Second merge of main to spatial-main

.github/workflows/pkgdown.yaml

@@ -4,7 +4,7 @@ on:
   push:
     branches: [main, prod]
   pull_request:
-    branches: [spatial-main, main, prod]
+    branches: [main, prod]
   release:
     types: [published]
   workflow_dispatch:
@@ -13,56 +13,171 @@ name: pkgdown
 
 jobs:
   build:
+
+    strategy:
+      matrix:
+        version:
+          - 'release'
+          - 'devel'
+
+    name: pkgdown site build (${{ matrix.version }})
+
     runs-on: ubuntu-latest
     # Only restrict concurrency for non-PR jobs
     concurrency:
-      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}-${{ matrix.version }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     permissions:
       contents: write
       id-token: write
       pages: write
-    outputs:
-      page_artifact_id: ${{ steps.upload-artifact.outputs.artifact_id }}
     steps:
+
+      ##########################################################################
+      # Identifying the latest and corresponding tag/sha to download
+      #########################################################################
+      - name: Check the repo to download
+        id: commit
+        run: |
+
+          gh api \
+            -H "Accept: application/vnd.github+json" \
+            -H "X-GitHub-Api-Version: 2022-11-28" \
+            /repos/CDCgov/ww-inference-model/releases/latest > \
+            latest_release
+
+          echo -n "This job is running on tag/sha: "
+          if [ "${{ matrix.version }}" = "release" ]; then
+            echo $(jq -r '.tag_name' latest_release)
+            echo "tag=$(jq -r '.tag_name' latest_release)" >> $GITHUB_OUTPUT
+          else
+            echo "tag=${{ github.sha }}" >> $GITHUB_OUTPUT
+            echo ${{ github.sha }}
+          fi
+
       - uses: actions/checkout@v4
+        with:
+          ref: ${{ steps.commit.outputs.tag }}
 
+      - name: Checkout the sha-associated repo
+        if: ${{ matrix.version == 'release' }}
+        uses: actions/checkout@v4
+        with:
+          sparse-checkout: './_pkgdown.yml'
+          path: pkgdown-${{ github.sha}}
+
+      - name: Overwriting the _pkgdown.yml
+        if: ${{ matrix.version == 'release' }}
+        run: |
+          cp pkgdown-${{ github.sha }}/_pkgdown.yml ./
+          rm -rf pkgdown-${{ github.sha }}
+
+      - name: Checking if the release is cached
+        if: ${{ matrix.version == 'release' }}
+        id: cache-hit
+        uses: actions/cache@v3
+        with:
+          key: pkgdown_site-${{ matrix.version }}-${{ steps.commit.outputs.tag }}-${{ hashFiles( './_pkgdown.yml' ) }}
+          path: './docs/'
+
+      # These steps only happen if the cache is not hit
       - uses: r-lib/actions/setup-pandoc@v2
+        if: ${{ matrix.version != 'release' || steps.cache-hit.outputs.cache-hit != 'true' }}
         with:
           pandoc-version: "2.19.2"
 
       - uses: r-lib/actions/setup-r@v2
+        if: ${{ matrix.version != 'release' || steps.cache-hit.outputs.cache-hit != 'true' }}
         with:
           r-version: "release"
           use-public-rspm: true
           install-r: false
           extra-repositories: "https://mc-stan.org/r-packages/"
       - uses: r-lib/actions/setup-r-dependencies@v2
+        if: ${{ matrix.version != 'release' || steps.cache-hit.outputs.cache-hit != 'true' }}
         with:
           pak-version: rc
           extra-packages: any::pkgdown local::.
           needs: website
 
       - name: "Install cmdstan via cmdstanr"
         uses: epinowcast/actions/install-cmdstan@v1
+        if: ${{ matrix.version != 'release' || steps.cache-hit.outputs.cache-hit != 'true' }}
         with:
           cmdstan-version: "latest"
 
       - name: Build site
-        run: "pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)"
-        shell: Rscript {0}
+        if: ${{ matrix.version != 'release' || steps.cache-hit.outputs.cache-hit != 'true' }}
+        run: |
+          # Changing the URL if it is a development build
+          if [ "${{ matrix.version }}" = "devel" ]; then
+            # Forcing the development mode
+            export PKGDOWN_DEV_MODE="devel"
+          else
+
+            # Setting the url
+            sed -i'' 's|url: https://cdcgov.github.io/ww-inference-model/|url: https://cdcgov.github.io/ww-inference-model/release/|' _pkgdown.yml
+
+            # Changing the navbar
+            sed -i'' 's|href: https://cdcgov.github.io/ww-inference-model/release|href: https://cdcgov.github.io/ww-inference-model/|' _pkgdown.yml
+
+            sed -i'' 's|text: (switch to release)|text: (switch to dev)|' _pkgdown.yml
+
+            sed -i'' 's|icon: fa-toggle-on|icon: fa-toggle-off|' _pkgdown.yml
+
+            # Forcing the release mode
+            export PKGDOWN_DEV_MODE="release"
+          fi
+          Rscript --vanilla -e \
+            "pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)"
+
+          if [ "${{ matrix.version }}" = "devel" ]; then
+            mv docs docs-tmp
+            mkdir docs
+            mv docs-tmp/dev/* docs
+          fi
 
       - name: Upload artifact for GH pages deployment
+        id: upload-artifact
+        uses: actions/upload-artifact@v4
+        with:
+          path: "./docs/"
+          name: pkgdown-site-${{ matrix.version }}
+
+  combine:
+    outputs:
+      page_artifact_id: ${{ steps.upload-artifact.outputs.artifact_id }}
+
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+
+      - name: Download dev artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: pkgdown-site-devel
+          path: ./docs/
+
+      - name: Download release artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: pkgdown-site-release
+          path: ./docs/release
+
+      - name: Upload pages artifact
         id: upload-artifact
         uses: actions/upload-pages-artifact@v3
         with:
-          path: "docs/"
+          path: ./docs/
+          name: github-pages
+          retention-days: 7
 
   deploy:
     # check builds on PRs but only deploy when main changes
     if: ${{ github.event_name != 'pull_request' }}
-    needs: build
+    needs: combine
     runs-on: ubuntu-latest
     permissions:
       pages: write
@@ -77,31 +192,23 @@ jobs:
         uses: actions/deploy-pages@v4
 
   post-page-artifact:
-    # only comment on PRs
-    if: ${{ github.event_name == 'pull_request' }}
-    needs: build
     runs-on: ubuntu-latest
+
+    if: ${{ github.event_name == 'pull_request' }}
+
+    # This job depends on the `build` job
+    needs: combine
+
+    # Required permissions
     permissions:
-        contents: read
-        pull-requests: write
-    env:
-      GH_TOKEN: ${{ github.token }}
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-      - name: Find Comment
-        uses: peter-evans/find-comment@v3
-        id: fc
-        with:
-           issue-number: ${{ github.event.pull_request.number }}
-           comment-author: 'github-actions[bot]'
-           body-includes: Your page is ready to preview
+      contents: read
+      pull-requests: write
 
-      - name: Create or update comment
-        uses: peter-evans/create-or-update-comment@v4
+    steps:
+      # Post the artifact pulling the id from the `readme` step.
+      # The msg will refer to the arfitact as 'README file'.
+      - name: Post the artifact
+        uses: CDCgov/cfa-actions/[email protected]
         with:
-          comment-id: ${{ steps.fc.outputs.comment-id }}
-          issue-number: ${{ github.event.pull_request.number }}
-          body: |
-            Thank you for your contribution, @${{ github.triggering_actor }} :rocket:! Your page is ready to preview [here](https://github.com/${{github.repository}}/actions/runs/${{ github.run_id }}/artifacts/${{ needs.build.outputs.page_artifact_id }})
-          edit-mode: replace
+          artifact-name: github-pages
+          gh-token: ${{ secrets.GITHUB_TOKEN }}

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: wwinference
 Title: Jointly infers infection dynamics from wastewater data and epidemiological indicators
-Version: 0.1.0
+Version: 0.1.0.99
 Authors@R: c(
     person(given = "Kaitlyn",
            family = "Johnson",

NEWS.md

@@ -1,3 +1,15 @@
+
+# wwinference 0.1.0.99 (dev)
+
+## User-visible changes
+- Add wastewater data into the forecast period to output in `generate_simulated_data()` function and as package data. Also adds subpopulation-level
+hospital admissions to output of function and package data. ([#184](https://github.com/CDCgov/ww-inference-model/issues/184))
+- `wwinference` now checks whether `site_pop` is fixed per site (see issue [#223](https://github.com/CDCgov/ww-inference-model/issues/226) reported by [@akeyel](https://github.com/akeyel)).
+
+## Internal changes
+- Updated the workflow for posting the pages artifact to PRs (issue [#229](https://github.com/CDCgov/ww-inference-model/issues/229)).
+- Modify `plot_forecasted_counts()` so that it does not require an evaluation dataset ([#218](https://github.com/CDCgov/ww-inference-model/pull/218))
+
 # wwinference 0.1.0
 
 This is the first major release, focused on providing an initial version of the package.
@@ -10,4 +22,7 @@ As it's written, the package is intended to allow users to do the following:
 - Validate input data validation with informative error messaging ([#37](https://github.com/CDCgov/ww-inference-model/issues/37), [#54](https://github.com/CDCgov/ww-inference-model/issues/54))
 - Provide a wrapper function to generate forward simulated data with user-specified variables. It calls a number of functions to perform specific model components ([#27](https://github.com/CDCgov/ww-inference-model/issues/27))
 - Contains S3 class methods applied to the output of the main model wrapper function, the `wwinference_fit` class object ([#58](https://github.com/CDCgov/ww-inference-model/issues/58)).
+<<<<<<< HEAD
 - Wastewater concentration data is expected to be in log scale ([#122](https://onetakeda.box.com/s/pju273g5khx3y3cwoae2zwv3e7vu03x3)).
+=======
+- Wastewater concentration data is expected to be in log scale ([#122](https://github.com/CDCgov/ww-inference-model/pull/122)).

R/data.R

@@ -32,13 +32,15 @@
 #'    units of log estimated genome copies per mL.}
 #'   \item{site_pop}{The population size of the wastewater catchment area
 #'   represented by the site variable}
+#'   \item{location}{ A string indicating the location that all of the
+#'   data is coming from. This is not a necessary column, but instead is
+#'   included to more realistically mirror a typical workflow}
 #'   }
 #' @source vignette_data.R
 "ww_data"
 
 
 
-
 #' Example wastewater dataset with independent site correlations.
 #'
 #' A dataset containing the simulated wastewater concentrations
@@ -135,9 +137,9 @@
 #'  to match this format.
 #'
 #' This data is generated via the default values in the
-#'  `generate_simulated_data()` function. They represent the bare minumum
+#'  `generate_simulated_data()` function. They represent the bare minimum
 #'  required fields needed to pass to the model, and we recommend that users
-#'  try to format their own data to match this formate.
+#'  try to format their own data to match this format.
 #'
 #' The variables are as follows:
 #' \describe{
@@ -147,6 +149,9 @@
 #'   hospital on that date, available as of the forecast date}
 #'   \item{state_pop}{The number of people contributing to the daily hospital
 #'   admissions}
+#'   \item{location}{ A string indicating the location that all of the
+#'   data is coming from. This is not a necessary column, but instead is
+#'   included to more realistically mirror a typical workflow}
 #'   }
 #' @source vignette_data.R
 "hosp_data_ind"
@@ -214,13 +219,19 @@
 
 
 
-#' Example hospital admissions dataset for evaluation spatially ind. sites.
+#' Example subpopulation level hospital admissions dataset
 #'
-#'  A dataset containing the simulated daily hospital admissions that the model
-#'  will be evaluated against (labeled here as `daily_hosp_admits_for_eval`)
-#'  by date of admission (`date`). This data is not needed to fit the model,
-#'  but is used in the Getting Started vignette to demonstrate the forecasted
-#'  hospital admissions compared to those later observed.
+#'  A dataset containing the simulated daily hospital admissions
+#' (labeled here as `daily_hosp_admits`) by date of admission (`date`) in
+#'  each subpopulation.
+#'  Additional columns that are the population size of the
+#'  population contributing to the hospital admissions. In this instance,
+#'  the subpopulations here are each of the wastewater catchment areas plus
+#'  an additional subpopulation for the portion of the population not captured
+#'  by wastewater surveillance. The data generated are daily hospital
+#'  admissions but they could be any other epidemiological count dataset e.g.
+#'  cases. This data should only contain hospital admissions that would have
+#'  been available as of the date that the forecast was made.
 #'
 #' This data is generated via the default values in the
 #'  `generate_simulated_data()` function.