[PRE REVIEW]: PyAMG: Algebraic Multigrid Solvers in Python about joss-reviews HOT 38 CLOSED

@danielskatz @jedbrown I'm happy to review this contribution.

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There had been a question, but turns out I'm not conflicted.

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@editorialbot assign @jedbrown as editor

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Hello human, 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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Software report:

github.com/AlDanial/cloc v 1.88  T=0.29 s (505.6 files/s, 159403.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         102           5135           9770          16204
C++                              9            505              9           4755
C/C++ Header                     9            764           3281           4150
CSS                              1            125             21            517
Markdown                        11            120              0            516
YAML                             7             46             13            313
TeX                              3             25              0            246
Bourne Shell                     2              1              0             27
reStructuredText                 2             33             35             22
TOML                             1              1              0             11
make                             1              4              6             10
-------------------------------------------------------------------------------
SUM:                           148           6759          13135          26771
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 1335

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

OK DOIs

- 10.1137/1.9781611971057 is OK
- 10.1007/BF02238511 is OK
- 10.1137/050626272 is OK
- 10.1137/16M1082706 is OK
- 10.1007/978-3-540-70529-1_337 is OK
- 10.1007/978-3-540-70529-1_338 is OK
- 10.1137/1.9780898719505 is OK
- 10.1109/MCSE.2006.105 is OK
- 10.1016/S0168-9274(01)00115-5 is OK
- 10.1137/140980260 is OK
- 10.1134/s1995080219050056 is OK
- 10.1137/110838844 is OK

MISSING DOIs

- 10.1137/17m1144350 may be a valid DOI for title: Nonsymmetric algebraic multigrid based on local approximate ideal restriction (\ell AIR)

INVALID DOIs

- None

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

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@lukeolson - thanks for your submission. Please add the missing DOI (found above) to the bib file. It also appears that the entry two about that one should have a DOI as well: 10.1137/18M119376

Finally, your submission message implies a previous version of this software (or a paper about it) has been published. Can you explain this a bit more, along with highlighting what is new since then, either in code, perhaps as a git diff, or just in words?

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👋 @lukeolson - In another week or so I will reject this submission, unless I hear from you. Of course, you can will be able resubmit it later when you have more time to participate in the review process.

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@editorialbot generate pdf

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

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@editorialbot check references

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

OK DOIs

- 10.1137/1.9781611971057 is OK
- 10.1007/BF02238511 is OK
- 10.1137/050626272 is OK
- 10.1137/16M1082706 is OK
- 10.1007/978-3-540-70529-1_337 is OK
- 10.1007/978-3-540-70529-1_338 is OK
- 10.1137/1.9780898719505 is OK
- 10.1109/MCSE.2006.105 is OK
- 10.1016/S0168-9274(01)00115-5 is OK
- 10.1137/140980260 is OK
- 10.1134/s1995080219050056 is OK
- 10.1137/110838844 is OK
- 10.1137/17M1144350 is OK
- 10.1137/18M1193761 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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@lukeolson - thanks for your submission. Please add the missing DOI (found above) to the bib file. It also appears that the entry two about that one should have a DOI as well: 10.1137/18M119376

Fixed. pyamg/pyamg@5ab16a5

Finally, your submission message implies a previous version of this software (or a paper about it) has been published. Can you explain this a bit more, along with highlighting what is new since then, either in code, perhaps as a git diff, or just in words?

The previous version, published in JOSS, covered v4. v5 of the code includes a series of hefty PRs that were several years in development and represent a major release. The new version adds the following main to the code:

• support for non-symmetric systems: previous solvers were limited to simply
  building a different restriction operator on A.T. In v5, approximate ideal restriction (AIR) solvers have been added with examples. PRs pyamg/pyamg#367 pyamg/pyamg#380

• complete CF AMG: v4 included only the basics of ruge-stuben (or CF) AMG. This version adds a full suite of interpolation operators, block support, C/F relaxation routines, etc, bringing CF-AMG up to a fully featured solver like SA-AMG in v4. PRs pyamg/pyamg#353 pyamg/pyamg#354 pyamg/pyamg#244

• new pairwise aggregation: v5 adds a new pairwise solver and supporting methods; PR pyamg/pyamg#360

• the full diff can be found here: pyamg/pyamg@v4.2.3...v5.0.0

We feel that v5 significally expands the suite of solvers in PyAMG in comparison to v4. This motivated the release to a new major version number and a resubmission of the article.

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Thanks for submitting your paper to JOSS @lukeolson. Currently, there isn't a JOSS editor assigned to your paper.

@lukeolson if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

mayrmt and mattmartineau provided reviews last time which may be efficient. From the list, victorapm may also be familiar with solvers

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Thanks @lukeolson - let's go ahead and review this

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👋 @mayrmt and @mattmartineau - since you reviewed the previous version of this software (https://doi.org/10.21105/joss.04142) about 15 months ago, would you be willing to review this new submission?

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👋 @victorapm - would you be willing to review this JOSS submission?

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Yes, it's a pleasure to review this work

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Thanks @victorapm - I'll add you, and once we get one or two more reviewers, we'll start the review.

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@editorialbot add @victorapm as reviewer

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Can't add reviewers: There is no editor assigned yet

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Oops. I shouldn't be editing this due to my affiliation conflict with @lukeolson. @jedbrown - Can you take on this new version?

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@editorialbot invite @jedbrown as editor

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Invitation to edit this submission sent!

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@editorialbot set @jedbrown as editor

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I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

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Assigned! @jedbrown is now the editor

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@editorialbot add @mayrmt as reviewer

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@mayrmt added to the reviewers list!

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@editorialbot add @Jeff-Hadley as reviewer

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@Jeff-Hadley added to the reviewers list!

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@editorialbot start review

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OK, I've started the review over in #5495.

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Hi @jedbrown, just checking if I am still supposed to review this work. I don't see my name listed in 5495. Thanks!

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Oops, I didn't see where it lost you. I'll add you in the review issue.

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Thanks, Jed!

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