just stash

Author: daeh

.projectignore

@@ -0,0 +1,14 @@
+# project-local contains your personal configuration choices and state
+/anaconda-project-local.yml
+
+# Files autocreated by Python
+__pycache__/
+*.pyc
+*.pyo
+*.pyd
+
+# Notebook stuff
+/.ipynb_checkpoints
+
+# Spyder stuff
+/.spyderproject

Dockerfile

@@ -71,6 +71,7 @@ RUN apt-get update -qq \
            libc-dev \
            git-annex-standalone \
            netbase \
+           vim \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 

environment27.yml

@@ -0,0 +1 @@
+/annex/objects/SHA256E-s3151--0270335bbbc9ae6db51a923b92854401449661dac8a9c98d25ed37466b3af141.yml

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 ..queue import queue_conversion
+from ..slurmqueue import queue_conversion
 
 import inspect
 import logging

heudiconv/queue.py

@@ -0,0 +1 @@
+/annex/objects/SHA256E-s1164--c0074611d4178ba7bf603159c93e65f7ee7aa7c2c339a30098a9cd7e20db4547.py

heudiconv/slurmqueue.py

@@ -0,0 +1 @@
+/annex/objects/SHA256E-s0--e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855.py

heudiconv/tests/data/__init__.py

@@ -0,0 +1 @@
+/annex/objects/SHA256E-s391--38015958888dd40f9c1872ee36a5a02587f010e0b2946be8ecd2f23c4970b07d.py

heudiconv/tests/data/anonymize_script.py

@@ -19,16 +19,17 @@
 
 @pytest.mark.parametrize('subject', ['sub-sid000143'])
 @pytest.mark.parametrize('heuristic', ['reproin.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):
+def test_conversion(tmpdir, subject, heuristic, anon_cmd):
     tmpdir.chdir()
     try:
         datadir = fetch_data(tmpdir.strpath, subject)
     except IncompleteResultsError as exc:
         pytest.skip("Failed to fetch test data: %s" % str(exc))
     outdir = tmpdir.mkdir('out').strpath
 
-    args = gen_heudiconv_args(datadir, outdir, subject, heuristic)
+    args = gen_heudiconv_args(datadir, outdir, subject, heuristic, anon_cmd)
     runner(args) # run conversion
 
     # verify functionals were converted

heudiconv/tests/test_regression.py

@@ -5,16 +5,21 @@
 TESTS_DATA_PATH = op.join(op.dirname(__file__), 'data')
 
 
-def gen_heudiconv_args(datadir, outdir, subject, heuristic_file, xargs=None):
+def gen_heudiconv_args(datadir, outdir, subject, heuristic_file, anon_cmd=None, xargs=None):
     heuristic = op.realpath(op.join(HEURISTICS_PATH, heuristic_file))
     args = ["-d", op.join(datadir, 'sourcedata/{subject}/*/*/*.tgz'),
             "-c", "dcm2niix",
             "-o", outdir,
             "-s", subject,
             "-f", heuristic,
             "--bids",]
+    if anon_cmd:
+        args += ["--anon-cmd", op.join(op.dirname(__file__), 'data', anon_cmd), "-a", outdir]
     if xargs:
         args += xargs
+    
+    print("DEBUGCUSTOM1")
+    print(args)
 
     return args