fix: Properly quote file paths with spaces

nipype/conftest.py

@@ -1,24 +1,45 @@
+import importlib
 import os
 import shutil
-from tempfile import mkdtemp
+import tempfile
 import pytest
 import numpy as np
 import py.path as pp
 
 NIPYPE_DATADIR = os.path.realpath(
     os.path.join(os.path.dirname(__file__), "testing/data")
 )
-temp_folder = mkdtemp()
-data_dir = os.path.join(temp_folder, "data")
-shutil.copytree(NIPYPE_DATADIR, data_dir)
+NIPYPE_TMPDIR = tempfile.mkdtemp()
+TMP_DATADIR = os.path.join(NIPYPE_TMPDIR, "data")
+
+
+def pytest_configure(config):
+    shutil.copytree(NIPYPE_DATADIR, TMP_DATADIR)
+
+    # Pytest uses gettempdir() to construct its tmp_paths, but the logic to get
+    # `pytest-of-<user>/pytest-<n>` directories is contingent on not directly
+    # configuring the `config.option.base_temp` value.
+    # Instead of replicating that logic, inject a new directory into gettempdir()
+    #
+    # Use the discovered temp dir as a base, to respect user/system settings.
+    if ' ' not in (base_temp := tempfile.gettempdir()):
+        new_base = os.path.join(base_temp, "nipype tmp")
+        os.makedirs(new_base, exist_ok=True)
+        os.environ['TMPDIR'] = os.path.join(base_temp, "nipype tmp")
+        importlib.reload(tempfile)
+        assert tempfile.gettempdir() == os.path.join(base_temp, "nipype tmp")
+
+
+def pytest_unconfigure(config):
+    shutil.rmtree(NIPYPE_TMPDIR)
 
 
 @pytest.fixture(autouse=True)
 def add_np(doctest_namespace):
     doctest_namespace["np"] = np
     doctest_namespace["os"] = os
     doctest_namespace["pytest"] = pytest
-    doctest_namespace["datadir"] = data_dir
+    doctest_namespace["datadir"] = TMP_DATADIR
 
 
 @pytest.fixture(scope='session', autouse=True)
@@ -33,7 +54,7 @@ def _docdir(request):
     doctest_plugin = request.config.pluginmanager.getplugin("doctest")
     if isinstance(request.node, doctest_plugin.DoctestItem):
         # Get the fixture dynamically by its name.
-        tmpdir = pp.local(data_dir)
+        tmpdir = pp.local(TMP_DATADIR)
 
         # Chdir only for the duration of the test.
         with tmpdir.as_cwd():
@@ -42,8 +63,3 @@ def _docdir(request):
     else:
         # For normal tests, we have to yield, since this is a yield-fixture.
         yield
-
-
-def pytest_unconfigure(config):
-    # Delete temp folder after session is finished
-    shutil.rmtree(temp_folder)

nipype/info.py

@@ -108,6 +108,7 @@ def get_nipype_gitversion():
 DATEUTIL_MIN_VERSION = "2.2"
 SIMPLEJSON_MIN_VERSION = "3.8.0"
 PROV_MIN_VERSION = "1.5.2"
+LXML_MIN_VERSION = "5.0"
 RDFLIB_MIN_VERSION = "5.0.0"
 CLICK_MIN_VERSION = "6.6.0"
 PYDOT_MIN_VERSION = "1.2.3"
@@ -139,6 +140,7 @@ def get_nipype_gitversion():
     "numpy>=%s" % NUMPY_MIN_VERSION,
     "packaging",
     "prov>=%s" % PROV_MIN_VERSION,
+    f"lxml>={LXML_MIN_VERSION}",  # prov < 2.0.2 depended on lxml, now it's an [xml] extra
     "pydot>=%s" % PYDOT_MIN_VERSION,
     "python-dateutil>=%s" % DATEUTIL_MIN_VERSION,
     "rdflib>=%s" % RDFLIB_MIN_VERSION,

nipype/interfaces/ants/utils.py

@@ -928,7 +928,7 @@ class LabelGeometry(ANTSCommand):
     >>> label_extract.inputs.dimension = 3
     >>> label_extract.inputs.label_image = 'atlas.nii.gz'
     >>> label_extract.cmdline
-    'LabelGeometryMeasures 3 atlas.nii.gz [] atlas.csv'
+    "LabelGeometryMeasures 3 atlas.nii.gz '[]' atlas.csv"
 
     >>> label_extract.inputs.intensity_image = 'ants_Warp.nii.gz'
     >>> label_extract.cmdline

nipype/interfaces/base/core.py

@@ -32,7 +32,7 @@
 
 from ...external.due import due
 
-from .traits_extension import traits, isdefined, Undefined
+from .traits_extension import traits, isdefined, BasePath, Undefined
 from .specs import (
     BaseInterfaceInputSpec,
     CommandLineInputSpec,
@@ -798,6 +798,13 @@ def _format_arg(self, name, trait_spec, value):
             # type-checking code here as well
             sep = trait_spec.sep if trait_spec.sep is not None else " "
 
+            if argstr == '%s':
+                inner_traits = getattr(trait_spec, "inner_traits", None)
+                if inner_traits and any(
+                    t.is_trait_type(BasePath) for t in inner_traits
+                ):
+                    values = [shlex.quote(elt) for elt in value]
+
             if argstr.endswith("..."):
                 # repeatable option
                 # --id %d... will expand to
@@ -807,6 +814,8 @@ def _format_arg(self, name, trait_spec, value):
             else:
                 return argstr % sep.join(str(elt) for elt in value)
         else:
+            if argstr == '%s' and trait_spec.is_trait_type(BasePath):
+                return shlex.quote(value)
             # Append options using format string.
             return argstr % value
 

nipype/interfaces/base/tests/test_core.py

@@ -608,3 +608,19 @@ def _run_interface(self, runtime):
 
     with pytest.raises(RuntimeError):
         BrokenRuntime().run()
+
+
+def test_CommandLine_escape(tmp_path):
+    test_file = tmp_path / "test file.txt"
+    test_file.write_text("content")
+
+    class InputSpec(nib.TraitedSpec):
+        in_file = nib.File(desc="a file", exists=True, argstr="%s")
+
+    class CatCommand(nib.CommandLine):
+        input_spec = InputSpec
+        _cmd = "cat"
+
+    command = CatCommand(in_file=str(test_file))
+    result = command.run()
+    assert result.runtime.stdout == "content"

nipype/interfaces/freesurfer/preprocess.py

@@ -1975,7 +1975,7 @@ def _list_outputs(self):
                 outputs["out_fsl_file"] = op.abspath(_in.out_fsl_file)
 
         if isdefined(_in.init_cost_file):
-            if isinstance(_in.out_fsl_file, bool):
+            if isinstance(_in.init_cost_file, bool):
                 outputs["init_cost_file"] = outputs["out_reg_file"] + ".initcost"
             else:
                 outputs["init_cost_file"] = op.abspath(_in.init_cost_file)

nipype/pipeline/plugins/base.py

@@ -5,6 +5,7 @@
 from copy import deepcopy
 from glob import glob
 import os
+import shlex
 import shutil
 from time import sleep, time
 from traceback import format_exception
@@ -564,7 +565,7 @@ def _submit_job(self, node, updatehash=False):
         batch_dir, name = os.path.split(pyscript)
         name = ".".join(name.split(".")[:-1])
         batchscript = "\n".join(
-            (self._template.rstrip("\n"), f"{sys.executable} {pyscript}")
+            (self._template.rstrip("\n"), shlex.join([sys.executable, pyscript]))
         )
         batchscriptfile = os.path.join(batch_dir, "batchscript_%s.sh" % name)
         with open(batchscriptfile, "w") as fp:

tox.ini

@@ -76,6 +76,7 @@ extras =
   full: ssh
   full: nipy
 setenv =
+  NO_ET=1
   FSLOUTPUTTYPE=NIFTI_GZ
   pre: PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
   pre: UV_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple