[REVIEW]: Results of the ISMRM 2020 joint Reproducible Research & Quantitative MR study groups reproducibility challenge on phantom and human brain T1 mapping #14
Comments
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Hello humans, I'm @roboneuro, a robot that can help you with some common editorial tasks. For a list of things I can do to help you, just type: For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type: |
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Wordcount for |
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Failed to discover a valid open source license |
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Error in the pdf requires change: @mathieuboudreau can you please edit ORCID IDs so that they are not URLs? - name: Chenyang Wang
orcid: https://orcid.org/0000-0001-6798-0857
- name: Ziwei Zhao
orcid: https://orcid.org/0000-0003-0281-1141 |
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looks like there is a similar problem in the DOI of the reference @mathieuboudreau |
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@roboneuro generate book |
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I'm sorry human, I don't understand that. You can see what commands I support by typing:
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@roboneuro build book |
⚪ Book Build (Preview)Status: Assigned to task |
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@pbellec this will trigger the book build as a background task, but will not post status at regular intervals yet because I need to move generator function (that connects to the binderhub buildstream) to the context of the background task. Mostly note for myself and heads up for you. |
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ok, will I get a notification when the book finishes building, or do we need access to the servers to check the logs at this stage? |
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IIRC this one requires a different book build command as @mathieuboudreau noted before, not the common one due to formatting. I think the following may be related to that: Book build is not reaching the notebook execution step. Full log below. |
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@mathieuboudreau can you remind me the Jupyter Book build command this submission needs and explain what/why additional arguments do to generalize it for the API? |
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@agahkarakuzu this is the line I've been using: https://github.com/rrsg2020/paper/blob/7e799ee79ab846345919e5ad2e7cbd75fb654a1c/.github/workflows/main.yml#L33 I had compare this suggested way by Jupyter Book for single pages, vs simply indicating single-page in the config file. If I recall, the issue with setting it in the config file (and using the default build command) is that it added a table of content on one of the sidebars, which I didn't want. I could double check though! |
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@mathieuboudreau I know the data for this one is coming from https://github.com/rrsg2020/analysis and data is localized thereafter, but as we cache data and archive it, this dynamic approach will not work. For data dependencies, we need a {
"src": "10.5281/zenodo.####", #or any other repo2data compatible source
"dst": "../../data",
"projectName": "rrsg-2020"
}Then, for example, the data should be accessible at You can get this programatically: from repo2data.repo2data import Repo2Data
import os
data_req_path = os.path.join("..","..", "binder", "data_requirement.json")
repo2data = Repo2Data(data_req_path)
data_path = repo2data.install()[0]That's why repo2data should be included in the |
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For the other issue, I will need to enhance our book build endpoint to pass custom build arguments to the binderhub cluster. Thanks for providing the resources! |
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For the data, does it need to be the original resource (eg all the different OSF files), or could I just run the notebook as is right now, and package all the data that gets downloaded and used into a new osf repo, just to package this as a one-off so that you can also package it as a one off to save the state |
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Even a public drive link would work, as long as the data needed bu this notebook provided. If the structure and content of the zenodo doi'd repository matches this one, we can just download the whole thing. Otherwise, not using zenodo would be a good idea as we'll need to archive it. |
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@agahkarakuzu I've updated my repo to adhere to the data requirements, added a postBuild command to clone my analysis repo for the tools needed in my book, and removed the duplicate requirements file. Let me know if it looks good to continue with the submission review! |
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@mathieuboudreau thank you! Can you push a book_layout: traditional
single_page: index.ipynb |
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@roboneuro commands |
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Done, docker archive is now 10.5281/zenodo.8419811 |
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@roboneuro set 10.5281/zenodo.8419809 as data archive |
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Done, data archive is now 10.5281/zenodo.8419809 |
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@roboneuro set 10.5281/zenodo.8419805 as repository archive |
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Done, repository archive is now 10.5281/zenodo.8419805 |
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@roboneuro set 10.5281/zenodo.8419803 as book archive |
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Done, book archive is now 10.5281/zenodo.8419803 |
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@roboneuro recommend-accept |
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The paper's PDF and metadata files generation produced some warnings that could prevent the final paper from being published. Please fix them before the end of the review process. |
IDREFS attribute rid references an unknown ID "ref-Project" |
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@roboneuro recommend-accept |
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👋 @openjournals/executable-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 neurolibre/preprints#54, then you can now move forward with accepting the submission by compiling again with the command |
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@roboneuro production sync pdf |
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🌱♻️📄 Synced the summary PDF from the source, should be now available at https://preprint.neurolibre.org/10.55458/neurolibre.00014.pdf?no-cache |
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@roboneuro commands |
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Hello @agahkarakuzu, here are the things you can ask me to do: |
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@roboneuro accept |
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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: CITATION.cff
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🌰🌱🌺 THIS IS NOT A DRILL, YOU HAVE JUST PUBLISHED A NEUROLIBRE REPRODUCIBLE PREPRINT! 🌺🌸🍀 Here's what you must now do:
Any issues? Notify your editorial technical team... |
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@agahkarakuzu the data "hack" you asked me to do for this submission (i.e. host it all in a zip file in a google drive) is an issue for developing new submissions; repeatedly doing builds while developing a new submission causes Google to get pissed off at you and lock you out of the file. i.e. I'm encountering build errors while trying it in a new repo: https://github.com/rrsg2020/note When I go to the download link ( https://drive.google.com/uc?id=1ICGD4rCDYIawgX_QkzmW-MTTvZY8dMjA ), I get this page: and by clicking "Download anyways", the file downloads. I've tried regenerating the share public link and keep getting the error locally when I run gdown on my laptop: Any thoughts? We probably need a new solution for dealing with the archived data, as for my upcoming submission as I can't get gdown to consistently work with my repo2data for my build anymore =( |
Submitting author: @mathieuboudreau (Mathieu Boudreau)
Repository: https://github.com/rrsg2020/paper
Branch with paper.md (empty if default branch): main
Version: v1.0.0
Editor: @pbellec
Reviewers: @pbellec
Reproducible preprint: https://preprint.neurolibre.org/10.55458/neurolibre.00014
Repository archive: 10.5281/zenodo.8419805
Data archive: 10.5281/zenodo.8419809
Book archive: 10.5281/zenodo.8419803
Docker archive: 10.5281/zenodo.8419811
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