Update documentation & revision guidance #693

dhimmel · 2017-11-06T18:09:15Z

semantic linefeeds GitHub PR review interface

cgreene · 2017-11-06T18:15:09Z

README.md

-pull request, and pitch in. Authorship criteria remain the same.
+We are currently working on manuscript revisions in response to two external peer reviews.
+See [Issue #678](https://github.com/greenelab/deep-review/issues/678) to coordinate this process.
+When addressing reviewer comments, please also update [`response-to-reviewers.md`](content/response-to-reviewers.md) as appropriate.


Do you want to make this stronger? We'd like to not accept PRs on new topics unless they directly address review comments? Basically just "may" -> "will"

cgreene

couple suggested changes - largely LGTM, so just a few points

cgreene · 2017-11-06T18:16:10Z

content/response-to-reviewers.md

+
+> The authors summarized over 400 literature references purely by narratives. The authors provided synopsis for each important reference, but lacks synthesis of related work. It would be better to synthesize related work into a table and analyze their characteristics. 
+
+TODO


For the ones that just say todo, do you want to add a link to the connected issue?

dhimmel · 2017-11-06T18:17:20Z

Code Climate

@agitter and @cgreene have you found that code climate is doing anything useful for this repo? Is this something we should keep enabled but change the line length setting or disable entirely?

cgreene · 2017-11-06T18:20:13Z

Do you want to use this as an opportunity to disable line length checks via codeclimate?
https://github.com/markdownlint/markdownlint/blob/master/docs/RULES.md#md013---line-length
https://docs.codeclimate.com/v1.0/docs/disabling-individual-checks

cgreene · 2017-11-06T18:38:40Z

@dhimmel : now that we have travis, i am fine with disabling codeclimate - @agitter, do you agree?

cgreene · 2017-11-06T18:39:23Z

LGTM now 👍

Refs greenelab#624

This will help if quoted paragraphs are split when responding.

agitter

Looks good. Feel free to disable code climate if you'd like. I rely on Travis testing more.

agitter · 2017-11-06T18:56:25Z

README.md


-#### More about the manuscript.
+**Manubot updates:**


Should we also remind contributors to pull the latest version of master before making revisions? This was always the recommendation but will be even more important after #681.

agitter · 2017-11-06T18:56:49Z

README.md

+We are currently working on manuscript revisions in response to two external peer reviews.
+See [Issue #678](https://github.com/greenelab/deep-review/issues/678) to coordinate this process.
+When addressing reviewer comments, please also update [`response-to-reviewers.md`](content/response-to-reviewers.md) as appropriate.
+At the moment, efforts are concentrated on revisions: content unrelated to revisions may be deferred or not accepted.


I also would like to focus on merging existing pull requests, but this text is okay.

agitter · 2017-11-06T18:58:59Z

content/01.abstract.md

@@ -1,20 +1,11 @@
 ## Abstract {.page_break_before}

-Deep learning, which describes a class of machine learning algorithms, has


Should we try to merge some of the outstanding pull requests first? That may take too long, so I'm okay updating the line wrapping now if you think that is most efficient. We will need to provide help with merge conflicts for those pull requests though.

I only reflowed the abstract assuming that none of the PRs touch the abstract. Yes, we should focus on reviewing existing PRs. They likely all have conflicts now. Tag me when it's time to merge and I will handle the conflict resolution. Sooner the better.

@dhimmel ah, I see. I reviewed this hastily between meetings.

agitter · 2017-11-06T18:59:57Z

content/response-to-reviewers.md

@@ -0,0 +1,48 @@
+# Response to Reviewers


This is great 👍

This build is based on f12c1d7. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/deep-review/builds/298164970 https://travis-ci.org/greenelab/deep-review/jobs/298164971 [ci skip] The full commit message that triggered this build is copied below: Update documentation & revision guidance (#693) * Add response to reviewers template Refs #678 * Update CONTRIBUTING.md semantic linefeeds GitHub PR review interface * Update README for current project status * Link issues in response to reviewers * Review formatting * Code Climate: disable line_length for markdown * Remove trailing whitespace * Reflow abstract: one line per sentence Refs #624 * Reviews: one line per sentence This will help if quoted paragraphs are split when responding. * Fix Blank line inside blockquote * Concentration on reviews wording * Prioritize open PR review * README: keep forks synced

dhimmel added 3 commits November 6, 2017 11:30

Add response to reviewers template

06bc20b

Update CONTRIBUTING.md

3607fed

semantic linefeeds GitHub PR review interface

Update README for current project status

cfaa370

dhimmel force-pushed the revision-status branch from 617a785 to cfaa370 Compare November 6, 2017 18:12

dhimmel requested review from cgreene and agitter November 6, 2017 18:12

cgreene reviewed Nov 6, 2017

View reviewed changes

cgreene requested changes Nov 6, 2017

View reviewed changes

dhimmel added 2 commits November 6, 2017 13:26

Link issues in response to reviewers

446e356

Review formatting

3b506fe

cgreene approved these changes Nov 6, 2017

View reviewed changes

Code Climate: disable line_length for markdown

54770b5

dhimmel force-pushed the revision-status branch from 4f0b4b4 to 54770b5 Compare November 6, 2017 18:43

dhimmel added 4 commits November 6, 2017 13:47

Remove trailing whitespace

0be5d3c

Reflow abstract: one line per sentence

5d98b23

Refs greenelab#624

Reviews: one line per sentence

bca5113

This will help if quoted paragraphs are split when responding.

Fix Blank line inside blockquote

8ed9960

agitter approved these changes Nov 6, 2017

View reviewed changes

dhimmel added 3 commits November 6, 2017 14:03

Concentration on reviews wording

ec0cee9

Prioritize open PR review

7343c6d

README: keep forks synced

15d483d

dhimmel merged commit f12c1d7 into greenelab:master Nov 6, 2017

dhimmel deleted the revision-status branch November 6, 2017 19:46

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Update documentation & revision guidance #693

Update documentation & revision guidance #693

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dhimmel Nov 6, 2017 •

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agitter Nov 6, 2017

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		> The authors summarized over 400 literature references purely by narratives. The authors provided synopsis for each important reference, but lacks synthesis of related work. It would be better to synthesize related work into a table and analyze their characteristics.

		TODO

		@@ -1,20 +1,11 @@
		## Abstract {.page_break_before}

		Deep learning, which describes a class of machine learning algorithms, has

Update documentation & revision guidance #693

Update documentation & revision guidance #693

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Code Climate

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