Merge pull request #138 from Gilead-BioStats/fix-137

Workflow updates

.github/ISSUE_TEMPLATE/qc.md

@@ -1,11 +1,11 @@
 ---
-name: "Assessment QC Issue Template"
-about: "Conduct a full QC of an Assessment"
+name: "QC Issue Template"
+about: "Update QC Framework: Documentation, Qualification, Automation etc.  "
 title: "QC: (fill in)"
 
 ---
 ## QC Details
-<!--- What assessment(s) is/are being submitted for QC -->
+<!--- What Updates are being made. Link to PR/Issues as appropriate. -->
 
 ## Additional Comments
-<!--- Not required, anything else import pertaining to this QC -->
+<!--- Not required, anything else import pertaining to this issue -->

.github/PULL_REQUEST_TEMPLATE/release.md

@@ -1,17 +1,48 @@
----
-name: "Release Pull Request Template"
-about: "Create a new package release"
-title: "Release: (fill in)"
----
-## Release Description
-<!--- What is being released.  Please include any new assessments or  -->
-<!--- fixes that have been added since the previous release  -->
-
-## Release Checklist
+# Release Description
+<!--- Summarize what is being released.  -->
+
+## Assessments Updated
+<!--- List all new/updated assessments and provide a brief description of the updates --->
+<!--- Add a section for "Other updates" if there are updates that are not related to a specific assessment --->
+
+## Milestone
+<!--- Link to the milestone for the release. ---> 
+<!--- Make sure all relevant issues/PRs are included on the linked pages. --->
+Milestone: [v1.0.0](https://github.com/Gilead-BioStats/gsm/milestone/1)
+
+# Overall Risk Assessment 
+<!--- Complete the following Risk Assessment for this Release-->
+<!--- Risk should generally be the highest risk among the `fix` PRs included in the release--->
+Overall Risk: Low/Medium/High
+
+Notes: 
+<!--- provide a quick description of the overall risk assessment -->
+
+## Assessment 1 Risk
+<!--- Make a separate section accessing risk for each assessment and "other" update. -->
+<!--- If selected, fill out the QC checklist in a comment on this PR. Add one comment per Assessment --->
+Overall Risk: Low/Medium/High
+Mitigation Strategy:
+- [ ] Qualification Testing
+- [ ] Unit Testing
+- [ ] Code Review
+- [ ] QC Checklist
+- [ ] Automated Testing
+
+Notes: 
+<!--- provide a quick description of what was done and why the -->
+<!--- risk level and mitigation strategies were chosen -->
+
+# Release Checklist
 <!--- Fill out the following Release checklist -->
+
 - [ ] Version number has been updated
 - [ ] NEWS.md has been updated
 - [ ] README.md has been updated (if applicable)
 - [ ] Ensure all unit tests are passing
 - [ ] Ensure all qualification tests are passing and report has been rerun
+- [ ] All QC Checklists in this PR are complete
+- [ ] GitHub actions on this PR are all passing
+- [ ] Run `spell_check()`
+- [ ] Draft GitHub release created using automatic template and updated with additional details. Remember to click "release" after PR is merged.  
 

.github/pull_request_template.md

@@ -1,60 +1,23 @@
----
-name: "Pull Request Template"
-about: "Create a Pull Request"
-title: ""
----
-## Details
+
+## Overview
 <!--- What was done in the source branch -->
 <!--- (i.e. bugfixes, feature additions, etc.) -->
 
+## Test Notes/Sample Code
+<!--- Notes about testing or code to reproduce new functionality --->
 
 ## Risk Assessment
-<!--- Complete the following Risk Assessment for this Pull Request-->
-Risk: Low/Medium/High
-Mitigation Strategy:
-- [ ] Qualification Testing
-- [ ] Unit Testing
-- [ ] Code Review
-- [ ] QC
-- [ ] Automated Testing
-Notes: 
-<!--- provide a quick description of what was done and why the -->
+<!--- Complete a Risk Assessment for this Pull Request-->
+<!--- Provide a quick description of what was done and why the -->
 <!--- risk level and mitigation strategies were chosen -->
+<!--- Each mitigation strategy should be given a status before PR is merged --->
+Risk: Low/Medium/High
+Mitigation Strategy: 
+- Qualification Testing - [Included/Issue #X Filed]
+- Unit Testing - [Included/Issue #X Filed]
+- Code Review - [Included via PR review]
+- QC Checklist - [To be included with Release/Included in Comment]
+- Automated Testing - [Package Checks via GitHub Actions]
 
-## QC Checklist
-<!--- Fill out the following QC checklist as you complete the QC items -->
-- [ ] Documentation
-    - [ ] Function name captured in [Roxygen title](https://cran.r-project.org/web/packages/roxygen2/vignettes/rd.html#the-description-block)(e.g. "Adverse Event Assessment")
-    - [ ] Assessment Purpose captured in [Roxygen description](https://cran.r-project.org/web/packages/roxygen2/vignettes/rd.html#the-description-block) (e.g. "Evaluates site-level level Adverse Event Rates and flags rates that are abnormally high or low."
-    - [ ] Input Data Requirements are described in the the [Roxygen details](https://cran.r-project.org/web/packages/roxygen2/vignettes/rd.html#the-description-block) under a Data section (`#' @details # Data Requirements`).
-    - [ ] Parameters have detailed documentation using `@param`. Each parameter should include: parameter name, brief description, usage details, the default value (if any), is it required, list of valid options (if applicable)
-    - [ ] All external dependencies are captured. Use `@importFrom` when importing 3 or fewer functions, and use `@import` otherwise. 
-    - [ ] Output Data Standards are described under `@returns`
-    - [ ] At least 1 example is provided under `@examples`
-- [ ] Error Checking
-    - [ ]  Basic checks for all all parameters should be included using `stopifnot()` or similar logic. (e.g. `stopifnot("dfInput is not a dataframe"=is.data.frame(dfInput))`)
-    - [ ] Basic tests should be included confirming that `stopifnot()` parameter checks are working as expected. 
-    - [ ] Basic tests should be included that confirm that the input data has required columns (if any)
-    - [ ] Basic tests should be included that confirm that the output data has the expected columns
-- [ ] Basic QC
-    - [ ] Code is well commented and easy to read
-    - [ ] No file paths or other company-specific data is present. 
-    - [ ] Function calls from non-tidyverse dependencies are called via `::`
-    - [ ] devtools::check() passes with no errors/warnings/notes
-    - [ ] package docs up to date. devtools::document() doesn't change any files
-    - [ ] Uses tidyverse best practices for standard data manipulation (start discussion thread if unclear)
-    - [ ] All new dependencies add significant value (start discussion thread)
-    - [ ] All GitHub Actions run with no errors
-- [ ] Process
-    - [ ] PR with approved code review ready to merge to dev
-    - [ ] All relevant issues linked to PR
-- [ ] Unit tests
-    - Confirm that informative errors are thrown when data standard is not met. 
-    - Confirm that output specifications are met using standard test data. 
-    - Confirm that tests confirm that missing data is handled appropriately.
-- [ ] Qualification tests
-    - [ ] Specifications have been created and entered into valtools framework
-    - [ ] Test Cases have been created and entered into valtools framework
-    - [ ] Test Code has been created
-    - [ ] Qualification Report has been rerun and all test are passing
+Notes: