Setup conda using github action for postbuild tests

kraemer-lab · Sep 13, 2024 · 860fdff · 860fdff
1 parent 8c293ba
commit 860fdff
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Showing 5 changed files with 38 additions and 11 deletions.
diff --git a/.github/workflows/nightly_build.yml b/.github/workflows/nightly_build.yml
@@ -47,10 +47,20 @@ jobs:
           yarn build
           yarn package
       # only publish builds if they pass post-build tests
+      - name: Set up Miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: build
+          miniforge-version: latest
+          auto-update-conda: true
+          python-version: 3.12
+          use-mamba: true
       - name: postbuild-tests
         working-directory: ./electron-app
         shell: bash
         run: |
+          conda init
+          source ~/.bashrc
           ./run_postbuild_tests.sh
       - name: Build distributables
         working-directory: ./electron-app

diff --git a/.github/workflows/postbuildchecks.yml b/.github/workflows/postbuildchecks.yml
@@ -28,26 +28,32 @@ jobs:
       - uses: nanasess/setup-chromedriver@v2
         with:
           chromedriver-version: "126.0.6478.185"
-      - name: Set up Python
-        uses: actions/setup-python@v5
+      - name: Set up Miniconda
+        uses: conda-incubator/setup-miniconda@v3
         with:
-          python-version: "3.12"
+          activate-environment: build
+          miniforge-version: latest
+          auto-update-conda: true
+          auto-activate-base: true
+          python-version: 3.12
+          use-mamba: true
       - name: Install the latest version of uv
         uses: astral-sh/setup-uv@v2
       - name: install MacOS (M1) build dependencies
-        shell: bash
+        shell: bash -el {0}  # required to sustain the conda environment
         run: |
           if [ "$RUNNER_OS" == "macOS" ] && [ "$RUNNER_ARCH" == "ARM64" ]; then
             brew install pango
           fi
       # setuptools needs to be available globally for the yarn build script
       - name: Install setuptools
+        shell: bash -el {0}  # required to sustain the conda environment
         run: |
           python -m pip install --upgrade pip
           python -m pip install setuptools
       - name: build
         working-directory: ./electron-app
-        shell: bash
+        shell: bash -el {0}  # required to sustain the conda environment
         run: |
           corepack enable
           ./build_deps.sh
@@ -56,7 +62,7 @@ jobs:
           yarn build
           yarn package
       - name: install docker MacOS (Intel chips)
-        shell: bash
+        shell: bash -el {0}  # required to sustain the conda environment
         run: |
           if [ "$RUNNER_OS" == "macOS" ] && [ "$RUNNER_ARCH" == "X64" ]; then
             brew install docker
@@ -68,6 +74,6 @@ jobs:
         if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled }}
       - name: postbuild-tests
         working-directory: ./electron-app
-        shell: bash
+        shell: bash -el {0}  # required to sustain the conda environment
         run: |
           ./run_postbuild_tests.sh
diff --git a/.github/workflows/publish_build.yml b/.github/workflows/publish_build.yml
@@ -48,13 +48,21 @@ jobs:
       - name: tmate debugging
         uses: mxschmitt/action-tmate@v3
         if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled }}
+      # only publish builds if they pass post-build tests
+      - name: Set up Miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: build
+          miniforge-version: latest
+          auto-update-conda: true
+          python-version: 3.12
+          use-mamba: true
       - name: postbuild-tests
         working-directory: ./electron-app
         shell: bash
-        # 'yarn package' is only run to allow build_testsuite.sh to run before
-        # the package is pushed for publishing ('yarn run publish' builds and
-        # publishes in one step)
         run: |
+          conda init
+          source ~/.bashrc
           yarn package
           ./run_postbuild_tests.sh
       - name: publish

diff --git a/electron-app/postbuild_tests/modules.test.ts b/electron-app/postbuild_tests/modules.test.ts
@@ -614,6 +614,8 @@ describe('modules', () => {
   ])(
     "Build and Test the conda workflow: module '%s'",
     async (modulenames, connections, outfiles) => {
+      console.log('::: test Build and Test the conda workflow');
+
       // Open settings pane
       await driver.findElement(By.xpath('//div[@id="btnSidenavSettings"]')).click();
 
@@ -627,6 +629,7 @@ describe('modules', () => {
 
       // Build and run workflow
       await BuildAndRun_MultiModuleWorkflow(driver, modulenames, connections, outfiles);
+      console.log('<<< test Build and Test the conda workflow');
     },
     5 * ONE_MINUTE,
   ); // long timeout

diff --git a/electron-app/run_postbuild_tests.sh b/electron-app/run_postbuild_tests.sh
@@ -17,7 +17,7 @@ RUNNER_OS=${RUNNER_OS:-$(uname)}
 # install miniforge if not already installed
 if ! command -v mamba &> /dev/null
 then
-    . ./install_miniforge.sh
+    source ./install_miniforge.sh
 fi
 
 # launch GRAPEVNE in the background and in debug mode