[PRE REVIEW]: LDDS: Python package for computing and visualizing Lagrangian Descriptors for Dynamical Systems

whedon commented 3 years ago

Submitting author: @Shibabrat (Shibabrat Naik) Repository: https://github.com/champsproject/ldds Version: v0.1.0 Editor: @richardjgowers Reviewers: @nicoguaro, @jmbr Managing EiC: Kyle Niemeyer

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

The author's suggestion for the handling editor is @dpsanders.

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whedon commented 3 years ago

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:

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whedon commented 3 years ago

PDF failed to compile for issue #3301 with the following error:

 /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:147:in `check_fields': Paper YAML header is missing expected fields: date (RuntimeError)
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:89:in `initialize'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/processor.rb:38:in `new'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/processor.rb:38:in `set_paper'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/bin/whedon:58:in `prepare'
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    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in `invoke_command'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:in `dispatch'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in `start'
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    from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `<main>'

whedon commented 3 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.12 s (366.0 files/s, 93000.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Jupyter Notebook                12              0           6577            749
Python                          13            515           1068            744
TeX                              1             61              0            563
Markdown                         5            167              0            352
reStructuredText                 9            192            174            165
YAML                             2              8             11             32
DOS Batch                        1              8              1             26
make                             1              4              7              9
Bourne Shell                     1              1              0              1
-------------------------------------------------------------------------------
SUM:                            45            956           7838           2641
-------------------------------------------------------------------------------

Statistical information for the repository 'd3ed551376e6408aca0c7b70' was
gathered on 2021/05/21.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Broncio                         58          3041            992            6.29
Víctor                           1             0            165            0.26
shibabrat                       29         28165          28485           88.35
vkrajnak                        76          1990           1284            5.11

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
Broncio                     930           30.6          4.8               12.04
shibabrat                   345            1.2          3.3               28.41
vkrajnak                   1052           52.9          3.8                6.84

whedon commented 3 years ago

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

OK DOIs

- 10.1103/RevModPhys.64.795 is OK
- 10.1111/j.1365-2966.2005.09237.x is OK
- 10.1063/1.166509 is OK
- 10.1063/1.4915831 is OK
- 10.5281/zenodo.4539666 is OK
- 10.1007/BF00375090 is OK
- 10.1134/S1560354716060034 is OK
- 10.5281/zenodo.3958985 is OK
- 10.1016/j.compfluid.2016.07.007 is OK
- 10.1016/j.jocs.2014.12.002 is OK
- 10.1063/1.4795749 is OK
- 10.1017/jfm.2020.737 is OK
- 10.1142/S0218127420300086 is OK
- 10.1142/S0218127420500765 is OK
- 10.1088/1751-8121/ab8b75 is OK
- 10.1039/D0CP01362E is OK
- 10.1007/s00382-019-04832-y is OK
- 10.1007/s00382-019-04833-x is OK
- 10.1103/PhysRevE.100.022204 is OK
- 10.1142/S021812741750225X is OK
- 10.1016/j.cnsns.2019.104907 is OK
- 10.1175/JAS-D-11-0142.1 is OK
- 10.1134/S1560354718050052 is OK
- 10.1016/j.marpolbul.2016.08.018 is OK
- 10.4249/scholarpedia.6327 is OK
- 10.1002/9780470977859 is OK
- 10.1016/j.physd.2005.10.007 is OK
- 10.1016/j.cnsns.2015.02.022 is OK
- 10.1142/S0218127417300014 is OK
- 10.1038/s41598-018-23028-8 is OK
- 10.1088/1751-8121/ab8b75 is OK

MISSING DOIs

- 10.1201/9781003069515-39 may be a valid DOI for title: Transport in Hamiltonian systems
- 10.1007/978-1-4612-4312-0 may be a valid DOI for title: Normally hyperbolic invariant manifolds in dynamical systems
- 10.1016/0167-2789(90)90040-v may be a valid DOI for title: Geometry and dynamics of stable and unstable cylinders in  Hamiltonian systems
- 10.1017/s0022112090000167 may be a valid DOI for title: An analytical study of transport, mixing and chaos in an unsteady vortical flow
- 10.1016/j.cnsns.2013.05.002 may be a valid DOI for title: Lagrangian Descriptors: A method for Revealing Phase Space Structures of General Time Dependent Dynamical Systems
- 10.1175/jas-d-12-0274.1 may be a valid DOI for title: Isentropic transport within the Antarctic polar night vortex: Rossby wave breaking evidence and Lagrangian structures.
- 10.1103/physreve.99.032221 may be a valid DOI for title: Unveiling the chaotic structure in phase space of molecular systems using Lagrangian descriptors
- 10.1142/s0218127416300366 may be a valid DOI for title: Lagrangian Descriptors for Stochastic Differential Equations: A Tool for Revealing the Phase Portrait of Stochastic Dynamical Systems
- 10.1039/c7cp05912d may be a valid DOI for title: Detecting reactive islands using Lagrangian descriptors and the relevance to transition path sampling
- 10.1016/j.cplett.2017.09.008 may be a valid DOI for title: Obtaining time-dependent multi-dimensional dividing surfaces using Lagrangian descriptors
- 10.1063/1.4997379 may be a valid DOI for title: Chemical dynamics between wells across a time-dependent barrier: Self-similarity in the Lagrangian descriptor and reactive basins
- 10.1103/physrevlett.115.148301 may be a valid DOI for title: Lagrangian descriptors of thermalized transition states on time-varying energy surfaces
- 10.1103/physreve.96.022222 may be a valid DOI for title: Lagrangian descriptors of driven chemical reaction manifolds
- 10.1039/c5cp06624g may be a valid DOI for title: Deconstructing field-induced ketene isomerization through Lagrangian descriptors
- 10.1007/s12043-008-0103-3 may be a valid DOI for title: Visual explorations of dynamics: The standard map
- 10.1086/109234 may be a valid DOI for title: The Applicability of the Third Integral Of Motion: Some Numerical Experiments

INVALID DOIs

- https://doi.org/10.1016/j.ijmecsci.2017.10.040 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.cnsns.2019.105033 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.cplett.2020.137199 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.cnsns.2020.105331 is INVALID because of 'https://doi.org/' prefix

kyleniemeyer commented 3 years ago

@whedon invite @richardjgowers as editor

@richardjgowers this is a bit outside your area, but could you edit this submission?

whedon commented 3 years ago

@richardjgowers has been invited to edit this submission.

whedon commented 3 years ago

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

whedon commented 3 years ago

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

richardjgowers commented 3 years ago

@kyleniemeyer yeah I'm a little busy this week but I can get the ball rolling this weekend.

broncio123 commented 3 years ago

Hi,

We would like to suggest as potential reviewers:

Brandon Behring, we couldn't find his email. Only contact through Linkedin
Josh Karpel, josh.karpel@gmail.com
Ingmar Schoegl, ischoegl@lsu.edu
Niall McGinness, njwmcginness@gmail.com
David Ignacio Cortes, dic1e13@soton.ac.uk
Nicolás Guarín-Zapata, nicoguarin@gmail.com
Jun Zhong, jun_zhong@brown.edu

broncio123 commented 3 years ago

PDF failed to compile for issue #3301 with the following error:

 /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:147:in `check_fields': Paper YAML header is missing expected fields: date (RuntimeError)
  from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:89:in `initialize'
  from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/processor.rb:38:in `new'
  from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/processor.rb:38:in `set_paper'
  from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/bin/whedon:58:in `prepare'
  from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:in `run'
  from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in `invoke_command'
  from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:in `dispatch'
  from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in `start'
  from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/bin/whedon:131:in `<top (required)>'
  from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `load'
  from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `<main>'

Added date to header of paper.md

broncio123 commented 3 years ago

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

OK DOIs

- 10.1103/RevModPhys.64.795 is OK
- 10.1111/j.1365-2966.2005.09237.x is OK
- 10.1063/1.166509 is OK
- 10.1063/1.4915831 is OK
- 10.5281/zenodo.4539666 is OK
- 10.1007/BF00375090 is OK
- 10.1134/S1560354716060034 is OK
- 10.5281/zenodo.3958985 is OK
- 10.1016/j.compfluid.2016.07.007 is OK
- 10.1016/j.jocs.2014.12.002 is OK
- 10.1063/1.4795749 is OK
- 10.1017/jfm.2020.737 is OK
- 10.1142/S0218127420300086 is OK
- 10.1142/S0218127420500765 is OK
- 10.1088/1751-8121/ab8b75 is OK
- 10.1039/D0CP01362E is OK
- 10.1007/s00382-019-04832-y is OK
- 10.1007/s00382-019-04833-x is OK
- 10.1103/PhysRevE.100.022204 is OK
- 10.1142/S021812741750225X is OK
- 10.1016/j.cnsns.2019.104907 is OK
- 10.1175/JAS-D-11-0142.1 is OK
- 10.1134/S1560354718050052 is OK
- 10.1016/j.marpolbul.2016.08.018 is OK
- 10.4249/scholarpedia.6327 is OK
- 10.1002/9780470977859 is OK
- 10.1016/j.physd.2005.10.007 is OK
- 10.1016/j.cnsns.2015.02.022 is OK
- 10.1142/S0218127417300014 is OK
- 10.1038/s41598-018-23028-8 is OK
- 10.1088/1751-8121/ab8b75 is OK

MISSING DOIs

- 10.1201/9781003069515-39 may be a valid DOI for title: Transport in Hamiltonian systems
- 10.1007/978-1-4612-4312-0 may be a valid DOI for title: Normally hyperbolic invariant manifolds in dynamical systems
- 10.1016/0167-2789(90)90040-v may be a valid DOI for title: Geometry and dynamics of stable and unstable cylinders in  Hamiltonian systems
- 10.1017/s0022112090000167 may be a valid DOI for title: An analytical study of transport, mixing and chaos in an unsteady vortical flow
- 10.1016/j.cnsns.2013.05.002 may be a valid DOI for title: Lagrangian Descriptors: A method for Revealing Phase Space Structures of General Time Dependent Dynamical Systems
- 10.1175/jas-d-12-0274.1 may be a valid DOI for title: Isentropic transport within the Antarctic polar night vortex: Rossby wave breaking evidence and Lagrangian structures.
- 10.1103/physreve.99.032221 may be a valid DOI for title: Unveiling the chaotic structure in phase space of molecular systems using Lagrangian descriptors
- 10.1142/s0218127416300366 may be a valid DOI for title: Lagrangian Descriptors for Stochastic Differential Equations: A Tool for Revealing the Phase Portrait of Stochastic Dynamical Systems
- 10.1039/c7cp05912d may be a valid DOI for title: Detecting reactive islands using Lagrangian descriptors and the relevance to transition path sampling
- 10.1016/j.cplett.2017.09.008 may be a valid DOI for title: Obtaining time-dependent multi-dimensional dividing surfaces using Lagrangian descriptors
- 10.1063/1.4997379 may be a valid DOI for title: Chemical dynamics between wells across a time-dependent barrier: Self-similarity in the Lagrangian descriptor and reactive basins
- 10.1103/physrevlett.115.148301 may be a valid DOI for title: Lagrangian descriptors of thermalized transition states on time-varying energy surfaces
- 10.1103/physreve.96.022222 may be a valid DOI for title: Lagrangian descriptors of driven chemical reaction manifolds
- 10.1039/c5cp06624g may be a valid DOI for title: Deconstructing field-induced ketene isomerization through Lagrangian descriptors
- 10.1007/s12043-008-0103-3 may be a valid DOI for title: Visual explorations of dynamics: The standard map
- 10.1086/109234 may be a valid DOI for title: The Applicability of the Third Integral Of Motion: Some Numerical Experiments

INVALID DOIs

- https://doi.org/10.1016/j.ijmecsci.2017.10.040 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.cnsns.2019.105033 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.cplett.2020.137199 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.cnsns.2020.105331 is INVALID because of 'https://doi.org/' prefix

Fixed DOIs in paper.bib

vkrajnak commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

PDF failed to compile for issue #3301 with the following error:

 Error reading bibliography file paper.bib:
(line 483, column 9):
unexpected "N"
expecting space, ",", white space or "}"
Looks like we failed to compile the PDF

vkrajnak commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

vkrajnak commented 3 years ago

The paper is all good now.

richardjgowers commented 3 years ago

@whedon assign @richardjgowers as editor

whedon commented 3 years ago

OK, the editor is @richardjgowers

richardjgowers commented 3 years ago

@nicoguaro @davidcortesortuno would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

nicoguaro commented 3 years ago

@richardjgowers, I think that I can review it.

Shibabrat commented 3 years ago

Hi @kyleniemeyer @richardjgowers, can we help with moving this pre-review to the next step? We appreciate your time and consideration in finding the reviewers.

Sincerely, Authors

richardjgowers commented 3 years ago

@whedon add @nicoguaro as reviewer

whedon commented 3 years ago

OK, @nicoguaro is now a reviewer

richardjgowers commented 3 years ago

@Shibabrat I'm trying a few more people to try and get a second reviewer for this, thanks for your patience.

richardjgowers commented 3 years ago

@jmbr would you be interested in reviewing this?

jmbr commented 3 years ago

@richardjgowers Yes, count me in.

richardjgowers commented 3 years ago

@whedon add @jmbr as reviewer

whedon commented 3 years ago

OK, @jmbr is now a reviewer

richardjgowers commented 3 years ago

@whedon start review

whedon commented 3 years ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/3482.

openjournals / joss-reviews

[PRE REVIEW]: LDDS: Python package for computing and visualizing Lagrangian Descriptors for Dynamical Systems #3301

Status