Publish 3 new examples (and some other changes)

.github/ISSUE_TEMPLATE/other-issue.md

@@ -8,13 +8,13 @@ assignees: ''
 ### Background
 
 <!-- What was the background and context that lead to this problem? -->
-<!-- Links to github comments or related issues are also helpful --> 
+<!-- Links to github comments or related issues are also helpful -->
 
 ### Problem
 
 <!-- Why does the current state of things not work?-->
 
-#### What potential "gotchas" do we know of?
+### What potential "gotchas" do we know of?
 
 <!-- Are there any potentially tricky things or unknowns that the person who takes on this issue should know? -->
 
@@ -23,4 +23,11 @@ assignees: ''
 <!-- If applicable, what steps would you need to take to get started? -->
 
 <!-- What other info is needed to complete this task (in however long an interval after the issue is written) -->
+
 <!-- Do you have helpful references and resources we should consult? -->
+
+### Is there a particular timeframe for this issue?
+
+<!-- Is there a particular timeframe that a strategy decision should be made about this issue? --> 
+
+<!-- Is there a particular timeframe that this issue should be acted upon? -->

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,28 +1,33 @@
-## Purpose:
-What issue(s) does your PR address?
 
-## Strategy
-What was your strategy for this new or edited analysis?
+## Use the 'Preview' view to click on a link below to choose an appropriate PR template:
 
-## Concerns/Questions for reviewers:
-What things should reviewers look out for?
+For any stage of adding a new analysis example:
+<a href="?expand=1&template=new-analysis-pr.md"> New analysis PR </a>
 
-## Analysis Pull Request Check List (roughly in order):
+For publishing changes to Github pages:
+<a href="?expand=1&template=publish-pr.md"> Publishing PR </a>
 
-### Content checks
-* [ ] All `{{BLANKS}}` have been replaced with the correct content.
-* [ ] [Sources are cited](https://github.com/AlexsLemonade/refinebio-examples/blob/master/CONTRIBUTING.md#citing-sources-in-text)
-* [ ] Seed is set (if applicable)
+For either stage of a hotfix PR -- something that is straightforward and needs to be user-facing quickly:
+<a href="?expand=1&template=hotfix-pr.md"> Hotfix PR </a>
 
-### Formatting Checks
-* [ ] Removed any manual numbering of sections.
-* [ ] Removed any instances of chunk naming.
-* [ ] Comments and documentation are up to date.
-* [ ] All links have been checked and are properly formatted.
+## For any other types of PRs that don't fit any of the above categories, delete the previous section (including this line) and use the template below.
 
-### Add datasets to S3
-* [ ] Added [data and metadata files to S3](https://github.com/AlexsLemonade/refinebio-examples/blob/master/CONTRIBUTING.md#adding-datasets-to-the-S3-bucket).
+### Purpose
 
-### Docker/Snakemake rendering components
-* [ ] Added the `.html` [link to the navigation bar](https://github.com/AlexsLemonade/refinebio-examples/blob/master/CONTRIBUTING.md#add-new-analyses-to-the-navbar).
-* [ ] Any not yet added packages needed for this analysis have been added to the Dockerfile and it successfully builds.
+<!-- What was the background and context that lead to this problem? -->
+
+<!-- Link to Github comments or related issues that are helpful -->
+
+### Issue addressed
+
+<!-- What is the Github issue being addressed here -->
+
+#### Gotchas the reviewer should know about
+
+<!-- Are there things that came up during development that you found tricky or that the reviewer should be informed about -->
+
+## Remaining concerns and questions
+
+<!-- Are there any outstanding issues you have questions about -->
+
+<!-- Are there follow-up issues that should be filed? -- perhaps related issues but outside the scope of this PR -->

.github/PULL_REQUEST_TEMPLATE/hotfix-pr.md

@@ -0,0 +1,23 @@
+## Hotfix Purpose
+
+<!-- What is the urgent and straightforward problem that requires hotfix; why is a hotfix needed? -->
+
+## Pull Request Stage
+
+<!-- Select one of these and delete the other to let the reviewer know what stage this analysis example is at -->
+
+This is the **first PR**, to `master` -- it has not been reviewed at all.
+
+This is the **second PR**, to `staging` -- it was reviewed for the `master` branch on <!--PR Link--> and now should be reviewed mostly for correct merge conflict resolutions.
+
+## Explain the Fix
+
+<!-- What have you done to test that your hotfix works and addresses the problem at hand? -->
+
+<!-- Attach any relevant screenshots or html's that show the before and after -->
+
+## Comments/Questions for the Reviewer
+
+<!-- Is there anything you are unsure about with this fix that you could use the reviewer's help double checking? -->
+
+<!-- Are there follow-up issues that should be filed? -- perhaps related issues but not meant to be addressed through hotfix -->

.github/PULL_REQUEST_TEMPLATE/new-analysis-pr.md

@@ -0,0 +1,47 @@
+## Analysis Purpose
+
+<!-- What new analysis issue(s) does your PR address? -->
+
+## Pull Request Stage
+
+<!-- Select one of these and delete the other to let the reviewer know what stage this analysis example is at -->
+
+This is a **Draft PR** - needs review of big concepts and outline
+
+This is a **Refined PR** - needs review of details and polishing
+
+<!-- In the case of the Refined PR, link the draft PR here -->
+
+## Strategy
+
+<!-- What was your strategy for this new or edited analysis? -->
+
+<!-- Is there anything you found out in implementation that required you to shift strategies from what was originally discussed? -->
+
+## Concerns/Questions for reviewers:
+
+<!-- Are there any items you would like the reviewer to take an extra close look? -->
+
+<!-- Any results that don't quite make sense? -->
+
+<!-- Anywhere that you are unsure about wording or how to guide the user? -->
+
+## Analysis Pull Request Check List (roughly in order):
+
+### Content checks
+* [ ] All `{{BLANKS}}` have been replaced with the correct content.
+* [ ] [Sources are cited](https://github.com/AlexsLemonade/refinebio-examples/blob/master/CONTRIBUTING.md#citing-sources-in-text)
+* [ ] Seed is set (if applicable)
+
+### Formatting Checks
+* [ ] Removed any manual numbering of sections.
+* [ ] Removed any instances of chunk naming.
+* [ ] Comments and documentation are up to date.
+* [ ] All links have been checked and are properly formatted.
+
+### Add datasets to S3
+* [ ] Added [data and metadata files to S3](https://github.com/AlexsLemonade/refinebio-examples/blob/master/CONTRIBUTING.md#adding-datasets-to-the-S3-bucket).
+
+### Docker/Snakemake rendering components
+* [ ] Added the `.html` [link to the navigation bar](https://github.com/AlexsLemonade/refinebio-examples/blob/master/CONTRIBUTING.md#add-new-analyses-to-the-navbar).
+* [ ] Any not yet added packages needed for this analysis have been added to the Dockerfile and it successfully builds.

.github/PULL_REQUEST_TEMPLATE/publish-pr.md

@@ -0,0 +1,19 @@
+## Changes Being Published
+
+<!-- What overall changes are being included in this "Publish" PR and are they all ready to be published? -->
+
+## List of Commits/PR's Included
+
+<!-- List the staging commits/PR #'s that are included with a general and quick summary of what each does -- start by finishing the prompt below -->
+
+- PR# Added such and such
+
+## Link to html Preview
+
+For reviewing purposes, you can take a browse through htmlpreview: http://htmlpreview.github.io/?https://github.com/AlexsLemonade/refinebio-examples/gh-pages-stages/01-getting-started/getting-started.html
+
+## Publishing Checklist:
+
+- [ ] Does everything look good using html preview -- having taken a particularly close look at any new html files?
+
+- [ ] Have any new examples been added to the [refinebio-examples feedback survey](https://app.hubspot.com/forms/5187852/a50f293c-1ef4-4ee1-b7ee-c563afe2ad5c/performance)? Ideally, don't click publish until this PR is merged (changes are autosaved).

.gitignore

@@ -21,3 +21,6 @@ _site
 
 # If spell check is run, we don't really have a need for tracking this
 spell_check_results.tsv
+
+# If git commit history is saved to file, ignore it
+git.log