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Origin/literate #67

Closed LSheneman closed 10 years ago

LSheneman commented 10 years ago

The complete literate code on that has been implemented and tested on all parts of the protocol.

LSheneman commented 10 years ago

After the header line insert:

.. shell:: start

at the end put: .. shell:: stop

For a block of code that needs to be tested format it like

+and also some mass combining : +::

All other blocks: Like normal::

camillescott commented 10 years ago

Very nice! Quite simple and elegant in the end, I can see how my idea of using includes would get very messy.

Mind if I comment on the diffs?

On Wed, Feb 26, 2014 at 7:41 PM, LSheneman notifications@github.com wrote:

After the header line insert:

.. shell:: start

at the end put: .. shell:: stop

For a block of code that needs to be tested format it like

+and also some mass combining : +::

All other blocks: Like normal::

Reply to this email directly or view it on GitHubhttps://github.com/ged-lab/khmer-protocols/pull/67#issuecomment-36197149 .

Camille Scott

Department of Computer Science and Engineering Lab for Genomics, Evolution, and Development Michigan State University

camille.scott.w@gmail.com

LSheneman commented 10 years ago

Go for it.

I think Titus is going to give them a try soon too.

From: Camille Scott notifications@github.com Reply-To: ged-lab/khmer-protocols <reply+i-27716875-aba86cb0d2912b873dddc96650d02cce68601894-4492432@reply.git hub.com> Date: Wednesday, February 26, 2014 at 7:48 PM To: ged-lab/khmer-protocols khmer-protocols@noreply.github.com Cc: Leigh Sheneman leighs@msu.edu Subject: Re: [khmer-protocols] Origin/literate (#67)

Very nice! Quite simple and elegant in the end, I can see how my idea of using includes would get very messy.

Mind if I comment on the diffs?

On Wed, Feb 26, 2014 at 7:41 PM, LSheneman notifications@github.com wrote:

After the header line insert:

.. shell:: start

at the end put: .. shell:: stop

For a block of code that needs to be tested format it like

+and also some mass combining : +::

All other blocks: Like normal::

Reply to this email directly or view it on GitHubhttps://github.com/ged-lab/khmer-protocols/pull/67#issuecomment-36197149 .

Camille Scott

Department of Computer Science and Engineering Lab for Genomics, Evolution, and Development Michigan State University

camille.scott.w@gmail.com

‹ Reply to this email directly or view it on GitHub https://github.com/ged-lab/khmer-protocols/pull/67#issuecomment-36197590 .

LSheneman commented 10 years ago

Hey Camille let me merge go ahead and merge this to the GED, it is just to take it from my account to a branch on master. Actually thought I had my bad

camillescott commented 10 years ago

Ah oops! Didn't notice.

LSheneman commented 10 years ago

Totally my fault, feel free to correct the "dummy errors". Big stuff lets talk about though.. cool?

camillescott commented 10 years ago

Don't sweat it. I didn't see anything major; it all looks pretty straight forward and well done. I notice you made some nice cosmetic changes to the code/literal blocks as well!

LSheneman commented 10 years ago

Thank you!