[REVIEW]: ticktack: A Python package for carbon box modelling

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@benjaminpope@dfm<!--end-editor-- Reviewers: @joshuakt, @dfm Archive: 10.5281/zenodo.7754438

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/457392fb96baf638d8a7cc74324c3bf5/status.svg)](https://joss.theoj.org/papers/457392fb96baf638d8a7cc74324c3bf5)

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

@joshuakt, 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:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @dfm 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 ✨

Checklists

📝 Checklist for @joshuakt

📝 Checklist for @dfm

editorialbot commented 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:

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.15 s (322.3 files/s, 83680.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           9            371           1184           1867
TeX                              1            155              0           1759
Jupyter Notebook                20              0           4565           1718
Markdown                        12             94              0            329
YAML                             3              9              7             84
JSON                             1              0              0             44
JavaScript                       1              1              0             16
-------------------------------------------------------------------------------
SUM:                            47            630           5756           5817
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 1149

dfm commented 1 year ago

@joshuakt — This is the review thread for the paper. All of our correspondence will happen here from now on. Thanks again for agreeing to participate!

👉 Please read the "Reviewer instructions & questions" in the first comment above, and generate your checklists by commenting @editorialbot generate my checklist on this issue ASAP. 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 and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#5084 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please try to make a start ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule. Please get your review started as soon as possible!

editorialbot commented 1 year ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1109/MCSE.2007.53 is OK
- 10.21105/joss.00045 is OK
- 10.1038/nature11123 is OK
- 10.1038/ncomms2783 is OK
- 10.1002/2012JA018320 is OK
- 10.1038/486473e is OK
- 10.1002/asna.201512208 is OK
- 10.1017/RDC.2018.74 is OK
- 10.1002/asna.201512205 is OK
- 10.1016/j.asr.2014.12.014 is OK
- 10.1667/rr1094.1 is OK
- 10.1017/rdc.2020.58 is OK
- 10.1038/srep03728 is OK
- 10.1088/1742-6596/1400/2/022034 is OK
- 10.1093/mnras/stz685 is OK
- 10.1016/j.icarus.2014.06.009 is OK
- 10.1007/s11207-019-1424-8 is OK
- 10.1038/ncomms9611 is OK
- 10.1029/2021JA029351 is OK
- 10.1002/2017JD027325 is OK
- 10.1017/S0033822200052176 is OK
- 10.1093/mnras/sts378 is OK
- 10.1093/mnras/stt1468 is OK
- 10.1038/nature11695 is OK
- 10.1051/0004-6361/201321080 is OK
- 10.1029/2021GL094848 is OK
- 10.1016/0771-050x(80)90013-3 is OK
- 10.1137/141000671 is OK
- 10.3402/tellusa.v9i1.9078 is OK
- 10.1007/978-1-4020-2113-8 is OK
- 10.1038/ncomms15423 is OK
- 10.5194/gmd-12-1541-2019 is OK
- 10.1016/0168-583x(87)90264-3 is OK
- 10.1038/s41561-020-00674-0 is OK
- 10.1038/s41467-022-28804-9 is OK
- 10.1038/s41467-021-27891-4 is OK
- 10.3847/1538-3881/ac5683 is OK
- 10.1029/2021gl097201 is OK
- 10.1177/095968369300300401 is OK
- 10.1016/j.nimb.2012.08.046 is OK
- 10.1016/j.epsl.2014.11.048 is OK
- 10.1073/pnas.1613144114 is OK
- 10.1038/s41467-018-05883-1 is OK
- 10.1038/s41467-018-06036-0 is OK
- 10.1002/2014GL062218 is OK
- 10.1029/2021GL093419 is OK
- 10.3389/fspas.2022.886140 is OK
- 10.1017/RDC.2018.53 is OK
- 10.1017/RDC.2017.59 is OK
- 10.3402/tellusa.v27i2.9900 is OK
- 10.1017/s0033822200009449 is OK
- 10.1038/s41598-019-53296-x is OK
- 10.1098/rspa.2016.0263 is OK
- 10.1017/rdc.2016.50 is OK
- 10.1002/asna.201412071 is OK
- 10.1038/s41586-021-03972-8 is OK
- 10.1017/RDC.2017.75 is OK
- 10.1073/pnas.1921301117 is OK
- 10.1038/s41586-021-04240-5 is OK
- 10.1017/S0007087420000011 is OK
- 10.1126/science.109.2827.227 is OK
- 10.1038/s43586-021-00058-7 is OK
- 10.1007/s41116-022-00033-8 is OK
- 10.2458/azu_js_rc.55.16947 is OK
- 10.1017/rdc.2020.41 is OK
- 10.1038/s41467-017-01698-8 is OK
- 10.1007/s11434-014-0345-z is OK
- 10.3847/1538-4357/ab55db is OK
- 10.1086/510482 is OK
- 10.1093/mnras/stv423 is OK
- 10.3847/2041-8205/826/1/L2 is OK
- 10.1038/nature16168 is OK
- 10.3847/2041-8213/ac794d is OK
- 10.1002/2017gl074208 is OK
- 10.1038/ncomms11058 is OK
- 10.1093/mnras/stab166 is OK
- 10.1093/pasj/psu012 is OK
- 10.3847/1538-4357/ab14e6 is OK
- 10.3847/1538-4357/abc8f5 is OK
- 10.1126/science.aay3821 is OK
- 10.1146/annurev-astro-112420-023324 is OK
- 10.1038/s41550-021-01335-x is OK
- 10.21105/joss.00248 is OK
- 10.21105/joss.00516 is OK
- 10.5334/jors.130 is OK
- 10.11141/ia.7.1 is OK
- 10.1038/s41467-020-20695-y is OK
- 10.1017/rdc.2020.46 is OK
- 10.1017/rdc.2020.59 is OK
- 10.1038/1741138a0 is OK
- 10.1029/2021JA029378 is OK
- 10.1029/2007ja012499 is OK
- 10.3847/1538-4357/abad93 is OK
- 10.1145/3452296.3472916 is OK
- 10.1038/srep45257 is OK
- 10.1029/2020JA027921 is OK
- 10.1017/CBO9781139165150.015 is OK
- 10.2140/camcos.2010.5.65 is OK
- 10.1063/1.1699114 is OK
- 10.5281/zenodo.6389738 is OK
- 10.1086/670067 is OK
- 10.1063/1.1835238 is OK
- 10.12688/f1000research.29032.2 is OK
- 10.3847/1538-3881/aa9332 is OK
- 10.3847/2515-5172/aaaf6c is OK
- 10.1038/195984a0 is OK
- 10.1017/RDC.2019.26 is OK
- 10.1038/s41598-019-57273-2 is OK
- 10.1007/s11207-021-01831-3 is OK
- 10.1051/swsc/2018014 is OK
- 10.1038/s41598-021-95235-9 is OK
- 10.1029/2020SW002665 is OK
- 10.1126/science.abd7096 is OK
- 10.1126/science.1185402 is OK
- 10.1086/367639 is OK
- 10.1017/RDC.2018.64 is OK
- 10.1017/RDC.2020.108 is OK
- 10.1126/science.1066114 is OK
- 10.1017/RDC.2020.49 is OK

MISSING DOIs

- 10.1109/mcse.2007.55 may be a valid DOI for title: Matplotlib: A 2D graphics environment
- 10.1109/mcse.2011.37 may be a valid DOI for title: The NumPy array: a structure for efficient numerical computation
- 10.3847/2041-8213/ac8b13 may be a valid DOI for title: HD 166620: Portrait of a Star Entering a Grand Magnetic Minimum
- 10.2307/211876 may be a valid DOI for title: Dendroclimatic changes in semiarid America
- 10.1017/s0033822200030903 may be a valid DOI for title: Radiocarbon calibration and analysis of stratigraphy: the OxCal program
- 10.2458/azu_js_rc.55.16215 may be a valid DOI for title: Recent and planned developments of the program OxCal

INVALID DOIs

- 10.1098/rspa.2022.0497. is INVALID
- https://doi.org/10.1016/j.quascirev.2016.12.024 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/0893-9659(89)90079-7 is INVALID because of 'https://doi.org/' prefix

editorialbot commented 1 year ago

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

dfm commented 1 year ago

@benjaminpope — Take a look at those DOI suggestions from the bot above and please remove any entries from the bibtex that aren't referenced in the text!

benjaminpope commented 1 year ago

Thanks - DOIs should be fixed now

dfm commented 1 year ago

@joshuakt — This is a ping to keep this on your radar. The first step of generating your checklist as described above, and starting on the first few boxes should be pretty quick. Let me know if you run into issues, and I'll send an email if we don't hear from you since I know GitHub notifications can get lost.

joshuakt commented 1 year ago

Hi Dan, thanks for the reminder - I will do this in the next couple of days.

On Thu, Jan 26, 2023 at 9:32 AM Dan Foreman-Mackey @.***> wrote:

@joshuakt https://github.com/joshuakt — This is a ping to keep this on your radar. The first step of generating your checklist as described above, and starting on the first few boxes should be pretty quick. Let me know if you run into issues, and I'll send an email if we don't hear from you since I know GitHub notifications can get lost.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/5084#issuecomment-1405354971, or unsubscribe https://github.com/notifications/unsubscribe-auth/AI6ANQWX76EGT2Z7K4GMQLTWUKYK3ANCNFSM6AAAAAAT6JIBT4 . You are receiving this because you were mentioned.Message ID: @.***>

-- Josh

joshuakt commented 1 year ago

Review checklist for @joshuakt

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/SharmaLlama/ticktack?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@benjaminpope) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

joshuakt commented 1 year ago

Some initial comments on code usability:

I had a few issues trying to get ticktack installed - I kept getting errors when I tried installing in my usual conda environment(s) because I had the wrong version of this or that. In the end, I had to create a new conda environment with most of the requirements from requirements.txt:

conda create -n tictac -c conda-forge python numpy scipy jax jaxlib astropy matplotlib diffrax emcee h5py==3.3.0 pandas seaborn tqdm tinygp pip

conda activate tictac

And then I had to install the remaining three packages (chainconsumer, hdfdict, jax-cosmo) with pip install. Only then did pip install ticktack work properly.

I found it was also necessary to pip install pytest to successfully run the tests in the tests folder.

After installation, I attempted to run joss_figure.py to reproduce the results in the manuscript. It took around 10 minutes to get through the burn-in and "running production" but then I got an error "NameError: name 'ChainConsumer' is not defined"

I attempted to fix this by adding the line "from chainconsumer import ChainConsumer" to joss_figure.py. This seems to work because the code finished running and reproduced Fig. 1 from the manuscript.

The manuscript itself is clear, contains a persuasive statement of need, and sufficient references for the reader to dig into the model details. Finally, I worked through the fitting documentation and everything was explained succinctly and the code ran without issue.

dfm commented 1 year ago

@benjaminpope — I haven't had any success finding a second reviewer for this submission so I propose that I will do a review myself. The only potential issue with this is that @benjaminpope and I have co-authored two (related) papers within the past 4 years (Nth authors in both cases):

I don't believe that these make me unable to provide impartial judgement, but I wanted to give @benjaminpope, any other authors, and @arfon (as an external JOSS editor) a chance to chime in with any concerns about this potential perceived conflict of interest.

dfm commented 1 year ago

@editorialbot add @dfm as reviewer

editorialbot commented 1 year ago

@dfm added to the reviewers list!

dfm commented 1 year ago

Review checklist for @dfm

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/SharmaLlama/ticktack?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@benjaminpope) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item. https://github.com/SharmaLlama/ticktack/issues/36
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[x] Installation: Does installation proceed as outlined in the documentation? https://github.com/SharmaLlama/ticktack/pull/35 https://github.com/SharmaLlama/ticktack/issues/38
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)? https://github.com/SharmaLlama/ticktack/issues/42
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified? https://github.com/SharmaLlama/ticktack/issues/40 https://github.com/SharmaLlama/ticktack/issues/44
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support https://github.com/SharmaLlama/ticktack/issues/41

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

dfm commented 1 year ago

@benjaminpope — (wearing my editor hat 🎩) I believe that we're still waiting on a response to @joshuakt's comments from above (https://github.com/openjournals/joss-reviews/issues/5084#issuecomment-1407296942). Please take a look at that and respond so that @joshuakt can continue with the review!

benjaminpope commented 1 year ago

Hi @dfm, @joshuakt,

My apologies for taking so long - last week was the first week of the teaching semester and things got on top of me a little.

Thank you both for your helpful and insightful comments and engagement with the code, and for carefully identifying issues with the initial submission.

We have now addressed and closed all the issues raised by @dfm. We have also fixed both the install issue and the joss_figure.py issue identified by @joshuakt. I want to explicitly acknowledge @sharmallama, @qingyuanzhang3, and @jordan-dennis for their work building this package and addressing the issues raised in review.

We are now happy to resubmit and continue the review.

All the best,

Ben

benjaminpope commented 1 year ago

Just checking in on this - is there anything else we need to do to complete this review?

Jordan-Dennis commented 1 year ago

The new docs need to be published. I couldn't replicate the local mkdocs environment easily, but I can try again tomorrow.

dfm commented 1 year ago

@benjaminpope — Besides @Jordan-Dennis' docs point, I think the ball is back to me an @joshuakt to finish going through our checklists. JOSS reviews are typically iterative so I expect that we'll have some more feedback as we go through the last steps. I'll aim to get back to it ASAP, and @joshuakt can you take a look again soon too? Thanks!

dfm commented 1 year ago

I've checked all but 2 of my review items:

I think that the documentation/licensing for the included data is still insufficient: https://github.com/SharmaLlama/ticktack/issues/36
The tests emit some deprecation warnings that can be easily fixed (there are also some caused by dependencies, but we'll have to live with those!): https://github.com/SharmaLlama/ticktack/issues/44

benjaminpope commented 1 year ago

Hi @dfm,

Docs are now published, including data provenance, and all warnings fixed.

Thank you again for identifying these issues.

Cheers,

Ben

dfm commented 1 year ago

Thanks @benjaminpope! I'm happy to finish checking all the items on my checklist.

@joshuakt — Can you try going through the rest of your checklist? It doesn't seem like there's much left to do. Please let me know if you run into any issues. Thanks!

joshuakt commented 1 year ago

Looks good to me! Checklist items have been addressed

dfm commented 1 year ago

@joshuakt — Great - thank you for the time you've volunteered to this!!

dfm commented 1 year ago

@editorialbot check references

dfm commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

editorialbot commented 1 year ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1109/MCSE.2007.53 is OK
- 10.21105/joss.00045 is OK
- 10.1038/nature11123 is OK
- 10.1038/ncomms2783 is OK
- 10.1002/2012JA018320 is OK
- 10.1038/486473e is OK
- 10.1002/asna.201512208 is OK
- 10.1017/RDC.2018.74 is OK
- 10.1002/asna.201512205 is OK
- 10.1016/j.asr.2014.12.014 is OK
- 10.1667/rr1094.1 is OK
- 10.1017/rdc.2020.58 is OK
- 10.1038/srep03728 is OK
- 10.1088/1742-6596/1400/2/022034 is OK
- 10.1093/mnras/stz685 is OK
- 10.1016/j.icarus.2014.06.009 is OK
- 10.1007/s11207-019-1424-8 is OK
- 10.1038/ncomms9611 is OK
- 10.1029/2021JA029351 is OK
- 10.1002/2017JD027325 is OK
- 10.1017/S0033822200052176 is OK
- 10.1093/mnras/sts378 is OK
- 10.1093/mnras/stt1468 is OK
- 10.1038/nature11695 is OK
- 10.1051/0004-6361/201321080 is OK
- 10.1029/2021GL094848 is OK
- 10.1016/0771-050x(80)90013-3 is OK
- 10.1137/141000671 is OK
- 10.3402/tellusa.v9i1.9078 is OK
- 10.1098/rspa.2022.0497 is OK
- 10.1007/978-1-4020-2113-8 is OK
- 10.1038/ncomms15423 is OK
- 10.5194/gmd-12-1541-2019 is OK
- 10.1016/0168-583x(87)90264-3 is OK
- 10.1038/s41561-020-00674-0 is OK
- 10.1038/s41467-022-28804-9 is OK
- 10.1038/s41467-021-27891-4 is OK
- 10.3847/1538-3881/ac5683 is OK
- 10.1029/2021gl097201 is OK
- 10.1177/095968369300300401 is OK
- 10.1016/j.nimb.2012.08.046 is OK
- 10.1016/j.epsl.2014.11.048 is OK
- 10.1073/pnas.1613144114 is OK
- 10.1038/s41467-018-05883-1 is OK
- 10.1038/s41467-018-06036-0 is OK
- 10.1002/2014GL062218 is OK
- 10.1029/2021GL093419 is OK
- 10.3389/fspas.2022.886140 is OK
- 10.1017/RDC.2018.53 is OK
- 10.1017/RDC.2017.59 is OK
- 10.3402/tellusa.v27i2.9900 is OK
- 10.1017/s0033822200009449 is OK
- 10.1038/s41598-019-53296-x is OK
- 10.1098/rspa.2016.0263 is OK
- 10.1017/rdc.2016.50 is OK
- 10.1002/asna.201412071 is OK
- 10.1038/s41586-021-03972-8 is OK
- 10.1016/j.quascirev.2016.12.024 is OK
- 10.1017/RDC.2017.75 is OK
- 10.1073/pnas.1921301117 is OK
- 10.1038/s41586-021-04240-5 is OK
- 10.1017/S0007087420000011 is OK
- 10.1126/science.109.2827.227 is OK
- 10.1038/s43586-021-00058-7 is OK
- 10.1007/s41116-022-00033-8 is OK
- 10.2458/azu_js_rc.55.16947 is OK
- 10.1017/rdc.2020.41 is OK
- 10.1038/s41467-017-01698-8 is OK
- 10.1007/s11434-014-0345-z is OK
- 10.3847/1538-4357/ab55db is OK
- 10.1086/510482 is OK
- 10.1093/mnras/stv423 is OK
- 10.3847/2041-8205/826/1/L2 is OK
- 10.1038/nature16168 is OK
- 10.3847/2041-8213/ac794d is OK
- 10.1002/2017gl074208 is OK
- 10.1038/ncomms11058 is OK
- 10.1093/mnras/stab166 is OK
- 10.1093/pasj/psu012 is OK
- 10.3847/1538-4357/ab14e6 is OK
- 10.3847/1538-4357/abc8f5 is OK
- 10.1126/science.aay3821 is OK
- 10.1146/annurev-astro-112420-023324 is OK
- 10.1038/s41550-021-01335-x is OK
- 10.21105/joss.00248 is OK
- 10.21105/joss.00516 is OK
- 10.5334/jors.130 is OK
- 10.11141/ia.7.1 is OK
- 10.1038/s41467-020-20695-y is OK
- 10.1017/rdc.2020.46 is OK
- 10.1017/rdc.2020.59 is OK
- 10.1038/1741138a0 is OK
- 10.1029/2021JA029378 is OK
- 10.1029/2007ja012499 is OK
- 10.3847/1538-4357/abad93 is OK
- 10.1145/3452296.3472916 is OK
- 10.1038/srep45257 is OK
- 10.1029/2020JA027921 is OK
- 10.1017/CBO9781139165150.015 is OK
- 10.2140/camcos.2010.5.65 is OK
- 10.1063/1.1699114 is OK
- 10.5281/zenodo.6389738 is OK
- 10.1086/670067 is OK
- 10.1063/1.1835238 is OK
- 10.12688/f1000research.29032.2 is OK
- 10.3847/1538-3881/aa9332 is OK
- 10.3847/2515-5172/aaaf6c is OK
- 10.1016/0893-9659(89)90079-7 is OK
- 10.1038/195984a0 is OK
- 10.1017/RDC.2019.26 is OK
- 10.1038/s41598-019-57273-2 is OK
- 10.1007/s11207-021-01831-3 is OK
- 10.1051/swsc/2018014 is OK
- 10.1038/s41598-021-95235-9 is OK
- 10.1029/2020SW002665 is OK
- 10.1126/science.abd7096 is OK
- 10.1126/science.1185402 is OK
- 10.1086/367639 is OK
- 10.1017/RDC.2018.64 is OK
- 10.1017/RDC.2020.108 is OK
- 10.1126/science.1066114 is OK
- 10.1017/RDC.2020.49 is OK

MISSING DOIs

- 10.1109/mcse.2007.55 may be a valid DOI for title: Matplotlib: A 2D graphics environment
- 10.1109/mcse.2011.37 may be a valid DOI for title: The NumPy array: a structure for efficient numerical computation
- 10.3847/2041-8213/ac8b13 may be a valid DOI for title: HD 166620: Portrait of a Star Entering a Grand Magnetic Minimum
- 10.2307/211876 may be a valid DOI for title: Dendroclimatic changes in semiarid America
- 10.1017/s0033822200030903 may be a valid DOI for title: Radiocarbon calibration and analysis of stratigraphy: the OxCal program
- 10.2458/azu_js_rc.55.16215 may be a valid DOI for title: Recent and planned developments of the program OxCal

INVALID DOIs

- None

dfm commented 1 year ago

@benjaminpope — Can you check those missing DOIs, and make sure that only references that are actually cited are included in the .bib file? It looks to me like there are some references that are included in the .bib file, but not cited. Thanks!

benjaminpope commented 1 year ago

@editorialbot generate pdf

benjaminpope commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1038/s41561-020-00674-0 is OK
- 10.1038/s41467-018-06036-0 is OK
- 10.1007/s41116-022-00033-8 is OK
- 10.1007/978-1-4020-2113-8 is OK
- 10.1086/670067 is OK
- 10.1016/j.epsl.2014.11.048 is OK
- 10.21105/joss.00045 is OK
- 10.1038/s41586-021-03972-8 is OK
- 10.1073/pnas.1613144114 is OK
- 10.1038/nature11123 is OK
- 10.1017/rdc.2020.41 is OK
- 10.2458/azu_js_rc.55.16947 is OK
- 10.1029/2021GL094848 is OK
- 10.1051/0004-6361/201321080 is OK
- 10.1098/rspa.2022.0497 is OK

MISSING DOIs

- None

INVALID DOIs

- None

benjaminpope commented 1 year ago

@dfm fixed references - short .bib file (didn't realise this was an issue), DOIs fixed. Thanks.

editorialbot commented 1 year ago

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

dfm commented 1 year ago

@benjaminpope — Perfect, thank you! I spotted one more tiny typesetting issue (sorry!) can you merge that and then I have a few final processing steps for you. Can you:

Take one last read through the manuscript to make sure that you're happy with it (it's harder to make changes later!), especially the author names and affiliations. I've taken a pass and it looks good to me!
Increment the version number of the software and report that version number back here.
Create an archived release of that version of the software (using Zenodo or something similar). Please make sure that the metadata (title and author list) exactly match the paper. Then report the DOI of the release back to this thread.

benjaminpope commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

benjaminpope commented 1 year ago

Merged your typesetting PR.

Incremented version number to 1.1.0.

Ping @sharmallama about Zenodo archive.

benjaminpope commented 1 year ago

DOI for Zenodo: 10.5281/zenodo.7754438

dfm commented 1 year ago

Thanks! Can you (perhaps @SharmaLlama or @benjaminpope) please update the Zenodo metadata so that the author list and title to exactly match the paper? You can click the "Edit" button at the top right of the Zenodo page if you the owner of the archive. Then we're good to go.

dfm commented 1 year ago

@editorialbot set 1.1.0 as version

editorialbot commented 1 year ago

Done! version is now 1.1.0

dfm commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1038/s41561-020-00674-0 is OK
- 10.1038/s41467-018-06036-0 is OK
- 10.1007/s41116-022-00033-8 is OK
- 10.1007/978-1-4020-2113-8 is OK
- 10.1086/670067 is OK
- 10.1016/j.epsl.2014.11.048 is OK
- 10.21105/joss.00045 is OK
- 10.1038/s41586-021-03972-8 is OK
- 10.1073/pnas.1613144114 is OK
- 10.1038/nature11123 is OK
- 10.1017/rdc.2020.41 is OK
- 10.2458/azu_js_rc.55.16947 is OK
- 10.1029/2021GL094848 is OK
- 10.1051/0004-6361/201321080 is OK
- 10.1098/rspa.2022.0497 is OK

MISSING DOIs

- None

INVALID DOIs

- None

SharmaLlama commented 1 year ago

@dfm I've appended the metadata for zenodo to have the authors and title matching the paper

dfm commented 1 year ago

@SharmaLlama — Thanks! For some reason (probably left over from my PRs), I'm still listed as an author on the Zenodo archive. I'm going to proceed with the final processing steps, but can you remove me from the author list ASAP? Thanks!

dfm commented 1 year ago

@editorialbot set 10.5281/zenodo.7754438 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.7754438

openjournals / joss-reviews