Merge pull request #725 from cmu-delphi/release/v3.0.26

Release v3.0.26

Author: krivard

.github/workflows/blog.yaml

@@ -7,39 +7,50 @@ on:
       - "environment.yml"
       - "dependencies.R"
       - ".github/workflows/blog.yaml"
+  workflow_dispatch:
 
 jobs:
   blog:
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    env:
+      RETICULATE_PYTHON: /usr/share/miniconda3/envs/www-main/bin/python
     steps:
       - uses: actions/checkout@v3
         with:
           # submodules: true  # Fetch Hugo themes (true OR recursive)
           fetch-depth: 3
-      - name: Cache Conda
-        uses: actions/[email protected]
-        with:
-          path: ~/conda_pkgs_dir
-          key: ${{ runner.os }}-conda6-${{ hashFiles('environment.yml') }}
-          restore-keys: |
-            ${{ runner.os }}-conda6-
       - uses: conda-incubator/setup-miniconda@v2
         with:
           python-version: 3.9
-          mamba-version: "*"
-          channels: conda-forge,defaults
-          channel-priority: true
           activate-environment: www-main
-          environment-file: environment.yml
-          auto-activate-base: false
+          miniforge-variant: Mambaforge
+          miniforge-version: latest
+          use-mamba: true
           use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
-      # - name: Conda info
-      #   shell: bash -l {0}
-      #   run: |
-      #     conda info
-      #     conda list
+      - name: Get Date
+        id: get-date
+        run: echo "name=today::$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
+        shell: bash
+      - name: Cache Conda env
+        uses: actions/cache@v3
+        with:
+          path: ${{ env.CONDA }}/envs
+          key: conda-${{ runner.os }}--${{ runner.arch }}--${{ steps.get-date.outputs.today }}-${{ hashFiles('environment.yml') }}-${{ env.CACHE_NUMBER }}
+        env:
+          # Increase this value to reset cache if etc/example-environment.yml has not changed
+          CACHE_NUMBER: 0
+        id: cache
+      - name: Update environment
+        run: mamba env update -n www-main -f environment.yml
+        if: steps.cache.outputs.cache-hit != 'true'
+      - name: Conda info
+        run: |
+          conda info
+          conda list
       - name: Install R dependencies
-        shell: bash -l {0}
         env:
           GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
         run: |
@@ -54,10 +65,8 @@ jobs:
             ${{ runner.os }}-blogdown2-${{ hashFiles('environment.yml') }}-
             ${{ runner.os }}-blogdown2-
       - name: Build site
-        shell: bash -l {0}
         run: |
           npm run build:blog
-
       - uses: actions/upload-artifact@v3
         with:
           name: blog
@@ -79,7 +88,6 @@ jobs:
         run: npm run lint
       - name: Build
         run: npm run build
-
       - uses: actions/upload-artifact@v3
         with:
           name: website

content/blog/2021-01-22-holiday-surveys.Rmd

@@ -108,7 +108,7 @@ regionmap <- travel %>%
   filter(geo_value %in% str_to_lower(statelist)) %>%
   mutate(value = plyr::mapvalues(geo_value, str_to_lower(statelist), regions),
          value = as.integer(factor(value)))
-
+attr(regionmap, "metadata") <- list(geo_type = "state")
 grid_label <- textGrob("Data from Delphi COVIDcast, delphi.cmu.edu",
                        hjust = 1, x = 1, gp = gpar(fontsize = 9))
 

content/covid19/ctis.md

@@ -59,6 +59,7 @@ Our primary description of the survey and its results over the first year of ope
 
 Other research publications using the survey data include:
 
+- C. Lupton-Smith, E. Badillo Goicoechea, M. Collins, J. Lessler, M. K. Grabowski & E. A. Stuart (2022). [Consistency between Household and County Measures of Onsite Schooling during the COVID-19 Pandemic](https://doi.org/10.1080/19345747.2022.2131660). *Journal of Research on Educational Effectiveness*.
 - Nguyen, Q.C., Yardi, I., Gutierrez, F.X.M. et al. (2022). [Leveraging 13 million responses to the U.S. COVID-19 Trends and Impact Survey to examine vaccine hesitancy, vaccination, and mask wearing, January 2021-February 2022](https://doi.org/10.1186/s12889-022-14286-3). *BMC Public Health* 22, 1911. 
 - J. G. Lu (2022). [Two large-scale global studies on COVID-19 vaccine hesitancy over time: Culture, uncertainty avoidance, and vaccine side-effect concerns](https://doi.org/10.1037/pspa0000320). *Journal of Personality and Social Psychology*.
 - J. M. Cox-Ganser, P. K. Henneberger, D. N. Weissman, G. Guthrie, and C. P. Groth (2022). [COVID-19 test positivity by occupation using the Delphi US COVID-19 Trends and Impact Survey, September–November 2020](https://doi.org/10.1002/ajim.23410). *American Journal of Industrial Medicine* 65 (9), 721-730.

content/people/index.md

@@ -516,7 +516,8 @@ people:
   image: duane-mengo.jpg
   affiliation: CMU/MLD
   team:
-  - core
+  - past
+  note: Core member, April-September 2022
 - key: lmorinishi
   firstName: Leanna
   lastName: Morinishi

dependencies.R

@@ -8,6 +8,6 @@ install.packages("covidcast", repo="http://cran.rstudio.com/")
 #                          upgrade = 'never',
 #                          subdir = "R-packages/covidcast")
 
-devtools::install_github("reichlab/zoltr", upgrade = 'never', quick = TRUE)
-devtools::install_github("reichlab/covidData", upgrade = 'never', quick = TRUE)
-devtools::install_github("reichlab/covidHubUtils", upgrade = 'never', quick = TRUE)
+devtools::install_github("reichlab/zoltr", upgrade = 'never')
+devtools::install_github("reichlab/covidData", upgrade = 'never')
+devtools::install_github("reichlab/covidHubUtils", upgrade = 'never')

environment.yml

@@ -6,7 +6,7 @@ dependencies:
   - gdal
   - python=3.9.1
   - pip
-  - r-base=3.6.3
+  - r-base
   - glib
   - mscorefonts
   - r-cairo
@@ -50,6 +50,7 @@ dependencies:
   - r-vroom
   - r-urltools
   - r-base64url
+  - r-readr >=2
   - pandoc
   - fiona
   - geopandas

package-lock.json

@@ -1,18 +1,18 @@
 {
   "name": "www-main",
-  "version": "3.0.25",
+  "version": "3.0.26",
   "private": true,
   "dependencies": {
     "@fortawesome/fontawesome-free": "^6.2.0",
     "highlight.js": "^11.6.0",
-    "katex": "^0.16.2",
-    "uikit": "^3.15.10",
+    "katex": "^0.16.3",
+    "uikit": "^3.15.11",
     "www-covidcast": "https://github.com/cmu-delphi/www-covidcast/releases/download/v3.2.3/www-covidcast-3.2.3.tgz",
     "www-covidcast-classic": "https://github.com/cmu-delphi/www-covidcast-classic/releases/download/v2.6.3/www-covidcast-classic-2.6.3.tgz",
     "www-epivis": "https://github.com/cmu-delphi/www-epivis/releases/download/v2.0.3/www-epivis-2.0.3.tgz"
   },
   "devDependencies": {
-    "hugo-bin": "^0.92.3",
+    "hugo-bin": "^0.93.0",
     "husky": "^8.0.1",
     "lint-staged": "^13.0.3",
     "prettier": "^2.7.1",