editorialbot commented 7 months ago

Submitting author: !--author-handle-->@victorapm@lucydot<!--end-editor-- Reviewers: @DamynChipman, @mayrmt Archive: 10.5281/zenodo.11657386

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/63cf7b829394f99d113c59cd13729290"><img src="https://joss.theoj.org/papers/63cf7b829394f99d113c59cd13729290/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/63cf7b829394f99d113c59cd13729290/status.svg)](https://joss.theoj.org/papers/63cf7b829394f99d113c59cd13729290)

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

@DamynChipman & @mayrmt, 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 @lucydot 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 @DamynChipman

📝 Checklist for @mayrmt

editorialbot commented 7 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:

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

@editorialbot generate pdf

editorialbot commented 7 months ago

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

OK DOIs

- 10.1109/ISPDC.2012.16 is OK
- 10.1145/2807591.2807623 is OK

MISSING DOIs

- No DOI given, and none found for title: high performance preconditioners
- No DOI given, and none found for title: YAML Ain’t Markup Language (YAML) Version 1.2

INVALID DOIs

- None

editorialbot commented 7 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (1774.5 files/s, 279516.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C                               22            869            935           3849
C/C++ Header                    22            294           1119            983
reStructuredText                 6            356            267            694
m4                               2             97             17            689
Markdown                         5             63              0            417
YAML                             9             23             12            269
Python                           2             65            105            180
Bourne Shell                     1             13             15             54
make                             2             10              8             48
TeX                              1              3              0             34
JavaScript                       1              0              3              8
-------------------------------------------------------------------------------
SUM:                            73           1793           2481           7225
-------------------------------------------------------------------------------

Commit count by author:

    72  Victor A. P. Magri

editorialbot commented 7 months ago

Paper file info:

📄 Wordcount for paper.md is 658

✅ The paper includes a Statement of need section

editorialbot commented 7 months ago

License info:

🟡 License found: Other (Check here for OSI approval)

editorialbot commented 7 months ago

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

DamynChipman commented 7 months ago

Review checklist for @DamynChipman

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/hypre-space/hypredrive?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@victorapm) 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?

DamynChipman commented 7 months ago

@lucydot, I want to disclose a potential perceived COI and request it to be waived in order to review this: I worked at LLNL in the summer of 2021 and 2022. This was over a year ago and in a different directorate than @victorapm.

lucydot commented 7 months ago

Hi @DamynChipman - thanks for the disclosure, and agreed that this does not meet bar for COI - please do continue with the review.

DamynChipman commented 6 months ago

@lucydot, I have completed my review. @victorapm addressed the comments I had in https://github.com/hypre-space/hypredrive/issues/60.

lucydot commented 6 months ago

@mayrmt how is your review going?

lucydot commented 6 months ago

That's great @DamynChipman, thanks for the update. Can I double check you were able to install and run through examples without any hiccups? I'm asking as it is unusual for everything to go so smoothly!

DamynChipman commented 6 months ago

Yeah, I was able to install hypredrive as detailed in the documentation without issue. I ran the built in unit tests with make test, then ran through each of the examples in examples using the files found in data. I also experimented a little bit some of the examples.

mayrmt commented 6 months ago

Review checklist for @mayrmt

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/hypre-space/hypredrive?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@victorapm) 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?

danielskatz commented 6 months ago

👋 @mayrmt - it looks like your review, and the process of reviewing this submission overall, is close to done, so as track editor, I'm just checking in to see if we can complete it. Is there anything I can do to help you?

mayrmt commented 6 months ago

@danielskatz thanks for asking! I have just re-done my tests of the software. One item remains open, that requires some clarification from the submitting author.

@victorapm While the code compiles and tests run nicely, one line of the installation instructions give me some trouble. In particular, make install yields the following terminal output:

$ make install
make[1]: Entering directory '/hdd/codes/hypredrive/src-hyperdrive'
 /usr/bin/mkdir -p '/usr/local/lib'
 /bin/bash ./libtool   --mode=install /usr/bin/install -c   libHYPREDRV.la '/usr/local/lib'
libtool: install: /usr/bin/install -c .libs/libHYPREDRV.lai /usr/local/lib/libHYPREDRV.la
/usr/bin/install: cannot create regular file '/usr/local/lib/libHYPREDRV.la': Permission denied
make[1]: *** [Makefile:532: install-libLTLIBRARIES] Error 1
make[1]: Leaving directory '/hdd/codes/hypredrive/src-hyperdrive'
make: *** [Makefile:1101: install-am] Error 2

I was wondering, whether I can change the installation directory, though I haven't found the necessary information in neither the documentation nor the code base itself. Am I missing something here?

Note: I can use the software without installing it.

victorapm commented 6 months ago

Hi Matthias,

make install failed because, by default, it installs the software at /usr/local, which requires admin privileges.

For a custom installation path, you can pass the option --prefix=${INSTALL_PATH} to the configure script, where ${INSTALL_PATH} is a destination folder set by the user, e.g., --prefix=${PWD}/install. This is mentioned in the Getting Started section, fourth enumerated point under "Note".

Hope this helps!

mayrmt commented 6 months ago

@victorapm, sorry for missing that! It works just fine.

@danielskatz @lucydot This completes my review. I am happy to recommend publication.

lucydot commented 6 months ago

Excellent work @mayrmt and @DamynChipman; on behalf of the JOSS team, thank you for your expertise and time.

lucydot commented 6 months ago

We are onto the final stages of the process now @victorapm I'll ask editorialbot to generate the post-review to-do list; let me know when each item is done.

lucydot commented 6 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Double check authors and affiliations (including ORCIDs)
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.
Archive the release on Zenodo/figshare/etc and post the DOI here.
Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
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 pull request)
[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
[ ] Recommend acceptance with @editorialbot recommend-accept

lucydot commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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

lucydot commented 6 months ago

@editorialbot check references

lucydot commented 6 months ago

@victorapm you have a very nicely written and concise JOSS paper 👍 One minor point - you do not use the acronym CSE defined at the start of the paper.

lucydot commented 6 months ago

@victorapm a little work is also needed on the references. I can see all but one reference points to a webpage. Are there outputs-with-a-DOI associated with any of these projects? As these would be our preferred sources. You can still link directly to any webpages directly by embedding a hyperlink in the main text.

lucydot commented 5 months ago

@victorapm a reminder ping. Few relatively small changes needed to paper and then we are ready to proceed with final steps.

lucydot commented 5 months ago

A quick note here to say I will be on Annual Leave for the next week, will be back on the 24th June.

victorapm commented 5 months ago

Hi Lucy, thank you for your kind comments and I apologize for the delay, the last couple of weeks have been busy to me!

I updated the references as you suggested, i.e., by using the ones with DOI.

The package version is v0.1.0 and published here

As for the zenodo archive, you can find it here. The title and author list, including ORCIDs, in the archive match those in the JOSS paper.

Please, let me know if there's something missing from my end. Thank you!

victorapm commented 5 months ago

@editorialbot generate pdf

editorialbot commented 5 months ago

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

victorapm commented 5 months ago

@editorialbot generate pdf

editorialbot commented 5 months ago

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

lucydot commented 5 months ago

@editorialbot set v0.1.0 as version

editorialbot commented 5 months ago

Done! version is now v0.1.0

lucydot commented 5 months ago

@editorialbot set 10.5281/zenodo.11657386 as archive

editorialbot commented 5 months ago

Done! archive is now 10.5281/zenodo.11657386

lucydot commented 5 months ago

@editorialbot generate pdf

lucydot commented 5 months ago

@editorialbot check references

editorialbot commented 5 months ago

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

OK DOIs

- 10.1007/3-540-47789-6_66 is OK
- 10.1145/1089014.1089021 is OK
- 10.2172/2205494 is OK
- 10.1145/2807591.2807623 is OK

MISSING DOIs

- None

INVALID DOIs

- None

lucydot commented 5 months ago

@victorapm - this all looks great 🥳

I'll recommend acceptance now -

lucydot commented 5 months ago

@editorialbot recommend-accept

editorialbot commented 5 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 5 months ago

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

OK DOIs

- 10.1007/3-540-47789-6_66 is OK
- 10.1145/1089014.1089021 is OK
- 10.2172/2205494 is OK
- 10.1145/2807591.2807623 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 5 months ago

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

editorialbot commented 5 months ago

:wave: @openjournals/csism-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/5532, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz commented 5 months ago

@victorapm - as track editor, I'll proofread the paper in the next couple of hours and let you know the next steps, if any are needed from you.

danielskatz commented 5 months ago

👋 @victorapm - the paper looks good, but I found two small issues in the bib to correct, as shown in https://github.com/hypre-space/hypredrive/pull/62. Please merge this, or let me know what you disagree with, then we can continue to acceptance and publication.

victorapm commented 5 months ago

Merged, thanks @danielskatz!

danielskatz commented 5 months ago

@editorialbot recommend-accept

openjournals / joss-reviews

[REVIEW]: Hypredrive: High-level interface for solving linear systems with hypre #6654

Status

Reviewer instructions & questions

Checklists

Review checklist for @DamynChipman

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @mayrmt

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