Merge pull request #1567 from yarikoptic/enh-consistent-citation

ENH: remove all prior existing citation files first

Author: oesteban

.zenodo.json

@@ -106,6 +106,11 @@
       "affiliation": "University College London",
       "orcid": "0000-0002-9699-9052"
     },
+    {
+      "name": "Halchenko, Yaroslav O.",
+      "affiliation": "Dartmouth College: Hanover, NH, United States",
+      "orcid": "0000-0003-3456-2493"
+    },
     {
       "name": "Poldrack, Russell A.",
       "affiliation": "Department of Psychology, Stanford University",

fmriprep/cli/run.py

@@ -786,7 +786,18 @@ def build_workflow(opts, retval):
     boilerplate = retval['workflow'].visit_desc()
 
     if boilerplate:
-        (logs_path / 'CITATION.md').write_text(boilerplate)
+        # To please git-annex users and also to guarantee consistency
+        # among different renderings of the same file, first remove any
+        # existing one
+        citation_files = {
+            ext: logs_path / ('CITATION.%s' % ext)
+            for ext in ('bib', 'tex', 'md', 'html')
+        }
+        for citation_file in citation_files.values():
+            if citation_file.exists() or citation_file.is_symlink():
+                citation_file.unlink()
+
+        citation_files['md'].write_text(boilerplate)
         logger.log(25, 'Works derived from this fMRIPrep execution should '
                    'include the following boilerplate:\n\n%s', boilerplate)
 
@@ -795,8 +806,8 @@ def build_workflow(opts, retval):
                pkgrf('fmriprep', 'data/boilerplate.bib'),
                '--filter', 'pandoc-citeproc',
                '--metadata', 'pagetitle="fMRIPrep citation boilerplate"',
-               str(logs_path / 'CITATION.md'),
-               '-o', str(logs_path / 'CITATION.html')]
+               str(citation_files['md']),
+               '-o', str(citation_files['html'])]
         try:
             check_call(cmd, timeout=10)
         except (FileNotFoundError, CalledProcessError, TimeoutExpired):
@@ -806,16 +817,16 @@ def build_workflow(opts, retval):
         # Generate LaTex file resolving citations
         cmd = ['pandoc', '-s', '--bibliography',
                pkgrf('fmriprep', 'data/boilerplate.bib'),
-               '--natbib', str(logs_path / 'CITATION.md'),
-               '-o', str(logs_path / 'CITATION.tex')]
+               '--natbib', str(citation_files['md']),
+               '-o', str(citation_files['tex'])]
         try:
             check_call(cmd, timeout=10)
         except (FileNotFoundError, CalledProcessError, TimeoutExpired):
             logger.warning('Could not generate CITATION.tex file:\n%s',
                            ' '.join(cmd))
         else:
             copyfile(pkgrf('fmriprep', 'data/boilerplate.bib'),
-                     (logs_path / 'CITATION.bib'))
+                     citation_files['bib'])
 
     return retval