Make tests deterministic

primer3/thermoanalysis.pyx

@@ -2423,3 +2423,14 @@ class ThermoAnalysis(_ThermoAnalysis):
         '''
         pywarnings.warn(SNAKE_CASE_DEPRECATED_MSG % 'calc_tm')
         return self.calc_tm(seq1)
+
+cdef extern from "libprimer3.h":
+    const char* libprimer3_release()
+
+def get_libprimer3_version() -> str:
+    '''Get the version of the underlying libprimer3 C library.
+
+    Returns:
+        str: The version string of libprimer3
+    '''
+    return libprimer3_release().decode('utf-8')

pyproject.toml

@@ -38,6 +38,7 @@ classifiers = [
 dev = [
     "pre-commit~=3.5.0",
     "pytest~=7.4.0",
+    "tomli~=2.0.0",
 ]
 docs = [
     "myst-parser",

tests/save_thermo_values.py

@@ -0,0 +1,153 @@
+# Copyright (C) 2020-2025. Ben Pruitt & Nick Conway; Wyss Institute
+# See LICENSE for full GPLv2 license.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along
+# with this program; if not, write to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+'''
+tests.save_thermo_values
+~~~~~~~~~~~~~~~~~~~~~~~
+
+Script to generate and save gold standard thermodynamic values for
+regression testing. Imports calculation and saving functions from
+test_sequences.
+
+'''
+
+import json
+import platform
+import subprocess
+import sys
+from datetime import datetime
+from importlib.metadata import (
+    PackageNotFoundError,
+    version,
+)
+from pathlib import Path
+from typing import Dict
+
+import tomli
+
+from primer3 import __version__ as primer3_py_version
+from primer3 import thermoanalysis
+
+# Add the project root to the Python path
+project_root = Path(__file__).parent.parent
+sys.path.insert(0, str(project_root))
+
+from tests.test_sequences import calculate_thermo_values
+
+
+def get_git_info() -> Dict[str, str]:
+    '''Get git branch and latest tag information.
+
+    Returns:
+        Dictionary containing git branch and latest tag
+    '''
+    try:
+        branch = subprocess.check_output(
+            ['git', 'rev-parse', '--abbrev-ref', 'HEAD'],
+            stderr=subprocess.DEVNULL,
+        ).decode('utf-8').strip()
+
+        latest_tag = subprocess.check_output(
+            ['git', 'describe', '--tags', '--abbrev=0'],
+            stderr=subprocess.DEVNULL,
+        ).decode('utf-8').strip()
+
+        return {
+            'branch': branch,
+            'latest_tag': latest_tag,
+        }
+    except subprocess.CalledProcessError:
+        return {
+            'branch': 'unknown',
+            'latest_tag': 'unknown',
+        }
+
+
+def get_dependency_versions() -> Dict[str, str]:
+    '''Get versions of dependencies from pyproject.toml.
+
+    Returns:
+        Dictionary containing versions of Python dependencies
+    '''
+    deps = {}
+
+    # Read pyproject.toml
+    pyproject_path = Path(__file__).parent.parent / 'pyproject.toml'
+    with open(pyproject_path, 'rb') as f:
+        pyproject = tomli.load(f)
+
+    # Get build dependencies
+    build_deps = pyproject.get('build-system', {}).get('requires', [])
+    for dep in build_deps:
+        name = dep.split('>=')[0].split('~=')[0].split('==')[0].strip()
+        try:
+            deps[name] = version(name)
+        except PackageNotFoundError:
+            deps[name] = 'Not installed'
+
+    # Get dev dependencies
+    dev_deps = pyproject.get('project', {}).get(
+        'optional-dependencies', {},
+    ).get('dev', [])
+    for dep in dev_deps:
+        name = dep.split('>=')[0].split('~=')[0].split('==')[0].strip()
+        try:
+            deps[name] = version(name)
+        except PackageNotFoundError:
+            deps[name] = 'Not installed'
+
+    return deps
+
+
+def save_thermo_values_with_metadata(
+        values,
+        filename='tests/thermo_standard_values.json',
+) -> None:
+    '''Save thermodynamic values with metadata to a JSON file.'''
+    metadata = {
+        'generation_timestamp': datetime.now().isoformat(),
+        'primer3_py_version': primer3_py_version,
+        'primer3_lib_version': thermoanalysis.get_libprimer3_version(),
+        'python_version': sys.version,
+        'platform': {
+            'system': platform.system(),
+            'release': platform.release(),
+            'version': platform.version(),
+            'machine': platform.machine(),
+        },
+        'dependencies': get_dependency_versions(),
+        'git_info': get_git_info(),
+    }
+
+    output = {
+        'metadata': metadata,
+        'values': values,
+    }
+
+    with open(filename, 'w') as f:
+        json.dump(output, f, indent=2)
+
+
+if __name__ == '__main__':
+    # Calculate standard values using the function from test_sequences
+    standard_values = calculate_thermo_values()
+
+    # Save standard values to a JSON file with metadata
+    save_thermo_values_with_metadata(
+        standard_values, 'tests/thermo_standard_values.json',
+    )
+
+    print('Gold standard values saved to tests/thermo_standard_values.json')

tests/test_primerdesign.py

@@ -58,6 +58,25 @@ def _get_mem_usage():
 
 class TestDesignBindings(unittest.TestCase):
 
+    def setUp(self) -> None:
+        '''Set up test case'''
+        random.seed(42)  # Make random operations deterministic
+
+    def _generate_quality_list(self, length: int) -> List[int]:
+        '''Generate a deterministic list of quality scores
+
+        Args:
+            length: Length of quality score list to generate
+
+        Returns:
+            List of quality scores between 30 and 50 with mean around 45
+        '''
+        # Use triangular distribution to cluster scores around 45
+        return [
+            int(random.triangular(30, 50, 45))
+            for _ in range(length)
+        ]
+
     def _compare_results(
         self,
         binding_res: Dict[str, Any],
@@ -208,10 +227,7 @@ def test_compare_sim(self):
             'TGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCA'
             'CACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG'
         )
-        quality_list = [
-            random.randint(20, 90)
-            for i in range(len(sequence_template))
-        ]
+        quality_list = self._generate_quality_list(len(sequence_template))
         seq_args = {
             'SEQUENCE_ID': 'MH1000',
             'SEQUENCE_TEMPLATE': sequence_template,