Merge pull request #383 from cmu-delphi/lcb/update-actions-and-pkgdown

Update pkgdown actions based on branch reorganization

Author: dshemetov

.github/workflows/R-CMD-check.yaml

@@ -4,9 +4,9 @@
 # Created with usethis + edited to run on PRs to dev, use API key.
 on:
   push:
-    branches: [main, master]
+    branches: [main, dev]
   pull_request:
-    branches: [main, master, dev]
+    branches: [main, dev]
 
 name: R-CMD-check
 

.github/workflows/pkgdown.yaml

@@ -4,9 +4,9 @@
 # Created with usethis + edited to run on PRs to dev, use API key.
 on:
   push:
-    branches: [main, master]
+    branches: [main, dev]
   pull_request:
-    branches: [main, master, dev]
+    branches: [main, dev]
   release:
     types: [published]
   workflow_dispatch:

DEVELOPMENT.md

@@ -0,0 +1,59 @@
+## Setting up the development environment
+
+```r
+install.packages(c('devtools', 'pkgdown', 'styler', 'lintr')) # install dev dependencies
+devtools::install_deps(dependencies = TRUE) # install package dependencies
+devtools::document() # generate package meta data and man files
+devtools::build() # build package
+```
+
+## Validating the package
+
+```r
+styler::style_pkg() # format code
+lintr::lint_package() # lint code
+
+devtools::test() # test package
+devtools::check() # check package for errors
+```
+
+## Developing the documentation site
+
+The [documentation site](https://cmu-delphi.github.io/epidatr/) is built off of the `main` branch. The `dev` version of the site is available at https://cmu-delphi.github.io/epidatr/dev.
+
+The documentation site can be previewed locally by running in R
+
+```r
+pkgdown::build_site(preview=TRUE)
+```
+
+The `main` version is available at `file:///<local path>/epidatr/docs/index.html` and `dev` at `file:///<local path>/epidatr/docs/dev/index.html`.
+
+You can also build the docs manually and launch the site with python. From the terminal, this looks like
+```bash
+R -e 'devtools::document()'
+python -m http.server -d docs
+```
+
+For `pkgdown` to correctly generate both public (`main`) and `dev` documentation sites, the package version in `DESCRIPTION` on `dev` must have four components, and be of the format `x.x.x.9000`. The package version on `main` must be in the format `x.x.x`.
+
+The documentation website is updated on push or pull request to the `main` and `dev` branches.
+
+## Release process
+
+### Manual
+
+TBD
+
+### Automated (currently unavailable)
+
+The release consists of multiple steps which can be all done via the GitHub website:
+
+1. Go to [create_release GitHub Action](https://github.com/cmu-delphi/epidatr/actions/workflows/create_release.yml) and click the `Run workflow` button. Enter the next version number or one of the magic keywords (patch, minor, major) and hit the green `Run workflow` button.
+2. The action will prepare a new release and will end up with a new [Pull Request](https://github.com/cmu-delphi/epidatr/pulls)
+3. Let the code owner review the PR and its changes and let the CI check whether everything builds successfully
+4. Once approved and merged, another GitHub action job starts which automatically will
+   1. create a git tag
+   2. create another [Pull Request](https://github.com/cmu-delphi/epidatr/pulls) to merge the changes back to the `dev` branch
+   3. create a [GitHub release](https://github.com/cmu-delphi/epidatr/releases) with automatically derived release notes
+5. Release to CRAN

NEWS.md

@@ -1,5 +1,4 @@
-
-# epiprocess 0.7.0.9999
+# epiprocess 0.7.0.9000
 
 ## Improvements
 

_pkgdown.yml

@@ -1,86 +1,90 @@
 template:
-  bootstrap: 5
-  bootswatch: cosmo
-  bslib:
-    font_scale: 1.0
-    primary: '#C41230'
-    link-color: '#C41230'
-    navbar-bg: '#C41230'
-    navbar-fg: '#f8f8f8'
+    bootstrap: 5
 
+development:
+    mode: auto
+
+# Colors from epipredict & epidatr, including Carnegie Red https://www.cmu.edu/brand/brand-guidelines/visual-identity/colors.html
 navbar:
-  bg: '#C41230'
-  fg: '#f8f8f8'
-  
+    bg: "#C41230"
+    fg: "#f8f8f8"
+    bootswatch: cosmo
+    bslib:
+        font_scale: 1.0
+        primary: "#C41230"
+        link-color: "#C41230"
+        navbar-bg: "#C41230"
+        navbar-fg: "#f8f8f8"
+
 url: https://cmu-delphi.github.io/epiprocess/
 
 home:
-  links:
-  - text: Introduction to Delphi's Tooling Work
-    href: https://cmu-delphi.github.io/delphi-tooling-book/
-  - text: Get the epipredict R package
-    href: https://cmu-delphi.github.io/epipredict/
-  - text: Get the epidatr R package
-    href: https://github.com/cmu-delphi/epidatr
+    links:
+        - text: Introduction to Delphi's Tooling Work
+          href: https://cmu-delphi.github.io/delphi-tooling-book/
+        - text: Get the epipredict R package
+          href: https://cmu-delphi.github.io/epipredict/
+        - text: Get the epidatr R package
+          href: https://github.com/cmu-delphi/epidatr
+        - text: Get the epidatasets R package
+          href: https://cmu-delphi.github.io/epidatasets/
 
 articles:
-- title: Using the package
-  desc: Basic usage and examples.
-  navbar: ~
-  contents:
-  - epiprocess
-  - slide
-  - growth_rate
-  - correlation
-  - aggregation
-  - outliers
-  - archive
-  - advanced
-  - compactify
+    - title: Using the package
+      desc: Basic usage and examples.
+      navbar: ~
+      contents:
+          - epiprocess
+          - slide
+          - growth_rate
+          - correlation
+          - aggregation
+          - outliers
+          - archive
+          - advanced
+          - compactify
 
 repo:
-  url:
-    home: https://github.com/cmu-delphi/epiprocess/tree/main/
-    source: https://github.com/cmu-delphi/epiprocess/blob/main/
-    issue: https://github.com/cmu-delphi/epiprocess/issues
-    user: https://github.com/
-
+    url:
+        home: https://github.com/cmu-delphi/epiprocess/tree/main/
+        source: https://github.com/cmu-delphi/epiprocess/blob/main/
+        issue: https://github.com/cmu-delphi/epiprocess/issues
+        user: https://github.com/
 
 reference:
-- title: "`epi_df` basics"
-  desc: Details on `epi_df` format, and basic functionality.
-- contents:
-  - matches("epi_df")
-- title: "`epi_*()` functions"
-  desc: Functions that act on `epi_df` objects.
-- contents:
-  - epi_slide
-  - epi_cor
-- title: Vector functions
-  desc: Functions that act directly on signal variables.
-- contents:
-  - growth_rate
-  - detect_outlr
-  - detect_outlr_rm
-  - detect_outlr_stl
-- title: "`epi_archive` basics"
-  desc: Details on `epi_archive`, and basic functionality.
-- contents:
-  - matches("archive")
-- title: "`epix_*()` functions"
-  desc: Functions that act on an `epi_archive` and/or `grouped_epi_archive` object.
-- contents:
-  - starts_with("epix")
-  - group_by.epi_archive
-- title: Example data
-- contents:
-  - archive_cases_dv_subset
-  - incidence_num_outlier_example
-  - contains("jhu_csse")
-- title: internal
-  contents:
-  - epiprocess
-  - max_version_with_row_in
-  - next_after
-  - guess_period
-
+    - title: "`epi_df` basics"
+      desc: Details on `epi_df` format, and basic functionality.
+    - contents:
+          - matches("epi_df")
+    - title: "`epi_*()` functions"
+      desc: Functions that act on `epi_df` objects.
+    - contents:
+          - epi_slide
+          - epi_cor
+    - title: Vector functions
+      desc: Functions that act directly on signal variables.
+    - contents:
+          - growth_rate
+          - detect_outlr
+          - detect_outlr_rm
+          - detect_outlr_stl
+    - title: "`epi_archive` basics"
+      desc: Details on `epi_archive`, and basic functionality.
+    - contents:
+          - matches("archive")
+    - title: "`epix_*()` functions"
+      desc: Functions that act on an `epi_archive` and/or `grouped_epi_archive` object.
+    - contents:
+          - starts_with("epix")
+          - group_by.epi_archive
+    - title: Example data
+    - contents:
+          - archive_cases_dv_subset
+          - incidence_num_outlier_example
+          - contains("jhu_csse")
+    - title: internal
+      contents:
+          - epiprocess
+          - max_version_with_row_in
+          - next_after
+          - guess_period