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datacarpentry / organization-genomics

Project Organization and Management for Genomics
https://datacarpentry.org/organization-genomics
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June 2019 Lesson Release checklist #108

Closed fmichonneau closed 5 years ago

fmichonneau commented 5 years ago

If your Maintainer team has decided not to participate in the June 2019 lesson release, please close this issue.

To have this lesson included in the 18 June 2019 release, please confirm that the following items are true:

When all checkboxes above are completed, this lesson will be added to the 18 June lesson release. Please leave a comment on carpentries/lesson-infrastructure#26 or contact Erin Becker with questions (ebecker@carpentries.org).

ErinBecker commented 5 years ago

Hi Maintainers! - Just confirming that you're still planning on including your lesson in the June 2019 release. We'll be putting out a blog post tomorrow inviting contributors to work on issues that have been tagged as part of the release milestone, so if there are specific issues you're looking for community help with, please add them to that milestone. It looks like this lesson is pretty clean and complete, so it may be that there isn't much need for community contributions. Please let me know if you have any questions!

hoytpr commented 5 years ago

Not going to go into minutia but a little wordsmithing is needed throughout e.g. “In order to be able to”. For the purpose of lesson release my assessment so far:

 * [ ]  Example code chunks run as expected

(Will have to check the .git/config code for fixing CR/LF tomorrow, but should note it’s not identical to the code in the linked examples. Also note that copy-paste resulted in doubly indented code for lines 2 & 3 which may or may not affect anything. Also note the lesson says Windows machines have export problems resulting in "data1, data2\r, 1, 2\r" which I have tested extensively and cannot reproduce in Windows, but the links point to problems with Macs exporting Excel files) ( Related to .csv files: C. Titus Brown recommended we include a link to: (https://donatstudios.com/Falsehoods-Programmers-Believe-About-CSVs))

 * [X]  Challenges / exercises run as expected

 * [ ]  Challenge / exercise solutions are correct

(00-intro/index.html has an exercise with no solution. Call this discussion or thought project? ) (I'll probably get some pushback on this but... considering our policies on inclusivity, is the "Example: You find one male, and one female of the same species. You enter this as 1M, 1F" perhaps too binary for our audience or am I being way too PC?)

 * [X]  Call out boxes (exercises, discussions, tips, etc) render correctly

 * [X]  A schedule appears on the lesson homepage (e.g. not “00:00”)

 * [x]  Each episode includes learning objectives

(Discussion page has no questions objectives times, or keypoints.)

 * [x]  Each episode includes questions

 * [x]  Each episode includes key points

 * [X]  Setup instructions are up-to-date, correct, clear, and complete

 * [X]  File structure is clean (e.g. delete deprecated files, insure filenames are consistent)

 * [X]  Some Instructor notes are provided

(But, formatting on Instructor notes is not exactly consistent. Needs bullets and Headers with same colors

 * [X]  Lesson links work as expected

(But, in 02, most links go directly to a source, rather than another lesson so OpenRefine should link to http://openrefine.org/download.html or be reworded.) (Also, the link to White, et al. 2013, goes to the preprint, not the final manuscript at Ecology and Evolution which is okay if the final version is pay-walled.)

ErinBecker commented 5 years ago

Thanks for your extensive work on this @hoytpr. A few responses to specific points:

hoytpr commented 5 years ago

Previous "Discussion" on page worked well with hidden "Solution", so left the format as is but changed the header to "Discusssion". (I've seen more than a few non-binary chimeric mice, but thanks for the "socially encoded" advice.)

ErinBecker commented 5 years ago

Hey Maintainers - just checking in to see if you're still planning on joining the release this month. We're asking that all lessons have completed the checklist by Tuesday, 4 June, Anywhere on Earth time in order to be included in the release. Please let me and @fmichonneau know if you have any questions or are running into any technical issues with preparing your lesson.

hoytpr commented 5 years ago

Yes. Will finish the code chunks analysis today. The Arizona Bug BBQ was fantastic. @fmichonneau did a great job getting through knitr. Can't wait until we have a Genomics Workshop at OKState! Wish we could have another BBQ here. The middle of the country needs this so much!

ErinBecker commented 5 years ago

@hoytpr - could you please confirm whether this lesson is ready for release? @fmichonneau and I are working on the releases this week.

hoytpr commented 5 years ago

Hi @ErinBecker
Set me up with an AWS and I'll go through it today completely.

ErinBecker commented 5 years ago

@hoytpr - I think your most recent message went to my email and not to this thread. From you email it looks like this lesson is complete and ready to go! So I'll check off those remaining items and we'll go ahead and include this lesson in the publication. Thanks @hoytpr!

ErinBecker commented 5 years ago

Awesome work @datacarpentry/organization-genomics-maintainers and everyone else who contributed! This is just a quick message confirming that this lesson will be included in the release that @fmichonneau and I are preparing this week. The release is scheduled to go through on the 18th and to be announced to the community on the 24th. Please let us know if you have any questions! And congratulations again!

fmichonneau commented 5 years ago

Lesson released! :tada: https://doi.org/10.5281/zenodo.3260317