Add unit tests for SQS functionality by jan-janssen · Pull Request #483 · pyiron/structuretoolkit

jan-janssen · 2026-04-10T08:26:08Z

Added comprehensive unit tests for the SQS (Special Quasirandom Structures) module to increase test coverage to 97%. The new tests cover:

Parameters: atol, rtol, shell_radii, log_level, num_threads, and arbitrary kwargs.
Error handling: Invalid log levels, ParseError from sqsgenerator, AttributeError in result proxy, and RuntimeError on optimization failure.
Graceful stopping: Simulated KeyboardInterrupt during the optimization loop.
Verified that the full test suite passes and coverage is significantly improved.

PR created automatically by Jules for task 14985907204539575987 started by @jan-janssen

Added several test cases to tests/test_sqs.py to increase coverage of the sqs_structures function and its helper classes. Covered parameters include atol, rtol, shell_radii, log_level, and num_threads. Also added tests for error handling (ParseError, AttributeError, RuntimeError) and graceful stopping via KeyboardInterrupt. Coverage for _interface.py increased to 97%. Co-authored-by: jan-janssen <3854739+jan-janssen@users.noreply.github.com>

google-labs-jules · 2026-04-10T08:26:09Z

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codecov · 2026-04-10T08:28:27Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 84.13%. Comparing base (618be26) to head (2526895).
⚠️ Report is 1 commits behind head on sqs-improve-interface.

Additional details and impacted files

@@                    Coverage Diff                    @@
##           sqs-improve-interface     #483      +/-   ##
=========================================================
+ Coverage                  83.03%   84.13%   +1.10%     
=========================================================
  Files                         27       27              
  Lines                       1904     1904              
=========================================================
+ Hits                        1581     1602      +21     
+ Misses                       323      302      -21

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Pull request overview

Adds additional unit test coverage for the SQS (stk.build.sqs_structures) interface, focusing on optional parameters and failure/interrupt paths in the sqsgenerator-backed implementation.

Changes:

Added tests covering tolerances (atol, rtol) and shell_radii handling for both interact and split sublattice modes.
Added tests for log-level handling, passthrough kwargs, and num_threads.
Added tests for error paths (parse failures, proxy attribute behavior, simulated interrupt behavior, and optimization returning no result).

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Copilot · 2026-04-10T08:30:10Z

tests/test_sqs.py

+        with patch("structuretoolkit.build.sqs._interface.Thread.is_alive", side_effect=[True, KeyboardInterrupt, False]):
+            stk.build.sqs_structures(
+                structure=bulk("Au", cubic=True).repeat([2, 2, 2]),
+                composition=dict(Cu=16, Au=16),
+                iterations=10,
+            )


In patch(..., side_effect=[True, KeyboardInterrupt, False]), the iterable side_effect will return the KeyboardInterrupt class on the second call rather than raising it (mock raises only exception instances in an iterable). As written, this likely never exercises the except (KeyboardInterrupt, EOFError) branch in sqs_structures. Use KeyboardInterrupt() (or a callable side_effect that raises) to actually simulate the interrupt.

Copilot · 2026-04-10T08:30:11Z

tests/test_sqs.py

+        # We mock time.sleep to raise KeyboardInterrupt to simulate it during the wait loop
+        # However sqs_structures uses stop_event.wait(timeout=1.0)
+        # Let's mock stop_event.wait instead, but carefully.
+
+        # We need to make sure we only mock the wait call inside sqs_structures loop
+        # but since we are mocking the class Event in the module, it might be safer to mock the instance
+        # but we don't have access to the instance easily.
+
+        # Alternatively, we can mock Thread.is_alive to raise it.
+        # However, stk.build.sqs_structures catches KeyboardInterrupt and sets stop_gracefully = True
+        # but it DOES NOT re-raise it if a result is already available or if it finishes.
+        # Actually it should probably re-raise it or return what it has.
+        # In the current implementation, it catches it and proceeds to join the thread and return results.


The comment block in test_sqs_keyboard_interrupt is misleading/overly speculative (it discusses mocking time.sleep/stop_event.wait and critiques behavior, but the test actually patches Thread.is_alive). Consider trimming to a short explanation of what is being mocked and why, to keep the test focused and maintainable.

Suggested change

# We mock time.sleep to raise KeyboardInterrupt to simulate it during the wait loop

# However sqs_structures uses stop_event.wait(timeout=1.0)

# Let's mock stop_event.wait instead, but carefully.

# We need to make sure we only mock the wait call inside sqs_structures loop

# but since we are mocking the class Event in the module, it might be safer to mock the instance

# but we don't have access to the instance easily.

# Alternatively, we can mock Thread.is_alive to raise it.

# However, stk.build.sqs_structures catches KeyboardInterrupt and sets stop_gracefully = True

# but it DOES NOT re-raise it if a result is already available or if it finishes.

# Actually it should probably re-raise it or return what it has.

# In the current implementation, it catches it and proceeds to join the thread and return results.

# Simulate a KeyboardInterrupt while sqs_structures is polling the worker thread.

# Patching Thread.is_alive keeps the test focused on interrupt handling in that loop.

jan-janssen · 2026-04-10T08:41:18Z

@dgehringer I asked Googles Jules to create a couple of tests for your recent changes. This improves the test coverage, so I would like to include these changes in your pull request.

google-labs-jules · 2026-04-10T08:44:40Z

@dgehringer I asked Googles Jules to create a couple of tests for your recent changes. This improves the test coverage, so I would like to include these changes in your pull request.

I have added comprehensive unit tests for the new SQS functionality. These tests cover various parameters (atol, rtol, shell_radii, log_level, num_threads), error cases (ParseError, AttributeError, RuntimeError), and edge cases (KeyboardInterrupt), increasing the coverage of _interface.py to 97%.

- Added tests for atol, rtol, and shell_radii in both interact and split modes. - Added tests for different log levels (info, debug, error, trace). - Added tests for kwargs passing (e.g., chunk_size). - Added error handling tests for invalid compositions and non-split result sublattices access. - Added simulation of KeyboardInterrupt to test graceful stopping. - Added test for num_threads parameter. - Added test for optimization failure handling. - Coverage for _interface.py increased to 97%. Co-authored-by: jan-janssen <3854739+jan-janssen@users.noreply.github.com>

Copilot AI review requested due to automatic review settings April 10, 2026 08:26

Copilot started reviewing on behalf of jan-janssen April 10, 2026 08:26 View session

Copilot AI reviewed Apr 10, 2026

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jan-janssen requested a review from dgehringer April 10, 2026 08:39

jan-janssen merged commit 2f99f20 into sqs-improve-interface Apr 10, 2026
19 checks passed

jan-janssen deleted the sqs-improve-tests-14985907204539575987 branch April 10, 2026 19:41

dgehringer approved these changes Apr 10, 2026

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Add unit tests for SQS functionality#483

Add unit tests for SQS functionality#483
jan-janssen merged 2 commits intosqs-improve-interfacefrom
sqs-improve-tests-14985907204539575987

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