pushed to main
!
Thanks for the update @abigailsnyder. Could you quickly outline how you addressed these items in https://github.com/JGCRI/stitches/issues/78 and close this issue if appropriate? I just quickly tried to install stitches-emulator
via pip and it seems like the requirements.txt
is missing from the code package hosted to pypi.
I will document and close the repo issue; Chris and I will try to trackdown what went wrong with the pypi hosting. Thanks!
@observingClouds we're still not sure why the distribution is ignoring the requirements.txt file but Chris figured out a work-around and has updated the distribution. I tested on my mac and the installation is successful now.
Thanks @abigailsnyder for the update. I can confirm that the installation is working also on my side. I just reached out to @Zeitsperre for some last comments. If all is well, we can move forward quickly.
Hello all, please excuse the lack of communication. I'll be resuming my review efforts tomorrow morning!
I've done a small pass-through now.
I think it's safe to say that when https://github.com/JGCRI/stitches/pull/97 and https://github.com/JGCRI/stitches/pull/98 are addressed, the majority of my boxes will be ticked. Moving onto the functionality now...
Thanks @Zeitsperre for the additional comments and PRs. Were you able to test the functionality as well?
Hi @observingClouds I haven't had a chance to check things since my initial testing. It looks as though many of my comments have been turned into issues within the repository, specifically the points concerning refactoring/optimizing calls for xarray
. If those are going to be addressed later, I imagine that it would be fine to click that box.
I've opened a few other issues and a Pull Request that have yet to be addressed. Once those are closed, I would be fine with checking the remaining issues.
@Zeitsperre I am so sorry - I do not get emails from github when an issue or PR gets opened in the stitches
repo and I'm just totally unused to actively checking. I will be able to look at these issues and PR next week. Thank you so much for pointing them out here.
@abigailsnyder
All good; People get busy. I'll be at a conference and taking a short vacation for the next two weeks. Feel free to ask any questions or request revisions in my PR, and I should be able to get back to you soon after I return. Have a good day!
@Zeitsperre Thank you! We have responded to all remaining items. For the contributor covenant https://github.com/JGCRI/stitches/issues/82#issuecomment-2045008798, we agree but we have to have appropriate language approved by our lab. For the QOL improvements https://github.com/JGCRI/stitches/issues/96, a PR addressing several of these has been reviewed and merged. For your PR, @crvernon caught one more typo but overall we are happy to merge this. I don't know the extent to which the JOSS process includes a copy-edit pass as other journals do but for the most part it seems like everything from this PR is very much in that space, to me at least?
Thank you so much for your feedback and your patience!
@abigailsnyder please merge the copy-editing PR. As an editor I will have a last read of the manuscript before publishing but we do not have a professional copy-editing service so I appreciate all edits that will be fixed and merged beforehand.
@observingClouds Thank you, done!
@abigailsnyder
Thanks for merging the final PR from me. I'll leave the QOL suggestions issue open on the repository (as there are a few things left to investigate) but I recommend the project for publication now.
Congratulations! Very fascinating library!
@Zeitsperre, @znicholls, @abigailsnyder thank you very much for hanging in here. I appreciate all your time you invested, particularly the reviewers @Zeitsperre and @znicholls with their valuable expertise and feedback.
I will now start the post-review phase where I will work together with @abigailsnyder to move this submission towards publication.
@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
@abigailsnyder could you please have a look at the above author tasks and post the DOI of the released archive here once you are done? Thank you!
The version is: 0.13
The DOI is: 10.5281/zenodo.11094934
And I will be getting on the other author items tomorrow hopefully
@editorialbot set 10.5281/zenodo.11094934 as archive
Done! archive is now 10.5281/zenodo.11094934
@editorialbot set v0.13 as version
Done! version is now v0.13
@editorialbot generate pdf
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.5194/esd-2022-14 is OK
- 10.1017/9781009157940.001 is OK
- 10.5194/gmd-9-1937-2016 is OK
- 10.5194/gmd-9-3461-2016 is OK
- 10.1038/nclimate3310 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.3509134 is OK
- 10.5334/jors.148 is OK
MISSING DOIs
- No DOI given, and none found for title: Emulating Earth system model temperatures with MES...
- 10.5194/esd-13-851-2022 may be a valid DOI for title: MESMER-M: an Earth system model emulator for spati...
- 10.1002/essoar.10511207.1 may be a valid DOI for title: Showcasing MESMER-X: Spatially Resolved Emulation ...
- No DOI given, and none found for title: A simple object-oriented and open-source model for...
- 10.5194/acp-11-1417-2011 may be a valid DOI for title: Emulating coupled atmosphere-ocean and carbon cycl...
- 10.5194/gmd-11-2273-2018 may be a valid DOI for title: FAIR v1. 3: a simple emissions-based impulse respo...
- No DOI given, and none found for title: The Climatic Impact-Driver Framework for Assessmen...
- 10.1002/wcc.457 may be a valid DOI for title: Characterizing half-a-degree difference: a review ...
- No DOI given, and none found for title: Climate Change 2021: the physical science basis. C...
- No DOI given, and none found for title: Ipcc, 2021: Summary for policymakers. in: Climate ...
- No DOI given, and none found for title: Scikit-learn: Machine Learning in Python
INVALID DOIs
- doi:10.59327/IPCC/AR6-9789291691647.001 is INVALID (failed connection)
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@abigailsnyder thanks for the release and the archive DOI. Could you also check your bibliography and add DOIs to all entries or if none is available provide a url. Thank you.
You can rerun @editorialbot check references
to see if the reference check succeeds successfully after you made the changes.
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.5194/esd-2022-14 is OK
- 10.1017/9781009157940.001 is OK
- 10.5194/gmd-9-1937-2016 is OK
- 10.5194/gmd-9-3461-2016 is OK
- 10.1038/nclimate3310 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.3509134 is OK
- 10.5334/jors.148 is OK
MISSING DOIs
- No DOI given, and none found for title: Emulating Earth system model temperatures with MES...
- 10.5194/esd-13-851-2022 may be a valid DOI for title: MESMER-M: an Earth system model emulator for spati...
- 10.1002/essoar.10511207.1 may be a valid DOI for title: Showcasing MESMER-X: Spatially Resolved Emulation ...
- No DOI given, and none found for title: A simple object-oriented and open-source model for...
- 10.5194/acp-11-1417-2011 may be a valid DOI for title: Emulating coupled atmosphere-ocean and carbon cycl...
- 10.5194/gmd-11-2273-2018 may be a valid DOI for title: FAIR v1. 3: a simple emissions-based impulse respo...
- No DOI given, and none found for title: The Climatic Impact-Driver Framework for Assessmen...
- 10.1002/wcc.457 may be a valid DOI for title: Characterizing half-a-degree difference: a review ...
- No DOI given, and none found for title: Climate Change 2021: the physical science basis. C...
- No DOI given, and none found for title: Ipcc, 2021: Summary for policymakers. in: Climate ...
- No DOI given, and none found for title: Scikit-learn: Machine Learning in Python
INVALID DOIs
- doi:10.59327/IPCC/AR6-9789291691647.001 is INVALID (failed connection)
@observingClouds I got the DOIs added in this morning and I have double checked Authors, affiliations, and ORCIDs. I believe @crvernon and I have checked everything else on the author task list and hopefully are good to go
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.5194/esd-2022-14 is OK
- 10.1017/9781009157940.001 is OK
- 10.5194/gmd-9-1937-2016 is OK
- 10.5194/gmd-9-3461-2016 is OK
- 10.1038/nclimate3310 is OK
- 10.5194/esd-11-139-2020 is OK
- 10.5194/esd-13-851-2022 is OK
- 10.1029/2022GL099012 is OK
- 10.5194/gmd-8-939-2015 is OK
- 10.5194/acp-11-1417-2011 is OK
- 10.5194/gmd-11-2273-2018 is OK
- 10.1029/2022EF002803 is OK
- 10.1002/wcc.457 is OK
- 10.1017/9781009157896.001 is OK
- 10.59327/IPCC/AR6-9789291691647.001 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.3509134 is OK
- 10.5334/jors.148 is OK
MISSING DOIs
- No DOI given, and none found for title: Climate Change 2021: the physical science basis. C...
- No DOI given, and none found for title: Scikit-learn: Machine Learning in Python
INVALID DOIs
- None
The two missing DOIs I couldn't track down but I did add URLs for them to the bib file
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
I believe you can use the Zenodo DOI for scikit-learn: https://zenodo.org/doi/10.5281/zenodo.591564 (all versions)
Additionally, for the IPCC reports, you can refer to this page: https://www.ipcc.ch/report/ar6/wg1/about/how-to-cite-this-report/
@abigailsnyder please also have a look at some editorial changes at https://github.com/JGCRI/stitches/pull/100.
@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 recommend-accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.5194/esd-2022-14 is OK
- 10.1017/9781009157940.001 is OK
- 10.5194/gmd-9-1937-2016 is OK
- 10.5194/gmd-9-3461-2016 is OK
- 10.1038/nclimate3310 is OK
- 10.5194/esd-11-139-2020 is OK
- 10.5194/esd-13-851-2022 is OK
- 10.1029/2022GL099012 is OK
- 10.5194/gmd-8-939-2015 is OK
- 10.5194/acp-11-1417-2011 is OK
- 10.5194/gmd-11-2273-2018 is OK
- 10.1029/2022EF002803 is OK
- 10.1002/wcc.457 is OK
- 10.1017/9781009157896.002 is OK
- 10.1017/9781009157896.001 is OK
- 10.59327/IPCC/AR6-9789291691647.001 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.10951361 is OK
- 10.5281/zenodo.3509134 is OK
- 10.5334/jors.148 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/5316, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept
Submitting author: !--author-handle-->@abigailsnyder<!--end-author-handle-- (Abigail Snyder) Repository: https://github.com/JGCRI/stitches Branch with paper.md (empty if default branch): main Version: v0.13 Editor: !--editor-->@observingClouds<!--end-editor-- Reviewers: @znicholls, @Zeitsperre Archive: 10.5281/zenodo.11094934
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