search

openjournals / joss-reviews

Reviews for the Journal of Open Source Software
Creative Commons Zero v1.0 Universal
703 stars 36 forks source link

[PRE REVIEW]: CategoricalTimeSeries.jl: A toolbox for categorical time-series analysis #3720

Closed whedon closed 2 years ago

whedon commented 2 years ago

Submitting author: @johncwok (Corentin Nelias) Repository: https://github.com/johncwok/CategoricalTimeSeries.jl Version: 1.0.0 Editor: @jbytecode Reviewers: @bkamins, @felixcremer Managing EiC: Kevin M. Moerman

: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.

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/919a3be5c11e2add7274a8517066361e"><img src="https://joss.theoj.org/papers/919a3be5c11e2add7274a8517066361e/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/919a3be5c11e2add7274a8517066361e/status.svg)](https://joss.theoj.org/papers/919a3be5c11e2add7274a8517066361e)

Author instructions

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

@johncwok 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 commented 2 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:

@whedon generate pdf
whedon commented 2 years ago

Wordcount for paper.md is 784

whedon commented 2 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.07 s (525.4 files/s, 136060.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              1              0              0           2671
JavaScript                       6            473           1213           2025
Julia                            8            183             17           1301
HTML                             7            272             18            950
Markdown                         8            134              0            513
CSS                              2             16             67             71
TeX                              1              8              0             65
YAML                             3             11              2             53
TOML                             1              5              0             20
XML                              1              0              0             11
JSON                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                            39           1102           1317           7681
-------------------------------------------------------------------------------

Statistical information for the repository 'ba0299fa7fab93bc7c126dce' was
gathered on 2021/09/12.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Corentin Nelias                  1          3711              0          100.00

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
Corentin Nelias            3711          100.0          0.0               32.69
whedon commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1137/141000671 is OK

MISSING DOIs

- 10.1093/biomet/80.3.611 may be a valid DOI for title: Spectral analysis for categorical time series: Scaling and the spectral envelope
- 10.1145/369133.369172 may be a valid DOI for title: Finding motifs using random projections
- 10.1162/neco_a_00961 may be a valid DOI for title: The deterministic information bottleneck

INVALID DOIs

- None
whedon commented 2 years ago

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

Kevin-Mattheus-Moerman commented 2 years ago

@johncwok thanks for this submission. I will be looking for a handling editor for this work. In the mean time can you work on fixing those references :point_up:. You can call @whedon generate pdf here to update the paper and call @whedon check references to check those DOI's. Thanks.

whedon commented 2 years ago

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

CNelias commented 2 years ago

Dear Kevin, I checked the existing DOIs and added the missing ones.

Kevin-Mattheus-Moerman commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

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

Kevin-Mattheus-Moerman commented 2 years ago

@whedon check references

whedon commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1137/141000671 is OK
- 10.1093/biomet/80.3.611 is OK
- 10.1002/9781119097013 is OK
- 10.1145/369133.369172 is OK
- 10.1162/neco_a_00961 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.1.1.91.5339 is INVALID
- 10.1.1.6.9199 is INVALID
Kevin-Mattheus-Moerman commented 2 years ago

@johncwok it looks like two still need some work, perhaps they need /..... FYI you can also run these commands I just ran yourself.

Kevin-Mattheus-Moerman commented 2 years ago

@whedon assign @jbytecode as editor

whedon commented 2 years ago

OK, the editor is @jbytecode

jbytecode commented 2 years ago

Dear @johncwok

You can use the site https://whedon.theoj.org/ to compile your paper and bibtex and then you can let the whedon dump the latest version here.

Do you have any suggestions for potential reviewers? If yes, please mention them here in this thread (without tagging them with an @ - we don't want to disturb them). 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).

In case you are unable to create a suitable list of referees, I will create one for you.

Thank you in advance.

jbytecode commented 2 years ago

@johncwok a small tip before inviting reviewers:

In tests of your package, it is a good practice to divide tests into categories like 

@testset "integerIB" begin
    @test ..... 
end

instead of commenting like 

#testing integerIB
@test ....
CNelias commented 2 years ago

@whedon check references

whedon commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1137/141000671 is OK
- 10.1093/biomet/80.3.611 is OK
- 10.1002/9781119097013 is OK
- 10.1145/369133.369172 is OK
- 10.1162/neco_a_00961 is OK

MISSING DOIs

- None

INVALID DOIs

- None
CNelias commented 2 years ago

@jbytecode I will have a look at potential reviewers this evening, and make test sets. Thanks for the feedback. I have another question: one of the papers I have in the references (The information bottleneck) doesn't seem to have a DOI. Is it an issue?

jbytecode commented 2 years ago

it seems it is an unpublished one and I couldn't find a crossref entry either. you can leave it as is.

jbytecode commented 2 years ago

@whedon check references

whedon commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1137/141000671 is OK
- 10.1093/biomet/80.3.611 is OK
- 10.1002/9781119097013 is OK
- 10.1145/369133.369172 is OK
- 10.1162/neco_a_00961 is OK

MISSING DOIs

- None

INVALID DOIs

- None
jbytecode commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

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

CNelias commented 2 years ago

Looking at the list (from the bottom), I think these people might be adapted referees: jiweiqi, metelkin, papachristoumarios Are 3 enough?

jbytecode commented 2 years ago

👋👋👋 Dear @jiweiqi, @metelkin, and @felixcremer 👋👋👋

Would you be willing to assist in reviewing this submission for JOSS (Journal of Open Source Software)?

JOSS publishes articles about open source research software. The submission I'd like you to review is titled: "CategoricalTimeSeries.jl: A toolbox for categorical time-series analysis". You can find more information at the top of this Github issue (https://github.com/openjournals/joss-reviews/issues/3720).

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know.

jiweiqi commented 2 years ago

Hi @jbytecode , thanks for your invitation. This package looks cool. However, I am not an expert in analyzing categorical time series (instead I am more familiar with dynamic systems with continuous variable). I would suggest someone else in this field review this paper. Thanks again and I am happy to involve in the future review processes.

jbytecode commented 2 years ago

Dear @jiweiqi, thank you for the quick response. Hope we will work together in later submissions. Who is your suggestion? Could you please mention the github id here without an @ symbol? Thank you in advance!

CNelias commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

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

jiweiqi commented 2 years ago

Dear @jiweiqi, thank you for the quick response. Hope we will work together in later submissions. Who is your suggestion? Could you please mention the github id here without an @ symbol? Thank you in advance!

Hi, I would recommend https://github.com/bkamins

jbytecode commented 2 years ago

Dear @bkamins 👋👋👋

Would you be willing to assist in reviewing this submission for JOSS (Journal of Open Source Software)?

JOSS publishes articles about open source research software. The submission I'd like you to review is titled: "CategoricalTimeSeries.jl: A toolbox for categorical time-series analysis". You can find more information at the top of this Github issue (https://github.com/openjournals/joss-reviews/issues/3720).

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know.

bkamins commented 2 years ago

Hi, I can review it. I have one question and two comments.

The question is: what exactly should I review (code, documentation, the article proof)?

The comments are:

Thank you!

jbytecode commented 2 years ago

Hi, I can review it. I have one question and two comments.

The question is: what exactly should I review (code, documentation, the article proof)?

@bkamins, Thank you for the reply. When the review starts, there will be 20 checkboxes for each reviewer that indicate the corresponding review item including the software, the paper, and the documentation. If you accept, I will be here to help you anytime.

The comments are:

  • it would be great to review the package against some release of it. Currently I do not see any releases nor tags for this package.
  • the current state of the package when added to an environment does not allow latest version of DataFrames.jl to be installed. It restricts it to 0.19 release. I think it would be good to try to fix that.

Since these are about reviewing, you will be able to interact with the author(s) and list a reviewing report during the process. This process will start whenever we set at least two reviewers for the submission.

Thank you!

do these answers fit your questions?

CNelias commented 2 years ago

Dear bkamins,

might I ask what you mean by release? The package was added to the julia registry some 10 months ago (https://github.com/JuliaRegistries/General/tree/master/C/CategoricalTimeSeries). I am a bit puzzled by the restrictions on the version of dataframes, since I didn't explicitly enforce any. I tried to explicitly make it work for later release, I hope this will fix it.

bkamins commented 2 years ago

do these answers fit your questions?

So I wait for the second reviewer. Right?

might I ask what you mean by release?

In https://github.com/JuliaRegistries/General/blob/master/C/CategoricalTimeSeries/Versions.toml you only have:

["0.1.0"]
git-tree-sha1 = "62468caf4b35c78a97dc7a5be9ea068a1f731a27"

while in your repo in https://github.com/johncwok/CategoricalTimeSeries.jl/blob/main/Project.toml you currently have:

name = "CategoricalTimeSeries"
uuid = "f5116226-a574-5b1a-a4a4-91edc520f498"

authors = ["Corentin Nelias <cwokpoubelle@laposte.net>"]
version = "1.0.0"

so as you can see the versions are inconsistent. And there is no tag for 0.1 release on your repository. Normally it is recommended to make a tag and a release on GitHub for each version of the package.

I am a bit puzzled by the restrictions on the version of dataframes

The reason is that in IntegerIB.jl in https://github.com/johncwok/IntegerIB.jl/blob/master/Project.toml you have:

[compat]
julia = "^1.0"
DataFrames = "^0.19"

which disallows latest version of DataFrames.jl.

In general I would recommend - as for the reviewed packages to make proper releases also for all packages that the reviewed package depends on as e.g. IntegerIB.jl does not have a proper release either.

To be clear, as is explained here https://github.com/JuliaRegistries/Registrator.jl/#note-on-git-tags-and-github-releases Julia package manager does not depend on GitHub tags, however, this is a good practice to have them and properly manage releases on GitHub (as users will normally check them when using your package). You can have a look at DataFrames.jl as an example how it looks like when this process is followed here: https://github.com/JuliaData/DataFrames.jl/releases.

The reason is that currently when you install your packages Julia installs some very old version of it (almost a year old) and not what is in main branch, as it currently uses the 62468caf4b35c78a97dc7a5be9ea068a1f731a27 git-tree-sha1 as a reference what should be installed (and it is dated Oct 28, 2020).

jbytecode commented 2 years ago

@whedon add @bkamins as reviewer

@bkamins yes, you are assigned as the first reviewer. When we set the second one, a new issue will be created. You can review the paper in there.

Thank you!

whedon commented 2 years ago

OK, @bkamins is now a reviewer

jbytecode commented 2 years ago

👋👋👋 Dear @papachristoumarios 👋👋👋

Would you be willing to assist in reviewing this submission for JOSS (Journal of Open Source Software)?

JOSS publishes articles about open source research software. The submission I'd like you to review is titled: "CategoricalTimeSeries.jl: A toolbox for categorical time-series analysis". You can find more information at the top of this Github issue (https://github.com/openjournals/joss-reviews/issues/3720).

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know.

jbytecode commented 2 years ago

👋👋👋 Dear @daviddewhurst 👋👋👋

Would you be willing to assist in reviewing this submission for JOSS (Journal of Open Source Software)?

JOSS publishes articles about open source research software. The submission I'd like you to review is titled: "CategoricalTimeSeries.jl: A toolbox for categorical time-series analysis". You can find more information at the top of this Github issue (https://github.com/openjournals/joss-reviews/issues/3720).

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know.

felixcremer commented 2 years ago

Dear @jbytecode,

I would be willing to review this submission, but I can only start doing the review two weeks from now.

Is it a conflict of interest, that I and the main author are both employed by the Max-Planck-Society? We are on different institutes and haven't met each other.

arfon commented 2 years ago

Is it a conflict of interest, that I and the main author are both employed by the Max-Planck-Society? We are on different institutes and haven't met each other.

Thank you for disclosing this @felixcremer. We are happy to waive this possible conflict (i.e., we are happy to have you as a reviewer!).

jbytecode commented 2 years ago

@whedon add @felixcremer as reviewer

Thank you @felixcremer, it is not a problem to wait until you are available. This deadline is reasonable for us. Thank you for accepting our invitation.

whedon commented 2 years ago

OK, @felixcremer is now a reviewer

jbytecode commented 2 years ago

@whedon start review

whedon commented 2 years ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/3733.