added anon-cmd unit test. verified in py36 and py27

ready for pr

Author: daeh

Dockerfile

@@ -71,7 +71,6 @@ RUN apt-get update -qq \
            libc-dev \
            git-annex-standalone \
            netbase \
-           vim \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
@@ -148,6 +147,7 @@ RUN echo '{ \
     \n          "traits>=4.6.0", \
     \n          "scipy", \
     \n          "numpy", \
+    \n          "pandas", \
     \n          "nomkl" \
     \n        ], \
     \n        "pip_install": [ \

heudiconv/cli/run.py

@@ -8,7 +8,7 @@
 from ..utils import load_heuristic, anonymize_sid, treat_infofile, SeqInfo
 from ..convert import prep_conversion
 from ..bids import populate_bids_templates, tuneup_bids_json_files
-from ..slurmqueue import queue_conversion
+from ..queue import queue_conversion
 
 import inspect
 import logging
@@ -306,12 +306,7 @@ def process_args(args):
 
         anon_sid = anonymize_sid(sid, args.anon_cmd) if args.anon_cmd else None
         if args.anon_cmd:
-            import sys
-            lgr.info('DEBUGC-version {}'.format(sys.version))
-            lgr.info('DEBUGC-execpath {}'.format(sys.executable))
             lgr.info('Anonymized {} to {}'.format(sid, anon_sid))
-            lgr.info('DEBUGC-type_to_match {}'.format(type(sid)))
-            lgr.info('DEBUGC-type_returned {}'.format(type(anon_sid)))
 
         study_outdir = op.join(outdir, locator or '')
         anon_outdir = args.conv_outdir or outdir

heudiconv/slurmqueue.py renamed to heudiconv/queue.py

@@ -0,0 +1 @@
+/annex/objects/SHA256E-s305--d13f986ddc4e3ba2a9fdea076834eb9861cddd365380d5675ebdf1177281f352.py

heudiconv/tests/anonymize_script.py

@@ -19,8 +19,7 @@
 
 @pytest.mark.parametrize('subject', ['sub-sid000143'])
 @pytest.mark.parametrize('heuristic', ['reproin.py'])
-# @pytest.mark.parametrize('anon_cmd', [None]) # ['anonymize_script.py']
-@pytest.mark.parametrize('anon_cmd', [None, 'anonymize_script.py']) #
+@pytest.mark.parametrize('anon_cmd', [None, 'anonymize_script.py'])
 @pytest.mark.skipif(not have_datalad, reason="no datalad")
 def test_conversion(tmpdir, subject, heuristic, anon_cmd):
     tmpdir.chdir()

heudiconv/tests/data/__init__.py

@@ -14,12 +14,9 @@ def gen_heudiconv_args(datadir, outdir, subject, heuristic_file, anon_cmd=None,
             "-f", heuristic,
             "--bids",]
     if anon_cmd:
-        args += ["--anon-cmd", op.join(op.dirname(__file__), 'data', anon_cmd), "-a", outdir]
+        args += ["--anon-cmd", op.join(op.dirname(__file__), anon_cmd), "-a", outdir]
     if xargs:
         args += xargs
-    
-    print("DEBUGC-args")
-    print(args)
 
     return args
 

heudiconv/tests/data/anonymize_script.py

@@ -103,25 +103,16 @@ def dec(obj):
 
 
 def anonymize_sid(sid, anon_sid_cmd):
-    from subprocess import check_output
     import sys
-    print('DEBUGC-version {}'.format(sys.version))
-    print('DEBUGC-execpath {}'.format(sys.executable))
-
-    type_to_match = type(sid)
+    from subprocess import check_output
 
     cmd = [anon_sid_cmd, sid]
     shell_return = check_output(cmd)
 
+    type_to_match = type(sid)
     type_returned = type(shell_return)
 
-    print('DEBUGC-type_to_match {}'.format(type_to_match))
-    print('DEBUGC-type_returned {}'.format(type_returned))
-    
-    # if type_to_match not type_returned:
-    #     if sys.version_info[0] < 3:
-    #         if type_to_match
-
+    ### Handle subprocess returning a bytes literal string to a python3 interpreter
     if all([sys.version_info[0] > 2, isinstance(shell_return, bytes), isinstance(sid, str)]):
         anon_sid = shell_return.decode()
     else: