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brettc / partitionfinder

PartitionFinder discovers optimal partitioning schemes for DNA sequences.
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Manual in md #120

Open alephreish opened 7 years ago

alephreish commented 7 years ago

Addresses https://github.com/brettc/partitionfinder/issues/113

brettc commented 7 years ago

This looks good, but I'd like to do a cleanup of the Markdown (long paras should be wrapped not broken + other stuff) and implement a build script for making a PDF. I think we should go ahead with pandoc as the default, as we can embed some font and other layout info into the header of the markdown (computer modern is icky). Perhaps we can publish the html somewhere too.

Once this is done we should ditch the docx, so we don't get out of sync.

Rob? Thoughts?

roblanf commented 7 years ago

This looks cool. Happy to leave this to you guys, since I'll be focussing on the v2 release for the next few weeks.

My suggestion is that you guys coordinate finishing this off, and just let me know when I'm to switch over from updating the manual in .docx to updating it in Markdown.

brettc commented 7 years ago

Okay -- will do. Try and refrain from editing the manual until I give the word. Or if you do -- let me know!

roblanf commented 7 years ago

just made a couple of small edits, but that should be it for now...

On 22 November 2016 at 16:37, Brett Calcott notifications@github.com wrote:

Okay -- will do. Try and refrain from editing the manual until I give the word. Or if you do -- let me know!

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/brettc/partitionfinder/pull/120#issuecomment-262152374, or mute the thread https://github.com/notifications/unsubscribe-auth/AA2pE_h0C4wmHWEiP-y9xZNnl6rQmml5ks5rAn-YgaJpZM4K3Zp7 .

Rob Lanfear Ecology, Evolution, and Genetics, The Australian National University, Canberra

www.robertlanfear.com

brettc commented 7 years ago

Andrey : how hard is it for you to regenerate this? (I'm assuming it was done using pandoc). Rob has made a few edits, but also markdown is much nicer in most editors when it is not hard-wrapped. You can use the pandoc option --wrap=none to do this I think. There are some odd remaining links in the code to, references to OLE objects...

alephreish commented 7 years ago

Sorry for the delay from my side, will do today.

alephreish commented 7 years ago

Hi everyone, please make a look at the current version. Besides, paragraph wrapping and some extra polishing I've added the recent PF2 paper - it seems to be the only addition in comparison to the docx version I originally took.

Concerning conversions to html and pdf: the main problem seems to be the toc. pandoc uses a different strategy to generate anchors for headers with markup. So, a pandoc MANUAL.md -o MANUAL.pdf -f markdown_github generates a nice pdf, but with some toc entries unclickable.

The github-like feel-and-look is obtained with e.g. grip (which uses github API): grip MANUAL.md --export MANUAL.html. The html version might then serve as the basis for a pdf version, but I have failed to find a converter which would be able preserve the toc (wkhtmltopdf and html-pdf do not support internal links, pandoc fails with an unrelated error [maybe repairable though]). gitprint produces a truncated pdf: https://gitprint.com/har-wradim/partitionfinder/blob/master/docs/MANUAL.md (see https://github.com/adamburmister/gitprint.com/issues/53).

brettc commented 7 years ago

Thanks for doing this -- I'll check this out (probably next week now).

brettc commented 7 years ago

Andrey : sorry again. Due to some issues with the k-means method, Rob has had to pull it from the 2.0 release. That meant he had to go and rapidly edit the manual (before anyone downloaded it). Can you (yet again) regenerate this (assuming it is easy to do). Don't worry about the Toc for now; I shall do that via LaTeX for the manual (in PDF).

roblanf commented 7 years ago

And I won't update the manual again for at least a couple of weeks - hopefully that will give us time to make the transition to the md manual, and I can do edits in there instead.

Rob

On 8 December 2016 at 19:59, Brett Calcott notifications@github.com wrote:

Andrey : sorry again. Due to some issues with the k-means method, Rob has had to pull it from the 2.0 release. That meant he had to go and rapidly edit the manual (before anyone downloaded it). Can you (yet again) regenerate this (assuming it is easy to do). Don't worry about the Toc for now; I shall do that via LaTeX for the manual (in PDF).

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/brettc/partitionfinder/pull/120#issuecomment-265688095, or mute the thread https://github.com/notifications/unsubscribe-auth/AA2pE7s8ON2TXVS_LHlG5zre5mO2a_nWks5rF8b-gaJpZM4K3Zp7 .

-- Rob Lanfear Ecology, Evolution, and Genetics, The Australian National University, Canberra

www.robertlanfear.com

alephreish commented 7 years ago

Hi guys, I'm a bit in a Zeitnot again, will have a look in a week or so.

alephreish commented 7 years ago

I've just synced the docx and the md versions. gitprint has been repaired, but it ignores any links.

brettc commented 7 years ago

Apologies -- I've dropped the ball on this. Both Rob and I are a bit swamped. It is not forgotten though. I'll chat with Rob soon about merging this in.