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Paper: pyFRET: A Python Library for Single Molecule Fluorescence Data Analysis (R. Murphy, S. Jackson, D. Klenerman) #34

Closed rebeccaroisin closed 9 years ago

rebeccaroisin commented 10 years ago

Paper for EuroScipy 2014 proceedings :)

NelleV commented 10 years ago

Hi Rebecca, Thank you for the submission. The review process will start on the 20th. Nelle

jni commented 10 years ago

Hi everyone! I intend to review this submission.

jni commented 10 years ago

@rebeccaroisin to start, could you hard wrap your text? Since git and GitHub operate on lines, tracking changes and comments over entire paragraphs can be difficult. I suggest you break on sentences. I know it can be ugly in a text editor but it'll render fine! =)

jni commented 10 years ago

Also, a few of the libraries you cite actually have associated papers — at the very least, SciPy and Matplotlib do. Please find and add what references you can find for software you used.

rebeccaroisin commented 10 years ago

Hi,

I've made the changes you need and pushed to my branch. Do I need to create a new pull request?

Cheers, Rebecca

On Sat, Aug 23, 2014 at 1:21 AM, Juan Nunez-Iglesias < notifications@github.com> wrote:

Also, a few of the libraries you cite actually have associated papers — at the very least, SciPy and Matplotlib do. Please find and add what references you can find for software you used.

— Reply to this email directly or view it on GitHub https://github.com/euroscipy/euroscipy_proceedings/pull/34#issuecomment-53136805 .

NelleV commented 10 years ago

Hello Rebecca, The pull request automatically updates itself, so no need to create a new one. Thanks, Nelle

khinsen commented 10 years ago

I will review this as well.

jni commented 10 years ago

@rebeccaroisin I've added some fairly minor comments/requests for clarification. Good stuff overall! Post a message here when you've addressed all the comments and I'll have another look. Thanks!

jni commented 10 years ago

@rebeccaroisin any interest in updating this? ;)

pdebuyl commented 10 years ago

Dear @khinsen and @jni , thank you for your reviews.

Dear @rebeccaroisin , please propose modifications addressing the comments made in the reviews.

Your updates should arrive for mid-october so that the reviewers can assess the update before the end of october.

rebeccaroisin commented 10 years ago

Sorry for the late modifications! Was very busy, then on vacation. Will address comments today!

Rebecca

On Fri, Sep 26, 2014 at 9:48 AM, Pierre de Buyl notifications@github.com wrote:

Dear @khinsen https://github.com/khinsen and @jni https://github.com/jni , thank you for your reviews.

Dear @rebeccaroisin https://github.com/rebeccaroisin , please propose modifications addressing the comments made in the reviews.

Your updates should arrive for mid-october so that the reviewers can assess the update before the end of october.

— Reply to this email directly or view it on GitHub https://github.com/euroscipy/euroscipy_proceedings/pull/34#issuecomment-56935293 .

pdebuyl commented 10 years ago

Hi @rebeccaroisin , is your update complete? Let me know if this is the case so that I can update the pdf file.

rebeccaroisin commented 10 years ago

Yes, this is complete now.

Rebecca

On Tue, Oct 7, 2014 at 7:22 AM, Pierre de Buyl notifications@github.com wrote:

Hi @rebeccaroisin https://github.com/rebeccaroisin , is your update complete? Let me know if this is the case so that I can update the pdf file.

— Reply to this email directly or view it on GitHub https://github.com/euroscipy/euroscipy_proceedings/pull/34#issuecomment-58142128 .

jni commented 10 years ago

@rebeccaroisin Thanks for the update! I hope you had a nice holiday. =)

It reads much better. I've pointed out a few stray typos. In addition, I would still prefer if the demo script would be made available with example data, but I understand that's not always possible. As it is, it reads a lot better with the parameter definitions, and even without the full data I feel more confident about replicating it. =)

Thanks again! Now if you could wrap up your excellent scikit-image PR, that would make for a great little end-of-summer package! =P

rebeccaroisin commented 10 years ago

OK, typos fixed.

The sample data would be a pretty big set of files, which is why I haven't included it.

Rebecca

On Tue, Oct 7, 2014 at 12:34 PM, Juan Nunez-Iglesias < notifications@github.com> wrote:

@rebeccaroisin https://github.com/rebeccaroisin Thanks for the update! I hope you had a nice holiday. =)

It reads much better. I've pointed out a few stray typos. In addition, I would still prefer if the demo script would be made available with example data, but I understand that's not always possible. As it is, it reads a lot better with the parameter definitions, and even without the full data I feel more confident about replicating it. =)

Thanks again! Now if you could wrap up your excellent scikit-image PR https://github.com/scikit-image/scikit-image/pull/1126, that would make for a great little end-of-summer package! =P

— Reply to this email directly or view it on GitHub https://github.com/euroscipy/euroscipy_proceedings/pull/34#issuecomment-58171012 .

jni commented 10 years ago

OK, typos fixed.

Great! Though it is hilarious that there was a typo in the commit message! =D

The sample data would be a pretty big set of files, which is why I haven't included it.

Understood. Thank you! =)

pdebuyl commented 10 years ago

@jni I understand that you are are ok with the current version. @khinsen a confirmation?

jni commented 10 years ago

@pdebuyl you understood correctly. =)

khinsen commented 10 years ago

@pdebuyl Yes, this version looks OK.

pdebuyl commented 10 years ago

Thanks @jni and @khinsen

@rebeccaroisin your paper is ready to be merged. There is no further action needed from your part, I will perform a general layout check on all papers before proceeding though.

Pierre

pdebuyl commented 9 years ago

Hi Rebecca,

The filesize of your paper is rather large, at 3 MB for the compiled pdf. Is it possible rework the figures for a lighter result? The main culprit is 6bp_example.pdf that weighs 2.6 MB by itself. I say this mostly for the convenience of readers as large file are sometimes annoying (data transfer and printing issues).

The resulting file should preferably still be in pdf (not png) to preserve vector rendering of the fonts.

pdebuyl commented 9 years ago

Thanks for the update. I don't receive notifications for updates on pull requests automatically so only noticed it now. I'll check this today.

pdebuyl commented 9 years ago

Hi Rebecca,

The bottom right part of the figure does not display correctly with the current file.

pdebuyl commented 9 years ago

Nevermind, I could re-compress directly the original 6bp_example.pdf from 2.6MB to about 0.6MB by using pdf2ps followed by ps2pdf. I'll put the file in the repository upon merging.

rebeccaroisin commented 9 years ago

Great -- thank you!

Rebecca

On Fri, Dec 5, 2014 at 11:30 AM, Pierre de Buyl notifications@github.com wrote:

Nevermind, I could re-compress directly the original 6bp_example.pdf from 2.6MB to about 0.6MB by using pdf2ps followed by ps2pdf. I'll put the file in the repository upon merging.

— Reply to this email directly or view it on GitHub https://github.com/euroscipy/euroscipy_proceedings/pull/34#issuecomment-65778315 .