From b1697b8afa49f3300bb4912adac41844be4f8274 Mon Sep 17 00:00:00 2001
From: Ben Wooding <38587669+Kiguli@users.noreply.github.com>
Date: Fri, 5 Sep 2025 10:13:04 +0100
Subject: [PATCH 1/5] Testing Workflow for versions

testing installation for python 3.9, 3.10 and 3.11.
---
 .github/workflows/python-package.yml | 40 ++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 .github/workflows/python-package.yml

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
new file mode 100644
index 0000000..e56abb6
--- /dev/null
+++ b/.github/workflows/python-package.yml
@@ -0,0 +1,40 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python package
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest

From 58133db2130020e1d4a911aaa62eb471048f1fc3 Mon Sep 17 00:00:00 2001
From: Ben Wooding <38587669+Kiguli@users.noreply.github.com>
Date: Fri, 5 Sep 2025 10:23:28 +0100
Subject: [PATCH 2/5] Modify linting and testing to exclude FOSSIL parts

---
 .github/workflows/python-package.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index e56abb6..9e34c50 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -32,9 +32,9 @@ jobs:
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --exclude fossil-main,ex/benchmarks-deterministic/FOSSIL-versions
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics --exclude fossil-main,ex/benchmarks-deterministic/FOSSIL-versions
     - name: Test with pytest
       run: |
-        pytest
+        pytest --ignore=fossil-main --ignore=ex/benchmarks-deterministic/FOSSIL-versions

From 8770039f62e45afd7aa83c3a72b067f42b23672d Mon Sep 17 00:00:00 2001
From: Ben Wooding <38587669+Kiguli@users.noreply.github.com>
Date: Fri, 5 Sep 2025 10:28:15 +0100
Subject: [PATCH 3/5] Create test for main.py execution

---
 tests/test_main.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)
 create mode 100644 tests/test_main.py

diff --git a/tests/test_main.py b/tests/test_main.py
new file mode 100644
index 0000000..1538dc8
--- /dev/null
+++ b/tests/test_main.py
@@ -0,0 +1,13 @@
+import subprocess
+import sys
+import os
+
+def test_main_runs():
+    """Check that main.py runs without errors."""
+    result = subprocess.run(
+        [sys.executable, os.path.join(os.path.dirname(__file__), "..", "main.py")],
+        capture_output=True,
+        text=True
+    )
+    # Assert that the script exits successfully
+    assert result.returncode == 0, f"main.py failed with error:\n{result.stderr}"

From 9a5f1f6bde80e31c8535960f028cca8158a4945b Mon Sep 17 00:00:00 2001
From: Ben Wooding <38587669+Kiguli@users.noreply.github.com>
Date: Fri, 5 Sep 2025 10:33:56 +0100
Subject: [PATCH 4/5] Rename test and check benchmark script execution

---
 tests/test_main.py | 21 ++++++++++++++++-----
 1 file changed, 16 insertions(+), 5 deletions(-)

diff --git a/tests/test_main.py b/tests/test_main.py
index 1538dc8..87bc86c 100644
--- a/tests/test_main.py
+++ b/tests/test_main.py
@@ -2,12 +2,23 @@
 import sys
 import os
 
-def test_main_runs():
-    """Check that main.py runs without errors."""
+def test_benchmark_runs():
+    """Check that the benchmark script runs without errors."""
+
+    # Path to the benchmark script (update if needed)
+    benchmark_path = os.path.join(
+        os.path.dirname(__file__),
+        "..", "ex", "benchmarks-deterministic", "PRoTECT-versions", "ex1_dt_DS.py"
+    )
+
+    # Verify the file exists before running
+    assert os.path.exists(benchmark_path), f"Benchmark script not found: {benchmark_path}"
+
     result = subprocess.run(
-        [sys.executable, os.path.join(os.path.dirname(__file__), "..", "main.py")],
+        [sys.executable, benchmark_path],
         capture_output=True,
         text=True
     )
-    # Assert that the script exits successfully
-    assert result.returncode == 0, f"main.py failed with error:\n{result.stderr}"
+
+    # Assert successful exit
+    assert result.returncode == 0, f"Benchmark failed with error:\n{result.stderr}"

From c916f5dae83475f1f7a24392894d56d879523cba Mon Sep 17 00:00:00 2001
From: Ben Wooding <38587669+Kiguli@users.noreply.github.com>
Date: Fri, 5 Sep 2025 10:36:27 +0100
Subject: [PATCH 5/5] Update test to include PYTHONPATH environment variable

---
 tests/test_main.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/tests/test_main.py b/tests/test_main.py
index 87bc86c..22bcb8f 100644
--- a/tests/test_main.py
+++ b/tests/test_main.py
@@ -5,20 +5,21 @@
 def test_benchmark_runs():
     """Check that the benchmark script runs without errors."""
 
-    # Path to the benchmark script (update if needed)
     benchmark_path = os.path.join(
         os.path.dirname(__file__),
         "..", "ex", "benchmarks-deterministic", "PRoTECT-versions", "ex1_dt_DS.py"
     )
 
-    # Verify the file exists before running
     assert os.path.exists(benchmark_path), f"Benchmark script not found: {benchmark_path}"
 
+    env = os.environ.copy()
+    env["PYTHONPATH"] = os.path.join(os.path.dirname(__file__), "..")
+
     result = subprocess.run(
         [sys.executable, benchmark_path],
         capture_output=True,
-        text=True
+        text=True,
+        env=env
     )
 
-    # Assert successful exit
     assert result.returncode == 0, f"Benchmark failed with error:\n{result.stderr}"