add quality checks

.github/workflows/quality_checks.yml

@@ -0,0 +1,46 @@
+# This is a basic workflow to help you get started with Actions
+
+name: quality checks
+
+# Controls when the workflow will run
+on:
+  # Triggers the workflow on push or pull request events but only for the master branch
+  push:
+    branches: [ main]
+  pull_request:
+    branches: [ main]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "build"
+  TestBuild:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.12"]
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v4
+
+      # Install python
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      # Install the package
+      - name: Install packages
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install pytest pandas f4enix
+
+      # Run pytest
+      - name: Testing
+        run: |
+          python -m pytest

.gitignore

@@ -1 +1,4 @@
-get_wwinp.py
+get_wwinp.py
+*pyc
+.vscode
+**/__pycache__/

tests/test_quality_jade.py

@@ -0,0 +1,132 @@
+import json
+import os
+from pathlib import Path
+import pandas as pd
+import re
+from f4enix import Input
+
+rmode_pat = re.compile(r"RMODE", re.IGNORECASE)
+
+ROOT = Path("jade_open_benchmarks")
+
+
+def test_metadata():
+    for folder in os.listdir(ROOT / "inputs"):
+        path_folder = ROOT / "inputs" / folder
+        if not path_folder.is_dir():
+            continue
+        with open(path_folder / "benchmark_metadata.json") as f:
+            data = json.load(f)
+        assert data["name"] == folder
+
+        # check internal structure
+        ref_set_flag = False
+        for subrun in os.listdir(path_folder):
+            if subrun == "benchmark_metadata.json":
+                continue
+
+            codes = os.listdir(path_folder / subrun)
+            if not ref_set_flag:
+                ref_codes = codes
+                ref_set_flag = True
+                continue
+
+            # check that in all subrun the same codes are implemented
+            assert codes == ref_codes, f"Subrun {subrun}"
+
+        # check that the version is specified for each code
+        for code in ref_codes:
+            assert data["version"][code]
+
+
+def test_error_relative():
+    absolute_errors = []
+
+    # these are exceptions where the rel error is indeed above 1
+    manually_checked = ["Tiara-BC", "FNS-TOF"]
+
+    for folder in os.listdir(ROOT / "exp_results"):
+        if folder in manually_checked:
+            continue
+        for file in os.listdir(ROOT / "exp_results" / folder):
+            file = ROOT / "exp_results" / folder / file
+            df = pd.read_csv(file)
+            if df["Error"].max() > 1:
+                absolute_errors.append(folder)
+                print(
+                    f"Absolute error found in {file}: max error = {df['Error'].max()}"
+                )
+    absolute_errors = list(set(absolute_errors))
+    assert len(absolute_errors) == 0, f"Folders with absolute errors: {absolute_errors}"
+
+
+def test_no_RMODE_card():
+    for file in mcnp_input_paths_generator():
+        with open(file) as f:
+            for line in f:
+                if rmode_pat.match(line):
+                    raise AssertionError(f"RMODE card found in {file}")
+
+
+def test_f4enix_readability():
+    """test that all MCNP input files can be read by f4enix"""
+    for file in mcnp_input_paths_generator():
+        _ = Input.from_input(file)
+
+
+def test_exp_data_naming_consistency():
+    """test that all files in exp_results have a corresponding input file with the
+    same name"""
+    known_exceptions = ["Oktavian_Pb"]
+    for folder in os.listdir(Path(ROOT, "exp_results")):
+        path_folder = Path(ROOT, "exp_results", folder)
+        for file in os.listdir(path_folder):
+            name = file.split(" ")[0]
+            if name in known_exceptions:
+                continue
+            assert Path(ROOT, "inputs", folder, name).exists(), (
+                f"File {file} in {folder} does not match any input file"
+            )
+
+
+def test_mcnp_filename_matches_subrun():
+    """Test that MCNP input file names match their parent subrun folder names."""
+    for folder in os.listdir(ROOT / "inputs"):
+        folder_path = ROOT / "inputs" / folder
+        if not folder_path.is_dir():
+            continue
+        for subrun in os.listdir(folder_path):
+            subrun_path = folder_path / subrun
+            if not subrun_path.is_dir():
+                continue
+            for code in os.listdir(subrun_path):
+                if code != "mcnp":
+                    continue
+                mcnp_path = subrun_path / code
+                # Get all .i files in the mcnp directory
+                i_files = list(mcnp_path.glob("*.i"))
+                assert len(i_files) == 1, (
+                    f"Expected exactly 1 .i file in {mcnp_path}, found {len(i_files)}"
+                )
+
+                expected_filename = f"{subrun}.i"
+                actual_filename = i_files[0].name
+                assert actual_filename == expected_filename, (
+                    f"File name mismatch in {mcnp_path}: expected '{expected_filename}', found '{actual_filename}'"
+                )
+
+
+def mcnp_input_paths_generator():
+    for folder in os.listdir(Path(ROOT, "inputs")):
+        folder_path = Path(ROOT, "inputs", folder)
+        if not folder_path.is_dir():
+            continue
+        for subrun in os.listdir(folder_path):
+            subrun_path = folder_path / subrun
+            if not subrun_path.is_dir():
+                continue
+            for code in os.listdir(subrun_path):
+                if code != "mcnp":
+                    continue
+
+                yield subrun_path / code / f"{subrun}.i"