Merge branch 'wrapper_to_cmd' into 'main'

Fix infinite regression error when pickling wrapper functions

See merge request fsl/fslpy!449

fsl/tests/test_run.py

@@ -20,6 +20,7 @@ import pytest
 import fsl.utils.tempdir                  as tempdir
 from   fsl.utils.platform import platform as fslplatform
 import fsl.utils.run                      as run
+import fsl.wrappers                       as wrappers
 
 from . import make_random_image, mockFSLDIR, CaptureStdout, touch
 
@@ -479,7 +480,7 @@ def test_hold():
             threading.Thread(target=create_holdfile).start()
             run.hold([1, 2, 3], holdfile, timeout=1)
 
-        cmds = list(run.dryrun.commands)
+        cmds = list(run.DRY_RUN_COMMANDS)
 
     # dryrun gathers all executed commands
     # in a list of (cmd, submit) tuples,
@@ -534,6 +535,11 @@ def test_func_to_cmd():
                 else:
                     assert op.exists(fn), f"Failing job got removed even with clean = {clean}"
 
+def test_wrapper_to_cmd():
+    fn = run.func_to_cmd(wrappers.bet)
+    assert op.exists(fn)
+    assert op.basename(fn).startswith("bet_")
+
 
 def test_job_output():
     with tempdir.tempdir() as td:

fsl/utils/run.py

@@ -53,6 +53,12 @@ DRY_RUN = False
 execute them.
 """
 
+DRY_RUN_COMMANDS = None
+"""Contains the commands that got logged during a dry run.
+
+Commands will be logged if :data:`DRY_RUN` is true, which can be set using :func:`dryrun`.
+"""
+
 
 FSL_PREFIX = None
 """Global override for the FSL executable location used by :func:`runfsl`. """
@@ -73,14 +79,14 @@ def dryrun(*_):
 
     After this function returns, each command that was executed while the
     dryrun is active, along with any submission parameters, will be accessible
-    within a list which is stored as an attribute of this function called
-    ``commands``.
+    within a list which is stored as :data:`DRY_RUN_COMMANDS`.
     """
-    global DRY_RUN  # pylint: disable=global-statement
+    global DRY_RUN, DRY_RUN_COMMANDS  # pylint: disable=global-statement
 
     oldval          = DRY_RUN
     DRY_RUN         = True
-    dryrun.commands = []
+    DRY_RUN_COMMANDS = []
+
 
     try:
         yield
@@ -106,7 +112,6 @@ def prepareArgs(args):
     return list(args)
 
 
-real_stdout = sys.stdout
 def _forwardStream(in_, *outs):
     """Creates and starts a daemon thread which forwards the given input stream
     to one or more output streams. Used by the :func:`run` function to redirect
@@ -269,7 +274,8 @@ def _dryrun(submit, returnStdout, returnStderr, returnExitcode, *args):
 
     # Save command/submit parameters -
     # see the dryrun ctx manager
-    getattr(dryrun, 'commands', []).append((args, submit))
+    if DRY_RUN_COMMANDS is not None:
+        DRY_RUN_COMMANDS.append((args, submit))
 
     if submit:
         return ('0',)