fix return-value/deprecated API bugs, accumulation lock leaks, code cleanup

- raise instead of silent None for unsupported operands and empty negation
- validate before acquiring lock in Accumulation operators (no RLock leak)
- Accumulation._copy_provenance helper, ADC_Result._copy_metadata for all result paths
- shared _sandbox_stdout_redirect contextmanager for sandboxed scripts
- TemperatureMonitor dead code removal (gtk helper, traceback, unused properties)
- new unit tests incl. lock-freedom regression test
- gitignore sphinx generated doc/_autosummary/ and doc/damaris/

src/damaris/gui/ExperimentHandling.py

@@ -5,6 +5,7 @@ import sys
 import time
 import logging
 import ast
+import contextlib
 from damaris.experiments.Experiment import Quit
 from damaris.experiments import Experiment
 
@@ -36,6 +37,19 @@ class _SandboxStdout:
         return False
 
 
+@contextlib.contextmanager
+def _sandbox_stdout_redirect(log_callback):
+    """Temporarily redirect process-global stdout/stderr to the sandbox log."""
+    old_stdout, old_stderr = sys.stdout, sys.stderr
+    sandbox = _SandboxStdout(log_callback)
+    try:
+        sys.stdout = sandbox
+        sys.stderr = sandbox
+        yield sandbox
+    finally:
+        sys.stdout, sys.stderr = old_stdout, old_stderr
+
+
 class ExperimentHandling(threading.Thread):
     """
     runs the experiment script in sandbox
@@ -52,17 +66,25 @@ class ExperimentHandling(threading.Thread):
             self.data["__recentexperiment"]=-1
 
     def synchronize(self, before=0, waitsteps=0.1):
-        while (self.data["__recentexperiment"]>self.data["__recentresult"]+before) and not self.quit_flag.isSet():
+        while (self.data["__recentexperiment"]>self.data["__recentresult"]+before) and not self.quit_flag.is_set():
             self.quit_flag.wait(waitsteps)
-        if self.quit_flag.isSet():
+        if self.quit_flag.is_set():
             raise StopExperiment
         
     def sleep(self, seconds):
         self.quit_flag.wait(seconds)
-        if self.quit_flag.isSet():
+        if self.quit_flag.is_set():
             raise StopExperiment
 
     def run(self):
+        # Redirect stdout/stderr so print() in sandboxed scripts goes to the GUI
+        if self._log_callback is not None:
+            with _sandbox_stdout_redirect(self._log_callback):
+                self._run_script()
+        else:
+            self._run_script()
+
+    def _run_script(self):
         dataspace={}
         exp_classes = __import__('damaris.experiments', dataspace, dataspace, ['Experiment'])
         for name in dir(exp_classes):
@@ -77,13 +99,6 @@ class ExperimentHandling(threading.Thread):
         self.location = None
         exp_iterator=None
 
-        # Redirect stdout/stderr so print() in sandboxed scripts goes to the GUI
-        _orig_stdout = sys.stdout
-        _orig_stderr = sys.stderr
-        if self._log_callback is not None:
-            sys.stdout = _SandboxStdout(self._log_callback)
-            sys.stderr = _SandboxStdout(self._log_callback)
-
         # check for time.sleep()
         try:
             tree = ast.parse(self.script)
@@ -131,7 +146,7 @@ class ExperimentHandling(threading.Thread):
                 traceback_file=None
                 return
         
-        while exp_iterator is not None and not self.quit_flag.isSet():
+        while exp_iterator is not None and not self.quit_flag.is_set():
             # get next experiment from script 
             try:
                 job=next(exp_iterator)
@@ -171,7 +186,7 @@ class ExperimentHandling(threading.Thread):
                     # relax for a short time
                     if "__resultsinadvance" in self.data and self.data["__resultsinadvance"]+100<job.job_id:
                         self.quit_flag.wait(0.05)
-                if self.quit_flag.isSet():
+                if self.quit_flag.is_set():
                     dataspace=None
                     exp_iterator=None
                     break
@@ -181,7 +196,3 @@ class ExperimentHandling(threading.Thread):
         dataspace=None
         self.exp_iterator=None
         self.writer=None
-
-        # Restore stdout/stderr
-        sys.stdout = _orig_stdout
-        sys.stderr = _orig_stderr