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SimonGoring / neotoma_paper

Repository for the neotoma package paper.
MIT License
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remove old, non-conformant-named file #36

Closed gavinsimpson closed 10 years ago

gavinsimpson commented 10 years ago

For consistency, Makefile can be used to render Word, PDF, or Markdown format files from the Neotoma_paper.Rmd sources. It named the outputs Neotoma_paper.foo where foof is the format extension. This PR deletes the now obsolete neomtoma_paper.docx file.

SimonGoring commented 10 years ago

My only concern is that we retain the "submitted" file, with pagination and figures at the end as in the submitted version. I have a docx and PDF like this. Would it be best to put those in a folder called "Submitted"? On Oct 9, 2014 10:08 PM, "Gavin Simpson" notifications@github.com wrote:

For consistency, Makefile can be used to render Word, PDF, or Markdown format files from the Neotoma_paper.Rmd sources. It named the outputs Neotoma_paper.foo where foof is the format extension. This PR deletes the

now obsolete neomtoma_paper.docx file.

You can merge this Pull Request by running

git pull https://github.com/gavinsimpson/neotoma_paper clean-up

Or view, comment on, or merge it at:

https://github.com/SimonGoring/neotoma_paper/pull/36 Commit Summary

  • remove old, non-conformant-named file

File Changes

Patch Links:

— Reply to this email directly or view it on GitHub https://github.com/SimonGoring/neotoma_paper/pull/36.

gavinsimpson commented 10 years ago

I don't think I've changed the files at all? I don't think you updated the PDF in the repo when you submitted so it may well be different now. In terms of recording things, that's why I've been mentioning tagging the repo. If you want to retain the docx file that I delete here, go to https://github.com/SimonGoring/neotoma_paper/releases and create a new tag/release called "submitted-version". Then you can merge this PR.

We really ought to have cleaned this up before we submitted if we wanted a version of record. But lets not worry about that now. Is Neotoma_paper.docx substantially different to the one you submitted? I'm not sure how if it is - I've only modified the Rmd to look in consistent places for figures and deleted stuff we don't use. Other than that the changes were to snapshot the data used in the submitted version.

SimonGoring commented 10 years ago

Sorry, can't do this tonight, I'll do it tomorrow morning, unless @karthik can in the meantime. @andydawson do you have access to this repo?

gavinsimpson commented 10 years ago

I think we'll need @karthik to comment now; he has pushed a new version of neotoma_paper.docx in 3c16ef0 (which is why this PR won't merge automagically any longer) so we just need to get our ducks in a row between ourselves on this one.

To be clear; the submitted version should be no different to Neomtoma_paper.docx, but should is a potentially large kettle of fish :-)

karthik commented 10 years ago

Sorry, I deleted that offending commit. This request should automatically merge again (i see that it can). But I'll let @SimonGoring do it.

gavinsimpson commented 10 years ago

Cheers @karthik and no rush @SimonGoring. I think I have left two minor changes to the .Rmd which force render() to use a single common fig.path for all formats and a single cache.path which will round out the clean-up. In addition, the figure-generating chunks were renamed (in the .Rmd of the submitted version) and we should commit the renamed figures and delete the old ones. We can tag the repo before or after we merge those (?) and @karthik wants to pakrat the repo so we have a snapshot of package versions used.

I'm happy to deal with the figures-renaming and the changes to fig.path and cache.path but agnostic as to whether I do this before we tag/pakrat or after.