First update

bulky.py

@@ -4,8 +4,9 @@
 from argparse import ArgumentParser, Namespace, ArgumentDefaultsHelpFormatter
 
 from chris_plugin import chris_plugin, PathMapper
+import shutil
 
-__version__ = '1.0.0'
+__version__ = "1.0.0"
 
 DISPLAY_TITLE = r"""
  _           _ _                                      
@@ -19,16 +20,16 @@
 """
 
 
-parser = ArgumentParser(description='!!!CHANGE ME!!! An example ChRIS plugin which '
-                                    'counts the number of occurrences of a given '
-                                    'word in text files.',
-                        formatter_class=ArgumentDefaultsHelpFormatter)
-parser.add_argument('-w', '--word', required=True, type=str,
-                    help='word to count')
-parser.add_argument('-p', '--pattern', default='**/*.txt', type=str,
-                    help='input file filter glob')
-parser.add_argument('-V', '--version', action='version',
-                    version=f'%(prog)s {__version__}')
+parser = ArgumentParser(
+    description="""
+    A dummy bulk processor. Move along. Not much to see here.
+                        """,
+    formatter_class=ArgumentDefaultsHelpFormatter,
+)
+parser.add_argument(
+    "--pattern", default="**/*.dcm", type=str, help="input file filter glob"
+)
+parser.add_argument("--version", action="version", version=f"%(prog)s {__version__}")
 
 
 # The main function of this *ChRIS* plugin is denoted by this ``@chris_plugin`` "decorator."
@@ -37,11 +38,11 @@
 # documentation: https://fnndsc.github.io/chris_plugin/chris_plugin.html#chris_plugin
 @chris_plugin(
     parser=parser,
-    title='A bulk processor',
-    category='',                 # ref. https://chrisstore.co/plugins
-    min_memory_limit='100Mi',    # supported units: Mi, Gi
-    min_cpu_limit='1000m',       # millicores, e.g. "1000m" = 1 CPU core
-    min_gpu_limit=0              # set min_gpu_limit=1 to enable GPU
+    title="A bulk processor",
+    category="",  # ref. https://chrisstore.co/plugins
+    min_memory_limit="100Mi",  # supported units: Mi, Gi
+    min_cpu_limit="1000m",  # millicores, e.g. "1000m" = 1 CPU core
+    min_gpu_limit=0,  # set min_gpu_limit=1 to enable GPU
 )
 def main(options: Namespace, inputdir: Path, outputdir: Path):
     """
@@ -53,7 +54,6 @@ def main(options: Namespace, inputdir: Path, outputdir: Path):
     :param inputdir: directory containing (read-only) input files
     :param outputdir: directory where to write output files
     """
-
     print(DISPLAY_TITLE)
 
     # Typically it's easier to think of programs as operating on individual files
@@ -63,15 +63,16 @@ def main(options: Namespace, inputdir: Path, outputdir: Path):
     #
     # Refer to the documentation for more options, examples, and advanced uses e.g.
     # adding a progress bar and parallelism.
-    mapper = PathMapper.file_mapper(inputdir, outputdir, glob=options.pattern, suffix='.count.txt')
+    mapper = PathMapper.file_mapper(
+        inputdir, outputdir, glob=options.pattern, suffix=".bak.dcm"
+    )
     for input_file, output_file in mapper:
         # The code block below is a small and easy example of how to use a ``PathMapper``.
         # It is recommended that you put your functionality in a helper function, so that
         # it is more legible and can be unit tested.
-        data = input_file.read_text()
-        frequency = data.count(options.word)
-        output_file.write_text(str(frequency))
+        print(f"copying {input_file} to {output_file}")
+        shutil.copy(input_file, output_file)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()