Merge pull request #706 from cmu-delphi/krivard/blog-workflow

Get blog workflow to work again

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))
 

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