[Re] Measures for investigating the contextual modulation of information transmission.

[sepehrmn]

Original article: Smyth, D., Phillips, W. A. and Kay, J.(1996) 'Measures for investigating the contextual modulation of information transmission', Network: Computation in Neural Systems, 7:2,307 — 316

PDF URL: https://github.com/sepehrmn/mahmoudian-2020-rescience/blob/master/article/Reproduction_of_Smyth_et_al__1996.pdf

Metadata URL: https://github.com/sepehrmn/mahmoudian-2020-rescience/blob/master/article/metadata.yaml

Code URL: https://github.com/sepehrmn/mahmoudian-2020-rescience/tree/master/code

Scientific domain: Computational Neuroscience

Programming language: Python

Suggested editor:

[rougier]

Do you have a new directory in the repo ?

[rougier]

Ok notification we for other papers so I think it's ok. I think the failed commit comes from other editors having commited while you were trying to push. Try a git fetch / git merge.

[oliviaguest]

Sorry — I tried pulling before I saw your message. Does any of this make sense for the question?

Do you have a new directory in the repo ?

(base) MBpro:articles olivia$ git pull
Warning: untrusted X11 forwarding setup failed: xauth key data not generated
remote: Enumerating objects: 15, done.
remote: Counting objects: 100% (15/15), done.
remote: Compressing objects: 100% (12/12), done.
remote: Total 14 (delta 4), reused 12 (delta 2), pack-reused 0
Unpacking objects: 100% (14/14), done.
From github.com:ReScience/articles
   39bf30e..fb3f574  master     -> origin/master
Updating 39bf30e..fb3f574
Fast-forward
 .../article.bib                                       |   2 +-
 .../article.pdf                                       | Bin
 .../article.yaml                                      |   2 +-
 10.5281_zenodo.3886447/article.bib                    |  22 +++++
 10.5281_zenodo.3886447/article.pdf                    | Bin 0 -> 198642 bytes
 10.5281_zenodo.3886447/article.yaml                   | 113 ++++++++++++++++++++++
 6 files changed, 137 insertions(+), 2 deletions(-)
 rename {0.5281_zenodo.3886412 => 10.5281_zenodo.3886412}/article.bib (95%)
 rename {0.5281_zenodo.3886412 => 10.5281_zenodo.3886412}/article.pdf (100%)
 rename {0.5281_zenodo.3886412 => 10.5281_zenodo.3886412}/article.yaml (99%)
 create mode 100644 10.5281_zenodo.3886447/article.bib
 create mode 100644 10.5281_zenodo.3886447/article.pdf
 create mode 100644 10.5281_zenodo.3886447/article.yaml
(base) MBpro:articles olivia$ git push 
Warning: untrusted X11 forwarding setup failed: xauth key data not generated
Everything up-to-date

[rougier]

I'm not sure about the X11 forxwarding part. Best would be to clone the repo into another place and check if they're the same (make lasy commit).

[khinsen]

1) It's me who published two papers this morning, so the three messages from Zenodo are OK. 2) The "X11 forwarding" warning comes from ssh configuration, so it's unrelated to the script. 3) To me the output from git pull looks good, but the freshly added article is not in the archive, so something did go wrong with git push.

@oliviaguest The error message AttributeError: 'Repository' object has no attribute 'swh' is due to article.py not being up to date. I have just pushed a fix (which I had made this morning for my own use but forgotten to push).

But... you can't just run publish.py again, because the first part of its work (publishing on Zenodo) is already done (and it looks correct). I'd say the best fix now is to create and push the directory for the new article by hand.

What I don't understand is why git flags your publish.py as modified. Did you change something?

[oliviaguest]

@khinsen:

What I don't understand is why git flags your publish.py as modified. Did you change something?

Yes, due to the "bug" (?) I described in https://github.com/ReScience/submissions/issues/29#issuecomment-641122552. I added a print statement. I didn't understand how to fix it and ran it with the --zenodo flag without getting the sandbox to work.

[oliviaguest]

@rougier I don't see a difference [using software tools not my eyes] between my local version and a fresh clone. Sorry. What can I do to fix this? I feel like this is the same bug I had last time (although it was not from my MBP, but from a Linux desktop).

[oliviaguest]

OK, I did this manually. I think it's OK! ☺️ https://github.com/ReScience/articles/tree/master/10.5281_zenodo.3885793

[sepehrmn]

Excellent. Many thanks everyone!

[oliviaguest]

@sepehrmn sorry about the teething problems — I seem to always find a way to screw up right before the end... 😆 BUT! Importantly your paper is published and I think it should appear on the website too soon. So... 🥳 congratulations! 👏

[rougier]

Did you add the bibtex entry on the website bibfile?

[oliviaguest]

No, what is needed to be done? Just copy-paste this one? https://github.com/ReScience/articles/blob/master/10.5281_zenodo.3885793/article.bib

[oliviaguest]

Are the keywords OK? Hmm... See: https://github.com/ReScience/rescience.github.io/commit/2f3b5b6a639f18cb13ed6a967c244b10999e4a20

[rougier]

Perfect. And yes, you only need to append it to the website bibfile (I'll regenerate the website)

[oliviaguest]

Great! Excited to see @sepehrmn's paper on the https://rescience.github.io site. 👏

[sepehrmn]

Excellent! Much appreciated @oliviaguest ! I guess the issue can be closed now!

[oliviaguest]

Let's make sure everything is OK first.

[sepehrmn]

Very well. I still can't see it on https://rescience.github.io/read/ .

[oliviaguest]

@rougier now sure what's up? Have you compiled and it's my manual editing of files that's screwy?

[oliviaguest]

@sepehrmn feel free to unsubscribe BTW. We will deal with this as it's a journal issue — congrats again and thank you for being so patient! 🥳

[rougier]

@oliviaguest I'm a bit lost now. What do I need to check exactly ?

[oliviaguest]

Ah, it's perfect! Sorry for some reason (maybe cache) I couldn't see it! I think everything is fine with this and we can close the issue.

[schmidDan]

@oliviaguest is it supposed to be published within the "Issue 2 (NeurIPS 2019 Reproducibility Challenge)" though?

[oliviaguest]

@schmidDan I am confused! I think I did something wrong again! @rougier? https://github.com/ReScience/ReScience/issues/48#issuecomment-640887146

[rougier]

Probably the issue number is wrong. I think it should be 3 and paper number should be #2. You can correct it directly on Zenodo and you'll need to update the published.bib on the rescience website (or I can do it, just tell me).

[oliviaguest]

@rougier looking on Zenodo, maybe I'm confused... but it looks right? I haven't changed anything.

[rougier]

Ok, it's only wrong in the bibtex for the website then. I'll correct it.

[oliviaguest]

Oh! Thank you, @rougier. 🌷

[rougier]

Done !

[oliviaguest]

Rejoice! Thanks! 🥳