Website updates (#350)

* updates

* removing docs folder

* Update _pkgdown.yml

* Update admiraldev-package.Rd

* url updates

* Update common.yml

* Update common.yml

.github/pull_request_template.md

@@ -1,16 +1,16 @@
-Thank you for your Pull Request! We have developed this task checklist from the [Development Process Guide](https://pharmaverse.github.io/admiraldev/devel/articles/development_process.html) to help with the final steps of the process. Completing the below tasks helps to ensure our reviewers can maximize their time on your code as well as making sure the admiral codebase remains robust and consistent.   
+Thank you for your Pull Request! We have developed this task checklist from the [Development Process Guide](https://pharmaverse.github.io/admiraldev/articles/development_process.html) to help with the final steps of the process. Completing the below tasks helps to ensure our reviewers can maximize their time on your code as well as making sure the admiral codebase remains robust and consistent.   
 
 Please check off each taskbox as an acknowledgment that you completed the task or check off that it is not relevant to your Pull Request. This checklist is part of the Github Action workflows and the Pull Request will not be merged into the `devel` branch until you have checked off each task.
 
 - [ ] Place Closes #<insert_issue_number> into the beginning of your Pull Request Title (Use Edit button in top-right if you need to update)
 - [ ] Code is formatted according to the [tidyverse style guide](https://style.tidyverse.org/). Run `styler::style_file()` to style R and Rmd files
-- [ ] Updated relevant unit tests or have written new unit tests, which should consider realistic data scenarios and edge cases, e.g. empty datasets, errors, boundary cases etc. - See [Unit Test Guide](https://pharmaverse.github.io/admiraldev/devel/articles/unit_test_guidance.html#tests-should-be-robust-to-cover-realistic-data-scenarios)
-- [ ] If you removed/replaced any function and/or function parameters, did you fully follow the [deprecation guidance](https://pharmaverse.github.io/admiraldev/devel/articles/programming_strategy.html#deprecation)?
-- [ ] Update to all relevant roxygen headers and examples, including keywords and families. Refer to the [categorization of functions](https://pharmaverse.github.io/admiraldev/devel/articles/programming_strategy.html#categorization-of-functions) to tag appropriate keyword/family.
+- [ ] Updated relevant unit tests or have written new unit tests, which should consider realistic data scenarios and edge cases, e.g. empty datasets, errors, boundary cases etc. - See [Unit Test Guide](https://pharmaverse.github.io/admiraldev/articles/unit_test_guidance.html#tests-should-be-robust-to-cover-realistic-data-scenarios)
+- [ ] If you removed/replaced any function and/or function parameters, did you fully follow the [deprecation guidance](https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html#deprecation)?
+- [ ] Update to all relevant roxygen headers and examples, including keywords and families. Refer to the [categorization of functions](https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html#categorization-of-functions) to tag appropriate keyword/family.
 - [ ] Run `devtools::document()` so all `.Rd` files in the `man` folder and the `NAMESPACE` file in the project root are updated appropriately
 - [ ] Address any updates needed for vignettes and/or templates
 - [ ] Update `NEWS.md` under the header `# admiral (development version)` if the changes pertain to a user-facing function (i.e. it has an `@export` tag) or documentation aimed at users (rather than developers)
-- [ ] Build admiral site `pkgdown::build_site()` and check that all affected examples are displayed correctly and that all new functions occur on the "[Reference](https://pharmaverse.github.io/admiraldev/devel/reference/index.html)" page. 
+- [ ] Build admiral site `pkgdown::build_site()` and check that all affected examples are displayed correctly and that all new functions occur on the "[Reference](https://pharmaverse.github.io/admiraldev/reference/index.html)" page. 
 - [ ] Address or fix all lintr warnings and errors - `lintr::lint_package()`
 - [ ] Run `R CMD check` locally and address all errors and warnings - `devtools::check()`
 - [ ] Link the issue in the Development Section on the right hand side.

.github/workflows/common.yml

@@ -35,7 +35,7 @@ concurrency:
 
 env:
   R_VERSION: "4.1"
-  
+
 jobs:
   get_r_version:
     name: Get R version

.gitignore

@@ -37,7 +37,6 @@ vignettes/*.pdf
 
 # Web Documentation files
 /docs/*
-!/docs/pkgdown.yml
 
 # R Environment Variables
 .Renviron

DESCRIPTION

@@ -24,7 +24,7 @@ Description: Utility functions to check data, variables and conditions for funct
  with maintaining documentation, testing and general upkeep of 'admiral' and 'admiral' extension packages.  
 License: Apache License (>= 2)
 BugReports: https://github.com/pharmaverse/admiraldev/issues
-URL: https://pharmaverse.github.io/admiraldev/main/, https://github.com/pharmaverse/admiraldev/
+URL: https://pharmaverse.github.io/admiraldev/, https://github.com/pharmaverse/admiraldev/
 Encoding: UTF-8
 Language: en-US
 LazyData: false

_pkgdown.yml

@@ -1,4 +1,4 @@
-url: https://pharmaverse.github.io/admiraldev
+url: https://pharmaverse.github.io/admiraldev/
 
 template:
   bootstrap: 5

vignettes/package_extensions.Rmd

@@ -56,8 +56,8 @@ _Note: The ordering numbers below are suggested but don't all need to strictly b
 
 1. Agree on a charter and expectations of each company, e.g. we usually ask for at least 3 developers with at least 25% capacity and a mix of R, GitHub and TA experience. Within the charter make sure the scope and timelines are clear. _It is important here not to try to boil the ocean. Focus first on the very common endpoints required as a foundation and then the package can build up from here via contributions from both the co-development companies and also the wider across-industry admiral community. If useful, the `{admiralonco}` charter could be shared as a guide._
 
-1. Each company should start to identify the required developer resources. Then each developer is required to complete the `{admiral`} [dummy issue for onboarding](https://github.com/pharmaverse/admiral/issues/1839), as well as reading up on the [admiraldev documentation](https://pharmaverse.github.io/admiraldev/devel/index.html), - especially the developer guides, which all need to be followed for package extensions.
-![Dummy issue for new developers](https://github.com/pharmaverse/admiraldev/raw/devel/vignettes/dummy_issue.png){width=100%}
+1. Each company should start to identify the required developer resources. Then each developer is required to complete the `{admiral`} [dummy issue for onboarding](https://github.com/pharmaverse/admiral/issues/1839), as well as reading up on the [admiraldev documentation](https://pharmaverse.github.io/admiraldev/index.html), - especially the developer guides, which all need to be followed for package extensions.
+![Dummy issue for new developers](https://github.com/pharmaverse/admiraldev/raw/vignettes/dummy_issue.png){width=100%}
 
 1. Optionally it can be useful to host a kick-off meeting to decide how the team will work, for which we recommend agile/scrum practices.
 
@@ -81,9 +81,9 @@ _Note: The ordering numbers below are suggested but don't all need to strictly b
 
 1. Assuming you work under agile/scrum, then create a product backlog, prioritize and make a sprint plan.
 
-1. The intention is always to re-use as much as possible from `{admiral}` core package. If you find anything additional needed for the package extension, you should first question whether it might be a common need for other TAs and if so consider instead raising an issue to `{admiral}` core. When designing new functions always try to stay aligned with the [Programming Strategy](https://pharmaverse.github.io/admiraldev/devel/articles/programming_strategy.html). 
+1. The intention is always to re-use as much as possible from `{admiral}` core package. If you find anything additional needed for the package extension, you should first question whether it might be a common need for other TAs and if so consider instead raising an issue to `{admiral}` core. When designing new functions always try to stay aligned with the [Programming Strategy](https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html). 
 
-1. Start development of your foundational first release 0.1.0. Follow a consistent [Development Process](https://pharmaverse.github.io/admiraldev/devel/articles/development_process.html) to `{admiral}`. 
+1. Start development of your foundational first release 0.1.0. Follow a consistent [Development Process](https://pharmaverse.github.io/admiraldev/articles/development_process.html) to `{admiral}`. 
 
 1. Line up testers from your companies and others and set expectations around when you believe a stable version would be available for user testing. You can use the admiral Slack community to raise interest to get involved.