[REVIEW]: Libscientific: A Powerful C Library for Multivariate Analysis

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@gmrandazzo@jbytecode<!--end-editor-- Reviewers: @mikeaalv, @faosorios Archive: 10.5281/zenodo.8436823

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/afc8dfc4cdd496f6f51813dbaa5ad310"><img src="https://joss.theoj.org/papers/afc8dfc4cdd496f6f51813dbaa5ad310/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/afc8dfc4cdd496f6f51813dbaa5ad310/status.svg)](https://joss.theoj.org/papers/afc8dfc4cdd496f6f51813dbaa5ad310)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@mikeaalv & @faosorios, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @jbytecode know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @mikeaalv

📝 Checklist for @faosorios

jbytecode commented 1 year ago

@gmrandazzo - Thank you for adding the new subsection now it is more clear to readers.

Please take a look at the comment and the PR:

https://github.com/gmrandazzo/libscientific/pull/10/files#r1318146613

It seems my corrections are not applied for a reason, so please apply the corrections manually:

Please use either libscientific or Libscientific in whole of the manuscript in a consistent way.
Please review the generated bibliography. It seems to contain some unnecessary characters or LaTeX directives. Please make the necessary changes or formatting adjustments to ensure a clean PDF output.
All of the programming language names should be in capital form, e.g., Pyhon but not python.
Please perform a full read and fix any typo if exists.
Put a space between the sentence and the citation, e.g., The sentece. (Author, year; ...)

Thank you in advance.

jbytecode commented 12 months ago

@gmrandazzo - could you please update your status? thank you in advance

gmrandazzo commented 12 months ago

@editorialbot generate pdf

editorialbot commented 12 months ago

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

jbytecode commented 12 months ago

@gmrandazzo- It looks better now. Thank you. By the way, there are still some issues which should be fixed:

The citation "Ke, Q., & Kanade, T. (2005). Robust l/sub 1/ norm factorization in the presence of outliers and missing data by alternative convex programming" still have LaTeX directives. Please fix.
There is a figure that shows computation times in pages 3-4 but this figure is not referenced from within the text. Please mention the figure in somewhere in text and set a caption and label to the figure, e.g., Figure 1. Description.
Please perform a full read and check whether the pdf renders correctly.
Please ping me when you've done with the manuscript.

Thank you in advance.

jbytecode commented 11 months ago

@gmrandazzo - Do you need help? Could you please consider applying the suggestions below?

jbytecode commented 11 months ago

@gmrandazzo - Could you please update your status?

gmrandazzo commented 11 months ago

Hi @jbytecode I will try to finish everything by the end of this week. Sorry.. busy time :) Tnx

jbytecode commented 11 months ago

@gmrandazzo - could you please update your status? would you like me to set the status of this submission as paused?

gmrandazzo commented 11 months ago

Hello @jbytecode done.

All the points were addressed. (latex directives in a citation, figure in 2 pages now is in one page, full read and ping to you now) For your knowledge, I have added some new text in the 'algorithm stability' and 'speed and memory comparison' with a new reference to justify some sentences that were not happy to me.

Back to you.

Thanks

gmrandazzo commented 11 months ago

@editorialbot generate pdf

editorialbot commented 11 months ago

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

jbytecode commented 11 months ago

Line 65 : Multivariate analyisis -> analysis
Line 98: libscientific is a numerical algorithm... -> is libscientific is an algorithm or a set of implementations of algorithms? By the way, it is not a good idea to add some piece of new text after the review and editorial stuff. I need to track and fix many things from scratch right now.

jbytecode commented 11 months ago

@editorialbot check references

editorialbot commented 11 months ago

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

OK DOIs

- 10.1016/0003-2670(86)80028-9 is OK
- 10.1002/cem.1180010107 is OK
- 10.1002/(SICI)1099-128X(199809/10)12:5<301::AID-CEM515>3.0.CO;2-S is OK
- 10.1088/0957-0233/12/10/708 is OK
- 10.1002/9781119013563 is OK
- 10.1109/CVPR.2005.309 is OK
- 10.1002/qsar.19960150402 is OK
- 10.1177/108705719600100308 is OK
- 10.1016/j.aca.2016.02.014 is OK
- 10.1016/j.chemolab.2016.11.010 is OK
- 10.1016/j.jchromb.2017.04.032 is OK
- 10.1016/j.chroma.2019.460661 is OK
- 10.1126/sciadv.abf2665 is OK
- 10.3389/fcimb.2022.897291 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1002/cem.1180010105 is INVALID because of 'https://doi.org/' prefix

jbytecode commented 11 months ago

@gmrandazzo - Here we go again! Please correct the typo and other things. Please update your bibliography as our editorialbot suggests.

I hope we are not in an infinite loop.

gmrandazzo commented 11 months ago

@editorialbot check references

editorialbot commented 11 months ago

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

OK DOIs

- 10.1016/0003-2670(86)80028-9 is OK
- 10.1002/cem.1180010107 is OK
- 10.1002/(SICI)1099-128X(199809/10)12:5<301::AID-CEM515>3.0.CO;2-S is OK
- 10.1088/0957-0233/12/10/708 is OK
- 10.1002/9781119013563 is OK
- 10.1109/CVPR.2005.309 is OK
- 10.1002/qsar.19960150402 is OK
- 10.1177/108705719600100308 is OK
- 10.1016/j.aca.2016.02.014 is OK
- 10.1016/j.chemolab.2016.11.010 is OK
- 10.1016/j.jchromb.2017.04.032 is OK
- 10.1016/j.chroma.2019.460661 is OK
- 10.1126/sciadv.abf2665 is OK
- 10.3389/fcimb.2022.897291 is OK
- 10.1002/cem.1180010105 is OK

MISSING DOIs

- None

INVALID DOIs

- None

gmrandazzo commented 11 months ago

@editorialbot generate pdf

editorialbot commented 11 months ago

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

gmrandazzo commented 11 months ago

@jbytecode many thanks! Apologies for the last-minute add. I know that is not correct. However, those sentences could have been more cool after rereading them, and I was unhappy with them. Now, they are more solid and well-justified.

Then, I have fixed everything again. This will not be an infinite loop. :)

jbytecode commented 11 months ago

@gmrandazzo - Thank you, seems better now.

Could you please perform the tasks given in https://github.com/openjournals/joss-reviews/issues/5420#issuecomment-1701232046

Create a release tag in the repo
Use this release tag to create a Zenodo archive.
Report the version and the Zenodo link, DOI here.

Thank you in advance.

gmrandazzo commented 11 months ago

here is the zenodo DOI link: https://10.5281/zenodo.8436823

jbytecode commented 11 months ago

@editorialbot set v1.6.0 as version

editorialbot commented 11 months ago

Done! version is now v1.6.0

jbytecode commented 11 months ago

In archive https://zenodo.org/record/8436823, the title of paper and the title of archive should match. Please correct.

gmrandazzo commented 11 months ago

Hi @jbytecode I'm still waiting to update the information on Zenodo. However is down since today morning. I will fix the title one everything will be back again. Thank you

jbytecode commented 10 months ago

@gmrandazzo - It seems the site is active now

gmrandazzo commented 10 months ago

@jbytecode unfortunatelly not... https://stats.uptimerobot.com/vlYOVuWgM/ :( When I click to modify the text of the abstract i receive the following message:

The server encountered an internal error and was unable to complete your request. Either the server is overloaded or there is an error in the application.

gmrandazzo commented 10 months ago

it is broken since friday...

gmrandazzo commented 10 months ago

@jbytecode done. Title changed.

jbytecode commented 10 months ago

@editorialbot set 10.5281/zenodo.8436823 as archive

editorialbot commented 10 months ago

Done! archive is now 10.5281/zenodo.8436823

jbytecode commented 10 months ago

@editorialbot check references

editorialbot commented 10 months ago

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

OK DOIs

- 10.1016/0003-2670(86)80028-9 is OK
- 10.1002/cem.1180010107 is OK
- 10.1002/(SICI)1099-128X(199809/10)12:5<301::AID-CEM515>3.0.CO;2-S is OK
- 10.1088/0957-0233/12/10/708 is OK
- 10.1002/9781119013563 is OK
- 10.1109/CVPR.2005.309 is OK
- 10.1002/qsar.19960150402 is OK
- 10.1177/108705719600100308 is OK
- 10.1016/j.aca.2016.02.014 is OK
- 10.1016/j.chemolab.2016.11.010 is OK
- 10.1016/j.jchromb.2017.04.032 is OK
- 10.1016/j.chroma.2019.460661 is OK
- 10.1126/sciadv.abf2665 is OK
- 10.3389/fcimb.2022.897291 is OK
- 10.1002/cem.1180010105 is OK

MISSING DOIs

- None

INVALID DOIs

- None

jbytecode commented 10 months ago

@editorialbot generate pdf

editorialbot commented 10 months ago

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

jbytecode commented 10 months ago

@gmrandazzo - The PR includes minor changes on manuscript text and citation notation PR. Please review and merge.

jbytecode commented 10 months ago

@editorialbot check references

editorialbot commented 10 months ago

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

OK DOIs

- 10.1016/0003-2670(86)80028-9 is OK
- 10.1002/cem.1180010107 is OK
- 10.1002/(SICI)1099-128X(199809/10)12:5<301::AID-CEM515>3.0.CO;2-S is OK
- 10.1088/0957-0233/12/10/708 is OK
- 10.1002/9781119013563 is OK
- 10.1109/CVPR.2005.309 is OK
- 10.1002/qsar.19960150402 is OK
- 10.1177/108705719600100308 is OK
- 10.1016/j.aca.2016.02.014 is OK
- 10.1016/j.chemolab.2016.11.010 is OK
- 10.1016/j.jchromb.2017.04.032 is OK
- 10.1016/j.chroma.2019.460661 is OK
- 10.1126/sciadv.abf2665 is OK
- 10.3389/fcimb.2022.897291 is OK
- 10.1002/cem.1180010105 is OK

MISSING DOIs

- None

INVALID DOIs

- None

jbytecode commented 10 months ago

@editorialbot generate pdf

editorialbot commented 10 months ago

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

jbytecode commented 10 months ago

@gmrandazzo - Both the manuscript and the bibtex look good to me. I am now recommending an acceptance. Our track editor will make the final decision. Thank you for submitting your work to JOSS.

@mikeaalv, @faosorios - Also thank to you for reviewing this submission for JOSS.

jbytecode commented 10 months ago

@editorialbot recommend-accept

editorialbot commented 10 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 10 months ago

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

OK DOIs

- 10.1016/0003-2670(86)80028-9 is OK
- 10.1002/cem.1180010107 is OK
- 10.1002/(SICI)1099-128X(199809/10)12:5<301::AID-CEM515>3.0.CO;2-S is OK
- 10.1088/0957-0233/12/10/708 is OK
- 10.1002/9781119013563 is OK
- 10.1109/CVPR.2005.309 is OK
- 10.1002/qsar.19960150402 is OK
- 10.1177/108705719600100308 is OK
- 10.1016/j.aca.2016.02.014 is OK
- 10.1016/j.chemolab.2016.11.010 is OK
- 10.1016/j.jchromb.2017.04.032 is OK
- 10.1016/j.chroma.2019.460661 is OK
- 10.1126/sciadv.abf2665 is OK
- 10.3389/fcimb.2022.897291 is OK
- 10.1002/cem.1180010105 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 10 months ago

:wave: @openjournals/dsais-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/4710, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

arfon commented 10 months ago

@gmrandazzo – I found a couple of minor typos. Could you merge this PR and I'll be able to proceed from here: https://github.com/gmrandazzo/libscientific/pull/15

arfon commented 10 months ago

@editorialbot recommend-accept

editorialbot commented 10 months ago

Attempting dry run of processing paper acceptance...

openjournals / joss-reviews