FIX: Build cmdline from working directory

Author: effigies

nipype/pipeline/engine/nodes.py

@@ -27,7 +27,7 @@
 from ...utils.filemanip import (md5, FileNotFoundError, filename_to_list,
                                 list_to_filename, copyfiles, fnames_presuffix,
                                 loadpkl, split_filename, load_json, makedirs,
-                                emptydirs, savepkl, to_str)
+                                emptydirs, savepkl, to_str, indirectory)
 
 from ...interfaces.base import (traits, InputMultiPath, CommandLine, Undefined,
                                 DynamicTraitedSpec, Bunch, InterfaceResult,
@@ -627,7 +627,8 @@ def _run_command(self, execute, copyfiles=True):
             self._interface.__class__.__name__)
         if issubclass(self._interface.__class__, CommandLine):
             try:
-                cmd = self._interface.cmdline
+                with indirectory(outdir):
+                    cmd = self._interface.cmdline
             except Exception as msg:
                 result.runtime.stderr = '{}\n\n{}'.format(
                     getattr(result.runtime, 'stderr', ''), msg)

nipype/utils/filemanip.py

@@ -18,6 +18,7 @@
 import os.path as op
 import re
 import shutil
+import contextlib
 import posixpath
 import simplejson as json
 import numpy as np
@@ -916,3 +917,11 @@ def relpath(path, start=None):
     if not rel_list:
         return os.curdir
     return op.join(*rel_list)
+
+
+@contextlib.contextmanager
+def indirectory(path):
+    cwd = os.getcwd()
+    os.chdir(path)
+    yield
+    os.chdir(cwd)

nipype/utils/tests/test_filemanip.py

@@ -14,7 +14,7 @@
     save_json, load_json, fname_presuffix, fnames_presuffix, hash_rename,
     check_forhash, _parse_mount_table, _cifs_table, on_cifs, copyfile,
     copyfiles, filename_to_list, list_to_filename, check_depends,
-    split_filename, get_related_files)
+    split_filename, get_related_files, indirectory)
 
 
 def _ignore_atime(stat):
@@ -490,3 +490,28 @@ def test_cifs_check():
 
     _cifs_table[:] = []
     _cifs_table.extend(orig_table)
+
+
+def test_indirectory(tmpdir):
+    tmpdir.chdir()
+
+    os.makedirs('subdir1/subdir2')
+    sd1 = os.path.abspath('subdir1')
+    sd2 = os.path.abspath('subdir1/subdir2')
+
+    assert os.getcwd() == tmpdir.strpath
+    with indirectory('/'):
+        assert os.getcwd() == '/'
+    assert os.getcwd() == tmpdir.strpath
+    with indirectory('subdir1'):
+        assert os.getcwd() == sd1
+        with indirectory('subdir2'):
+            assert os.getcwd() == sd2
+            with indirectory('..'):
+                assert os.getcwd() == sd1
+                with indirectory('/'):
+                    assert os.getcwd() == '/'
+                assert os.getcwd() == sd1
+            assert os.getcwd() == sd2
+        assert os.getcwd() == sd1
+    assert os.getcwd() == tmpdir.strpath