Closed whedon closed 4 years ago
Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @juliohm, @matbesancon it looks like you're currently assigned to review this paper :tada:.
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Attempting to check references...
Attempting PDF compilation. Reticulating splines etc...
OK DOIs
- 10.1287/mnsc.47.2.295.9834 is OK
- 10.1007/s10479-015-1994-2 is OK
- 10.1007/s101070000202 is OK
- 10.1137/080718401 is OK
- 10.1137/110825054 is OK
- 10.1007/s10589-015-9758-0 is OK
- 10.1137/15M1043376 is OK
- 10.1137/141000671 is OK
- 10.1016/j.ejor.2016.11.028 is OK
- https://doi.org/10.1016/0167-7152(92)90006-Q is OK
MISSING DOIs
- None
INVALID DOIs
- None
@whedon generate pdf
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
Attempting PDF compilation. Reticulating splines etc...
Hi all, just checking in to see if there's anything I can help you with.
@melissawm a bunch of issues were opened, some being "nice-to-have" improvements on the package, but some being fairly necessary to navigate through the package and understand what is going on, how to use it & for which classes of problems. My opinion is that there is a fair bit of polishing still to do but I'll let the author voice in
cc @kirui93
@matbesancon Thank you so much for mentioning that. I think I have implemented all the review comments that you had stated and that has enabled us to bump up the package. If you update to the new version, you will see that almost all the details are incorporated. What we are remaining with only is to change to use Plots.jl instead of PyPlot.jl which we will do it in some time to come as for now PyPlot.jl works well.
@matbesancon I also did polish the paper and I think it is much of straightforward and to the point now.
@matbesancon @juliohm I really believe that everything is now up to standard of the package we wanted to create. Your insightful review comments have been of great help.
@kirui93 please comment on each open issue to explain how you addressed them. There are many open issues still.
@juliohm I think most of the issues I have dealt with. So I will comment and close them if it is up to my side.
@matbesancon @juliohm I did comment on the issues created and closed most of them as I had already dealt with them.
@kirui93 you didn't address many issues raised in the software paper for example. You also didn't mention how you addressed each issue on GitHub before closing them.
Please report on each issue above how you addressed the review comments, otherwise it is difficult to approve the paper for publication in JOSS.
@kirui93 you didn't address many issues raised in the software paper for example. You also didn't mention how you addressed each issue on GitHub before closing them.
Please report on each issue above how you addressed the review comments, otherwise it is difficult to approve the paper for publication in JOSS.
General comments about the documentation - Initially, I had my docstrings placed in a wrong manner and with the help of @matbesancon I was able to rewrite the docstrings in the correct manner. And also @juliohm had mentioned briefly about the usage of "library" instead of "package" in most parts of the documentation, which I addressed accordingly.
@matbesancon indicated about the title and the project set up. He was suggesting to name the package from "ScenTrees.jl" to something like "ScenarioTrees.jl". Initially, we had a lot of suggestions for the name of the package but we decided to go with "ScenTrees.jl" as it is unique and also in a way describes to our goal.
On naming and conventions, @matbesancon indicated about the function Children{Vector{Int64}}
which looked like a constructor. As indicated, this function is an internal function of Tree and its main purpose is to reduce the number of times we are going to use the function in the stochastic approximation process. We access the children of the nodes each time in stochastic approximation iteration and hence saving the children as a vector at first with the "Chidren" function provides an easier and less expensive manner.
Another issue concerned incorporating AbstractTrees.jl. Though it was not a major issue, but as I had indicated, this package seems it is no longer maintained. And I couldn't find the documentation to detail its usage.
One of the most important issue that @matbesancon had stated was every function which performs a random sampling should take in parameter the Random Number Generator (which is usually a subtype of Random.AbstractRNG)
. I found this as a good first issue as as he had indicated making function runs deterministic
makes it really important. With this I used the package Random.jl
. As stated in their documentation, random number generation in Julia uses the Mersenne Twister library via MersenneTwister objects
and thus I employed this for every function that involves random number generation.
There was quite a mislead regarding the Wasserstein distance and we thank @matbesancon for noting this out. In our code, we had used the term "WassersteinDistance" which was inappropriate. I stated in the issue that this was supposed to be the multistage distance and is duly corrected in the code. There is also the parameter r
which is used for multistage distance and is also corrected well in all the codes.
The final issue that @juliohm opened was about improvements for the software paper. All the corrections he suggested are duly represented in the paper. The current version of the paper has all the corrections implemented.
Thank you so much @matbesancon and @juliohm for your patience as well as insightful comments about the software paper as well as the package in general.
@kirui93 can you please add these comments to the issues in your project repo instead? It is quite hard to follow any text here without context. Please understand that we have limited time to review.
I will try to read the issues again in the following weeks.
Thank you.
@whedon generate pdf
Attempting PDF compilation. Reticulating splines etc...
@juliohm @matbesancon Thank you so much for your patience. I have re-commented again on the important issues and re-opened them.
Some other issues are general comments that were just suggestions for improving the documentation as well as docstrings which I did implement immediately on statement.
@whedon generate pdf
Attempting PDF compilation. Reticulating splines etc...
Hello all, just checking in on this review, is there anything I can help you with?
still a few code-related issues we are discussing with the author on my side
Thank you for checking the status of the submission Melissa. The author didn't address all the issues raised. I can take a look again if any update is triggered.
On Fri, Jan 10, 2020, 09:29 Mathieu Besançon notifications@github.com wrote:
still a few code-related issues we are discussing with the author on my side
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Hello @juliohm, I addressed all the issues that you had raised concerning the software paper. All the other issues also that were raised concerning the package are also addressed. You had mentioned some times back that I should comment on all the issues raised on how I addressed them and I did. Please have a look on my comments on the way I addressed the issues.
Hello @matbesancon, I gave you a reply on what we were threading on last time. Please have a look on it.
Hi @melissawm, thank you for reaching out again
Thank you @kirui93 for the update. On my side you are ready to go, let's wait for @matbesancon 's comments, he may have further comments to improve the work.
@juliohm Thank you so much for your insightful comments as well as your time to review our package and the paper.
@whedon generate pdf
As an update, only https://github.com/kirui93/ScenTrees.jl/issues/15 remains on the documentation side, I'll do a last pass on the paper but it starts to all look good to me, @juliohm do you have something more?
Everything is good to go on my side @matbesancon , thanks for pinging.
@whedon generate pdf
@whedon check references
Reference check summary:
OK DOIs
- 10.1287/mnsc.47.2.295.9834 is OK
- 10.1007/s10479-015-1994-2 is OK
- 10.1007/s101070000202 is OK
- 10.1137/080718401 is OK
- 10.1137/110825054 is OK
- 10.1007/s10589-015-9758-0 is OK
- 10.1137/15M1043376 is OK
- 10.1137/141000671 is OK
- 10.1016/j.ejor.2016.11.028 is OK
MISSING DOIs
- None
INVALID DOIs
- https://doi.org/10.1016/0167-7152(92)90006-Q is INVALID because of 'https://doi.org/' prefix
@kirui93 can you check the DOI above, there is one that needs removing the https://doi.org prefix
Yeah. It was a slight mistake in the .bib file. I have removed it.
@whedon check references
Submitting author: @kirui93 (Kipngeno ) Repository: https://github.com/kirui93/ScenTrees.jl Version: v0.2.2 Editor: @melissawm Reviewer: @juliohm, @matbesancon Archive: 10.5281/zenodo.3672205
Status
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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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@juliohm & @matbesancon, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:
The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @melissawm know.
✨ Please try and complete your review in the next two weeks ✨
Review checklist for @juliohm
Conflict of interest
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Documentation
Software paper
Review checklist for @matbesancon
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper