[PRE REVIEW]: PyStokes: Stokesian hydrodynamics in Python

[whedon]

Submitting author: @rajeshrinet (Rajesh Singh) Repository: https://github.com/rajeshrinet/pystokes Version: v2.1.1 Editor: @harpolea Reviewers: @fcooper8472, @khinsen Managing EiC: Kyle Niemeyer

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[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.35 s (282.8 files/s, 110132.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                      11           2201           2239           8337
TeX                              1            558              0           5304
Cython                          20           1441           1617           4963
HTML                            15           1751             15           3304
SVG                              1              0              0           2671
Python                          13            221            151            831
CSS                              4            165             34            645
Jupyter Notebook                10              0           1037            426
Markdown                         6             85              0            190
reStructuredText                12             64             57             76
YAML                             3             12              5             56
make                             2             14              8             41
DOS Batch                        1              8              1             26
-------------------------------------------------------------------------------
SUM:                            99           6520           5164          26870
-------------------------------------------------------------------------------

Statistical information for the repository '2299' was gathered on 2020/06/07.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Rajesh Singh                    63        420260         406280          100.00

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
Rajesh Singh              13980            3.3          0.5               16.87

[whedon]

PDF failed to compile for issue #2299 with the following error:

[WARNING] Could not convert image '/tmp/tex2pdf.-4e06424784e541bb/6d52616db8c85286870de3cf0a4c8d54044a4fd0.svg': check that rsvg-convert is in path. rsvg-convert: createProcess: runInteractiveProcess: exec: does not exist (No such file or directory) Error producing PDF. ! LaTeX Error: Cannot determine size of graphic in /tmp/tex2pdf.-4e06424784e541 bb/6d52616db8c85286870de3cf0a4c8d54044a4fd0.svg (no BoundingBox).

See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ...

l.408 ...16db8c85286870de3cf0a4c8d54044a4fd0.svg}}

Looks like we failed to compile the PDF

[kyleniemeyer]

👋 @rajeshrinet - Thanks for your submission to JOSS. As described in our blog post announcing the reopening of JOSS, we're currently working in a "reduced service mode", limiting the number of papers assigned to any individual editor.

Since reopening JOSS we've had > 60 papers submitted and as such, yours has been put in our backlog that we will be working through over the coming weeks and months.

Thanks in advance for your patience!

[kyleniemeyer]

@rajeshrinet regarding the paper build error, I think the issue is the SVG badge you are trying to include. Can you remove, or convert to a PNG (for example)?

[whedon]

Reference check summary:

OK DOIs

- 10.1017/CBO9780511813467 is OK
- 10.1007/978-3-319-12787-3 is OK
- 10.1002/cite.330641004 is OK
- 10.1007/978-3-540-87706-6_2 is OK
- 10.1007/978-3-540-72308-0 is OK
- 10.1017/CBO9780511624124 is OK
- 10.1137/1.9780898718003.bm is OK
- 10.1002/bbpc.197800142 is OK
- 10.1007/978-3-642-61544-3 is OK
- 10.1017/CBO9780511608810 is OK
- 10.1007/978-1-4757-6639-4_11 is OK
- 10.1002/cpa.3160050201 is OK
- 10.1002/andp.19053220806 is OK
- 10.1063/1.864051 is OK
- 10.1021/la00050a035 is OK
- 10.1146/annurev.fl.21.010189.000425 is OK
- 10.1103/PhysRevLett.82.1590 is OK
- 10.1002/adma.200501767 is OK
- 10.1039/B414896G is OK
- 10.1002/smll.200400061 is OK
- 10.1039/B505092H is OK
- 10.1021/ja047697z is OK
- 10.1103/PhysRevLett.92.118101 is OK
- 10.1063/1.3122346 is OK
- 10.1103/PhysRevLett.89.058101 is OK
- 10.1016/S0378-4371(02)00503-4 is OK
- 10.1103/PhysRevLett.100.178103 is OK
- 10.1063/1.3041776 is OK
- 10.1002/smll.201000415 is OK
- 10.1126/science.1203963 is OK
- 10.1103/PhysRevLett.104.258101 is OK
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- 10.1017/S0022112075000614 is OK
- 10.1017/S0022112076000475 is OK
- 10.1103/PhysRevLett.94.148104 is OK
- 10.1063/1.868116 is OK
- 10.1103/PhysRevE.82.016309 is OK
- 10.1103/PhysRevE.76.051905 is OK
- 10.1016/j.jcp.2003.10.017 is OK
- 10.1103/PhysRevLett.87.198301 is OK
- 10.1073/pnas.0900451106 is OK
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- 10.1063/1.1613939 is OK
- 10.1038/38532 is OK
- 10.1103/PhysRevE.78.036704 is OK
- 10.1063/1.3251771 is OK
- 10.1063/1.480156 is OK
- 10.1016/0370-1573(92)90090-M is OK
- 10.1146/annurev-fluid-121108-145519 is OK
- 10.1073/pnas.1200843109 is OK
- 10.1007/s12551-011-0046-7 is OK
- 10.1016/0065-227X(91)90022-6 is OK
- 10.1016/S0006-3495(98)74062-7 is OK
- 10.1080/01411599308223720 is OK
- 10.1073/pnas.251530598 is OK
- 10.1073/pnas.96.25.14306 is OK
- 10.1146/annurev.mi.19.100165.000321 is OK
- 10.1016/S0959-4388(97)80026-8 is OK
- 10.1126/science.1173869 is OK
- 10.1126/science.175.4019.337 is OK
- 10.1242/jeb.02131 is OK
- 10.1063/1.2751388 is OK
- 10.1146/annurev.fluid.37.061903.175725 is OK
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- 10.1063/1.1564047 is OK
- 10.1146/annurev.ph.58.030196.003415 is OK
- 10.1103/PhysRevE.80.036704 is OK
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- 10.1017/S0022112072001612 is OK
- 10.1016/0021-9290(75)90023-8 is OK
- 10.1146/annurev.fl.09.010177.002011 is OK
- 10.1039/c1sm90014e is OK
- 10.1146/annurev-conmatphys-070909-104101 is OK
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- 10.1103/PhysRevE.47.1815 is OK
- 10.1103/PhysRevE.49.2941 is OK
- 10.1103/PhysRevE.64.031203 is OK
- 10.1088/0034-4885/72/9/096601 is OK
- 10.1083/jcb.39.1.77 is OK
- 10.1085/jgp.50.6.241 is OK
- 10.1006/jtbi.2000.2182 is OK
- 10.1146/annurev.biochem.72.121801.161737 is OK
- 10.1016/S0006-3495(78)85431-9 is OK
- 10.1126/science.178.4060.455 is OK
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- 10.1002/cm.20313 is OK
- 10.1017/S0022112080002716 is OK
- 10.1017/S0022112079002482 is OK
- 10.1017/S002211207900104X is OK
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- 10.1038/nature11591 is OK
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- 10.1038/nature04090 is OK
- 10.1103/PhysRevLett.77.4102 is OK
- 10.1016/0378-4371(76)90104-7 is OK
- 10.1016/0378-4371(77)90111-X is OK
- 10.1063/1.1742462 is OK
- 10.1063/1.454658 is OK
- 10.1016/0378-4371(82)90127-3 is OK
- 10.1016/0378-4371(83)90061-4 is OK
- 10.1103/PhysRevB.2.1091 is OK
- 10.1063/1.433207 is OK
- 10.1080/00018737800101454 is OK
- 10.1016/j.crhy.2013.04.001 is OK
- 10.1017/S0022112006002631 is OK
- 10.1002/cpa.3160050201 is OK
- 10.1103/PhysRevLett.105.168102 is OK
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- 10.1016/0009-2509(64)85084-3 is OK
- 10.1016/0009-2509(64)85084-3 is OK
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- 10.1103/PhysRevLett.102.168101 is OK
- 10.1103/PhysRevE.83.061403 is OK
- 10.1146/annurev-fluid-121108-145434 is OK
- 10.1073/pnas.1019079108 is OK
- 10.1038/srep01964 is OK
- 10.1103/RevModPhys.85.1143 is OK
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- 10.1063/1.4812822 is OK
- 10.1098/rspa.1922.0078 is OK
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- 10.1103/PhysRevLett.92.078101 is OK
- 10.1140/epje/e2005-00002-5 is OK
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- 10.1088/1367-2630/9/11/422 is OK
- 10.1017/S0022112082000627 is OK
- 10.1063/1.2803837 is OK
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- 10.1103/PhysRevLett.112.118102 is OK
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- 10.1016/0021-9797(82)90127-8 is OK
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- 10.1017/S0022112088002411 is OK
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- 10.1103/PhysRevLett.109.158302 is OK
- 10.1103/PhysRevLett.108.268303 is OK
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- 10.1126/science.1230020 is OK
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- 10.1017/S0022112075001486 is OK
- 10.1002/andp.18792430702 is OK
- 10.1016/0378-4371(80)90067-9 is OK
- 10.1016/0378-4371(82)90007-3 is OK
- 10.1016/0378-4371(82)90236-9 is OK
- 10.1002/aic.690340704 is OK
- 10.1017/S002211208700171X is OK
- 10.1063/1.466366 is OK
- 10.1017/S0022112084001105 is OK
- 10.1017/S0022112001006735  is OK
- 10.1039/C6SM02104B is OK
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- 10.1063/1.1746947 is OK
- 10.1137/0147047 is OK
- 10.1140/epje/i2006-10009-1 is OK
- 10.1103/PhysRevLett.75.1226 is OK
- 10.1103/PhysRevLett.92.025702 is OK
- 10.1088/0034-4885/75/4/042601 is OK
- 10.1103/PhysRevLett.75.4326 is OK
- 10.1103/PhysRevLett.112.238104 is OK
- 10.1209/epl/i2006-10201-y is OK
- 10.1073/pnas.0906586106 is OK
- 10.1103/PhysRevLett.100.088103 is OK
- 10.1017/S0022112008003807 is OK
- 10.1103/PhysRevLett.100.218103 is OK
- 10.1021/la8038335 is OK
- 10.1103/PhysRevLett.114.158102 is OK
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- 10.1146/annurev-fluid-010313-141426 is OK
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- 10.1103/PhysRevE.84.040301 is OK
- 10.1103/PhysRevLett.108.235702 is OK
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- 10.1103/PhysRevLett.83.1239 is OK
- 10.1016/0021-9797(79)90336-9 is OK
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- 10.1006/jcph.1997.5706 is OK
- 10.1063/1.1331320 is OK
- 10.1016/j.jcp.2015.09.020 is OK
- 10.1063/1.4944962 is OK
- 10.1103/PhysRevE.88.012301 is OK
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- 10.1145/365723.365727 is OK

MISSING DOIs

- https://doi.org/10.1007/3-540-27223-2_1 may be missing for title: Fluid mechanics
- https://doi.org/10.1109/tit.2004.834752 may be missing for title: Information theory, inference and learning algorithms
- https://doi.org/10.1038/086105a0 may be missing for title: Brownian movement and molecular reality
- https://doi.org/10.2307/3613759 may be missing for title: The mathematical theory of viscous incompressible flow
- https://doi.org/10.1002/9780470241066.ch2 may be missing for title: Hydrodynamics
- https://doi.org/10.1016/0032-3861(81)90183-x may be missing for title: Scaling concepts in polymer physics
- https://doi.org/10.1016/0021-8502(75)90096-8 may be missing for title: Low Reynolds number hydrodynamics: with special applications to particulate media
- https://doi.org/10.1007/978-94-011-0195-0_9 may be missing for title: On the Motion of Small Particles of Elongated Form. Suspended in a Viscous Liquid
- https://doi.org/10.1201/9781315120195-1 may be missing for title: Introduction to Numerical Analysis
- https://doi.org/10.1007/978-3-540-39895-0_9 may be missing for title: Lattice Boltzmann modeling of complex fluids: Colloidal suspensions and fluid mixtures
- https://doi.org/10.1016/0021-9797(81)90146-6 may be missing for title: Concentration dependence of electrophoretic mobility
- https://doi.org/10.1016/0301-9322(85)90026-6 may be missing for title: Droplet interactions in thermocapillary motion
- https://doi.org/10.1201/9781351069397-24 may be missing for title: Methods of conjugate gradients for solving linear systems
- https://doi.org/10.1006/jsvi.1999.2257 may be missing for title: Dynamics of transversely vibrating beams using four engineering theories
- https://doi.org/10.1007/bf02025577 may be missing for title: Die Knicklast des einseitig eingespannten, tangential gedrückten Stabes
- https://doi.org/10.1523/jneurosci.23-11-04533.2003 may be missing for title: Spontaneous oscillation by hair bundles of the bullfrog’s sacculus
- https://doi.org/10.1016/s0006-3495(92)81683-1 may be missing for title: Ciliary motion modeling, and dynamic multicilia interactions.
- https://doi.org/10.1006/jtbi.1994.1097 may be missing for title: A "Geometric Clutch" Hypothesis to Explain Oscillations of the Axoneme of Cilia and Flagella
- https://doi.org/10.1016/j.bpj.2008.12.1051 may be missing for title: How molecular motors shape the flagellar beat.
- https://doi.org/10.1073/pnas.68.12.3092 may be missing for title: Adenosine triphosphate-induced sliding of tubules in trypsin-treated flagella of sea-urchin sperm
- https://doi.org/10.1103/physrevlett.94.148104 may be missing for title: Hydrodynamic induced deformation and orientation of a microscopic elastic filament
- https://doi.org/10.1215/ijm/1258138354 may be missing for title: Symmetry of a boundary integral operator and a characterization of a ball
- https://doi.org/10.1080/00018737800101454 may be missing for title: The description of the physical properties of condensed matter using irreducible tensors
- https://doi.org/10.1146/annurev.fl.24.010192.001525 may be missing for title: Hydrodynamic phenomena in suspensions of swimming microorganisms
- https://doi.org/10.1017/s0022112006001066 may be missing for title: Antisymmetric stresses in suspensions: Vortex viscosity and energy dissipation
- https://doi.org/10.1103/physreve.83.011907 may be missing for title: Nonlinear rheology of active particle suspensions: Insights from an analytical approach
- https://doi.org/10.1016/s0378-4371(02)01145-7 may be missing for title: Complex fluid behavior: coupling of the shear stress with order parameter tensors of ranks two and three in nematic liquid crystals and in tetradic fluids
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INVALID DOIs

- 10.1093/humupd is INVALID
- 10.1209/epl is INVALID
- 10.1209/0295-5075 is INVALID
- 10.1088/1367-2630 is INVALID
- 10.1007%2FBF01535657 is INVALID
- 10.1017/S096249290200007 is INVALID
- 10.1088/1367-2630/aa5f80/meta is INVALID
- 10.1038/s41567 is INVALID

[kyleniemeyer]

@rajeshrinet also, can you perhaps pare your bib file down to only those cited in the paper?

[rajeshrinet]

@rajeshrinet regarding the paper build error, I think the issue is the SVG badge you are trying to include. Can you remove, or convert to a PNG (for example)?

@kyleniemeyer thanks very much for your comments. I have removed the badge and pared down the bib file. I hope that solves the PDF compilation.

[kyleniemeyer]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[rajeshrinet]

@kyleniemeyer it seems I need use [@article1CITE] for each citation. It can not be done in a bunch like [@article1CITE, @article2CITE]?

[kyleniemeyer]

@rajeshrinet You can include multiple citations together, but you need semicolons rather than commas between each citation: https://joss.readthedocs.io/en/latest/submitting.html#example-paper-and-bibliography

[rajeshrinet]

@kyleniemeyer thanks very much for your prompt response. I will fix that now.

[rajeshrinet]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[rajeshrinet]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[rajeshrinet]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[rajeshrinet]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[rajeshrinet]

@kyleniemeyer and @whedon thanks for the article proof and this awesome interface.

Here is a list of suggested referees:

• Fergus Cooper. Email: fergus.cooper@cs.ox.ac.uk, University of Oxford

• Konrad Hinsen. Email : konrad.hinsen@cnrs.fr. Centre de Biophysique Moléculaire (UPR4301 CNRS), Orléans, France.

• Daniel Lagrava. Emai: .dlagrava@gmail.com. Research Software Engineer, NIWA, NZ

• Dave Pine. Email: pine@nyu.edu. Chemical and Biomolecular Engineering Department, New York University, USA.

• Martin Robinson. Email: martinjrobins@gmail.com, University of Oxford

[kyleniemeyer]

Hi @harpolea, apologies for simultaneous invitations, but this looks like it might be in your wheelhouse. Can you edit this submission as well?

[kyleniemeyer]

@whedon invite @harpolea as editor

[whedon]

@harpolea has been invited to edit this submission.

[rajeshrinet]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #2299 with the following error:

Error reading bibliography ./paper.bib (line 269, column 1): unexpected end of input expecting "\"", "\" or "{" Error running filter pandoc-citeproc: Filter returned error status 1 Looks like we failed to compile the PDF

[rajeshrinet]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[arfon]

@rajeshrinet - also, it would be very helpful if you could truncate your BibTeX file to only include the actual papers/entities that you're citing in the JOSS paper.

[rajeshrinet]

@arfon I have now removed all the remaining entries from bib which were not cited in JOSS paper.

@whedon generate pdf

[rajeshrinet]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[harpolea]

@kyleniemeyer I'd be happy to edit this one as well!

[harpolea]

@whedon assign @harpolea as editor

[whedon]

OK, the editor is @harpolea

[harpolea]

Hi @rajeshrinet - thanks for the reviewer suggestions! I shall reach out to them now

[rajeshrinet]

Hi @harpolea - thanks very much!

[harpolea]

@whedon assign @fcooper8472 as reviewer

[whedon]

OK, @fcooper8472 is now a reviewer

[harpolea]

Hi @rajeshrinet, it's come to my attention that a paper on this library has already been submitted to arXiv (https://arxiv.org/abs/1910.00909). Has this paper been accepted by another journal? If so, then I'm afraid we may not be able to accept this submission as it would involve a significant amount of overlap and duplication with an existing publication.

[rajeshrinet]

Hi @harpolea,

No https://arxiv.org/abs/1910.00909 has not been accepted (or under consideration) for publication elsewhere. In fact, our submission to JOSS is based on https://arxiv.org/abs/1910.00909 and has been reduced in size to match the word limit. We cite it in the submission as it contains more details. I hope that is okay?

Edit I can add a line in the submission to explicitly mention the point that an expanded version of this manuscript is available on arxiv.

[kyleniemeyer]

@harpolea @rajeshrinet this seems fine to me. @harpolea is right that it would not be appropriate to have an equivalent software paper under review (or published) at a different journal, but a preprint, whether extended or not, is fine.

I think citing the arXiv eprint in this article as a sort of extended documentation/additional examples is a good idea.

[rajeshrinet]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[harpolea]

Hi @rajeshrinet, thanks for your reply - that all sounds fine to me!

[harpolea]

@whedon add @khinsen as reviewer

[whedon]

OK, @khinsen is now a reviewer

[harpolea]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/2318.