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biocore / American-Gut

American Gut open-access data and IPython notebooks
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Preprocessing #120

Closed jwdebelius closed 9 years ago

jwdebelius commented 9 years ago

The preprocessing notebook for the American Gut data. A version of the notebook text can be found on google docs.

wasade commented 9 years ago

Done with review. It looks like this won't run as the necessary americangut modules are not there. Are they part of a different PR that should be reviewed and merged prior to this one?

josenavas commented 9 years ago

Can this notebook be renderer in some place? It will make the review way faster.

jwdebelius commented 9 years ago

@wasade: Just added geography_lib.py. Sorry it's been such a nightmare with the different pull requests. This does rely on diversity_analysis.py being merged from elsewhere.

@josenavas: Text can be found in the google doc linked in the description. There's an NBviewer version here.

wasade commented 9 years ago

Thanks, what PR specifically? On Dec 3, 2014 1:09 PM, "J W Debelius" notifications@github.com wrote:

@wasade https://github.com/wasade: Just added geography_lib.py. Sorry it's been such a nightmare with the different pull requests. This does rely on diversity_analysis.py being merged from elsewhere.

@josenavas https://github.com/josenavas: Text can be found in the google doc linked in the description. There's an NBviewer version here http://nbviewer.ipython.org/github/JWDebelius/American-Gut/blob/Preprocessing/ipynb/Preprocessing.ipynb .

— Reply to this email directly or view it on GitHub https://github.com/biocore/American-Gut/pull/120#issuecomment-65480472.

jwdebelius commented 9 years ago

I think the current version is in #121. But, I was testing the figures and found a bug with the way the significance bars are rendering, and I want to get that right before I push to that branch, again.

josenavas commented 9 years ago

I did not finished the review; but I need to work on other stuff. I'd recommend to address the comments that has been already done (@wasade's and mine) and I will go again over it. I also recommend that you read carefully the text and fix any typos and/or sentences that are not completely correct. It will increase the efficiency of the reviews. I've not gone over your other PR but probably you should do the same, in interest of developers time.

Thanks!

jwdebelius commented 9 years ago

As with every other notebook pull request I have submitted and will submit, final text is in the google doc linked at the top. There is no possible way for me to do copy editing in the notebook and have it come out correct, and it's a pain to make the changes both places and preserve formatting. Once the code is correct here and the text is correct there, the two can be combined.

josenavas commented 9 years ago

Ok. But why to keep things in two different places? It will be easier to review if everything is here... I will go over the text and the code tomorrow then...

wasade commented 9 years ago

I don't fully understand the issue with copy editing in the notebook. We're able to do it in the scikit-bio-cookbook repo, for instance.

I'd like to reiterate @josenavas point though that it is important to try and resolve typos and grammar before issuing a PR. This is analogous to submitting a manuscript: typos can suggest the document was submitted prematurely and have a negative impact on the reviewer due to the time they require to address.