ENH: Use duecredit - provide zenodo DOI as citation target

Here is how it would look ATM if you disregard some warnings from
duecredit about outdated injections (that is their cons, need to be
fixed up: duecredit/duecredit#170) and
datalad about datasets without aggregated metadata
(need to be fixed up: datalad/datalad#4562),
but otherwise -- works!  Ideally for this particular use case we
should have forced .duecredit.p to be stored within produced path, not
in curdir... later

    > DUECREDIT_ENABLE=1 heudiconv -o /tmp/out -f reproin --datalad --files QA/sourcedata/sub-qa/ses-20190930/anat/sub-qa_ses-20190930_acq-MPRAGE_T1w.dicom.tgz
...
    DueCredit Report:
    - DataLad - Data management and distribution platform / datalad (v 0.12.6) [1]
    - Flexible DICOM converter for organizing brain imaging data / heudiconv (v 0.8.0) [2]
    - I/O library to access to common neuroimaging file formats / nibabel (v 3.0.1) [3]
    - Scientific tools library / numpy (v 1.17.4) [4]

    4 packages cited
    0 modules cited
    0 functions cited

    References
    ----------

    [1] Halchenko, Y.O. et al., 2019. datalad/datalad 0.12.0rc6.
    [2] Halchenko, Y. et al., 2020. nipy/heudiconv v0.8.0.
    [3] Brett, M. et al., 2015. Nibabel 2.0.1.
    [4] Van Der Walt, S., Colbert, S.C. & Varoquaux, G., 2011. The NumPy array: a structure for efficient numerical computation. Computing in Science & Engineering, 13(2), pp.22–30.
    DUECREDIT_ENABLE=1 heudiconv -o /tmp/out -f reproin --datalad --files   15.50s user 8.34s system 104% cpu 22.917 total

Author: yarikoptic

heudiconv/cli/run.py

@@ -11,6 +11,7 @@
 from ..convert import prep_conversion
 from ..bids import populate_bids_templates, tuneup_bids_json_files
 from ..queue import queue_conversion
+from ..due import due, Doi
 
 import inspect
 import logging
@@ -244,6 +245,12 @@ def get_parser():
     return parser
 
 
+@due.dcite(
+    Doi('10.5281/zenodo.1012598'),
+    path='heudiconv',
+    description='Flexible DICOM converter for organizing brain imaging data',
+    version=__version__,
+    cite_module=True)
 def process_args(args):
     """Given a structure of arguments from the parser perform computation"""
 

heudiconv/due.py

@@ -0,0 +1,74 @@
+# emacs: at the end of the file
+# ex: set sts=4 ts=4 sw=4 et:
+# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### #
+"""
+
+Stub file for a guaranteed safe import of duecredit constructs:  if duecredit
+is not available.
+
+To use it, place it into your project codebase to be imported, e.g. copy as
+
+    cp stub.py /path/tomodule/module/due.py
+
+Note that it might be better to avoid naming it duecredit.py to avoid shadowing
+installed duecredit.
+
+Then use in your code as
+
+    from .due import due, Doi, BibTeX, Text
+
+See  https://github.com/duecredit/duecredit/blob/master/README.md for examples.
+
+Origin:     Originally a part of the duecredit
+Copyright:  2015-2019  DueCredit developers
+License:    BSD-2
+"""
+
+__version__ = '0.0.8'
+
+
+class InactiveDueCreditCollector(object):
+    """Just a stub at the Collector which would not do anything"""
+    def _donothing(self, *args, **kwargs):
+        """Perform no good and no bad"""
+        pass
+
+    def dcite(self, *args, **kwargs):
+        """If I could cite I would"""
+        def nondecorating_decorator(func):
+            return func
+        return nondecorating_decorator
+
+    active = False
+    activate = add = cite = dump = load = _donothing
+
+    def __repr__(self):
+        return self.__class__.__name__ + '()'
+
+
+def _donothing_func(*args, **kwargs):
+    """Perform no good and no bad"""
+    pass
+
+
+try:
+    from duecredit import due, BibTeX, Doi, Url, Text
+    if 'due' in locals() and not hasattr(due, 'cite'):
+        raise RuntimeError(
+            "Imported due lacks .cite. DueCredit is now disabled")
+except Exception as e:
+    if not isinstance(e, ImportError):
+        import logging
+        logging.getLogger("duecredit").error(
+            "Failed to import duecredit due to %s" % str(e))
+    # Initiate due stub
+    due = InactiveDueCreditCollector()
+    BibTeX = Doi = Url = Text = _donothing_func
+
+# Emacs mode definitions
+# Local Variables:
+# mode: python
+# py-indent-offset: 4
+# tab-width: 4
+# indent-tabs-mode: nil
+# End:

heudiconv/info.py

@@ -39,7 +39,9 @@
 
 EXTRA_REQUIRES = {
     'tests': TESTS_REQUIRES,
-    'extras': [],  # Requires patched version ATM ['dcmstack'],
+    'extras': [
+        'duecredit',  # optional dependency
+    ],  # Requires patched version ATM ['dcmstack'],
     'datalad': ['datalad >=0.12.3']
 }