Create benchmarks

.github/workflows/benchmarks.yml

@@ -0,0 +1,42 @@
+name: Benchmarks
+on:
+  # TODO remove pull_request once it's consistent.
+  pull_request:
+    branches: ["*"]
+  schedule:
+    - cron: "0 5 * * WED"
+
+jobs:
+  run:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Setup Julia
+        uses: julia-actions/setup-julia@v2
+      - uses: julia-actions/cache@v2
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.13"
+          cache: "pip"
+      - name: Setup optimizers
+        uses: ./.github/actions/setup_optimizers_linux
+        with:
+          GUROBI_WLS: ${{ secrets.GUROBI_WLS }}
+          COPT_LICENSE_KEY: ${{ secrets.COPT_LICENSE_KEY }}
+          COPT_LICENSE_DAT: ${{ secrets.COPT_LICENSE_DAT }}
+          CHECK_LICENSE: true
+      - name: Install dependencies
+        run: |
+          pip install -e .
+          cd benchmarks
+          pip install -e .
+      - name: Install Julia packages
+        run: |
+          julia --project=benchmarks -e 'using Pkg; Pkg.instantiate()'
+      - name: Run benchmarks
+        run: |
+          cd benchmarks
+          cp config.testing.yaml config.yaml
+          snakemake --cores all

.vscode/launch.json

@@ -12,6 +12,29 @@
             "args": [
                 "serve"
             ]
+        },
+        {
+            "name": "Snakemake",
+            "type": "debugpy",
+            "request": "launch",
+            "module": "snakemake",
+            "cwd": "${workspaceFolder}/benchmarks",
+            "args": [
+                "--cores",
+                "all"
+            ],
+        },
+        {
+            "name": "Python Debugger: Snakemake",
+            "type": "debugpy",
+            "request": "launch",
+            "module": "snakemake",
+            "cwd": "${workspaceFolder}/benchmarks",
+            "args": [
+                "--cores",
+                "1",
+                "--debug"
+            ]
         }
     ]
 }

benchmarks/.gitignore

@@ -0,0 +1,3 @@
+results/**
+src/*/input_data/**
+!src/*/input_data/final_inputs/**