Closed editorialbot closed 6 months ago
Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.
For a list of things I can do to help you, just type:
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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
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Software report:
github.com/AlDanial/cloc v 1.88 T=0.16 s (715.6 files/s, 173540.8 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
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Python 49 1835 2843 4696
SVG 1 0 0 2671
HTML 13 294 39 1750
Markdown 4 235 0 995
JavaScript 12 131 221 880
CSS 4 190 35 780
Jupyter Notebook 13 0 8915 522
TeX 1 5 0 92
reStructuredText 8 59 106 77
TOML 1 16 49 71
YAML 2 4 0 36
DOS Batch 1 8 1 26
JSON 1 0 0 10
make 1 4 7 9
INI 1 0 0 8
Bourne Shell 2 9 12 7
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SUM: 114 2790 12228 12630
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gitinspector failed to run statistical information for the repository
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.5281/ZENODO.7213391 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.21105/joss.01026 is OK
- 10.21105/joss.03021 is OK
- 10.18637/jss.v059.i10 is OK
MISSING DOIs
- None
INVALID DOIs
- None
Wordcount for paper.md
is 1662
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@gmrandazzo and @SunnyXu, let me know if you have any questions about how to get your reviews started!
@rkurchin @markur4 plotastic is a solid Python package bridging the gap between seaborn and pingouin to offer a unified environment for plotting and statistical analysis. It is good that there are the testing section and codecov on GitHub. Please see my comments (linked to issues) below to improve. Please let me know if anything is unclear.
@SunnyXu Thanks a lot for the great feedback! I appreciate the detail!
@rkurchin I worked through all points. Should I close them once the reviewer is satisfied?
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@markur4 Thanks for the improvement. I like your improvement regarding issue 3 and issue 6 especially. @rkurchin Martin has addressed all the issues except the second one (PYPI) which might get improved later. Please let me know if I need to do anything else. Thanks again for considering me as a reviewer. Hope to help with another review again in the future.
@SunnyXu, are you satisfied on the community guidelines point? If so, please check off that last box. If not, please leave any additional comments/feedback necessary.
@gmrandazzo, do you think you'll be able to start your review fairly soon?
@rkurchin Thanks for the reminder. I am satisfied and checked the last box. I do not have additional comments regarding.
I'm sorry @gmrandazzo, I'm afraid I can't do that. That's something only editors are allowed to do.
@markur4 and @rkurchin
Thanks for the chance to review this paper. Here are my comments:
1) The summary is OK; however, there needs to be a reason why it would be good to use plastic instead of seaborn+pingouin. This important statement is written in lines 54, 55, and 56 of the manuscript. Please report them also in the summary. The rest of the manuscripts seem fine to me.
2) Installation is fine. However, this package works only for Python >=3.11, and I need clarification on why older Python, i.e., 3.9, is not OK. If there is any specific reason, please state this in the installation document, specifying also the minimum Python version. Can you please fix that?
from pyproject.toml
[...]
#' Specify version only if concrete incompatibilities exist
requires-python = ">=3.11"
Is there any specific incompatibility? If yes, state this. If not, please fix that.
3) I have opened a shell. I copied and pasted the script you presented in the paper, and the Python shell became unusable. I'm not able to see the final plot. Can you check what is going on?
4) Functional documentation seems poor. Please improve it.
Thanks! Best regards
@markur4 Ah last comment. Please clean the package directory from .vscode and .DS_Store and other garbage files. Add them to the .gitignore
@gmrandazzo @rkurchin
Thank you very much for the valuable feedback!
That's a good point, I included the rationale in the last sentence of the summary:
Before: [...]This approach streamlines the process, translating seaborn
parameters into statistical terms, providing researchers and data scientists with a cohesive and user-friendly solution in python.
After: [...] This approach streamlines the process, translating seaborn
parameters into statistical terms, allowing researchers to focus on correct statistical testing and less about specific syntax and implementations.
I haven't tested plotastic on any other version than 3.11. I revised pyproject.toml to reduce confusion:
### Python version
#' Lower versions than 3.11 have not been tested
requires-python = ">=3.11"
Please let me know if testing on older python versions is required to pass the review.
Interesting, I have never executed plotastic in a shell. Here's what I did:
python _paper_test.py
this worked! (no plot shows up, but shell remains usable)python _paper_test.py
in both shell and vscode: this worked, tooimport seaborn as sns
sns.catplot(data=DF, **_dims)
Summary:
The screenshots do not refer to the correct documentation, but preliminary experiments with sphinx. I git removed them completely to prevent confusion.
Please use the documentations and examples found in the README.md as a guide to use plotastic. Let me know if they are clear!
Thanks for pointing out the garbage files! I git removed them from src, if you find any more, let me know!
@markur4 ok for point 2. State the minimum version in the README in the section "REQUIREMENTS" or something like that. Try to harmonize everything. Remember that someone landing your GitHub page should be able to install the software without somersault.
Then @rkurchin fine to me. Accepted.
@gmrandazzo @rkurchin
Ok, I'm happy that it's working! Also, I've added a requirements section to the README.md! Thanks a lot!
@editorialbot set <DOI here> as archive
@editorialbot set <version here> as version
@editorialbot generate pdf
@editorialbot check references
and ask author(s) to update as needed@editorialbot recommend-accept
Thanks again reviewers! @markur4, you can see above a few things you'll need to do (and in some cases, send me info in a comment here) to finalize this submission. I'll do a read over the manuscript itself and send any editorial comments shortly!
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.5281/ZENODO.7213391 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.21105/joss.01026 is OK
- 10.21105/joss.03021 is OK
- 10.18637/jss.v059.i10 is OK
MISSING DOIs
- None
INVALID DOIs
- None
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@rkurchin
Here's what I did:
Let me know if I missed something!
@editorialbot set 0.1.1 as version
Done! version is now 0.1.1
@editorialbot set 10.5281/zenodo.10775033 as archive
Done! archive is now 10.5281/zenodo.10775033
Apologies that this took a little while!
Editorial comments:
seaborn
seaborn
is a ` instead of a 'plotastic
@rkurchin
No problem, thanks for the feedback!
I made these revisions, let me know if I missed something!
* line 9: I think you can remove the "a" before "syntax" since I usually parse that as a collective noun
I removed the "a"
* line 12-13: I'm not sure if "analyses" is the plural of "analysis" (and hence an additional object of the verb "conducts") or the British English spelling of the third-person singular of the verb "analyzes" β in any case, the parallelization of the sentence is a bit broken. I would suggest rewriting/splitting it. One possibility: "The library systematically groups the data according to the needs of statistical tests and plots. It can perform these analyses and visualize the results and also supports extensive customization options"
I agree, the point that I wanted to convey doesn't come across at all.
Before: The library systematically groups the data according to the needs of statistical tests and plots, conducts visualisation, analyses and supports extensive customization options. In essence, plotastic establishes a protocol for configuring statical analyses through plotting parameters. This approach streamlines the process, translating seaborn parameters into statistical terms, [...].
After: Hence, statistics and plotting are performed on the same set of parameters, so that the strength of seaborn
in visualising multidimensional data is extended onto statistical analysis. In essence, plotastic
translates seaborn
parameters into statistical terms, configures statistical protocols based on intuitive plotting syntax and returns a matplotlib
figure with known customization options and more. This approach streamlines data analysis, [...].
* 22-25: not sure what's going on with the line spacing thing here, but perhaps double-check if there's anything goofy about your source file?
I removed unnecessary newlines
* 28: remove extra period before citation
Done
* 31: missing a "with" before `seaborn`
Done
* figure 1: Why is the whole of the plotting block in parentheses?
It's python syntax that allows for methods to be chained in newlines. Without parentheses, the methods need to be in one line and that becomes unreadable very quickly.
* 42: I think the apostrophe after `seaborn` is a ` instead of a '
It's a ', but I rephrased it to prevent confusion:
Before: plotastic
was inspired by seaborn
's intuitive and consistent usage of the same set of parameters
After: plotastic
was inspired by seaborn
using the same set of intuitive and consistent parameters
* 67: "per axes" --> "per axis"
Done
* 71-72: add "a" after "initializes"
Done
* 77, 91: plotastic --> `plotastic`
Done
* 78: remove "in"
Done
* 82: there's a word missing in this sentence...statistical what? Perhaps information? Indicators? Parameters?
Done
* References: [pandas requests](https://pandas.pydata.org/about/citing.html) two particular things be cited when acknowledging it, please replace your citation with those two
Done
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@editorialbot recommend-accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.5281/ZENODO.7213391 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.5281/zenodo.3509134 is OK
- 10.21105/joss.01026 is OK
- 10.21105/joss.03021 is OK
- 10.18637/jss.v059.i10 is OK
MISSING DOIs
- No DOI given, and none found for title: Pandas: A Foundational Python Library for Data Ana...
INVALID DOIs
- None
: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/5105, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept
@editorialbot accept
Doing it live! Attempting automated processing of paper acceptance...
Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.
If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.
You can copy the contents for your CITATION.cff file here:
``` cff-version: "1.2.0" authors: - family-names: Kuric given-names: Martin orcid: "https://orcid.org/0009-0009-7292-7714" - family-names: Ebert given-names: Regina orcid: "https://orcid.org/0000-0002-8192-869X" contact: - family-names: Kuric given-names: Martin orcid: "https://orcid.org/0009-0009-7292-7714" doi: 10.5281/zenodo.10775033 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Kuric given-names: Martin orcid: "https://orcid.org/0009-0009-7292-7714" - family-names: Ebert given-names: Regina orcid: "https://orcid.org/0000-0002-8192-869X" date-published: 2024-03-09 doi: 10.21105/joss.06304 issn: 2475-9066 issue: 95 journal: Journal of Open Source Software publisher: name: Open Journals start: 6304 title: "plotastic: Bridging Plotting and Statistics in Python" type: article url: "https://joss.theoj.org/papers/10.21105/joss.06304" volume: 9 title: "`plotastic`: Bridging Plotting and Statistics in Python" ```
If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.
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@gmrandazzo, @SunnyXu β many thanks for your reviews here and to @rkurchin for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you β¨
@markur4 β your paper is now accepted and published in JOSS :zap::rocket::boom:
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[![DOI](https://joss.theoj.org/papers/10.21105/joss.06304/status.svg)](https://doi.org/10.21105/joss.06304)
HTML:
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<img src="https://joss.theoj.org/papers/10.21105/joss.06304/status.svg" alt="DOI badge" >
</a>
reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06304/status.svg
:target: https://doi.org/10.21105/joss.06304
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The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:
Submitting author: !--author-handle-->@markur4<!--end-author-handle-- (Martin Kuric) Repository: https://github.com/markur4/plotastic Branch with paper.md (empty if default branch): Version: 0.1.1 Editor: !--editor-->@rkurchin<!--end-editor-- Reviewers: @gmrandazzo, @SunnyXu Archive: 10.5281/zenodo.10775033
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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.)
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@gmrandazzo & @SunnyXu, 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:
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