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[REVIEW]: Melissa: coordinating large-scale ensemble runs for deep learning and sensitivity analyses #5291
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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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Review checklist for @acrlakshmanConflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
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Thank you @acrlakshman and @NoujoudNader for accepting the review :-) While we are available for any questions you may have (here or in our Melissa discourse https://melissa.discourse.group/ ), I’d like to help you test the code as efficiently as possible. If you do not have a supercomputer that you can install Melissa on, it is OK, Melissa can be run locally as well :-). https://melissa.gitlabpages.inria.fr/melissa/first-dl-study/ this tutorial is executed locally with MPI, and our CI runs the same example with only 3 cores required. On the other hand, if you have access to a supercomputer, we have templates for OAR and Slurm schedulers: https://gitlab.inria.fr/melissa/melissa/-/tree/develop/examples/heat-pde/heat-pde-dl Most of this will be repeated in the documentation but I just wanted to make sure you knew that a supercomputer is great (it’s the target usecase for sure) but not required for running/testing/debugging Melissa machinery. Thanks again and do not hesitate to reach out during your review! |
Review checklist for @NoujoudNaderConflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
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@diehlpk - How is this review coming along? The progress appears somewhat slow. |
Hi @acrlakshman, @NoujoudNader how is your review going? |
Just checked in with the reviewers. |
Hi, sorry for the delay. This slipped my calendar, shall get back to this over the weekend. |
@editorialbot generate pdf |
Hey, Thank you |
Hi @acrlakshman how is your review going? |
@robcaulk would it be possible to add instructions for Windows and Mac OS? Or mention that you are not supporting these? |
Hey @diehlpk , yes, I have created the PR for warning users against Windows and MacOS here. I am also working on making a pre built docker image available for these Windows/Mac users - I hope to have that completed in the near future. I will update here if we are successful distributing it properly and adding usage instructions :-). |
Hi @acrlakshman how is your review going? |
Sorry for the delay @diehlpk . I shall get back to this, over the remaining part of this week. |
Doing some final tests, faced some issues while running |
Hello, The docker solution is still not fully supported beyond our CI. But we do, however, fully support running an LXD container. We have a tutorial for installation and running LXD here: https://melissa.gitlabpages.inria.fr/melissa/virtual-cluster/ I hope it helps, Robert |
@acrlakshman could you please have a look? |
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👋 @openjournals/csism-eics, this paper is ready to be accepted and published. Check final proof 👉📄 Download article If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4318, then you can now move forward with accepting the submission by compiling again with the command |
Looks great to me. |
@robcaulk - I was going to make a PR to suggest some text changes in the paper, but I can't make a PR to the repo without getting an account from an INRIA member, it says. I think this goes against JOSS requirements, at least in spirit (see https://joss.readthedocs.io/en/latest/submitting.html). How would users make PRs/contributions to the code if they are not at INRIA? |
Since I can't make a PR, here is an updated paper.md with my suggested changes. |
Also, here's an updated paper.bib with some more minor changes (except github won't let me upload a .bib extension, so I've added an extra .md extension that you can remove... |
You are right that it is a frustrating hurdle for a user who wants to quickly submit a PR. However, we do encourage users to contact us for a free account with the following instructions here. We use this same approach for another software, SPAM, which we published on JOSS a few years back. Both projects, SPAM and Melissa are institutional softwares which means they benefit from living on the institutional gitlab servers (where the runners and storage are free and supporting the open-source nature of the project). In an effort to make it even easier to report issues, at Melissa we have the discourse which does not require any permissions to log in and report issues or discuss enhancements. I would be happy to make you an account on the INRIA gitlab if you would like to share your email (you can privately message me at if this is an avenue you wish to follow). Otherwise, I am happy to incorporate the changes you provided here directly into the JOSS branch. |
I guess that's meeting the strict requirements for JOSS... Please go ahead and check my changes, and either merge them or let me know what you disagree with. |
Thanks for those improvements @danielskatz - here is the MR: https://gitlab.inria.fr/melissa/melissa/-/merge_requests/130 I believe this means I should tag a new version JOSS_v3 and update the sources + DOI on zenodo, right? |
No, we don't even need the paper source in the repo, as we archive the PDF generated from it separately. Though you can if you want to. |
Great, I just merged in edits, so we can have the bot rebuild the PDF. |
@editorialbot recommend-accept |
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👋 @openjournals/csism-eics, this paper is ready to be accepted and published. Check final proof 👉📄 Download article If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4319, then you can now move forward with accepting the submission by compiling again with the command |
@robcaulk - please take a look at this and make sure you are ok with it - I will do the same |
looks good to me :) |
@editorialbot accept |
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Congratulations to @robcaulk (Robert Caulk) and co-authors on your JOSS publication!! And thanks to @acrlakshman and @NoujoudNader for reviewing, and to @diehlpk for editing. |
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Thanks @danielskatz @diehlpk @acrlakshman and @NoujoudNader for all your help on reviewing and publishing this paper! The badge looks pretty, we will add it to our README/doc :-) |
Submitting author: @robcaulk (Robert Caulk)
Repository: https://gitlab.inria.fr/melissa/melissa
Branch with paper.md (empty if default branch): JOSS-paper
Version: JOSS_v2
Editor: @diehlpk
Reviewers: @acrlakshman, @NoujoudNader
Archive: 10.5281/zenodo.8046630
Status
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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
@acrlakshman & @NoujoudNader, 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 @diehlpk 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 @acrlakshman
📝 Checklist for @NoujoudNader
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