Merge pull request #350 from SysBioChalmers/fix/failing-workflows

fix: failing workflows

.github/workflows/memote-history.yml

@@ -8,9 +8,11 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v3
+        # MEMOTE wants to fetch all branches
         with:
           fetch-depth: 0
 
+
       - name: Set up Python 3
         uses: actions/setup-python@v4
         with:
@@ -19,19 +21,12 @@ jobs:
       - name: Install memote
         run: pip install -r code/requirements/ci-requirements.txt
 
-      - name: Setup variables
-        id: setup
-        run: |
-          echo "::set-output name=history::history_report.html"
-          echo "::set-output name=deployment::$(awk -F '=' '{if (! ($0 ~ /^;/) && $0 ~ /deployment/) print $2}' memote.ini | tr -d ' ')"
-          echo "::set-output name=other-repo::gh-pages-repo"
-
       - name: Checkout repo for gh-pages branch
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           repository: ${{ github.repository }}
-          ref: ${{ steps.setup.outputs.deployment }}
-          path: ${{ steps.setup.outputs.other-repo }}
+          ref: gh-pages
+          path: gh-pages-repo
 
       # - name: Convert model
       #   run: |
@@ -40,21 +35,26 @@ jobs:
 
       - name: Memote short run
         run: |
-          git config --global user.name "memote-bot"
-          memote run --skip-unchanged --solver-timeout 30
+          memote run --ignore-git --skip-unchanged --solver-timeout 30
 
       - name: Compute Memote history on push
         run: |
           # Generate the history report on the deployment branch
-          memote report history --filename="${{ steps.setup.outputs.other-repo }}/${{ steps.setup.outputs.history }}"
+          git config --global user.name "memote-bot"
+          memote report history --filename="gh-pages-repo/history_report.html"
+
+      - name: Fetch async changes in gh-pages
+        run: |
+          cd gh-pages-repo
+          git pull
 
       - name: Auto-commit results
         uses: stefanzweifel/git-auto-commit-action@v4
         with:
           commit_user_name: memote-bot
           commit_message: "chore: update memote history report"
-          file_pattern: ${{ steps.setup.outputs.history }}
-          branch: ${{ steps.setup.outputs.deployment }}
-          repository: ${{ steps.setup.outputs.other-repo }}
+          file_pattern: history_report.html
+          branch: gh-pages
+          repository: gh-pages-repo
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/memote-release.yml

@@ -24,13 +24,21 @@ jobs:
         with:
           python-version: "3.9"
 
+      - name: Create .env
+        run: touch .env
+
       - name: Install memote
         run: pip install -r code/requirements/requirements.txt
 
       - name: Memote run
         run: |
           memote report snapshot --solver-timeout 30 --filename="gh-pages-repo/release_report.html"
 
+      - name: Fetch async changes in gh-pages
+        run: |
+          cd gh-pages-repo
+          git pull
+
       - name: Auto-commit results
         uses: stefanzweifel/git-auto-commit-action@v4
         with:

.github/workflows/memote-run.yml

@@ -5,21 +5,20 @@ on: pull_request
 jobs:
   memote-run:
     runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/metabolicatlas/memote-docker:0.13
+      volumes:
+        - ${{ github.workspace }}:/project:rw
+      options: --user root --workdir /project
+
     steps:
       - name: Checkout
         uses: actions/checkout@v3
 
       - name: Create .env
-        run: touch .env
-
-      - name: Memote on PR
-        uses: addnab/docker-run-action@v3
-        with:
-          image: ghcr.io/metabolicatlas/memote-docker:0.13
-          options: -v ${{ github.workspace }}:/opt
-          shell: bash
-          run: |
-            cd /opt
-            pip install -r code/requirements/ci-requirements.txt
-            python -c 'import code.io as io; model = io.read_yeast_model(make_bigg_compliant=True); io.write_yeast_model(model)'
-            memote run --ignore-git --solver-timeout 30
+        run: |
+          touch .env
+          cd /project
+          pip install -r code/requirements/ci-requirements.txt
+          python -c 'import code.io as io; model = io.read_yeast_model(make_bigg_compliant=True); io.write_yeast_model(model)'
+          memote run --ignore-git --solver-timeout 30