[PRE REVIEW]: PySensors: A Python Package for Sparse Sensor Placement

[whedon]

Submitting author: @briandesilva (Brian de Silva) Repository: https://github.com/dynamicslab/pysensors/ Version: v.0.3.0 Editor: @pdebuyl Reviewers: @jordanperr, @tuelwer Managing EiC: Arfon Smith

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[whedon]

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

:warning: JOSS reduced service mode :warning:

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[whedon]

Failed to discover a Statement of need section in paper

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.29 s (143.0 files/s, 27858.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          24            533            798           1215
Jupyter Notebook                 7              0           3465            774
TeX                              1             78              0            649
reStructuredText                 3             86             61            122
YAML                             4              8              0            103
Markdown                         1             13              0             66
TOML                             1              2              0             16
-------------------------------------------------------------------------------
SUM:                            41            720           4324           2945
-------------------------------------------------------------------------------

Statistical information for the repository 'c365e0f424edc2c4ed1d7f06' was
gathered on 2020/10/27.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
briandesilva                    95          5713           3251           98.61
emilyclark012                    8           106             20            1.39

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
Brian                      2510          100.0          1.8                7.09
emilyclark012                36           34.0          3.0               16.67

[whedon]

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

[whedon]

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

OK DOIs

- 10.1073/pnas.1517384113 is OK
- 10.1109/access.2018.2886528 is OK
- 10.1126/science.1165893 is OK
- 10.1103/physrevmaterials.2.083802 is OK
- 10.1111/j.2517-6161.1996.tb02080.x is OK
- 10.5281/zenodo.1173754 is OK
- 10.1364/oe.24.030433 is OK
- 10.1063/1.5066099 is OK
- 10.1063/1.4977057 is OK
- 10.1016/j.ymssp.2018.08.033 is OK
- 10.1126/sciadv.1602614 is OK
- 10.1098/rspa.2016.0446 is OK
- 10.1137/16m1086637 is OK
- 10.1137/18m116798x is OK
- 10.1017/jfm.2017.823 is OK
- 10.1063/1.5018409 is OK
- 10.1016/j.ifacol.2016.10.249 is OK
- 10.1103/physreve.96.023302 is OK
- 10.1016/j.jcp.2018.10.045 is OK
- 10.1098/rspa.2018.0335 is OK
- 10.1016/j.jcp.2019.07.049 is OK
- 10.1103/physreve.101.010203 is OK
- 10.1115/1.4043148 is OK

MISSING DOIs

- 10.1109/mcs.2018.2810460 may be a valid DOI for title: Data-driven sparse sensor placement for reconstruction: Demonstrating the benefits of exploiting known patterns
- 10.1017/jfm.2011.195 may be a valid DOI for title: H 2 optimal actuator and sensor placement in the linearised complex Ginzburg-Landau system
- 10.2514/6.2004-2415 may be a valid DOI for title: Unsteady flow sensing and estimation via the gappy proper orthogonal decomposition
- 10.1109/access.2020.3023625 may be a valid DOI for title: A unified sparse optimization framework to learn parsimonious physics-informed models from data
- 10.1007/s00162-020-00536-w may be a valid DOI for title: Data-driven modeling of the chaotic thermal convection in an annular thermosyphon
- 10.1016/j.ocemod.2009.01.001 may be a valid DOI for title: Efficient sensor placement for ocean measurements using low-dimensional concepts
- 10.1109/cdc.2014.7040017 may be a valid DOI for title: An ADMM algorithm for optimal sensor and actuator selection
- 10.1017/jfm.2017.137 may be a valid DOI for title: Local flow characterization using bioinspired sensory information
- 10.1073/pnas.1808909115 may be a valid DOI for title: Neural-inspired sensors enable sparse, efficient classification of spatiotemporal data
- 10.1016/j.jmsy.2018.01.011 may be a valid DOI for title: Predicting shim gaps in aircraft assembly with machine learning and sparse sensing
- 10.1017/jfm.2018.147 may be a valid DOI for title: Sparse reduced-order modeling: sensor-based dynamics to full-state estimation
- 10.1007/s00162-020-00520-4 may be a valid DOI for title: Deep model predictive flow control with limited sensor data and online learning
- 10.1002/cpa.20124 may be a valid DOI for title: Stable signal recovery from incomplete and inaccurate measurements
- 10.1016/0167-7152(84)90020-8 may be a valid DOI for title: Optimal monitoring network designs
- 10.1016/j.crma.2004.08.006 may be a valid DOI for title: An ‘empirical interpolation’method: application to efficient reduced-basis discretization of partial differential equations
- 10.1162/0899766053723032 may be a valid DOI for title: Asymptotic theory of information-theoretic experimental design
- 10.1109/tit.2006.885507 may be a valid DOI for title: Near optimal signal recovery from random projections: Universal encoding strategies?
- 10.1109/tit.2005.862083 may be a valid DOI for title: Robust uncertainty principles: exact signal reconstruction from highly incomplete frequency information
- 10.1109/tit.2009.2034811 may be a valid DOI for title: Beyond Nyquist: Efficient sampling of sparse bandlimited signals
- 10.1016/j.acha.2010.10.002 may be a valid DOI for title: Compressed sensing with coherent and redundant dictionaries
- 10.1145/1879141.1879192 may be a valid DOI for title: Estimating and Sampling Graphs with Multidimensional Random Walks
- 10.1137/090766498 may be a valid DOI for title: Nonlinear model reduction via discrete empirical interpolation
- 10.1111/j.1467-9868.2011.00783.x may be a valid DOI for title: Penalized classification using Fisher’s linear discriminant
- 10.1137/110822724 may be a valid DOI for title: A state space error estimate for POD-DEIM nonlinear model reduction
- 10.1109/tsipn.2016.2614903 may be a valid DOI for title: Signal recovery on graphs: Fundamental limits of sampling strategies
- 10.1109/sam.2016.7569707 may be a valid DOI for title: Subsampling for graph power spectrum estimation
- 10.1137/16m1081270 may be a valid DOI for title: Householder QR Factorization With Randomization for Column Pivoting (HQRRP)

INVALID DOIs

- None

[briandesilva]

@whedon generate pdf

[whedon]

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

[arfon]

Failed to discover a Statement of need section in paper

:wave: @briandesilva - could you please make sure your paper has a clear statement of need for a general, non-specialist audience?

[briandesilva]

@arfon, I just added a statement of need section to the paper.

[arfon]

@whedon generate pdf

[whedon]

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

[arfon]

@whedon invite @drvinceknight as editor

:wave: @drvinceknight - would you be able to take on this submission?

[whedon]

@drvinceknight has been invited to edit this submission.

[Kevin-Mattheus-Moerman]

@drvinceknight @pdebuyl could one of you edit this submission?

[pdebuyl]

@whedon assing me as editor

[whedon]

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

@whedon commands

[pdebuyl]

@whedon commands

[whedon]

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[pdebuyl]

@whedon assign @pdebuyl as editor

[whedon]

OK, the editor is @pdebuyl

[pdebuyl]

Hi @briandesilva thank you for submitting to JOSS. I will look for reviewers shortly.

In the meantime, I have a few comments

• The second paragraph of the article is a laundry list of citations. JOSS papers should be written for a non-specialist audience and include "a list of key references".
• The list of author of the fourth reference is lacking full names.
• Please also check that the DOI are properly formatted for all references.
• You do not cite scikit-learn despite having prepared your library for interacting with it. This should be fixed.

[pdebuyl]

@stsievert , @jordanperr can you review the article "PySensors: A Python Package for Sparse Sensor Placement" for JOSS ?

[jordanperr]

@pdebuyl Happy to review this, but I'm not very familiar with the process. I am aware of the reviewer checklist, but It would be helpful if you could please guide me through the procedure.

[pdebuyl]

Thank you for the reply @jordanperr . We have documentation for authors / reviewers / editors at https://joss.readthedocs.io/en/latest/index.html

The high-level view is this: when we have two reviewers, I start the review. There will be a new github issue with the checklist and a link to the instructions. The issue page serves as the communication channel for all involved and I'll be available to reply to questions. You can have a look at accepted papers reviews if you wish https://github.com/openjournals/joss-reviews/issues?page=5&q=+label%3Aaccepted

For now, you should just wait for the review to start :-)

[briandesilva]

@whedon generate pdf

[whedon]

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

[briandesilva]

@pdebuyl, I just pushed the changes you requested. Please let me know if the DOIs aren't formatted the way you had in mind.

[pdebuyl]

Thank you @briandesilva , apart from Karniadakis 2009 and Tao the references are fine and my other comments addressed.

[stsievert]

I'll have to decline the review; I'm already on a different JOSS review and have limited bandwidth.

[briandesilva]

@whedon generate pdf

[briandesilva]

apart from Karniadakis 2009 and Tao the references are fine and my other comments addressed.

Good catch—fixed.

[whedon]

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

[pdebuyl]

Thank you @briandesilva

[pdebuyl]

@tuelwer can you review the article "PySensors: A Python Package for Sparse Sensor Placement" for JOSS ?

[tuelwer]

@pdebuyl sure, I can write a review for this paper!

[pdebuyl]

Thank you @tuelwer

[pdebuyl]

@whedon assign @jordanperr as reviewer

[whedon]

OK, @jordanperr is now a reviewer

[pdebuyl]

@whedon add @tuelwer as reviewer

[whedon]

OK, @tuelwer is now a reviewer

[pdebuyl]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/2828.