[PRE REVIEW]: PyNumDiff: A Python package for numerical differentiation of noisy time-series data

[whedon]

Submitting author: @florisvb (Floris van Breugel)
Repository: https://github.com/florisvb/PyNumDiff
Version: v0.0.3
Editor: @christinahedges
Reviewers: @pmli, @billtubbs
Managing EiC: Arfon Smith

⚠️ JOSS reduced service mode ⚠️

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.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/102257ee4b0142bf49bc18d7c810e9d5"><img src="https://joss.theoj.org/papers/102257ee4b0142bf49bc18d7c810e9d5/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/102257ee4b0142bf49bc18d7c810e9d5/status.svg)](https://joss.theoj.org/papers/102257ee4b0142bf49bc18d7c810e9d5)

Author instructions

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

@florisvb 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.

⚠️ JOSS reduced service mode ⚠️

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]

Wordcount for paper.md is 741

[whedon]

PDF failed to compile for issue #3922 with the following error:

 /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:456:in `parse': (c3fa3df322ad5171f67cce41/paper.md): did not find expected key while parsing a block mapping at line 2 column 1 (Psych::SyntaxError)
	from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:456:in `parse_stream'
	from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:390:in `parse'
	from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:277:in `load'
	from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:578:in `block in load_file'
	from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:577:in `open'
	from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:577:in `load_file'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:127:in `load_yaml'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:87:in `initialize'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/processor.rb:38:in `new'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/processor.rb:38:in `set_paper'
	from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/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-c5c16aedb3d6/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>'

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.13 s (591.6 files/s, 74938.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          40           1216           1904           2320
Jupyter Notebook                 3              0           2989            413
Markdown                         2             51              0            182
reStructuredText                27             94             98            147
TeX                              1             14              0            131
DOS Batch                        1              8              1             26
YAML                             1              3              0             10
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            76           1390           4999           3238
-------------------------------------------------------------------------------


Statistical information for the repository 'b1774cd1a49cf4a3510dac50' was
gathered on 2021/11/18.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Floris van Breugel              48          7985            786           10.99
floris                           4             8             21            0.04
luckystarufo                    18         34640          36398           88.98

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
Floris van Breugel          554            6.9          6.3                4.69
Yuying                     4886          100.0          1.6               15.78

[arfon]

@florisvb – thanks for your submission to JOSS. It looks like the paper can't be compiled because the indentation in the YAML header for this row is off:

- name: Department of Biology, University of Washington
   index: 3

Could you take a look at fixing this please?

[florisvb]

Hi Arfon, I just fixed that issue. Let me know if anything else comes up. fyi - the paper compiled for me when I ran it through the whedon.theoj.org link both before and after I made that change, which seems odd. - Floris

…

On Thu, Nov 18, 2021 at 4:52 AM Arfon Smith ***@***.***> wrote: @florisvb <https://github.com/florisvb> – thanks for your submission to JOSS. It looks like the paper can't be compiled because the indentation in the YAML header for this row is off: - name: Department of Biology, University of Washington index: 3 Could you take a look at fixing this please? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#3922 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAB4EPCFYTABPP73IGL7BALUMTZI3ANCNFSM5IJQ4ROA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

-- Floris van Breugel | http://www.florisvanbreugel.com Assistant Professor of Mechanical Engineering & Graduate Program for Neuroscience University of Nevada, Reno Wildlife and Landscape Photography Galleries: http://www.ArtInNaturePhotography.com/ Blog: http://www.ArtInNaturePhotography.com/wordpress/

[arfon]

@whedon invite @christinahedges as editor

👋 @christinahedges – would you be able to take on this submission for us?

[whedon]

@christinahedges has been invited to edit this submission.

[christinahedges]

@whedon assign me as editor

[whedon]

OK, the editor is @christinahedges

[christinahedges]

@whedon generate pdf

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[christinahedges]

@whedon check references

[whedon]

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

OK DOIs

- None

MISSING DOIs

- 10.1109/access.2020.3034077 may be a valid DOI for title: Numerical differentiation of noisy data: A unifying multi-objective optimization framework
- 10.1515/9783110226157.263 may be a valid DOI for title: An introduction to total variation for image analysis
- 10.1073/pnas.1517384113 may be a valid DOI for title: Discovering governing equations from data by sparse identification of nonlinear dynamical systems
- 10.1016/j.cpc.2007.03.009 may be a valid DOI for title: Numerical differentiation of experimental data: local versus global methods
- 10.1109/msp.2011.941097 may be a valid DOI for title: What is a Savitzky-Golay filter?[lecture notes]
- 10.1021/ac60214a047 may be a valid DOI for title: Smoothing and differentiation of data by simplified least squares procedures.
- 10.1109/9780470544334.ch9 may be a valid DOI for title: A new approach to linear filtering and prediction problems
- 10.1016/j.automatica.2017.08.011 may be a valid DOI for title: Generalized Kalman smoothing: Modeling and algorithms
- 10.1016/0167-2789(92)90242-f may be a valid DOI for title: Nonlinear total variation based noise removal algorithms

INVALID DOIs

- None

[christinahedges]

Hello @florisvb, welcome to JOSS! Thanks for your submission. Taking a look at your paper submission I can see a few fixable issues that you may want to work on while I find reviewers:

1. The references are missing DOIs (see whedon's comments above)
2. In your submission we usually encourage a state of the field section or paragraph which references common software that is use to solve similar problems in the field. You should add some references to the tools you mention in your submission.

I will get to work finding some reviewers.

[florisvb]

Sorry for the delay -- I have added in DOIs based on whedon's comments, as well as a state of the field section with some additional software references. - Floris

…

On Fri, Nov 19, 2021 at 9:28 AM Christina Hedges ***@***.***> wrote: Hello @florisvb <https://github.com/florisvb>, welcome to JOSS! Thanks for your submission. Taking a look at your paper submission I can see a few fixable issues that you may want to work on while I find reviewers: 1. The references are missing DOIs (see whedon's comments above) 2. In your submission we usually encourage a state of the field section or paragraph which references common software that is use to solve similar problems in the field. You should add some references to the tools you mention in your submission. I will get to work finding some reviewers. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#3922 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAB4EPFKLONDAPXEPKOTSI3UM2CMNANCNFSM5IJQ4ROA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

-- Floris van Breugel | http://www.florisvanbreugel.com Assistant Professor of Mechanical Engineering & Graduate Program for Neuroscience University of Nevada, Reno Wildlife and Landscape Photography Galleries: http://www.ArtInNaturePhotography.com/ Blog: http://www.ArtInNaturePhotography.com/wordpress/

[christinahedges]

@whedon check references

[whedon]

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

OK DOIs

- 10.1109/access.2020.3034077 is OK
- 10.1515/9783110226157.263 is OK
- 10.1073/pnas.1517384113 is OK
- 10.1016/j.cpc.2007.03.009 is OK
- 10.1109/msp.2011.941097 is OK
- 10.1021/ac60214a047 is OK
- 10.1109/9780470544334.ch9 is OK
- 10.1017/S000192400001232X is OK
- 10.1016/j.automatica.2017.08.011 is OK
- 10.1016/0167-2789(92)90242-f is OK
- 10.5402/2011/164564 is OK
- 10.1038/s41586-020-2649-2 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.21105/joss.00530 is INVALID because of 'https://doi.org/' prefix

[christinahedges]

@florisvb, thank you for fixing your DOIs (it looks like there's one invalid DOI that is easily fixed.)

I see from your submission that you have published a paper on this topic in another journal. There may be some concern from JOSS that this is not a unique submission. Could you please justify that this submission to JOSS is unique, and separate from the previously published article? I will then discuss with the rest of the JOSS team.

[florisvb]

I fixed the DOI issue. Regarding the previous IEEE paper. The previous paper was a scientific advance in optimization methods for numerical differentiation, which we illustrated using 4 differentiation methods. Our PyNumDiff package, on the other hand, provides 22 differentiation methods, organized documentation, and is compliant with all the open source software requirements. Together, this represents a substantial effort beyond the original scientific advance. These improvements were made possible by substantial new contributions from an additional author, Yuying Liu, who was not a part of the original author list for the scientific advance. A comparable example would be this scientific paper, https://www.pnas.org/content/113/15/3932.short, which was followed up by this JOSS paper, https://joss.theoj.org/papers/10.21105/joss.02104. Please let me know if I can expand on any of these details. Cheers, - Floris

…

On Wed, Nov 24, 2021 at 9:55 AM Christina Hedges ***@***.***> wrote: @florisvb <https://github.com/florisvb>, thank you for fixing your DOIs (it looks like there's one invalid DOI that is easily fixed.) I see from your submission that you have published a paper <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7899139/> on this topic in another journal. There may be some concern from JOSS that this is not a unique submission. Could you please justify that this submission to JOSS is unique, and separate from the previously published article? I will then discuss with the rest of the JOSS team. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#3922 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAB4EPGY2QX6H7Z4BNHDCTLUNURIPANCNFSM5IJQ4ROA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

-- Floris van Breugel | http://www.florisvanbreugel.com Assistant Professor of Mechanical Engineering & Graduate Program for Neuroscience University of Nevada, Reno Wildlife and Landscape Photography Galleries: http://www.ArtInNaturePhotography.com/ Blog: http://www.ArtInNaturePhotography.com/wordpress/

[christinahedges]

Hi @florisvb, I spoke with the editorial team, and we agree this is acceptable. I am looking for reviewers for this work, please would you let me know your suggestions for anyone in your field who is not conflicted with this work, and able to give an impartial review.

[florisvb]

Great! Here are some potential reviewers. Frank Noe, FU Berlin, ***@***.*** Benjamin Peherstorfer, Courant Institute NYU, ***@***.*** Peter Benner, Magdeburg ***@***.*** Hayden Schaeffer, Carnegie Mellon, ***@***.*** - Floris

…

On Tue, Nov 30, 2021 at 9:53 AM Christina Hedges ***@***.***> wrote: Hi @florisvb <https://github.com/florisvb>, I spoke with the editorial team, and we agree this is acceptable. I am looking for reviewers for this work, please would you let me know your suggestions for anyone in your field who is not conflicted with this work, and able to give an impartial review. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#3922 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAB4EPGF7UDAUO4RKBPUQC3UOUFRPANCNFSM5IJQ4ROA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

-- Floris van Breugel | http://www.florisvanbreugel.com Assistant Professor of Mechanical Engineering & Graduate Program for Neuroscience University of Nevada, Reno Wildlife and Landscape Photography Galleries: http://www.ArtInNaturePhotography.com/ Blog: http://www.ArtInNaturePhotography.com/wordpress/

[christinahedges]

@whedon assign @pmli as reviewer

[whedon]

OK, @pmli is now a reviewer

[christinahedges]

Hello @florisvb and @pmli, thank you for your patience in getting this review started. Unfortunately, perhaps because of the holidays, I've struggled finding a reviewer for this submission despite quite a lot of digging. @florisvb if you have any further suggestions of unconflicted reviewers please do let me know otherwise I think we will have to be patient. I will also see if I can rope in some other JOSS editors so we can get this kicked off.

Thanks again for your patience!

[florisvb]

Hi Christina, What qualifications do you typically look for in JOSS reviewers? Should they be people that hold academic positions, or are people in data science / software development positions also eligible? If the latter, I may be able to come up with additional candidates. Thanks! - Floris

…

On Tue, Jan 18, 2022 at 9:34 AM Christina Hedges ***@***.***> wrote: Hello @florisvb <https://github.com/florisvb> and @pmli <https://github.com/pmli>, thank you for your patience in getting this review started. Unfortunately, perhaps because of the holidays, I've struggled finding a reviewer for this submission despite quite a lot of digging. @florisvb <https://github.com/florisvb> if you have any further suggestions of unconflicted reviewers please do let me know otherwise I think we will have to be patient. I will also see if I can rope in some other JOSS editors so we can get this kicked off. Thanks again for your patience! — Reply to this email directly, view it on GitHub <#3922 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAB4EPFQRIBC3W5ZVZ73P33UWWQDRANCNFSM5IJQ4ROA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.Message ID: ***@***.***>

-- Floris van Breugel | http://www.florisvanbreugel.com Assistant Professor of Mechanical Engineering & Graduate Program for Neuroscience University of Nevada, Reno Wildlife and Landscape Photography Galleries: http://www.ArtInNaturePhotography.com/ Blog: http://www.ArtInNaturePhotography.com/wordpress/

[christinahedges]

If there are people in your field you feel have used the tool in their work, but are not conflicted with you, that would be ideal. Anyone in data science and software would still be totally fine, so long as it's clear they are an expert reviewer for some aspect of the tool. I will continue to ping people, thanks for your help!

[christinahedges]

@whedon add @biletubes as reviewer

[whedon]

OK, @biletubes is now a reviewer

[christinahedges]

@whedon assign @pmli as reviewer

[whedon]

OK, @pmli is now a reviewer

[christinahedges]

@whedon add @billtubbs as reviewer

[whedon]

OK, @billtubbs is now a reviewer

[christinahedges]

Hi @florisvb I was able to find our second reviewer who has experience in running this tool. Thanks so much @pmli and @billtubbs for joining us! I'll be kicking off the review now, which will start a new issue with a new number. You'll get a notification for the review issue, please join me over there and there will be further instructions!

[christinahedges]

@whedon start review

[whedon]

OK, I've started the review over in #4078.

[billtubbs]

Hi @christinahedges . Just realized I asked a question to a bot (@whedon). I have a problem in the #4708 review: See this comment.

Should this checklist be clickable by me?