Improved caching of RDS files, specificity of keys in the testing wor…

…kflow.

- fixed the publication workflow to use the new containers and caches.
- rerun the unit tests before publication, just in case.

.github/workflows/publish-npm.yaml

@@ -10,33 +10,16 @@ jobs:
   build:
     runs-on: ubuntu-latest
     if: ${{ github.event.workflow_run.conclusion == 'success' }}
-    container: ghcr.io/kanaverse/scran.js-docker/builder:master
-    defaults:
-      run:
-        working-directory: /scran.js
+    container: ghcr.io/kanaverse/emcmake-docker/builder:${{ needs.prepare-version.outputs.version }}
 
     steps:
-    - name: Get to the right branch
-      run: |
-        git fetch --all
-        git checkout $GITHUB_SHA
-
-    # We run the various preparatory steps to ensure that they do, in fact, run.
-    # This avoids nasty surprises when we actually do want to publish something.
-    - name: Update node build 
-      run: bash build.sh main
-
-    - name: Update browser build
-      run: bash build.sh browser
+    - name: Checkout repo
+      uses: actions/checkout@v4
 
     - name: Set up Node
-      uses: actions/setup-node@v3
+      uses: actions/setup-node@v4
       with:
-        registry-url: 'https://registry.npmjs.org'
-        node-version: 16
-
-    - name: Update NPM packages
-      run: npm i --include=dev
+        node-version: 18
 
     # We only run the remaining (remote-touching) steps if the version has actually changed.
     - name: Extract package versions
@@ -49,6 +32,43 @@ jobs:
         echo "UPDATE_SCRANJS=${update}" >> $GITHUB_ENV
         echo "Current version is ${current_version} (published ${old_version})"
 
+    - name: Cache installed
+      if: env.UPDATE_SCRANJS == 1
+      uses: actions/cache@v4
+      with:
+        path: extern/installed
+        key: deps-${{ hashFiles('extern/**/build.sh') }}-${{ env.IMAGE_VERSION }}
+
+    - name: Cache Modules
+      if: env.UPDATE_SCRANJS == 1
+      uses: actions/cache@v4
+      with:
+        path: '**/node_modules'
+        key: npm-${{ hashFiles('package.json') }}
+
+    - name: Update NPM packages
+      if: env.UPDATE_SCRANJS == 1
+      run: npm i --include=dev
+
+    - name: Update node build 
+      if: env.UPDATE_SCRANJS == 1
+      run: bash build.sh main
+
+    - name: Update browser build
+      if: env.UPDATE_SCRANJS == 1
+      run: bash build.sh browser
+
+    - name: Cache RDS files
+      if: env.UPDATE_SCRANJS == 1
+      uses: actions/cache@v4
+      with:
+        path: tests/rds/*.rds
+        key: rds-${{ hashFiles('tests/rds/generate.R') }}
+
+    - name: Double-checking tests
+      if: env.UPDATE_SCRANJS == 1
+      run: CHECK_RDS=1 npm run test
+
     - name: Publish to NPM
       if: env.UPDATE_SCRANJS == 1
       run: npm publish

.github/workflows/run-tests.yaml

@@ -26,17 +26,19 @@ jobs:
     - name: Checkout repo
       uses: actions/checkout@v4
 
+    - name: Cache RDS files
+      id: cache-rds
+      uses: actions/cache@v4
+      with:
+        path: tests/rds/*.rds
+        key: rds-${{ hashFiles('tests/rds/generate.R') }}
+
     - name: Build RDS files
+      if: steps.cache-rds.outputs.cache-hit != 'true'
       run: |
         cd tests/rds
         R -f generate.R
 
-    - name: Upload RDS files
-      uses: actions/upload-artifact@v4
-      with:
-        name: rds-files
-        path: tests/rds/*.rds
-
   build_deps:
     runs-on: ubuntu-latest
     needs: [prepare-version]
@@ -51,7 +53,7 @@ jobs:
       uses: actions/cache@v4
       with:
         path: extern/installed
-        key: deps-${{ hashFiles('**/extern/**/build.sh') }}-${{ env.IMAGE_VERSION }}
+        key: deps-${{ hashFiles('extern/**/build.sh') }}-${{ env.IMAGE_VERSION }}
 
     - name: Build HDF5
       if: steps.installed.outputs.cache-hit != 'true'
@@ -83,7 +85,7 @@ jobs:
       uses: actions/cache@v4
       with:
         path: '**/node_modules'
-        key: npm-${{ hashFiles('**/package.json') }}
+        key: npm-${{ hashFiles('package.json') }}
 
     - name: Update NPM packages
       run: npm i --include=dev
@@ -92,25 +94,25 @@ jobs:
       uses: actions/cache@v4
       with:
         path: extern/installed
-        key: deps-${{ hashFiles('**/extern/**/build.sh') }}-${{ env.IMAGE_VERSION }}
+        key: deps-${{ hashFiles('extern/**/build.sh') }}-${{ env.IMAGE_VERSION }}
+
+    - name: Cache RDS files
+      uses: actions/cache@v4
+      with:
+        path: tests/rds/*.rds
+        key: rds-${{ hashFiles('tests/rds/generate.R') }}
 
     - name: Cache node build
       id: wasm-build
       uses: actions/cache@v4
       with:
         path: js/wasm
-        key: wasm-${{ hashFiles('**/build.sh', '**/CMakeLists.txt', '**/src/*') }}-${{ env.IMAGE_VERSION }}
+        key: wasm-${{ hashFiles('build.sh', 'extern/**/build.sh', 'CMakeLists.txt', 'extern/CMakeLists.txt', 'src/*') }}-${{ env.IMAGE_VERSION }}
 
     - name: Update node build 
       if: steps.wasm-build.outputs.cache-hit != 'true'
       run: bash build.sh main
 
-    - name: Download RDS files
-      uses: actions/download-artifact@v4
-      with:
-        name: rds-files
-        path: tests/rds
-
     - name: Run tests
       run: |
         export CHECK_RDS=1