added test from pymbar issue 419

openmmtools/tests/test_sampling.py

@@ -22,12 +22,14 @@
 import shutil
 import sys
 import tempfile
+import time
 from io import StringIO
 
 import numpy as np
 import yaml
 
 import pytest
+import requests
 
 try:
     import openmm
@@ -1861,7 +1863,7 @@ def test_analysis_opens_without_checkpoint(self):
             del reporter
             self.REPORTER(storage_path, checkpoint_storage=cp_file_mod, open_mode="r")
 
-    @pytest.mark.flaky(reruns=3)
+    @pytest.mark.skipif(sys.platform == "darwin", reason="seg faults on osx sometimes")
     def test_storage_reporter_and_string(self):
         """Test that creating a MultiState by storage string and reporter is the same"""
         thermodynamic_states, sampler_states, unsampled_states = copy.deepcopy(
@@ -2612,6 +2614,42 @@ def test_resume_velocities_from_legacy_storage(self):
                     state.velocities.value_in_unit_system(unit.md_unit_system) != 0
                 ), "At least some velocity in sampler state from new checkpoint is expected to different from zero."
 
+@pytest.fixture
+def download_nc_file(tmpdir):
+    FILE_URL = "https://github.com/user-attachments/files/17156868/ala-thr.zip"
+    MAX_RETRIES = 3
+    RETRY_DELAY = 2  # Delay between retries (in seconds)
+    file_name = os.path.join(tmpdir, "ala-thr.nc")
+    retries = 0
+    while retries < MAX_RETRIES:
+        try:
+          # Send GET request to download the file
+            response = requests.get(FILE_URL, timeout=20)  # Timeout to avoid hanging
+            response.raise_for_status()  # Raise HTTPError for bad responses (4xx/5xx)
+            with open(file_name, "wb") as f:
+                f.write(response.content)
+            # File downloaded successfully, break out of retry loop
+            break
+
+        except (requests.exceptions.RequestException, requests.exceptions.HTTPError) as e:
+            retries += 1
+            if retries >= MAX_RETRIES:
+                pytest.fail(f"Failed to download file after {MAX_RETRIES} retries: {e}")
+            else:
+                print(f"Retrying download... ({retries}/{MAX_RETRIES})")
+                time.sleep(RETRY_DELAY)  # Wait before retrying
+    yield file_name
+
+
+def test_pymbar_issue_419(download_nc_file):
+    from openmmtools.multistate import MultiStateReporter, MultiStateSamplerAnalyzer
+
+    n_iterations = 1000
+    reporter_file = download_nc_file
+    reporter = MultiStateReporter(reporter_file)
+    analyzer = MultiStateSamplerAnalyzer(reporter, max_n_iterations=n_iterations)
+    f_ij, df_ij = analyzer.get_free_energy()
+
 
 # ==============================================================================
 # MAIN AND TESTS