[PRE REVIEW]: PyAMG: Algebraic Multigrid Solvers in Python

[whedon]

Submitting author: @lukeolson (Luke Olson) Repository: https://github.com/pyamg/pyamg/ Version: v4.2.2 Editor: @jedbrown Reviewers: @mayrmt Managing EiC: Kevin M. Moerman

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Author instructions

Thanks for submitting your paper to JOSS @lukeolson. Currently, there isn't an 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).

Editor instructions

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

For a list of things I can do to help you, just type:

@whedon commands

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

@whedon generate pdf

[whedon]

PDF failed to compile for issue #4125 with the following error:

 Can't find any papers to compile :-(

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.27 s (472.3 files/s, 146625.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          92           4732           8962          14640
C++                              8            423              8           3553
C/C++ Header                     8            601           2568           3110
CSS                              1            125             21            517
Markdown                         8             73              0            269
YAML                             5             39              0            262
Bourne Shell                     2              1              0             26
reStructuredText                 2             29             31             20
TOML                             1              1              0             12
make                             1              4              6             10
TeX                              1              0              0              7
-------------------------------------------------------------------------------
SUM:                           129           6028          11596          22426
-------------------------------------------------------------------------------

Statistical information for the repository '5e61014456ad07e20b867fed' was
gathered on 2022/02/02.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Ben Southworth                   7           770            433            0.77
Christian Zielinski              1             7              4            0.01
Guillaume Lemaitre               1            68             63            0.08
Isuru Fernando                   1             2              2            0.00
Jacob Schroder                 188         35814          10495           29.55
Luke Olson                     672         31913          34797           42.56
Marek Wojciechowski              1             3              3            0.00
Martin Fergie                    4            46             40            0.05
Matthew West                     1           377             82            0.29
Nathan Bell                    237         19585           8741           18.07
Nico Schlömer                   10            59            184            0.16
Oliver Krzysik                   1            14              7            0.01
Schroder                        22          1024            914            1.24
Scott MacLachlan                 2           121              5            0.08
Southworth                      16           440            286            0.46
Tristan Konolige                 1           136             37            0.11
Wolfgang Noichl                  1             2              1            0.00
ben-s-southworth                 1             9              3            0.01
ekmolloy                         2             2              2            0.00
lukeolson                      124          7313           2934            6.54

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Ben Southworth              476           61.8         66.5               17.44
Christian Zielinski           6           85.7         77.9               50.00
Guillaume Lemaitre           52           76.5         24.3                1.92
Isuru Fernando                2          100.0         37.7                0.00
Jacob Schroder            11716           32.7        138.6               20.16
Martin Fergie                31           67.4         86.2                0.00
Matthew West                304           80.6         21.9               44.41
Nathan Bell                5644           28.8        138.1               19.53
Nico Schlömer                25           42.4         18.4                0.00
Schroder                    582           56.8        101.2               18.21
Scott MacLachlan             23           19.0         22.5               34.78
Southworth                   80           18.2         67.3                5.00
Tristan Konolige            114           83.8         68.9               10.53
Wolfgang Noichl               2          100.0          4.0                0.00
ben-s-southworth            226         2511.1         37.7               25.22
ekmolloy                      1           50.0         83.4                0.00
lukeolson                 19313          264.1         56.0                7.97

[Kevin-Mattheus-Moerman]

@whedon generate pdf from branch joss-paper

[whedon]

Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...

[whedon]

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

[Kevin-Mattheus-Moerman]

@whedon check references from branch joss-paper

[whedon]

Attempting to check references... from custom branch joss-paper

[whedon]

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "," (COMMA) [#, "@", #, {:title=>["An Introduction to Algebraic Multigrid"], :author=>["Falgout, R D"], :doi=>[""], :url=>["https://www.osti.gov/biblio/897960"], :journal=>["Computing in Science and Engineering, vol. 8, no. 6, November 1, 2006, pp. 24-33"]}, ",", "number", "="]

[Kevin-Mattheus-Moerman]

@openjournals/dev can you see what happened here with the reference check?

[Kevin-Mattheus-Moerman]

@whedon invite @jedbrown as editor

[whedon]

@jedbrown has been invited to edit this submission.

[danielskatz]

@Kevin-Mattheus-Moerman & @lukeolson - the error says the last bib entry is the problem. I suggest changing it to

@article{amgintro,
  title   = {An Introduction to Algebraic Multigrid},
  author  = {Falgout, R. D.},
  url     = {https://www.osti.gov/biblio/897960},
  journal = {Computing in Science \& Engineering},
  doi = {10.1109/MCSE.2006.105},
  volume = 8,
  number = 6,
  pages = {24-33},
  place   = {United States},
  year    = 2006,
  month   = oct,
}

[lukeolson]

@Kevin-Mattheus-Moerman & @lukeolson - the error says the last bib entry is the problem. I suggest changing it to

@article{amgintro,
  title   = {An Introduction to Algebraic Multigrid},
  author  = {Falgout, R. D.},
  url     = {https://www.osti.gov/biblio/897960},
  journal = {Computing in Science \& Engineering},
  doi = {10.1109/MCSE.2006.105},
  volume = 8,
  number = 6,
  pages = {24-33},
  place   = {United States},
  year    = 2006,
  month   = oct,
}

Thanks @danielskatz . I made this change.

[Kevin-Mattheus-Moerman]

@whedon check references from branch joss-paper

[whedon]

Attempting to check references... from custom branch joss-paper

[whedon]

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
- 10.1137/1.9780898719505 is OK
- 10.1109/MCSE.2006.105 is OK

MISSING DOIs

- 10.1007/978-3-540-70529-1_338 may be a valid DOI for title: Multigrid Methods: Geometric

INVALID DOIs

- None

[Kevin-Mattheus-Moerman]

@lukeolson can you check that missing DOI?

[lukeolson]

@lukeolson can you check that missing DOI?

done. added two additional DOI

[danielskatz]

@lukeolson - you can use the command @whedon check references from branch joss-paper to check again, and the command @whedon generate pdf from branch joss-paper after making changes to the .md file or when the references are right to make a new PDF. Whedon commands need to be the first entry in a new comment.

[lukeolson]

@danielskatz gotcha (I wasn't sure if I was allowed to interact with whedon)

[lukeolson]

@whedon check references from branch joss-paper

[whedon]

Attempting to check references... from custom branch joss-paper

[whedon]

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

MISSING DOIs

- None

INVALID DOIs

- None

[lukeolson]

@whedon generate pdf from branch joss-paper

[whedon]

Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...

[whedon]

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

[danielskatz]

@danielskatz gotcha (I wasn't sure if I was allowed to interact with whedon)

Yes, and encouraged, to make the journal as scalable as possible. Whedon has some controls, so different roles can do different things, but these commands related to the paper are open to authors.

[jedbrown]

@whedon assign @jedbrown as editor

[whedon]

OK, the editor is @jedbrown

[jedbrown]

Welcome, @lukeolson! :wave: I'll get started finding reviewers.

[jedbrown]

@mayrmt :wave: Would you by chance be not-conflicted (with Luke or Jacob) and available to review this submission?

[mayrmt]

@jedbrown I don't have a conflict of interest and I'm happy to review this submission. Can you please provide more details on the review process for JOSS?

[jedbrown]

Certainly. The review will be coordinated through a GitHub issue, with possible issues filed directly to upstream. Your review covers the (short) paper, but also the project documentation, and we expect reviewers to experiment with running the software. https://joss.readthedocs.io/en/latest/review_criteria.html

[jedbrown]

@whedon add @mayrmt as reviewer

[whedon]

OK, @mayrmt is now a reviewer

[lukeolson]

@jedbrown @mayrmt scipy 1.8 was released yesterday, causing an import issue with pyamg. I rolled out a new release today 4.2.1 -> 4.2.2. Just a heads-up in case the version needs to change here.

[jedbrown]

@whedon set v4.2.2 as version

[whedon]

OK. v4.2.2 is the version.

[jedbrown]

Thanks, Luke. It's common that there are updates during review and we'll set the version when it's time to archive for acceptance.

[mayrmt]

@jedbrown I have started to look into the proposed code etc. Should I kick-off the official review process via [at]whedon start review or are there any other steps that have to happen before that?

[jedbrown]

Sure, I'll start it now and add another reviewer when I get replies.

[jedbrown]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/4142.