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[REVIEW]: yadg: yet another datagram #4166

Closed whedon closed 2 years ago

whedon commented 2 years ago

Submitting author: !--author-handle-->@PeterKraus<!--end-author-handle-- (Peter Kraus) Repository: https://github.com/dgbowl/yadg Branch with paper.md (empty if default branch): Version: v4.0.0 Editor: !--editor-->@galessiorob<!--end-editor-- Reviewers: @aozorahime, @1mikegrn, @pythonpanda2 Archive: 10.5281/zenodo.6413504

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@aozorahime, @pythonpanda2 & @1mikegrn, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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Review checklist for @aozorahime

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @1mikegrn

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @pythonpanda2

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 2 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @aozorahime, @1mikegrn it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

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whedon commented 2 years ago

Wordcount for paper.md is 1191

whedon commented 2 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=4.54 s (29.7 files/s, 133925.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JSON                            34              0              0         596261
Python                          67           1203           2252           6820
reStructuredText                21            245            360            587
SVG                              2              2              2            349
YAML                             7              9             20            224
TeX                              1             21              0            205
Markdown                         2             23              0             70
TOML                             1              0              0              6
-------------------------------------------------------------------------------
SUM:                           135           1503           2634         604522
-------------------------------------------------------------------------------

Statistical information for the repository '546042009554621630cac07e' was
gathered on 2022/02/15.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Kraus                            1            74             73            0.48
Kraus, Peter                    16          3924           1935           19.10
Nicolas Vetsch                   1           544              0            1.77
Peter Kraus                     29          3410           1290           15.32
Vetsch, Nicolas                  2          1940            169            6.87
krpe                            88          6880           4842           38.21
vetschn                         44          2983           2617           18.25

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
Kraus, Peter               6626          168.9          3.0                2.81
Nicolas Vetsch              544          100.0          0.9                6.25
Peter Kraus                 336            9.9          5.5               12.50
Vetsch, Nicolas            2764          142.5          1.4                6.22
vetschn                       5            0.2          3.2                0.00
whedon commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1038/s41586-020-2649-2 is OK
- 10.33774/chemrxiv-2021-mh17g is OK
- 10.1002/cctc.202001132 is OK
- 10.1186/1471-2105-13-115 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.1007/s11244-020-01380-2 is OK
- 10.1038/sdata.2016.18 is OK

MISSING DOIs

- None

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:

galessiorob commented 2 years ago

👋 @aozorahime, @1mikegrn, @pythonpanda2

Thanks again for volunteering to review this paper. Could you please update us in your ETA? Also, let me know if you have any questions ion the criteria or the process. 🙇‍♀️

mgdotdev commented 2 years ago

Hi everyone 👋🏻 @galessiorob I'm hoping to get my initial review at least started today, hopefully finished as well.

mgdotdev commented 2 years ago

Overall I feel like this is a very well put together package - most of my critiques are minor things like unused imports and whatnot. I don't have any major concerns for which I would expect any sort of revision. 👍🏻 I also noticed that there's some CI/CD built in from gitlab, I don't use gitlab so I didn't verify any of that, but I was able to easily install the package and run the test suite in a generic docker container, so I'd call it close enough 🤷🏻‍♂️.

aozorahime commented 2 years ago

Hi, i am doing this right now. hopefully can finish it tonight or tomorrow @galessiorob

PeterKraus commented 2 years ago

Overall I feel like this is a very well put together package - most of my critiques are minor things like unused imports and whatnot. I don't have any major concerns for which I would expect any sort of revision. 👍🏻 I also noticed that there's some CI/CD built in from gitlab, I don't use gitlab so I didn't verify any of that, but I was able to easily install the package and run the test suite in a generic docker container, so I'd call it close enough 🤷🏻‍♂️.

We've moved the package from our internal gitlab server back to github fairly recently. The gitlab repo is now archived and only the main repo on here is used. I forgot to remove the gitlab CI files after the migration. The github actions now replicate the CI functionality (with testing of every PR on Windows and Linux), including a docs deployment after every commit to master. If you have any suggestions how to improve this, I'm all ears!

pythonpanda2 commented 2 years ago

I will start taking a look at this latest on monday.

pythonpanda2 commented 2 years ago

@galessiorob I don't think I am able to work on the checklist. Please let me know if I have been removed from the review service or if my service is no longer required ? (That would make my life a bit easier. A major funding call opened up this week and now its grant writing season).

galessiorob commented 2 years ago

@editorialbot list reviewers

editorialbot commented 2 years ago

Here's the current list of reviewers: https://bit.ly/joss-reviewers

galessiorob commented 2 years ago

@editorialbot commands

editorialbot commented 2 years ago

Hello @galessiorob, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Add to this issue's reviewers list
@editorialbot add @username as reviewer

# Remove from this issue's reviewers list
@editorialbot remove @username from reviewers

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Assign a user as the editor of this submission
@editorialbot assign @username as editor

# Remove the editor assigned to this submission
@editorialbot remove editor

# Remind an author or reviewer to return to a review after a 
# certain period of time (supported units days and weeks)
@editorialbot remind @reviewer in 2 weeks

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

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@editorialbot set v1.0.0 as version

# Set a value for archive
@editorialbot set 10.21105/zenodo.12345 as archive

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galessiorob commented 2 years ago

@editorialbot add @pythonpanda2 as reviewer

editorialbot commented 2 years ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

galessiorob commented 2 years ago

@whedon add @pythonpanda2 as reviewer

editorialbot commented 2 years ago

My name is now @editorialbot

galessiorob commented 2 years ago

@arfon running into some issues trying to re-add pythonpanda2 as a reviewer so they can work on their checklist

galessiorob commented 2 years ago

@editorialbot add @pythonpanda2 to reviewers

editorialbot commented 2 years ago

@pythonpanda2 is already included in the reviewers list

galessiorob commented 2 years ago

@pythonpanda2 could you try again and let me know if the issue persists, please? We'd really appreciate having your review 🙏

pythonpanda2 commented 2 years ago

@galessiorob Thanks a lot. I will have a look at it now.

pythonpanda2 commented 2 years ago

@galessiorob Not sure if this is an issue due to Safari. I still cannot select the tick option in check list. I am going to try again in Firefox.

pythonpanda2 commented 2 years ago

@galessiorob I am not able to get the checklist sorted out even after switching to Firefox. I am just going to skip ahead and start the review. Thanks a lot for your patience.

galessiorob commented 2 years ago

@pythonpanda2 thank you!

galessiorob commented 2 years ago

@kyleniemeyer could you help us troubleshoot please?

kyleniemeyer commented 2 years ago

@galessiorob @pythonpanda2 I think the issue is that since we switched to the new editorialbot infrastructure, the checklists at the top no longer work (@arfon is that right?)

Instead, @pythonpanda2 can you comment @editorialbot generate my checklist ? This will generate one for you that you can edit.

pythonpanda2 commented 2 years ago

Review checklist for @pythonpanda2

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

pythonpanda2 commented 2 years ago

@PeterKraus https://github.com/dgbowl/yadg/issues/43

pythonpanda2 commented 2 years ago

@PeterKraus

https://github.com/dgbowl/yadg/issues/45

https://github.com/dgbowl/yadg/issues/46

PeterKraus commented 2 years ago

~Alright, I'm losing my mind trying to get the conference proceedings formatted properly for https://github.com/dgbowl/yadg/issues/45. @galessiorob, @kyleniemeyer does either of you know how to do this? The following bibtex doesn't seem to work well:~

@inproceedings{Draxl2020,
  title = {{FAIRmat [Presentation]}},
  author = {Draxl, Claudia},
  crossref = {nfdiconf:20},
  langid = {german},
  howpublished = {https://www.dfg.de/download/pdf/foerderung/programme/nfdi/nfdi_konferenz_2020/fairmat_abstract.pdf},
  file = {C\:\\Users\\krpe\\Zotero\\storage\\5AXGYX4G\\fairmat_abstract.pdf}
}

@proceedings{nfdiconf:20,
  title = {{2. NFDI Conference}},
  publisher = {{Deutsche Forschungsgemeinschaft}},
  venue = {online},
  month = jul,
  year = {2020},
  langid = german
}

~The title of the conference gets pulled out properly, but publisher and howpublished do not.~

I got around the issue by using @unpublished instead of @inproceedings and @proceedings.

PeterKraus commented 2 years ago

@editorialbot generate pdf

editorialbot 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:

pythonpanda2 commented 2 years ago

Thank you @PeterKraus

I think my part is done @galessiorob

PeterKraus commented 2 years ago

@pythonpanda2 I think there are a couple unticked/unchecked items wrt. documentation. The testing/CI is done via github actions, and the example usage is now included in a short section in the paper, and it will be added to the docs. See: DOI

galessiorob commented 2 years ago

@editorialbot generate pdf

editorialbot 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:

galessiorob commented 2 years ago

Hi @PeterKraus,

We're almost at the finish line! I put together a few edit suggestions and typo corrections in this PR. Please merge as much as you like, and after that, we'll review once more and start the publishing process.

PeterKraus commented 2 years ago

Hi @galessiorob, are there any outstanding issues that I should address? I'm only asking cause I'm giving a talk next week for which it'd be great to have a DOI to point folks to. But if it's not yet ready, I understand!

galessiorob commented 2 years ago

@editorialbot generate pdf

editorialbot 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:

galessiorob commented 2 years ago

@PeterKraus 🙈 I am very sorry I missed this question. I apologize for the delay and hope you have more upcoming talks where you can point the audience to your paper. I'm a Chemical Engineer and this paper is awesome! I'm sure it'll be very well received.

The next thing we need from you is to deposit your software in Zenodo and post the DOI here and the most recent version. After that, we can set the final version, generate a final proof, and have an Editor in Chief do the publishing.

@aozorahime @pythonpanda2 @1mikegrn Thank you so much for lending your expertise and reviewing this paper 🚀

PeterKraus commented 2 years ago

Hi @galessiorob, no worries about the delay. Glad you like the paper/software! I have uploaded all published versions of yadg to https://doi.org/10.5281/zenodo.5894822 (with version 4.0.0 being https://doi.org/10.5281/zenodo.6413504). We're working on getting v4.1.0 out, which will have some of the suggestions from reviewers merged in, but it's not ready yet as we need to finish a couple of features. Do I need to add the DOIs to the paper, or are the links here enough?

galessiorob commented 2 years ago

Great! I think the links are enough, but I'll ask the editor in chief.

galessiorob commented 2 years ago

@editorialbot set v4.0.0 as version

editorialbot commented 2 years ago

Done! version is now v4.0.0

galessiorob commented 2 years ago

@editorialbot recommend-accept