1.2.2 release

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

@@ -5,6 +5,14 @@ on:
     branches: [main, dev]
   pull_request:
     branches: [main, dev]
+    paths:
+      - '**.R'
+      - '**.Rmd'
+      - DESCRIPTION
+      - NAMESPACE
+      - man/**
+      - R/**
+      - tests/**
   workflow_dispatch:
 
 name: R-CMD-check

.github/workflows/lint.yaml

@@ -5,6 +5,13 @@ on:
     branches: [main, dev]
   pull_request:
     branches: [main, dev]
+    paths:
+      - '**.R'
+      - '**.Rmd'
+      - DESCRIPTION
+      - NAMESPACE
+      - man/**
+      - R/**
   workflow_dispatch:
 
 name: lint

.github/workflows/pkgdown.yaml

@@ -8,6 +8,14 @@ on:
     branches: [main, dev]
   pull_request:
     branches: [main, dev]
+    paths:
+      - '**.R'
+      - '**.Rmd'
+      - DESCRIPTION
+      - NAMESPACE
+      - man/**
+      - R/**
+      - _pkgdown.yml
   release:
     types: [published]
   workflow_dispatch:

.github/workflows/pr-commands.yaml

@@ -0,0 +1,149 @@
+# 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
+# Modifications:
+# - Allow more roles to trigger each PR command
+# - Document builds README.md from README.Rmd with devtools::build_readme()
+# - Include a doc-preview command (uses Netlify to preview the docs)
+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: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::roxygen2
+          needs: pr-document
+
+      - name: Document
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
+
+      - name: Build README.md from README.Rmd
+        run: Rscript -e 'if (file.exists("README.Rmd")) devtools::build_readme()'
+
+      - name: commit
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          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 "$GITHUB_ACTOR@users.noreply.github.com"
+          git add \*.R
+          git commit -m 'Style'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+  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/actions-netlify@v3.0
+        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/test-coverage.yml

@@ -5,7 +5,14 @@ on:
   push:
     branches: [main, dev]
   pull_request:
-
+    paths:
+      - '**.R'
+      - '**.Rmd'
+      - DESCRIPTION
+      - NAMESPACE
+      - man/**
+      - R/**
+      - tests/**
 name: test-coverage
 
 jobs:

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: epidatr
 Title: Client for Delphi's 'Epidata' API
-Version: 1.2.1
+Version: 1.2.2
 Authors@R: c(
     person("Logan", "Brooks", , "lcbrooks@andrew.cmu.edu", role = "aut"),
     person("Dmitry", "Shemetov", , "dshemeto@andrew.cmu.edu", role = "aut"),
@@ -68,7 +68,7 @@ Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Collate:
     'auth.R'
     'avail_endpoints.R'

NEWS.md

@@ -1,4 +1,22 @@
+# epidatr 1.2.2
+
+## Changes
+
+- Add `reference_week_day` argument to `fetch_args_list` and `fetch` functions.
+
+## Patches
+
+- Validate that `time_type` is one of "day" or "week" in `pub_covidcast`.
+- Validate that `time_type` is "week" when source is "nssp" in `pub_covidcast`.
+- Allow `hsa_nci` as a `geo_type` in `pub_covidcast`.
+- Allow `hsa_nci` as a `geo_type` in `pub_covidcast_meta`.
+- `pub_covidcast_meta` now returns `min_time`, `max_time`, `max_issue` as
+  integers rather than Dates. Because these fields can mix YYYYMMDD and YYYYWW
+  values, we recommend you parse them yourself.
+ - add new fields for `flusurv` endpoint.
+
 # epidatr 1.2.1
+
 ## Patches
 - Fix so that `covidcast_epidata()` will still print if fields are missing.