Merge pull request #467 from cmu-delphi/dev

Bump main

Author: dajmcdon

.Rbuildignore

@@ -20,4 +20,5 @@
 ^doc$
 ^Meta$
 ^.lintr$
-^.venv$
+^.venv$
+^inst/templates$

.github/workflows/doc-preview.yaml

@@ -0,0 +1,65 @@
+on:
+  issue_comment:
+    types: [created]
+
+name: doc-preview.yaml
+
+permissions: read-all
+
+jobs:
+  preview:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'COLLABORATOR' || github.event.comment.author_association == 'CONTRIBUTOR' || github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/preview-docs') }}
+
+    runs-on: ubuntu-latest
+    permissions:
+      # Needed to write a comment on the PR
+      pull-requests: write
+      # Needed to read the PR branch
+      contents: read
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          # Checkout the PR branch
+          ref: refs/pull/${{ github.event.issue.number }}/head
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to Netlify
+        uses: nwtgck/[email protected]
+        with:
+          # Standard config
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          deploy-message: "Deploy from GitHub Actions"
+          # 'docs/' is the default directory for pkgdown::build_site()
+          # we add 'dev' because _pkgdown.yml has 'development: mode: devel'
+          publish-dir: './docs/dev'
+          # Development deploys only
+          production-deploy: false
+          # Enable pull request comment (default)
+          enable-pull-request-comment: true
+          # Overwrite the pull request comment with updated link (default)
+          overwrites-pull-request-comment: true
+          # Don't deploy to GitHub
+          enable-github-deployment: false
+          # Don't update the status of the commit
+          enable-commit-status: false
+          # Don't comment on the commit
+          enable-commit-comment: false
+        env:
+          # Netlify credentials (currently from Dmitry's account)
+          NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
+          NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}
+        timeout-minutes: 1

.github/workflows/pr-commands.yaml

@@ -0,0 +1,85 @@
+# 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
+on:
+  issue_comment:
+    types: [created]
+
+name: pr-commands.yaml
+
+permissions: read-all
+
+jobs:
+  document:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'COLLABORATOR' || github.event.comment.author_association == 'CONTRIBUTOR' || github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}
+    name: document
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::roxygen2
+          needs: pr-document
+
+      - name: Document
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
+
+      - name: commit
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
+          git add man/\* NAMESPACE
+          git commit -m 'Document'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+  style:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'COLLABORATOR' || github.event.comment.author_association == 'CONTRIBUTOR' || github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/style') }}
+    name: style
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - name: Install dependencies
+        run: install.packages("styler")
+        shell: Rscript {0}
+
+      - name: Style
+        run: styler::style_pkg()
+        shell: Rscript {0}
+
+      - name: commit
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
+          git add \*.R
+          git commit -m 'Style'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/styler.yml

@@ -10,3 +10,4 @@ inst/doc
 .Rprofile
 renv.lock
 renv/
+.Renviron

.gitignore

@@ -1,11 +1,11 @@
 Package: epipredict
 Title: Basic epidemiology forecasting methods
-Version: 0.1.0
+Version: 0.2.0
 Authors@R: c(
     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("Dmitry", "Shemetov", , "[email protected]", role = "aut"),
+    person("David", "Weber", , "[email protected]", role = "aut"),
     person("Delphi Research Group", role = c("cph", "fnd")),
     person("Logan", "Brooks", role = "aut"),
     person("Rachel", "Lobay", role = "aut"),
@@ -24,21 +24,22 @@ URL: https://github.com/cmu-delphi/epipredict/,
     https://cmu-delphi.github.io/epipredict
 BugReports: https://github.com/cmu-delphi/epipredict/issues/
 Depends:
-    epiprocess (>= 0.9.0),
+    epidatasets,
     parsnip (>= 1.0.0),
     R (>= 3.5.0)
 Imports:
     checkmate,
     cli,
-    distributional,
     dplyr,
+    epiprocess (>= 0.11.2),
     generics,
     ggplot2,
     glue,
-    hardhat (>= 1.3.0),
+    hardhat (>= 1.4.1),
     lifecycle,
+    lubridate,
     magrittr,
-    recipes (>= 1.0.4),
+    recipes (>= 1.1.1),
     rlang (>= 1.1.0),
     stats,
     tibble,
@@ -48,18 +49,18 @@ Imports:
     vctrs,
     workflows (>= 1.0.0)
 Suggests:
-    covidcast,
     data.table,
     epidatr (>= 1.0.0),
     fs,
     grf,
+    here,
     knitr,
-    lubridate,
     poissonreg,
     purrr,
     quantreg,
     ranger,
     RcppRoll,
+    readr,
     rmarkdown,
     smoothqr,
     testthat (>= 3.0.0),
@@ -69,12 +70,12 @@ VignetteBuilder:
     knitr
 Remotes:
     cmu-delphi/delphidocs,
+    cmu-delphi/epidatasets,
     cmu-delphi/epidatr,
     cmu-delphi/epiprocess,
     dajmcdon/smoothqr
-Config/testthat/edition: 3
 Config/Needs/website: cmu-delphi/delphidocs
+Config/testthat/edition: 3
 Encoding: UTF-8
-LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2