Merge branch 'master' into AC-aws

Author: Acribbs

.github/workflows/cgatcore_python.yml

@@ -26,17 +26,25 @@ jobs:
           CACHE_NUMBER: 0
         with:
           path: ~/conda_pkgs_dir
-          key:
-            ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
-            hashFiles('conda/environments/cgat-core.yml') }}
+          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('conda/environments/cgat-core.yml') }}
+      - name: Set installer URL
+        id: set-installer-url
+        run: |
+          if [[ "${{ matrix.os }}" == "ubuntu-latest" ]]; then
+            echo "installer-url=https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh" >> $GITHUB_ENV
+          elif [[ "${{ matrix.os }}" == "macos-latest" ]]; then
+            echo "installer-url=https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-arm64.sh" >> $GITHUB_ENV
+          fi
       - uses: conda-incubator/setup-miniconda@v2
         with:
+          installer-url: ${{ env.installer-url }}
           python-version: ${{ matrix.python-version }}
           channels: conda-forge, bioconda, defaults
           channel-priority: true
           activate-environment: cgat-core
           environment-file: conda/environments/cgat-core.yml
-          miniforge-variant: Mambaforge
+      - name: Configure Conda Paths
+        run: echo "/usr/share/miniconda3/condabin" >> $GITHUB_PATH
       - name: Show conda
         run: |
           conda info

cgatcore/pipeline/execution.py

@@ -1038,10 +1038,16 @@ def _convert(key, v):
             data.update(dict([(x[0], _convert(x[0], x[1]))
                               for x in pairs if len(x) == 2]))
 
-            # remove % sign
+            cpu_value = data.get("percent_cpu", "0")
+            # Strip potential '%' symbols, handle non-numeric cases gracefully
+            try:
+                percent_cpu = int(re.sub("%", "", cpu_value)) if cpu_value.replace("%", "").strip().isdigit() else 0
+            except ValueError:
+                percent_cpu = 0  # Default or fallback value, adjust as necessary
+
             data.update(
-                {"percent_cpu": int(re.sub("%", "", data.get("percent_cpu", 0))),
-                 "cpu_t": float(data["user_t"]) + float(data["sys_t"])})
+                {"percent_cpu": percent_cpu,
+                 "cpu_t": float(data.get("user_t", 0)) + float(data.get("sys_t", 0))})
 
         return JobInfo(jobId=process.pid, resourceUsage=data)