[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 Reviewer: @nicoguaro, @jmbr Archive: 10.5281/zenodo.5519579

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Review checklist for @nicoguaro

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@Shibabrat) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @jmbr

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@Shibabrat) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

whedon commented 3 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @nicoguaro, @jmbr it looks like you're currently assigned to review this paper :tada:.

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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
- 10.1016/0167-2789(84)90270-7 is OK
- 10.1063/1.166509 is OK
- 10.1016/j.ijmecsci.2017.10.040 is OK
- 10.1016/j.cnsns.2019.105033 is OK
- 10.1063/1.4915831 is OK
- 10.5281/zenodo.4539666 is OK
- 10.1007/978-1-4612-4312-0 is OK
- 10.1016/0167-2789(90)90040-V is OK
- 10.1007/BF00375090 is OK
- 10.1017/S0022112090000167 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
- 10.1016/j.cnsns.2013.05.002 is OK
- 10.1016/j.cplett.2020.137199 is OK
- 10.1142/S0218127420300086 is OK
- 10.1016/j.cnsns.2020.105331 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-12-0274.1 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
- 10.1103/PhysRevE.99.032221 is OK
- 10.1142/S0218127416300366 is OK
- 10.1039/C7CP05912D is OK
- 10.1016/j.cplett.2017.09.008 is OK
- 10.1063/1.4997379 is OK
- 10.1103/physrevlett.115.148301 is OK
- 10.1103/PhysRevE.96.022222 is OK
- 10.1039/C5CP06624G is OK
- 10.1007/s12043-008-0103-3 is OK
- 10.1086/109234 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

- None

INVALID DOIs

- None

whedon commented 3 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.22 s (204.0 files/s, 51892.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Jupyter Notebook                12              0           6577            749
Python                          13            515           1068            744
TeX                              1             61              0            567
Markdown                         5            169              0            358
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            958           7838           2651
-------------------------------------------------------------------------------

Statistical information for the repository 'd96755ba38e02ac536fc633d' was
gathered on 2021/07/11.
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

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

nicoguaro commented 3 years ago

@richardjgowers, do you have a proposed time frame for this review?

richardjgowers commented 3 years ago

@nicoguaro we usually aim to get reviews done within 6 weeks at the most

nicoguaro commented 3 years ago

I followed the installation described in the README and got the following

(ldds_joss) nguarinz@cocorna ~/ldds $ python -m unittest

----------------------------------------------------------------------
Ran 0 tests in 0.000s

OK

whedon commented 3 years ago

:wave: @nicoguaro, please update us on how your review is going (this is an automated reminder).

whedon commented 3 years ago

:wave: @jmbr, please update us on how your review is going (this is an automated reminder).

nicoguaro commented 3 years ago

@richardjgowers, @Shibabrat, I have already added some updates in my review.

vkrajnak commented 3 years ago

I followed the installation described in the README and got the following
(ldds_joss) nguarinz@cocorna ~/ldds $ python -m unittest

----------------------------------------------------------------------
Ran 0 tests in 0.000s

OK

@nicoguaro Thank you for finding the unittest issue. In case it is acceptable to run unittest from a subfolder of the package, I've amended the README file to say

cd ldds/tests
python -m unittest

Then it works.

Shibabrat commented 3 years ago

@richardjgowers @nicoguaro, just wondering if we are required to make any additional changes at this stage to help with the review? Thank you.

nicoguaro commented 3 years ago

@richardjgowers @nicoguaro, just wondering if we are required to make any additional changes at this stage to help with the review? Thank you.

@Shibabrat, I have moved forward in the review. This is reflected in the boxes checked above. Currently, I am reading the companion book showed in the documentation.

broncio123 commented 3 years ago

Hi @jmbr hope everything is OK. Just wondering if there has been any progress on the review checklist. This hasn't been updated since 12 July (5 weeks ago).

As @Shibabrat mentioned above, if there's anything we can help out with, let us know. We're happy to do so.

@richardjgowers have you heard anything from @jmbr by any chance? It doesn't seem that he has made any comment at all in the thread.

jmbr commented 3 years ago

Hi @broncio123, All is OK, thanks. I will be able to complete the review this week. Hope that's alright.

broncio123 commented 3 years ago

Hi @broncio123, All is OK, thanks. I will be able to complete the review this week. Hope that's alright.

Alright, sure. Thanks a lot for letting us know :+1: And again, don't hesitate to give us a shout.

b

jmbr commented 3 years ago

I've checked off all the items in the review checklist. Here are some comments:

SLOCCount says that there are 742 lines of code (LOC) while the guidelines for JOSS say that submissions below 1000 LOC should be flagged.

python_count `git ls-files | grep -E '\.py$'`
21 docs/conf.py
9 ldds/__init__.py
223 ldds/base.py
66 ldds/base_discrete.py
33 ldds/discrete_maps.py
56 ldds/hamiltonians.py
44 ldds/testing_scripts.py
103 ldds/tools.py
79 ldds/vector_fields.py
29 setup.py
27 tests/separable_quadratic_hamiltonian.py
45 tests/test_uncoup_quad_ham2dof.py
7 tests/utils.py
Total:
742

Sphinx gives some warnings while building the documentation.


$ make html
Running Sphinx v4.1.2
loading translations [python]... not available for built-in messages
WARNING: html_static_path entry '_static' does not exist
loading intersphinx inventory from https://docs.python.org/3/objects.inv...
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 8 source files that are out of date
updating environment: [new config] 8 added, 0 changed, 0 removed
reading sources... [100%] user_guide                                                                                                                                                                               
/workspace/math/ldds/docs/examples.rst:4: WARNING: Unknown directive type "examples".

.. examples:: /workspace/math/ldds/docs/examples.rst:20: WARNING: Explicit markup ends without a blank line; unexpected unindent. /workspace/math/ldds/docs/examples.rst:96: WARNING: Inline interpreted text or phrase reference start-string without end-string. /workspace/math/ldds/ldds/base.py:docstring of base.fit_vector_field:6: WARNING: Unexpected indentation. /home/jmbr/python-venvs/ldds/lib/python3.8/site-packages/ldds-0.1.0-py3.8.egg/ldds/base.py:docstring of ldds.base.fit_vector_field:6: WARNING: Unexpected indentation. looking for now-outdated files... none found pickling environment... done checking consistency... /workspace/math/ldds/docs/modules.rst: WARNING: document isn't included in any toctree /workspace/math/ldds/docs/introduction.rst:59: WARNING: Citation [junginger2016lagrangian] is not referenced. done preparing documents... done writing output... [100%] user_guide
/workspace/math/ldds/docs/introduction.rst:6: WARNING: citation not found: demian2017 generating indices... genindex py-modindex done highlighting module code... [100%] vector_fields
writing additional pages... search done copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 9 warnings.


* In the documentation, the function :math:`\mathcal{L}^{(\cdot)}(\mathbf{x}_0, t_0, \tau)` is used prior to being defined.
* There are typos in the documentation (enconded, accummulating, etc.). I recommend you spell check the docs and the Jupyter notebooks.
* I miss some structure in the code. For instance, I'd advice that you aim for an interface to solvers (e.g., Euler-Maruyama) that mirrors that of scipy.integrate or, perhaps better, rely on `sdeint` (https://github.com/mattja/sdeint/) as a dependency.
* Neither `fit_pes` nor `fit_vector_field` work after installation because the HDF5 files are not copied to the appropriate paths outside the source tree.

broncio123 commented 3 years ago

Thanks a lot for your feedback @jmbr We will address each of your points promptly.

Hey @nicoguaro , hope everything is OK? Any further progress on reviewing the functionality, documentation, and paper? If there's anything we can help out with let us know, please.

nicoguaro commented 3 years ago

I have marked most of the checklist above. Following are some comments that I would add to @jmbr's ones.

Regarding the size (lines of code) of the package. I think that it is OK. The guideline suggests that number as a rule of thumb. In this case, I would say that it is clear the package has scientific value.
For me, the documentation is confusing.
- There isn't an example in the doc site, I was expecting one in the section "Getting started" or maybe on "Examples". I know that the examples are provided as notebooks, but having an introductory example in the docs helps a first-time user.
- It is common to have the documentation for the API organized in modules. There is a file named modules.rst but it is not invoked in index.rst.
- The format required in vector_field in the function compute_lagrange_descriptor is not clear enough in the docstrings. Although, you get the idea in tutorial-4.ipynb.
- I tried to compute the descriptor for a "user-defined" system for a simple pendulum for a 50×50 grid in [-4, 4]² and tau=1 but it ran for 5 hours without finishing. Maybe the selection of parameters is sub-optimal for this problem, but I couldn't find how to pick them in the documentation.

Shibabrat commented 3 years ago

Thank you @jmbr and @nicoguaro for the comments. We will be making appropriate revisions and post when the revisions are finished for you both to have a look.

richardjgowers commented 3 years ago

Hi @nicoguaro @jmbr thanks for your work in reviewing things. This seems like great feedback to improve the work. Regarding the SLOC criteria, this is a guideline and the editors have decided that this package is suitable.

broncio123 commented 3 years ago

I have marked most of the checklist above. Following are some comments that I would add to @jmbr's ones.

Regarding the size (lines of code) of the package. I think that it is OK. The guideline suggests that number as a rule of thumb. In this case, I would say that it is clear the package has scientific value.

For me, the documentation is confusing.

There isn't an example in the doc site, I was expecting one in the section "Getting started" or maybe on "Examples". I know that the examples are provided as notebooks, but having an introductory example in the docs helps a first-time user.

It is common to have the documentation for the API organized in modules. There is a file named modules.rst but it is not invoked in index.rst.

The format required in vector_field in the function compute_lagrange_descriptor is not clear enough in the docstrings. Although, you get the idea in tutorial-4.ipynb.

I tried to compute the descriptor for a "user-defined" system for a simple pendulum for a 50×50 grid in [-4, 4]² and tau=1 but it ran for 5 hours without finishing. Maybe the selection of parameters is sub-optimal for this problem, but I couldn't find how to pick them in the documentation.

Hi @nicoguaro , as for the last point, could you share with us a jupyter notebook or script with the setup of your simulation? Thanks! :)

broncio123 commented 3 years ago

Hi @jmbr , I'm probably not understanding your comment

I miss some structure in the code. For instance, I'd advice that you aim for an interface to solvers (e.g., Euler-Maruyama) that mirrors that of scipy.integrate or, perhaps better, rely on sdeint (https://github.com/mattja/sdeint/) as a dependency.

By mirroring the interface, do you mean that for the function base.EulerMaruyama_solver the ordering and the format of the input parameters

(t_initial, u_initial, vector_field, ...)

should match the ordering and the format of the input parameters of something like

scipy.integrate.solve_ivp(fun, t_span, y0, method='RK45', t_eval=None, dense_output=False, events=None, vectorized=False, args=None, **options)?

Is this correct? otherwise, please, clarify.

nicoguaro commented 3 years ago

Hi @nicoguaro , as for the last point, could you share with us a jupyter notebook or script with the setup of your simulation? Thanks! :)

The notebook is in the following link: https://gist.github.com/nicoguaro/9dcd8900427e923a077bd0617dfa7bd2

broncio123 commented 3 years ago

Hi @nicoguaro , as for the last point, could you share with us a jupyter notebook or script with the setup of your simulation? Thanks! :)

The notebook is in the following link: https://gist.github.com/nicoguaro/9dcd8900427e923a077bd0617dfa7bd2

Hi @nicoguaro

Thanks! I made some small tweaks to your setup here

https://github.com/champsproject/ldds/blob/test_pendulum/tutorials/demo/simple_pendulum.ipynb

Let us know if it worked. b

nicoguaro commented 3 years ago

Hi @nicoguaro

Thanks! I made some small tweaks to your setup here

https://github.com/champsproject/ldds/blob/test_pendulum/tutorials/demo/simple_pendulum.ipynb

Let us know if it worked.

Yes, it worked. It seems that I missed some details but it works and for larger tau I get what is expected from that system.

broncio123 commented 3 years ago

Hi @jmbr , I hope you're doing well.

I wondering if you could help me with this query of mine, please. https://github.com/openjournals/joss-reviews/issues/3482#issuecomment-910322939

If there's any other issue, please, just give us a shout and we'll look into it :)

broncio123 commented 3 years ago

Hi @nicoguaro Thanks! I made some small tweaks to your setup here https://github.com/champsproject/ldds/blob/test_pendulum/tutorials/demo/simple_pendulum.ipynb

Let us know if it worked.

Yes, it worked. It seems that I missed some details but it works and for larger tau I get what is expected from that system.

Awesome! 😎

jmbr commented 3 years ago

Hi @broncio123,

This was more of a stylistic suggestion. Since I checked all the boxes in the review list, you're good to go as far as I'm concerned.

FWIW, my statement is that it feels that the current interface isn't well established (by contrast to odeint or the newer scipy interface for ode solvers) but, as I said, this isn't critical for me.

Shibabrat commented 3 years ago

Hi @nicoguaro, we've updated the documentation with a new structure and hope this is less confusing. Please have a look around at https://ldds.readthedocs.io/en/latest/ and let us know if any other formatting change/s that will improve readability. Thanks.

nicoguaro commented 3 years ago

Hi @nicoguaro, we've updated the documentation with a new structure and hope this is less confusing. Please have a look around at https://ldds.readthedocs.io/en/latest/ and let us know if any other formatting change/s that will improve readability. Thanks.

I think that this new structure works better. I see some placeholders but I guess that you will fill them while completing the reviewing.

@richardjgowers, I have marked all the boxes above and consider that we can move forward with publication.

broncio123 commented 3 years ago

Hello! @richardjgowers @nicoguaro @jmbr Thank you very much for your time and energy in reviewing our work.

Now, what can we do to proceed with the publication?

richardjgowers commented 3 years ago

@whedon generate pdf

richardjgowers commented 3 years ago

@whedon check references

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
- 10.1016/0167-2789(84)90270-7 is OK
- 10.1063/1.166509 is OK
- 10.1016/j.ijmecsci.2017.10.040 is OK
- 10.1016/j.cnsns.2019.105033 is OK
- 10.1063/1.4915831 is OK
- 10.5281/zenodo.4539666 is OK
- 10.1007/978-1-4612-4312-0 is OK
- 10.1016/0167-2789(90)90040-V is OK
- 10.1007/BF00375090 is OK
- 10.1017/S0022112090000167 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
- 10.1016/j.cnsns.2013.05.002 is OK
- 10.1016/j.cplett.2020.137199 is OK
- 10.1142/S0218127420300086 is OK
- 10.1016/j.cnsns.2020.105331 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-12-0274.1 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
- 10.1103/PhysRevE.99.032221 is OK
- 10.1142/S0218127416300366 is OK
- 10.1039/C7CP05912D is OK
- 10.1016/j.cplett.2017.09.008 is OK
- 10.1063/1.4997379 is OK
- 10.1103/physrevlett.115.148301 is OK
- 10.1103/PhysRevE.96.022222 is OK
- 10.1039/C5CP06624G is OK
- 10.1007/s12043-008-0103-3 is OK
- 10.1086/109234 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

- None

INVALID DOIs

- None

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

@broncio123 @Shibabrat paper looks good now. Can you update the software repo to match the v0.1.0 version that this paper references? After that if you can create a release and archive that on something like zenodo and then report the DOI of that archive we can proceed.

broncio123 commented 3 years ago

Thanks, @richardjgowers, we'll do it promptly.

broncio123 commented 3 years ago

@broncio123 @Shibabrat paper looks good now. Can you update the software repo to match the v0.1.0 version that this paper references? After that if you can create a release and archive that on something like zenodo and then report the DOI of that archive we can proceed.

The software is up-to-date and now a release is available here https://github.com/champsproject/ldds/releases/tag/v0.1.0

I have also archived the source code of this release on ZENODO with URL https://zenodo.org/record/5519580

Let me know if there's anything else we need to do.

b

Shibabrat commented 3 years ago

@whedon generate pdf

Shibabrat commented 3 years ago

@whedon check references

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
- 10.1016/0167-2789(84)90270-7 is OK
- 10.1063/1.166509 is OK
- 10.1016/j.ijmecsci.2017.10.040 is OK
- 10.1016/j.cnsns.2019.105033 is OK
- 10.1063/1.4915831 is OK
- 10.5281/zenodo.4539666 is OK
- 10.1007/978-1-4612-4312-0 is OK
- 10.1016/0167-2789(90)90040-V is OK
- 10.1007/BF00375090 is OK
- 10.1017/S0022112090000167 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
- 10.1016/j.cnsns.2013.05.002 is OK
- 10.1016/j.cplett.2020.137199 is OK
- 10.1142/S0218127420300086 is OK
- 10.1016/j.cnsns.2020.105331 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-12-0274.1 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
- 10.1103/PhysRevE.99.032221 is OK
- 10.1142/S0218127416300366 is OK
- 10.1039/C7CP05912D is OK
- 10.1016/j.cplett.2017.09.008 is OK
- 10.1063/1.4997379 is OK
- 10.1103/physrevlett.115.148301 is OK
- 10.1103/PhysRevE.96.022222 is OK
- 10.1039/C5CP06624G is OK
- 10.1007/s12043-008-0103-3 is OK
- 10.1086/109234 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

- None

INVALID DOIs

- None

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

@broncio123 sorry I should have been clearer, I think you've manually set the DOI on the zenodo archive to the JOSS DOI? I need the zenodo archive to have its own DOI (zenodo will auto generate one iirc) then the paper will point to that DOI (associated with the software archive) to generate the DOI associated with the paper.

broncio123 commented 3 years ago

@broncio123 sorry I should have been clearer, I think you've manually set the DOI on the zenodo archive to the JOSS DOI? I need the zenodo archive to have its own DOI (zenodo will auto generate one iirc) then the paper will point to that DOI (associated with the software archive) to generate the DOI associated with the paper.

No problem, @richardjgowers
The ZENODO DOI is:

10.5281/zenodo.5519580

The JOSS DOI no longer appears on the Zenodo record https://zenodo.org/record/5519580

broncio123 commented 3 years ago

@whedon generate pdf

broncio123 commented 3 years ago

@whedon check references

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
- 10.1016/0167-2789(84)90270-7 is OK
- 10.1063/1.166509 is OK
- 10.1016/j.ijmecsci.2017.10.040 is OK
- 10.1016/j.cnsns.2019.105033 is OK
- 10.1063/1.4915831 is OK
- 10.5281/zenodo.4539666 is OK
- 10.1007/978-1-4612-4312-0 is OK
- 10.1016/0167-2789(90)90040-V is OK
- 10.1007/BF00375090 is OK
- 10.1017/S0022112090000167 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
- 10.1016/j.cnsns.2013.05.002 is OK
- 10.1016/j.cplett.2020.137199 is OK
- 10.1142/S0218127420300086 is OK
- 10.1016/j.cnsns.2020.105331 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-12-0274.1 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
- 10.1103/PhysRevE.99.032221 is OK
- 10.1142/S0218127416300366 is OK
- 10.1039/C7CP05912D is OK
- 10.1016/j.cplett.2017.09.008 is OK
- 10.1063/1.4997379 is OK
- 10.1103/physrevlett.115.148301 is OK
- 10.1103/PhysRevE.96.022222 is OK
- 10.1039/C5CP06624G is OK
- 10.1007/s12043-008-0103-3 is OK
- 10.1086/109234 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

- None

INVALID DOIs

- None

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

@whedon set 10.5281/zenodo.5519579 as archive

openjournals / joss-reviews