fix flaky pixi toml query (#74)

Author: irm-codebase

.github/workflows/pr-ci.yml

@@ -12,10 +12,9 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.12"]
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7
       - name: setup-pixi
-        uses: prefix-dev/setup-pixi@v0.8.3
+        uses: prefix-dev/setup-pixi@v0.9.6
       - name: Run tests
         run: pixi run test

template/.github/workflows/pr-ci.yml

@@ -13,11 +13,10 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.12"]
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7
       - name: Setup pixi
-        uses: prefix-dev/setup-pixi@v0.8.3
+        uses: prefix-dev/setup-pixi@v0.9.6
       - name: Run integration tests
         id: tests
         run: pixi run test-integration
@@ -30,7 +29,7 @@ jobs:
         continue-on-error: true
       - name: Save integration logs
         if: ${{ always() }}
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: integration-test-logs-${{ matrix.os }}
           path: tests/integration/resources/module/logs

template/tests/integration_test.py

@@ -4,31 +4,22 @@
 Contents may be updated in future template updates.
 """
 
-import json
 import subprocess
+import tomllib
 from pathlib import Path
 
 import pytest
 from clio_tools.data_module import ModuleInterface
 
 
 @pytest.fixture(scope="module")
-def pixi_environments(module_path) -> dict:
-    """Pixi environments defined for this project."""
-    process = subprocess.run(
-        ["pixi", "info", "--json"],
-        check=True,
-        cwd=module_path,
-        capture_output=True,
-        text=True,
-    )
-    return {
-        environment["name"]: environment
-        for environment in json.loads(process.stdout)["environments_info"]
-    }
+def pixi_platforms(module_path) -> list[str]:
+    """Pixi platforms defined for this project."""
+    with (module_path / "pixi.toml").open("rb") as pixi_config:
+        return tomllib.load(pixi_config)["workspace"]["platforms"]
 
 
-def test_snakemake_environments(module_path, pixi_environments, tmp_path):
+def test_snakemake_environments(module_path, pixi_platforms, tmp_path):
     """All Snakemake environment files should be based on pixi counterparts."""
     env_dir = module_path / "workflow/envs"
     env_files = sorted(env_dir.glob("*.yaml"))
@@ -47,7 +38,7 @@ def test_snakemake_environments(module_path, pixi_environments, tmp_path):
         generated_yaml = output_dir / env_file.name
         assert generated_yaml.read_text() == env_file.read_text()
 
-        for platform in pixi_environments[env_name]["platforms"]:
+        for platform in pixi_platforms:
             pin_file = env_dir / f"{env_name}.{platform}.pin.txt"
             assert pin_file.exists(), f"{env_name} has no conda pins for {platform}"