Merge pull request #391 from cmu-delphi/dev

Sync main with dev, epiprocess 0.9.0

Author: dshemetov

.Rbuildignore

@@ -3,6 +3,7 @@
 ^epipredict\.Rproj$
 ^\.Rproj\.user$
 ^LICENSE\.md$
+^DEVELOPMENT\.md$
 ^drafts$
 ^\.Rprofile$
 ^man-roxygen$
@@ -15,5 +16,8 @@
 ^data-raw$
 ^vignettes/articles$
 ^.git-blame-ignore-revs$
+^DEVELOPMENT\.md$
 ^doc$
 ^Meta$
+^.lintr$
+^.venv$

.github/pull_request_template.md

@@ -0,0 +1,24 @@
+### Checklist
+
+Please:
+
+- [ ] Make sure this PR is against "dev", not "main".
+- [ ] Request a review from one of the current epipredict main reviewers:
+      dajmcdon.
+- [ ] Make sure to bump the version number in `DESCRIPTION` and `NEWS.md`.
+      Always increment the patch version number (the third number), unless you are
+      making a release PR from dev to main, in which case increment the minor
+      version number (the second number).
+- [ ] Describe changes made in NEWS.md, making sure breaking changes
+      (backwards-incompatible changes to the documented interface) are noted.
+      Collect the changes under the next release number (e.g. if you are on
+      0.7.2, then write your changes under the 0.8 heading).
+- [ ] Consider pinning the `epiprocess` version in the `DESCRIPTION` file if
+  - You anticipate breaking changes in `epiprocess` soon
+  - You want to co-develop features in `epipredict` and `epiprocess`
+
+### Change explanations for reviewer
+
+### Magic GitHub syntax to mark associated Issue(s) as resolved when this is merged into the default branch
+
+- Resolves #{issue number}

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

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

.github/workflows/pkgdown.yaml

@@ -1,10 +1,10 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 #
-# Created with usethis + edited to use API key.
+# Created with usethis + edited to run on PRs to dev, use API key.
 on:
   push:
-    branches: [main, master]
+    branches: [main, dev]
   release:
     types: [published]
   workflow_dispatch:
@@ -13,14 +13,16 @@ name: pkgdown
 
 jobs:
   pkgdown:
+    # only build docs on the main repository and not forks
+    if: github.repository_owner == 'cmu-delphi'
     runs-on: ubuntu-latest
     # Only restrict concurrency for non-PR jobs
     concurrency:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -35,13 +37,19 @@ jobs:
 
       - name: Build site
         env:
-          DELPHI_EPIDATA_KEY: ${{ secrets.SECRET_EPIPREDICT_GHACTIONS_DELPHI_EPIDATA_KEY }}
-        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+          DELPHI_EPIDATA_KEY: ${{ secrets.SECRET_EPIPROCESS_GHACTIONS_DELPHI_EPIDATA_KEY }}
+        run: |
+          if (startsWith("${{ github.event_name }}", "pull_request")) {
+              mode <- ifelse("${{ github.base_ref }}" == "main", "release", "devel")
+          } else {
+              mode <- ifelse("${{ github.ref_name }}" == "main", "release", "devel")
+          }
+          pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE, override=list(PKGDOWN_DEV_MODE=mode))
         shell: Rscript {0}
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/[email protected].4
+        uses: JamesIves/github-pages-deploy-action@v4.4.1
         with:
           clean: false
           branch: gh-pages

.lintr

@@ -0,0 +1,9 @@
+linters: linters_with_defaults(
+  line_length_linter(120),
+  cyclocomp_linter = NULL,
+  object_length_linter(length = 40L)
+  )
+exclusions: list(
+  "renv",
+  "venv"
+  )

DESCRIPTION

@@ -1,13 +1,14 @@
 Package: epipredict
 Title: Basic epidemiology forecasting methods
-Version: 0.0.8
+Version: 0.1.0
 Authors@R: c(
-    person("Daniel", "McDonald", , "[email protected]", role = c("aut", "cre")),
+    person("Daniel J.", "McDonald", , "[email protected]", role = c("aut", "cre")),
     person("Ryan", "Tibshirani", , "[email protected]", role = "aut"),
+    person("Dmitry", "Shemetov", email = "[email protected]", role = "aut"),
+    person("David", "Weber", email = "[email protected]", role = "aut"),
+    person("CMU's Delphi Research Group", role = c("cph", "fnd")),
     person("Logan", "Brooks", role = "aut"),
     person("Rachel", "Lobay", role = "aut"),
-    person("Dmitry", "Shemetov", email = "[email protected]", role = "ctb"),
-    person("David", "Weber", email = "[email protected]", role = "ctb"),
     person("Maggie", "Liu", role = "ctb"),
     person("Ken", "Mawer", role = "ctb"),
     person("Chloe", "You", role = "ctb"),
@@ -23,43 +24,46 @@ URL: https://github.com/cmu-delphi/epipredict/,
     https://cmu-delphi.github.io/epipredict
 BugReports: https://github.com/cmu-delphi/epipredict/issues/
 Depends:
-    epiprocess (>= 0.6.0),
+    epiprocess (>= 0.9.0),
     parsnip (>= 1.0.0),
     R (>= 3.5.0)
 Imports:
+    checkmate,
     cli,
     distributional,
     dplyr,
-    fs,
     generics,
+    ggplot2,
     glue,
     hardhat (>= 1.3.0),
     lifecycle,
     magrittr,
-    methods,
-    quantreg,
     recipes (>= 1.0.4),
-    rlang,
-    smoothqr,
+    rlang (>= 1.1.0),
     stats,
     tibble,
     tidyr,
     tidyselect,
-    usethis,
+    tsibble,
     vctrs,
     workflows (>= 1.0.0)
 Suggests:
     covidcast,
     data.table,
     epidatr (>= 1.0.0),
-    ggplot2,
+    fs,
+    grf,
     knitr,
     lubridate,
     poissonreg,
+    purrr,
+    quantreg,
     ranger,
     RcppRoll,
     rmarkdown,
+    smoothqr,
     testthat (>= 3.0.0),
+    usethis,
     xgboost
 VignetteBuilder:
     knitr
@@ -71,4 +75,4 @@ Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.2

DEVELOPMENT.md

@@ -0,0 +1,45 @@
+## 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/epipredict/) is built off of the `main` branch. The `dev` version of the site is available at https://cmu-delphi.github.io/epipredict/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/epipredict/index.html` and `dev` at `file:///<local path>/epipredict/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
+```
+
+## Versioning
+
+Please follow the guidelines in the [PR template document](.github/pull_request_template.md).
+
+## Release process
+
+TBD