init GHA

.github/workflows/build-deploy-pr.yaml

@@ -0,0 +1,40 @@
+name: build-deploy-pr
+on:
+  pull_request:
+jobs:
+  deploy-images:
+    runs-on: ubuntu-latest
+    env:
+      registry: ghcr.io
+      username: degauss-org
+      repository: daymet_chicago
+    strategy:
+      fail-fast: false
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: create latest tag variable
+        run: |
+          container="${{ env.registry }}/${{ env.username}}/${{ env.repository }}:latest"
+          echo "container=${container}" >> $GITHUB_ENV
+      - name: create pull request tag variable based on name of associated branch
+        if: github.event_name == 'pull_request'
+        run: |
+          versioned="${{ env.registry }}/${{ env.username}}/${{ env.repository }}:${GITHUB_HEAD_REF}"
+          echo "versioned=${versioned}" >> $GITHUB_ENV
+      - name: build container
+        run: |
+          docker build -t ${{ env.container }} .
+      - name: test run container
+        run: |
+          docker run --rm -v "${PWD}/test":/tmp ${{ env.container }} loyalty_degauss.csv
+      - name: login to ghcr
+        uses: docker/login-action@v1
+        with:
+          registry: ${{ env.registry }}
+          username: ${{ env.username }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      - name: deploy pull request container
+        run: |
+          docker tag ${{ env.container }} ${{ env.versioned }}
+          docker push ${{ env.versioned }}

.github/workflows/build-deploy-release.yaml

@@ -0,0 +1,42 @@
+name: build-deploy-release
+on:
+  release:
+    types: [published]
+jobs:
+  deploy-images:
+    runs-on: ubuntu-latest
+    env:
+      registry: ghcr.io
+      username: degauss-org
+      repository: daymet_chicago
+    strategy:
+      fail-fast: false
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: create latest tag variable
+        run: |
+          container="${{ env.registry }}/${{ env.username}}/${{ env.repository }}:latest"
+          echo "container=${container}" >> $GITHUB_ENV
+      - name: create release tag variable
+        if: github.event_name == 'release'
+        run: |
+          versioned="${{ env.registry }}/${{ env.username}}/${{ env.repository }}:${GITHUB_REF##*/}"
+          echo "versioned=${versioned}" >> $GITHUB_ENV
+      - name: build container
+        run: |
+          docker build -t ${{ env.container }} .
+      - name: test container
+        run: |
+          docker run --rm -v "${PWD}/test":/tmp ${{ env.container }} loyalty_degauss.csv
+      - name: login to ghcr
+        uses: docker/login-action@v1
+        with:
+          registry: ${{ env.registry }}
+          username: ${{ env.username }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      - name: deploy release (and latest) container
+        run: |
+          docker tag ${{ env.container }} ${{ env.versioned }}
+          docker push ${{ env.versioned }}
+          docker push ${{ env.container }}

Makefile

@@ -1,13 +1,13 @@
-.PHONY: build test shell clean
-
-build:
-	docker build -t daymet_chicago .
-
-test:
-	docker run --rm -v "${PWD}":/tmp daymet_chicago loyalty_degauss.csv
-
-shell:
-	docker run --rm -it --entrypoint=/bin/bash -v "${PWD}":/tmp daymet_chicago
-
-clean:
-	docker system prune -f
+.PHONY: build test shell clean
+
+build:
+	docker build -t daymet_chicago .
+
+test:
+	docker run --rm -v "${PWD}/test":/tmp daymet_chicago loyalty_degauss.csv
+
+shell:
+	docker run --rm -it --entrypoint=/bin/bash -v "${PWD}":/tmp daymet_chicago
+
+clean:
+	docker system prune -f

entrypoint.R

@@ -140,10 +140,10 @@ import_data <- function(.csv_filename = opt$filename, .min_lon = min_lon, .max_l
   return(out)
 }
 
-# Creating function to load the Daymet NetCDF data
+# Create function to load the Daymet NetCDF data
 daymet_load <- function() {
   # Loading the NetCDF files downloaded from Daymet as a SpatRaster raster stack
-  netcdf_list <- list.files(pattern = "_ncss.nc$")
+  netcdf_list <- list.files(path = "/app", pattern = "_ncss.nc$")
   # Initializing a time dictionary
   time_dict <- tibble(number = 1:365)
   for (i in 1:length(netcdf_list)) {
@@ -154,7 +154,7 @@ daymet_load <- function() {
     layer_names <- as.character(1:365)
     layer_names <- paste0(dm_var, "_", layer_names, "_", yr)
     # Loading the Daymet data
-    daymet_load <- rast(netcdf_list[i])
+    daymet_load <- rast(paste0("/app/", netcdf_list[i]))
     names(daymet_load) <- layer_names
     # Creating a dictionary to link numbers 1–365 to a date in a year (time dictionary)
     origin <- as_date(paste0(yr, "-01-01")) - 1 # Numbers count days since origin