editorialbot commented 1 year ago

Submitting author: !--author-handle-->@tenemark@jsta<!--end-editor-- Reviewers: @aleaf, @ecomodeller Archive: 10.5281/zenodo.8412800

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/5f05b2f8f2dbd9e9f69b9181bdcb3359"><img src="https://joss.theoj.org/papers/5f05b2f8f2dbd9e9f69b9181bdcb3359/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/5f05b2f8f2dbd9e9f69b9181bdcb3359/status.svg)](https://joss.theoj.org/papers/5f05b2f8f2dbd9e9f69b9181bdcb3359)

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

@aleaf & @ecomodeller, 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 @jsta 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 @ecomodeller

📝 Checklist for @aleaf

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:

@editorialbot commands

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

@editorialbot generate pdf

editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (536.5 files/s, 159061.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           7            460            918           1634
Markdown                         3             31              0            436
HTML                             8             50             70            252
TeX                              1              0              0             76
Jupyter Notebook                 1              0           3095             64
YAML                             1              1              4             18
XML                              3              0              0              6
-------------------------------------------------------------------------------
SUM:                            24            542           4087           2486
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 561

editorialbot commented 1 year ago

Failed to discover a Statement of need section in paper

editorialbot commented 1 year ago

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

OK DOIs

- 10.1016/S0309-1708(02)00092-1 is OK

MISSING DOIs

- 10.1111/gwat.12360 may be a valid DOI for title: Calibration and uncertainty analysis for complex environmental models
- 10.25080/majora-92bf1922-00a may be a valid DOI for title: Data structures for statistical computing in python

INVALID DOIs

- http://dx.doi.org/10.5066/F7RF5S7G is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.envsoft.2021.105022 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:

ecomodeller commented 1 year ago

Review checklist for @ecomodeller

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/tenemark/mikecalsetup?
[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 (@tenemark) 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?
[ ] 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?

ecomodeller commented 1 year ago

@editorialbot commands

editorialbot commented 1 year ago

Hello @ecomodeller, 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

aleaf commented 1 year ago

Review checklist for @aleaf

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/tenemark/mikecalsetup?
[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 (@tenemark) 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?

aleaf commented 1 year ago

I was not able to confirm the functional claims of the software tenemark/mikecalsetup#2; tenemark/mikecalsetup#3; tenemark/mikecalsetup#5.

aleaf commented 1 year ago

The readme has a statement of need, but it could be improved: tenemark/mikecalsetup#4

aleaf commented 1 year ago

The package needs a list of dependencies, ideally in the form of a conda environment file: tenemark/mikecalsetup#1

aleaf commented 1 year ago

While the package includes a minimal working example, it could ideally be improved to be a complete working example that included execution of a forward model run with PEST or OSTRICH tenemark/mikecalsetup#5.

aleaf commented 1 year ago

Most functions and classes are documented with numpy-style docstrings, but I would highly encourage the author to add HTML documentation, which can be easily set up with the Scientific Python Cookiecutter or perhaps other tools tenemark/mikecalsetup#7.

aleaf commented 1 year ago

While there is one test file, it didn't execute successfully, and there is no test coverage reporting or CI tenemark/mikecalsetup#3, tenemark/mikecalsetup#7.

aleaf commented 1 year ago

The documentation does not have community guidelines tenemark/mikecalsetup#8

aleaf commented 1 year ago

State of the field: While the paper mentions the PstFrom module in pyEMU, the comparison is not entirely correct. While PstFrom was initially developed (and possibly most often used) for MODFLOW models, it is now model-agnostic in the sense that it accepts text files containing numerical arrays or tabular input (as can be read by numpy.loadtxt() and pandas.read_csv(), for example). PstFrom and more generally pyEMU has benefited from substantial development effort by some of the top scientists in the parameter estimation/uncertainty quantification space, and offer relatively easy, mostly automated hooks into many cutting edge techniques such as the high-dimensional parameterization, the iterative ensemble smoother, multi-objective optimization under uncertainty, etc. As a result it is widely used, and has good prospects for continued development.

Which I guess leads to a larger question of the focus of mikecalsetup. It clearly seems like there is a need to make parameter estimation easier for MIKE SHE models. Is there a way to do this that would also allow MIKE SHE users to also access the functionality in pyEMU, and reduce code duplication for more mundane tasks like managing the PEST control file or providing a python API for various PEST or PEST++ features?

aleaf commented 1 year ago

Quality of writing: the paper has some mostly minor grammatical issues, and could benefit from an edit by a native English speaker.

aleaf commented 1 year ago

It looks like there are some issues with the reference DOIs, as flagged by @editorialbot. pyEMU should probably be cited:

White, J.T., Fienen, M.N., Doherty, J.E., 2016. A python framework for environmental model uncertainty analysis. Environmental modeling and Software 85, 217–228. https://doi.org/10.1016/j.envsoft.2016.08.017.

jsta commented 1 year ago

Thank you to both reviewers for their careful and thorough work!

@tenemark please let myself or the reviewers know if you need clarification on any of the points they've raised.

tenemark commented 1 year ago

Hi, I understand the comments and will work on improving the package and manuscript accordingly. Thank you for the helpful suggestions. I will get back to you in a couple of weeks.

On Sat, Jul 8, 2023 at 4:00 AM Jemma Stachelek @.***> wrote:

Thank you to both reviewers for their careful and thorough work!

@tenemark https://github.com/tenemark please let myself or the reviewers know if you need clarification on any of the points they've raised.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/5548#issuecomment-1626450907, or unsubscribe https://github.com/notifications/unsubscribe-auth/A35QM7XXUV2QOIGB62REEZ3XPC5NHANCNFSM6AAAAAAZD6PV6M . You are receiving this because you were mentioned.Message ID: @.***>

tenemark commented 1 year ago

Thank you again very much for your thorough review! Following your comments, I have made some revisions, which I will summarize here: I have addressed the raised issues on github. I have improved testing of the package with additional tests and coverage reporting. I have added a conda environment file, which will ease installation of the package. By installing mikecalsetup in this environment, the test file will run successfully. I have added some extra examples and moved them to the folder "examples". The examples now also include execution of a forward model run with PEST and OSTRICH. Also, an example (example_PEST_with_PstFrom.ipynb) shows how users of MIKE SHE can access the functionality of pyEMU and mikecalsetup at the same time. I have changed the state of the field description to better convey how this package relate to pyEMU. The focus of mikecalsetup is to setup calibration files for the nested header text file format used in MIKE SHE files, which is not supported by pyEMU. Spatially distributed and time dependent data found in the dfs file format of MIKE SHE can be handled with pyEMU if they are converted to text files (which we now show in the example “example_PEST_with_PstFrom.ipynb”). mikecalsetup has therefore not been developed to handle these files. I have edited the reference list and validated the DOIs.

jsta commented 1 year ago

Sounds great @tenemark! I'll have a look over the next couple days.

jsta 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:

jsta 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

- 10.1016/S0309-1708(02)00092-1 is OK
- 10.1016/j.envsoft.2021.105022 is OK
- 10.1016/j.envsoft.2016.08.017 is OK

MISSING DOIs

- 10.1111/gwat.12360 may be a valid DOI for title: Calibration and uncertainty analysis for complex environmental models
- 10.25080/majora-92bf1922-00a may be a valid DOI for title: Data structures for statistical computing in python

INVALID DOIs

- None

jsta commented 1 year ago

The updated changes look great to me.

@aleaf or @ecomodeller can either of you verify that the installation file and tests work?

jsta 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:

jsta 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

- 10.1016/S0309-1708(02)00092-1 is OK
- 10.1016/j.envsoft.2021.105022 is OK
- 10.1016/j.envsoft.2016.08.017 is OK

MISSING DOIs

- 10.1111/gwat.12360 may be a valid DOI for title: Calibration and uncertainty analysis for complex environmental models
- 10.25080/majora-92bf1922-00a may be a valid DOI for title: Data structures for statistical computing in python

INVALID DOIs

- None

jsta commented 1 year ago

I have verified that the installation file and tests work. As an aside, the coverage reporting didn't work for me but that's not critical.

From my perspective, this paper is ready to move on to the next steps of post-review, acceptance, etc. @aleaf, @ecomodeller do either of you feel differently?

ecomodeller commented 1 year ago

No, please proceed.

aleaf commented 1 year ago

yes, please proceed.

On Wed, Oct 4, 2023 at 11:56 PM Henrik Andersson @.***> wrote:

No, please proceed.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/5548#issuecomment-1748032001, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA553O4X35SDPL2HHU622O3X5Y4ZJAVCNFSM6AAAAAAZD6PV6OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONBYGAZTEMBQGE . You are receiving this because you were mentioned.Message ID: @.***>

jsta commented 1 year ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

[x] Double check authors and affiliations (including ORCIDs)
[x] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
[x] Archive the release on Zenodo/figshare/etc and post the DOI here.
[x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
[x] Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

[x] Read the text of the paper and offer comments/corrections (as either a list or a PR)
[x] Check the references in the paper for corrections (e.g. capitalization)
[x] Check that the archive title, author list, version tag, and the license are correct
[x] Set archive DOI with @editorialbot set <DOI here> as archive
[x] Set version with @editorialbot set <version here> as version
[x] Double check rendering of paper with @editorialbot generate pdf
[x] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[x] Recommend acceptance with @editorialbot recommend-accept

jsta commented 1 year ago

@tenemark The next step is for you to create a GitHub/Zenodo release: https://github.com/tenemark/mikecalsetup/releases

tenemark commented 1 year ago

Thank you! I have made a release.

On Thu, Oct 5, 2023 at 5:49 PM Jemma Stachelek @.***> wrote:

@tenemark https://github.com/tenemark The next step is for you to create a GitHub/Zenodo release: https://github.com/tenemark/mikecalsetup/releases

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/5548#issuecomment-1749174256, or unsubscribe https://github.com/notifications/unsubscribe-auth/A35QM7QATESUCVUHBYPNNR3X53JI5AVCNFSM6AAAAAAZD6PV6OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONBZGE3TIMRVGY . You are receiving this because you were mentioned.Message ID: @.***>

jsta commented 1 year ago

@editorialbot set v0.1 as version

editorialbot commented 1 year ago

Done! version is now v0.1

jsta commented 1 year ago

Great, next step @tenemark is making a DOI archive in Zenodo/Figshare/Etc. One critical piece of this step is that the archival deposit must have 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.

tenemark commented 1 year ago

I am unsure how to do this. I have changed the metadata of my Zenodo upload to correspond to what you requested. The DOI is 10.5281/zenodo.8412800. If this is not what you meant, could you please provide me with a link to a guideline of what to do.

On Fri, Oct 6, 2023 at 2:51 PM Jemma Stachelek @.***> wrote:

Great, next step @tenemark https://github.com/tenemark is making a DOI archive in Zenodo/Figshare/Etc. One critical piece of this step is that the archival deposit must have 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.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/5548#issuecomment-1750623612, or unsubscribe https://github.com/notifications/unsubscribe-auth/A35QM7UHJEMYS24SIQYXKR3X575F7AVCNFSM6AAAAAAZD6PV6OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONJQGYZDGNRRGI . You are receiving this because you were mentioned.Message ID: @.***>

jsta commented 1 year ago

@editorialbot set 10.5281/zenodo.8412800 as archive

editorialbot commented 1 year ago

Done! archive is now 10.5281/zenodo.8412800

jsta 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:

jsta commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.1016/S0309-1708(02)00092-1 is OK
- 10.1016/j.envsoft.2021.105022 is OK
- 10.1016/j.envsoft.2016.08.017 is OK

MISSING DOIs

- 10.1111/gwat.12360 may be a valid DOI for title: Calibration and uncertainty analysis for complex environmental models
- 10.25080/majora-92bf1922-00a may be a valid DOI for title: Data structures for statistical computing in python

INVALID DOIs

- None

openjournals / joss-reviews

[REVIEW]: mikecalsetup: an open-source python tool for automatically creating calibration setups of MIKE SHE models in PEST or OSTRICH #5548

Status

Reviewer instructions & questions

Checklists

Review checklist for @ecomodeller

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @aleaf

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance