alternative aws download

saeyslab · Sep 3, 2024 · 65810bc · 65810bc
1 parent 1dcc82c
commit 65810bc
Showing 1 changed file with 20 additions and 16 deletions.
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -16,8 +16,6 @@ jobs:
       - name: Check out repository
         uses: actions/checkout@v4
 
-      - name: Install AWS CLI
-        uses: unfor19/install-aws-cli-action@v1
 
       - name: Set up specific version of Python
         uses: actions/setup-python@v5
@@ -30,6 +28,26 @@ jobs:
       - name: Set up Quarto
         uses: quarto-dev/quarto-actions/setup@v2
 
+      # - name: Install AWS CLI
+      #   uses: unfor19/install-aws-cli-action@v1
+      - name: Cache usecase_data
+        uses: actions/cache@v2
+        with:
+          path: |
+            notebooks/usecase_data
+          key: usecase_data_${{ runner.os }}
+
+      - name: Make sure data is available
+        run: |
+          if [[ ! -f notebooks/usecase_data/sc_counts_reannotated_with_counts.h5ad ]]; then
+            wget https://openproblems-bio.s3.amazonaws.com/public/neurips-2023-competition/sc_counts_reannotated_with_counts.h5ad \
+              -O notebooks/usecase_data/sc_counts_reannotated_with_counts.h5ad
+          fi
+          # aws s3 cp \
+          #   --no-sign-request \
+          #   s3://openproblems-bio/public/neurips-2023-competition/sc_counts_reannotated_with_counts.h5ad \
+          #   notebooks/usecase_data/sc_counts_reannotated_with_counts.h5ad
+
       # attempt with pixi:
 
       # - name: Install pixi
@@ -59,20 +77,6 @@ jobs:
           path: |
             _freeze
           key: renv_${{ runner.os }}
-
-      - name: Cache usecase_data
-        uses: actions/cache@v2
-        with:
-          path: |
-            notebooks/usecase_data
-          key: usecase_data_${{ runner.os }}
-
-      - name: Make sure data is available
-        run: |
-          aws s3 cp \
-            --no-sign-request \
-            s3://openproblems-bio/public/neurips-2023-competition/sc_counts_reannotated_with_counts.h5ad \
-            notebooks/usecase_data/sc_counts_reannotated_with_counts.h5ad
 
       - name: Render slides
         run: |