ENH: remove all prior existing citation files first

- makes it friendly to the cases where all output is under git-annex.
  .write_text() just opens a file in "w" mode so it would fail on
  annex protected file.

- if previous run did succeed generating e.g. .html file, if subsequent run
  fails, updated version of .html would not be generated and provided
  CITATION files could get out of sync.

Removing all CITATION* files prior generation resolves both of the issues.

Author: yarikoptic

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: str(logs_path / 'CITATION.' + ext)
+            for ext in ('bib', 'tex', 'md', 'html')
+        }
+        for citation_file in citation_files.values():
+            if op.lexists(citation_file):
+                citation_file.unlink()
+
+        Path(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')]
+               citation_files['md'],
+               '-o', 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', citation_files['md'],
+               '-o', 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