Replace third-party ssh and rsync actions with access-nri/setup-ssh a…

…ctions
ACCESS-NRI · Sep 26, 2024 · 344637c · 344637c
1 parent 1ee2fba
commit 344637c
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Showing 6 changed files with 122 additions and 77 deletions.
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -9,18 +9,24 @@ jobs:
   build:
     name: Build environment
     runs-on: ubuntu-latest
+    environment: Gadi
     steps:
-      - name: Build environment
-        uses: appleboy/[email protected]
+      - name: Setup SSH
+        uses: access-nri/actions/.github/actions/setup-ssh@main
+        id: ssh
         with:
-          host: gadi.nci.org.au
-          username: ${{secrets.GADI_USER}}
-          key: ${{secrets.DEPLOY_KEY}}
-          command_timeout: 120m
-          script: |
-            export SCRIPT_DIR=${{secrets.GADI_REPO_PATH}}/scripts
-            eval $( grep ADMIN_DIR $SCRIPT_DIR/install_config.sh )
-            eval $( grep JOB_LOG_DIR $SCRIPT_DIR/install_config.sh )
-            cd $JOB_LOG_DIR
-            # TODO: Replace with gdata/vk83
-            qsub -N build_${{ inputs.environment }} -lncpus=1,mem=20GB,walltime=2:00:00,jobfs=50GB,storage=scratch/tm70 -v SCRIPT_DIR,CONDA_ENVIRONMENT=${{ inputs.environment }} -P tm70 -q copyq -Wblock=true -Wumask=037 "${SCRIPT_DIR}"/build.sh
+          hosts: ${{ secrets.HOST }}
+          private-key: ${{ secrets.SSH_KEY }}
+
+      - name: Build environment
+        run: |
+          ssh ${{ secrets.USER }}@${{ secrets.HOST }} -i ${{ steps.ssh.outputs.private-key-path }} /bin/bash <<'EOT'
+
+          export SCRIPT_DIR=${{secrets.REPO_PATH}}/scripts
+          eval $( grep ADMIN_DIR $SCRIPT_DIR/install_config.sh )
+          eval $( grep JOB_LOG_DIR $SCRIPT_DIR/install_config.sh )
+          cd $JOB_LOG_DIR
+          # TODO: Replace with gdata/vk83
+          qsub -N build_${{ inputs.environment }} -lncpus=1,mem=20GB,walltime=2:00:00,jobfs=50GB,storage=scratch/tm70 -v SCRIPT_DIR,CONDA_ENVIRONMENT=${{ inputs.environment }} -P tm70 -q copyq -Wblock=true -Wumask=037 "${SCRIPT_DIR}"/build.sh
+
+          EOT
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -9,16 +9,23 @@ jobs:
   deploy:
     name: Deploy environment
     runs-on: ubuntu-latest
+    environment: Gadi
     steps:
-      - name: Deploy environment
-        uses: appleboy/[email protected]
+      - name: Setup SSH
+        uses: access-nri/actions/.github/actions/setup-ssh@main
+        id: ssh
         with:
-          host: gadi.nci.org.au
-          username: ${{secrets.GADI_USER}}
-          key: ${{secrets.DEPLOY_KEY}}
-          script: |
-            export SCRIPT_DIR=${{secrets.GADI_REPO_PATH}}/scripts
-            export CONDA_ENVIRONMENT=${{ inputs.environment }}
-            eval $( grep ADMIN_DIR $SCRIPT_DIR/install_config.sh )
-            eval $( grep BUILD_STAGE_DIR $SCRIPT_DIR/install_config.sh )
-            "${SCRIPT_DIR}"/deploy.sh
+          hosts: ${{ secrets.HOST }}
+          private-key: ${{ secrets.SSH_KEY }}
+
+      - name: Deploy environment
+        run: |
+          ssh ${{ secrets.USER }}@${{ secrets.HOST }} -i ${{ steps.ssh.outputs.private-key-path }} /bin/bash <<'EOT'
+
+          export SCRIPT_DIR=${{ secrets.REPO_PATH }}/scripts
+          export CONDA_ENVIRONMENT=${{ inputs.environment }}
+          eval $( grep ADMIN_DIR $SCRIPT_DIR/install_config.sh )
+          eval $( grep BUILD_STAGE_DIR $SCRIPT_DIR/install_config.sh )
+          "${SCRIPT_DIR}"/deploy.sh
+
+          EOT
diff --git a/.github/workflows/manual_trigger.yml b/.github/workflows/manual_trigger.yml
@@ -10,27 +10,36 @@ on:
 jobs:
   setup:
     runs-on: ubuntu-latest
+    environment: Gadi
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
+
+      - name: Setup SSH
+        uses: access-nri/actions/.github/actions/setup-ssh@main
+        id: ssh
+        with:
+          hosts: |
+            ${{ secrets.HOST }}
+            ${{ secrets.HOST_DATA }}
+          private-key: ${{ secrets.SSH_KEY }}
+
       - name: Sync repository to Gadi
-        uses: up9cloud/[email protected]
-        env:
-          HOST: gadi.nci.org.au
-          TARGET: ${{secrets.GADI_REPO_PATH}}
-          KEY: ${{secrets.DEPLOY_KEY}}
-          USER: ${{secrets.GADI_USER}}
+        run: |
+          rsync -e 'ssh -i ${{ steps.ssh.outputs.private-key-path }}' \
+            ./ \
+            ${{ secrets.USER }}@${{ secrets.HOST_DATA }}:${{ secrets.REPO_PATH }}
+
       - name: Create Admin dirs on Gadi
-        uses: appleboy/[email protected]
-        with:
-          host: gadi.nci.org.au
-          username: ${{secrets.GADI_USER}}
-          key: ${{secrets.DEPLOY_KEY}}
-          script: |
-            source ${{secrets.GADI_REPO_PATH}}/scripts/install_config.sh
-            source ${{secrets.GADI_REPO_PATH}}/scripts/functions.sh
-            mkdir -p $ADMIN_DIR $JOB_LOG_DIR $BUILD_STAGE_DIR
-            set_admin_perms $ADMIN_DIR $JOB_LOG_DIR $BUILD_STAGE_DIR
+        run: |
+          ssh ${{ secrets.USER }}@${{ secrets.HOST }} -i ${{ steps.ssh.outputs.private-key-path }} /bin/bash <<'EOT'
+
+          source ${{ secrets.REPO_PATH }}/scripts/install_config.sh
+          source ${{ secrets.REPO_PATH }}/scripts/functions.sh
+          mkdir -p $ADMIN_DIR $JOB_LOG_DIR $BUILD_STAGE_DIR
+          set_admin_perms $ADMIN_DIR $JOB_LOG_DIR $BUILD_STAGE_DIR
+
+          EOT
 
   build:
     needs: setup

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
@@ -11,41 +11,51 @@ jobs:
     container:
       image: quay.io/singularity/singularity:v3.11.4
       options: --privileged
+    environment: Gadi
     steps:
       - name: Checkout repository
         ### Latest at time of writing
         uses: actions/checkout@v4
+
       - name: Check if container definition has changed
         id: changed-container-def
         uses: tj-actions/changed-files@v41
         with:
           files_yaml: |
             containerdef:
               - container/container.def
+
       - name: Build container if definition has changed
         if: steps.changed-container-def.outputs.containerdef_any_changed == 'true'
         run: |
             echo ${{ needs.generate_matrix.outputs.matrix }}
             sudo -E singularity build container/base.sif container/container.def
+
+      - name: Setup SSH
+        uses: access-nri/actions/.github/actions/setup-ssh@main
+        id: ssh
+        with:
+          hosts: |
+            ${{ secrets.HOST }}
+            ${{ secrets.HOST_DATA }}
+          private-key: ${{ secrets.SSH_KEY }}
+
       - name: Sync repository to Gadi
-        ### Latest at time of writing
-        uses: up9cloud/[email protected]
-        env:
-          HOST: gadi.nci.org.au
-          TARGET: ${{secrets.GADI_REPO_PATH}}
-          KEY: ${{secrets.DEPLOY_KEY}}
-          USER: ${{secrets.GADI_USER}}
+        run: |
+          rsync -e 'ssh -i ${{ steps.ssh.outputs.private-key-path }}' \
+            ./ \
+            ${{ secrets.USER }}@${{ secrets.HOST_DATA }}:${{ secrets.REPO_PATH }}
+
       - name: Create Admin dirs on Gadi
-        uses: appleboy/[email protected]
-        with:
-          host: gadi.nci.org.au
-          username: ${{secrets.GADI_USER}}
-          key: ${{secrets.DEPLOY_KEY}}
-          script: |
-            source ${{secrets.GADI_REPO_PATH}}/scripts/install_config.sh
-            source ${{secrets.GADI_REPO_PATH}}/scripts/functions.sh
-            mkdir -p $ADMIN_DIR $JOB_LOG_DIR $BUILD_STAGE_DIR
-            set_admin_perms $ADMIN_DIR $JOB_LOG_DIR $BUILD_STAGE_DIR
+        run: |
+          ssh ${{ secrets.USER }}@${{ secrets.HOST }} -i ${{ steps.ssh.outputs.private-key-path }} /bin/bash <<'EOT'
+
+          source ${{ secrets.REPO_PATH }}/scripts/install_config.sh
+          source ${{ secrets.REPO_PATH }}/scripts/functions.sh
+          mkdir -p $ADMIN_DIR $JOB_LOG_DIR $BUILD_STAGE_DIR
+          set_admin_perms $ADMIN_DIR $JOB_LOG_DIR $BUILD_STAGE_DIR
+
+          EOT
 
   build:
     needs: [ generate_matrix, setup ]

diff --git a/.github/workflows/push_to_main.yml b/.github/workflows/push_to_main.yml
@@ -8,19 +8,25 @@ jobs:
 
   setup:
     runs-on: ubuntu-latest
+    environment: Gadi
     steps:
       - name: Checkout repository
         ### Latest at time of writing
         uses: actions/checkout@v4
+
+      - name: Setup SSH
+        uses: access-nri/actions/.github/actions/setup-ssh@main
+        id: ssh
+        with:
+          hosts: ${{ secrets.HOST_DATA }}
+          private-key: ${{ secrets.SSH_KEY }}
+
       - name: Sync repository to Gadi
-        ### Latest at time of writing
-        uses: up9cloud/[email protected]
-        env:
-          HOST: gadi.nci.org.au
-          TARGET: ${{secrets.GADI_REPO_PATH}}
-          KEY: ${{secrets.DEPLOY_KEY}}
-          USER: ${{secrets.GADI_USER}}
-
+        run: |
+          rsync -e 'ssh -i ${{ steps.ssh.outputs.private-key-path }}' \
+            ./ \
+            ${{ secrets.USER }}@${{ secrets.HOST_DATA }}:${{ secrets.REPO_PATH }}
+
   deploy:
     needs: [ generate_matrix, setup ]
     uses: ./.github/workflows/deploy.yml

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -9,17 +9,24 @@ jobs:
   test:
     name: Test environment
     runs-on: ubuntu-latest
+    environment: Gadi
     steps:
-      - name: Test environment
-        uses: appleboy/[email protected]
+      - name: Setup SSH
+        uses: access-nri/actions/.github/actions/setup-ssh@main
+        id: ssh
         with:
-          host: gadi.nci.org.au
-          username: ${{secrets.GADI_USER}}
-          key: ${{secrets.DEPLOY_KEY}}
-          script: |
-            export SCRIPT_DIR=${{secrets.GADI_REPO_PATH}}/scripts
-            eval $( grep ADMIN_DIR $SCRIPT_DIR/install_config.sh )
-            eval $( grep JOB_LOG_DIR $SCRIPT_DIR/install_config.sh )
-            cd $JOB_LOG_DIR
-            # TODO: Update storage flags?
-            qsub -N test_${{ inputs.environment }} -lncpus=4,mem=20GB,walltime=0:20:00,jobfs=50GB,storage=scratch/tm70 -v SCRIPT_DIR,CONDA_ENVIRONMENT=${{ inputs.environment }} -P tm70 -Wblock=true -Wumask=037 "${SCRIPT_DIR}"/test.sh
+          hosts: ${{ secrets.HOST }}
+          private-key: ${{ secrets.SSH_KEY }}
+
+      - name: Test environment
+        run: |
+          ssh ${{ secrets.USER }}@${{ secrets.HOST }} -i ${{ steps.ssh.outputs.private-key-path }} /bin/bash <<'EOT'
+
+          export SCRIPT_DIR=${{secrets.REPO_PATH}}/scripts
+          eval $( grep ADMIN_DIR $SCRIPT_DIR/install_config.sh )
+          eval $( grep JOB_LOG_DIR $SCRIPT_DIR/install_config.sh )
+          cd $JOB_LOG_DIR
+          # TODO: Update storage flags?
+          qsub -N test_${{ inputs.environment }} -lncpus=4,mem=20GB,walltime=0:20:00,jobfs=50GB,storage=scratch/tm70 -v SCRIPT_DIR,CONDA_ENVIRONMENT=${{ inputs.environment }} -P tm70 -Wblock=true -Wumask=037 "${SCRIPT_DIR}"/test.sh
+
+          EOT