Closed jasmainak closed 4 years ago
Merging #313 into master will not change coverage. The diff coverage is
n/a
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Coverage 75.66% 75.66%
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Branches 149 149
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Partials 37 37
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Thanks @jasmainak ! Looks good to me
wow this is great! Syracuse University is good.. but how do I compile the paper? #noob
That's a fantastic question @daniel-acuna . Here's how:
paper
Compile!
I'll update this in the first comment so others can see it too.
I am getting "Your paper failed to compile with the following errors:
Can't find any papers to compile. Make sure there's a file named paper.md in your repository."
On Mon, Nov 4, 2019 at 12:09 AM Mainak Jas notifications@github.com wrote:
That's a fantastic question @daniel-acuna https://github.com/daniel-acuna . Here's how:
- go to: https://whedon.theoj.org/
- in the paper repository address, enter: https://github.com/jasmainak/pyglmnet/
- in the custom branch, enter: paper
Compile!
I'll update this in the first comment so others can see it too.
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-- I love those that desire the impossible - Goethe.
Konrad Kording @kordinglab, UPenn, Richards 404b cell:773 - liberat (5423728) office:(215) 898-5826 kordinglab.com
@koerding You have to select the paper
branch. Works like a charm
ah yes thanks. it does work great. Should the paper contain more information on potential usage scenarios or is it good like this?
On Mon, Nov 4, 2019 at 8:43 AM Daniel E. Acuna notifications@github.com wrote:
@koerding https://github.com/koerding You have to select the paper branch. Works like a charm
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Konrad Kording @kordinglab, UPenn, Richards 404b cell:773 - liberat (5423728) office:(215) 898-5826 kordinglab.com
Thanks everyone especially jasmainak and pavanramkumar for spearheading this great project. I confirm my name and affiliation. I added my orcid as a code suggestion (0000-0003-1762-3450). Reviewing the manuscript now.
I totally agree with @koerding. I think it would be great to add usage
or example usage
section similar to examples in README
and documentation. Additionally, we can provide examples in the summary section on use cases where distribution and regularization are not provided in statsmodels
or scikit-learn
.
I made a few stylistic suggestions in this PR: https://github.com/jasmainak/pyglmnet/pull/1
I like the current usage example with glm.fit and glm.predict. I think it might be nice to add a few lines that demonstrate the different noise models (poisson, binomial, etc) and different regularization terms (L1, L2, etc) since those are the main features that are emphasized in the text.
hey. I can' seem to edit it. I forked pyglmnet but the paper does not seem to be there. Can I provide feedback in a google doc or by email? sorry, my github skills are not-so-elite
On Mon, Nov 4, 2019 at 10:21 AM Titipat Achakulvisut < notifications@github.com> wrote:
I totally agree with @koerding https://github.com/koerding. I think it would be great to add usage or example usage section similar to examples in README and documentation. Additionally, we can provide examples in the summary section on use cases where distribution and regularization are not provided in statsmodels or scikit-learn.
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-- I love those that desire the impossible - Goethe.
Konrad Kording @kordinglab, UPenn, Richards 404b cell:773 - liberat (5423728) office:(215) 898-5826 kordinglab.com
@koerding if you go here, you should be able to edit the paper and submit a pull request. Can you give it a try? If it doesn't work, we can do this over email or google doc
ah that is great. Thanks! Sorry.
On Mon, Nov 4, 2019 at 10:57 AM Mainak Jas notifications@github.com wrote:
@koerding https://github.com/koerding if you go here https://github.com/jasmainak/pyglmnet/edit/paper/paper/paper.md, you should be able to edit the paper and submit a pull request. Can you give it a try? If it doesn't work, we can do this over email or google doc
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-- I love those that desire the impossible - Goethe.
Konrad Kording @kordinglab, UPenn, Richards 404b cell:773 - liberat (5423728) office:(215) 898-5826 kordinglab.com
When I try to compile the paper on Whedon, I get the error message:
Your paper failed to compile with the following errors:
Author (Peter Foley) is missing affiliation
Please try again. Looks like some of the "code suggestions" were in the incorrect format which broke the compilation. Sorry about that.
Hey @koerding we'll email you a markdown draft to make it easier!
@titipata @koerding thanks for your comments: happy to receive edits / suggestions!
Have a look here at paper content expectations here: https://joss.readthedocs.io/en/latest/submitting.html
Unlike typical journal papers, JOSS is meant to be a very thin wrapper around the documentation / examples of the OSS project: the latter is peer reviewed and expected to describe use cases and provide examples. Our example gallery currently provides one application with matrix reg (Tikhonov) and one with group lasso: both of which expand the scope of status quo glm libraries significantly
Hi! Sorry just saw this. Is there something you need me to submit?
hi @themantalope can you read the first comment and confirm your authorship by checking the affiliation and adding the orcid? Thanks.
I will be completely out until next thursday. Sorry guys. Huge grant deadlin
On Fri, Nov 8, 2019 at 9:28 AM Mainak Jas notifications@github.com wrote:
hi @themantalope https://github.com/themantalope can you read the first comment https://github.com/glm-tools/pyglmnet/pull/313#issue-319008762 and confirm your authorship by checking the affiliation and adding the orcid? Thanks.
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-- I love those that desire the impossible - Goethe.
Konrad Kording @kordinglab, UPenn, Richards 404b cell:773 - liberat (5423728) office:(215) 898-5826 kordinglab.com
no worries, we are expecting you to make at least two pull requests since you are taking extra time now ;)
I have done my orcid ;) so just one?
On Fri, Nov 8, 2019 at 4:08 PM Mainak Jas notifications@github.com wrote:
no worries, we are expecting you to make at least two pull requests since you are taking extra time now ;)
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@AnchorBlues @BeibinLi @DreHar @the872 @themantalope @marquesVF @evadyer @tommyod @ravigarg27 @timshell
I have not heard from you in this thread. We do need you to confirm your name and affiliation if you want to be included as an author.
@jasmainak I am in a conference with one of the assoc. editors in chief of JOSS. perhaps there is some way of receiving feedback? maybe email me to deacuna@syr.edu
Thanks @daniel-acuna for offering to do this. The JOSS review process seems super straightforward and transparent: one of the reasons why we chose the venue. @jasmainak will be in touch!
Yes, my name and affiliation is correct as written. Thanks!
On Sat, Nov 9, 2019 at 2:05 PM Pavan Ramkumar notifications@github.com wrote:
Thanks @daniel-acuna https://github.com/daniel-acuna for offering to do this. The JOSS review process seems super straightforward and transparent: one of the reasons why we chose the venue. @jasmainak https://github.com/jasmainak will be in touch!
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Name and affiliation are good for me. Thanks for including me! Not sure why I'm not showing up in the contributor graph. Perhaps the e-mail I used for that was my undergraduate university e-mail (which I don't have access to anymore)
@timshell okay then we have to do this by updating the .mailmap. Are you up to make a PR to fix it? If not, just tell me your new email address and I'll do it.
Thanks! I would like to be part of this. My name and affiliation look all right.
Verifying that my name and affiliation is correct as written. Thanks!
Thank you for including me. My name and affiliation are right.
Thanks for including me for the paper.
I verified that my name and affiliation are correct.
Thanks for the update, will be happy to represent the Loyola University Chicago commits.
@the872 thanks! any idea how we can reach out to @marquesVF -- pending confirmation needed from him
Hi guys!
Thanks for reaching me. That's correct. I was at Loyola.
I would only suggest to use my full name as Vinicius de F. Marques
Thanks and great work!
@pavanramkumar
closes #297
Hi everyone,
@pavanramkumar and I created a first draft of our paper for submission to JOSS. If you want to be listed as an author, please read the draft and leave comments. More importantly:
pyglmnet
The guidelines for JOSS submission are here.
Compiling the paper
If you want to compile the paper
Compile!
Tagging all contributors (check mark if we got a response)