Closed editorialbot closed 3 months ago
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Software report:
github.com/AlDanial/cloc v 1.88 T=0.71 s (76.5 files/s, 434739.9 lines/s)
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JSON 2 0 0 293408
Python 19 819 1731 2189
Jupyter Notebook 10 0 6359 1181
Markdown 4 110 0 440
reStructuredText 12 142 136 206
TeX 1 19 0 164
YAML 3 4 3 64
DOS Batch 1 8 1 26
make 1 4 7 9
Bourne Shell 1 0 0 5
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SUM: 54 1106 8237 297692
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gitinspector failed to run statistical information for the repository
Wordcount for paper.md
is 2363
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1214/21-BA1287 is OK
- 10.1103/PhysRevC.106.044002 is OK
- 10.1088/1361-6471/abf1df is OK
- 10.1080/00401706.2023.2257765 is OK
- 10.1016/j.jmva.2019.104555 is OK
- 10.1214/17-BA1091 is OK
- 10.1175/MWR3441.1 is OK
- 10.3389/fnhum.2014.00457 is OK
- 10.1016/j.cpc.2021.108168 is OK
MISSING DOIs
- None
INVALID DOIs
- https://doi.org/10.1111/insr.12243 is INVALID because of 'https://doi.org/' prefix
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@ominusliticus, be sure to fix that one DOI when you have a moment.
The DOI has been updated :+1:
Hi @rkurchin and @ominusliticus , I've finished what I can of the review for Taweret
as of now. I've opened several issues with #51 and #52 currently blocking for acceptance (discussed below). My comments on the paper (#54) are minor and non-blocking--I will leave them up to the discretion of @rkurchin, but having a statement of contribution with this many co-first authors feels important.
To finish my review, I need to sufficiently assess functionality. To do so, I would like to be able to run and toy with the example models provided with the documentation, but I run into ptemcee
errors when running a notebook locally. As I discuss in that issue, I suspect this is on my end but having ptemcee
not be included within the requirements.txt
file during installation I think makes it relevant to the review, i.e. if I ran into this error, end-users will certainly run into it as well.
I view issues#51 and #52 as blocking because they are critical to use of the software. Installing Taweret
is a bit of a bear as I have to clone the repository, add it to my PATH
, and then hunt down a binary to run the regression trees. Unless I am missing something big (which is totally plausible), this could be greatly simplified for the end-user by packaging Taweret
on pip
and then defining a build_taweret
command that does the full regression tree configuration. For comparison, cmdstanpy
(a industry-standard library for Bayesian inference via Hamiltonian MCMC) has a function for installing the cmdstan
toolchain in a platform-agnostic manner. Something similar for Taweret
would enormously simplify installation for the end user.
Finally, I am concerned that the current version of Taweret
does not have a CI/CD pipeline. The authors discuss this as a goal for the software in the paper, but I think the authors should really prioritize it. The tests are currently failing (see #52), which would have been caught with CI/CD in place.
Thanks, @gchure. @ominusliticus, take note!
@julienmalard, any sense when you'll be able to start working on your review?
Would 2-3 weeks from now be too late?
Earlier would certainly be better (even if you can only get started but maybe file a few issues that @ominusliticus would be able to start working on), but if you need to wait that long, that's okay.
Hi all, my co-authors and I have started to address/implement @gchure comments/suggestions. Everything should be up-to-date this weekend.
@ominusliticus checking in on the status of these updates!
@rkurchin we responded to @gchure 's comments today and included is suggestion. I will have the bot generate a new draft. The biggest thing is getting CI/CD working, which is the goal for this week.
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Hi @rkurchin, I've played around with Taweret more and am happy with the software (good work to @ominusliticus and everyone else!). The remaining blocking issue on my end is i) implementation of CI/CD and ii) release of Taweret on PyPi. Once those are configured (and I can test installation one more time), I'll finish my review and recommend Taweret for publication in JOSS.
I have finished my initial review (see https://github.com/bandframework/Taweret/issues/56 and https://github.com/bandframework/Taweret/issues/55).
Hi @julienmalard, @gchure and @rkurchin, thank you for your patience! I just wanted to post a quick update: we are nearing completion of making the python packages available via PyPI. Our playing around TestPyPI seems to be promising. We still have to update the documentation with all the changes we have made regarding installation instructions and CI/CD. We are hoping to able to finalize everything next week.
🔔 Hi @ominusliticus, just checking in on the progress here!
Hey @rkurchin, we are having trouble building wheels for the one of the dependencies of Taweret. Trying to resolve as quickly as possible! The documentation has been updated with new installation instructions. Once the dependency is successfully built, we can publish the packages and have people pip install them.
@ominusliticus Let me know if you have any particular difficulties with building the wheel that I could help out with..
@rkurchin @gchure @julienmalard we are happy to announce that all the recommended changes have been implemented, along with the corresponding changes to the documentation. Taweret is now pip installable!
We found throughout the CI/CD process that having a copy of OpenMPI was necessary for the test_trees.py to pass. So if you wish to run these tests yourself, please be sure to have an installation.
Thank you for your patience!
Great! @julienmalard and @gchure, please take a look and see if this suffices to finish up your review checklists!
Hi @rkurchin, I will make sure to look at this by the end of the week.
Looks like there's still an issue with pip installation on MacOS, I think due to mismatched versioning in the metadata for openBT. I've commented on this here.
Hi @rkurchin! The installation problem has been fixed, and I can mark my review as complete. Congrats to @ominusliticus and the rest of the authors on a nice piece of software.
Thanks @gchure! @julienmalard, what are your thoughts?
Installation looks good on my end! When running the tests, I get the following error: https://github.com/bandframework/Taweret/issues/80
Hi @julienmalard and @ominusliticus, checking in on the status of the issue reference above?
Hi @rkurchin, we think all @julienmalard needs to do is update Taweret via pip install Taweret --upgrade
. The openbtmixing package was not installed when the tests were run. The newest version of Taweret includes openbtmixing as a dependency, so things should be installed properly if Taweret is upgraded.
Hi @julienmalard, have you had a chance to try this?
Pinging @julienmalard on this again!
Yes, just tried again (see comment in issue).
Thanks for trying the code again! The issue was related to the dependency, so we will close the issue as you have instructed.
Perfect; my review is now done.
@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
@ominusliticus, we're almost ready to go here! I'll send some editorial comments when I can; in the meantime, you can get going on the other pieces of info I need, summarized in the list above.
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1214/21-BA1287 is OK
- 10.1103/PhysRevC.106.044002 is OK
- 10.1088/1361-6471/abf1df is OK
- 10.1080/00401706.2023.2257765 is OK
- 10.1016/j.jmva.2019.104555 is OK
- 10.1214/17-BA1091 is OK
- 10.1175/MWR3441.1 is OK
- 10.3389/fnhum.2014.00457 is OK
- 10.1016/j.cpc.2021.108168 is OK
MISSING DOIs
- No DOI given, and none found for title: \textttloo: Efficient leave-one-out cross-validati...
- No DOI given, and none found for title: SAMBA: SAndbox for Mixing using Bayesian Analysis
- No DOI given, and none found for title: BANDFramework: An Open-Source Framework for Bayesi...
- No DOI given, and none found for title: Multifaceted study of ultrarelativistic heavy ion ...
- Entry without DOI or title found
- No DOI given, and none found for title: Taweret: A Python Package for Bayesian Model Mixin...
- No DOI given, and none found for title: Open Bayesian Trees Project
- No DOI given, and none found for title: BMA: Bayesian Model Averaging
INVALID DOIs
- doi.org/10.1111/insr.12243 is INVALID because of 'doi.org/' prefix
@ominusliticus please fix up those DOI issues when you can!
@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 will do. We will have a meeting tomorrow to try and finalize the release version!
Regarding the MISSING DOIs
misc
. Hopefully that will kill the DOI warningmisc
. Hopefully that will kill the DOI warningmisc
... misc
....misc
....I have pushed to commits
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1111/insr.12243 is OK
- 10.1214/21-BA1287 is OK
- 10.1103/PhysRevC.106.044002 is OK
- 10.1088/1361-6471/abf1df is OK
- 10.1080/00401706.2023.2257765 is OK
- 10.1016/j.jmva.2019.104555 is OK
- 10.1214/17-BA1091 is OK
- 10.1175/MWR3441.1 is OK
- 10.3389/fnhum.2014.00457 is OK
- 10.1016/j.cpc.2021.108168 is OK
MISSING DOIs
- No DOI given, and none found for title: \textttloo: Efficient leave-one-out cross-validati...
- No DOI given, and none found for title: SAMBA: SAndbox for Mixing using Bayesian Analysis
- No DOI given, and none found for title: BANDFramework: An Open-Source Framework for Bayesi...
- No DOI given, and none found for title: Multifaceted study of ultrarelativistic heavy ion ...
- No DOI given, and none found for title: Taweret: A Python Package for Bayesian Model Mixin...
- No DOI given, and none found for title: Open Bayesian Trees Project
- No DOI given, and none found for title: BMA: Bayesian Model Averaging
INVALID DOIs
- None
Some editorial comments on the manuscript:
References:
I will note that this paper is on the long side for JOSS. I don't think there's inherently a problem with that, but I certainly encourage you to make sure that the more pedagogical content is also incorporated into the package docs so it is easy for users to find and for package maintainers to keep updated! The paper will be somewhat of a static document, useful for citation of course, but not really able to be updated in any kind of incremental way.
Submitting author: !--author-handle-->@ominusliticus<!--end-author-handle-- (Kevin Ingles) Repository: https://github.com/bandframework/Taweret.git Branch with paper.md (empty if default branch): joss-submission Version: 1.0.2 Editor: !--editor-->@rkurchin<!--end-editor-- Reviewers: @julienmalard, @gchure Archive: 10.5281/zenodo.11254359
Status
Status badge code:
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
@julienmalard & @gchure, 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:
The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @rkurchin 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 @gchure
📝 Checklist for @julienmalard