Refactor code for tidyness points

nf_core/create.py

@@ -3,7 +3,6 @@
 organization's specification based on a template.
 """
 from genericpath import exists
-from pathlib import Path
 import git
 import jinja2
 import logging
@@ -108,31 +107,32 @@ def render_template(self):
             output_path = os.path.join(self.outdir, template_fn)
             os.makedirs(os.path.dirname(output_path), exist_ok=True)
 
-            # Just copy binary files
-            (ftype, encoding) = mimetypes.guess_type(template_fn_path, strict=False)
-            if encoding is not None or (ftype is not None and any([ftype.startswith(ft) for ft in binary_ftypes])):
-                log.debug(f"Copying binary file: '{output_path}'")
-                shutil.copy(template_fn_path, output_path)
-                continue
+            try:
+                # Just copy certain file extensions
+                filename, file_extension = os.path.splitext(template_fn_path)
+                if file_extension in binary_extensions:
+                    raise AttributeError(f"File extension: {file_extension}")
 
-            if Path(template_fn_path).suffix in binary_extensions:
-                log.debug(f"Copying binary file: '{output_path}'")
-                shutil.copy(template_fn_path, output_path)
-                continue
+                # Try to detect binary files
+                (ftype, encoding) = mimetypes.guess_type(template_fn_path, strict=False)
+                if encoding is not None or (ftype is not None and any([ftype.startswith(ft) for ft in binary_ftypes])):
+                    raise AttributeError(f"Encoding: {encoding}")
 
-            # Render the template
-            try:
+                # Got this far - render the template
                 log.debug(f"Rendering template file: '{template_fn}'")
                 j_template = env.get_template(template_fn)
                 rendered_output = j_template.render(object_attrs)
-            except UnicodeDecodeError as e:
-                log.error(f"Could not decode file {template_fn_path} {e}")
-                sys.exit(1)
 
-            # Write to the pipeline output file
-            with open(output_path, "w") as fh:
-                log.debug(f"Writing to output file: '{output_path}'")
-                fh.write(rendered_output)
+                # Write to the pipeline output file
+                with open(output_path, "w") as fh:
+                    log.debug(f"Writing to output file: '{output_path}'")
+                    fh.write(rendered_output)
+
+            # Copy the file directly instead of using Jinja
+            except (AttributeError, UnicodeDecodeError) as e:
+                log.debug(f"Copying file without Jinja: '{output_path}' - {e}")
+                shutil.copy(template_fn_path, output_path)
+                continue
 
         # Make a logo and save it
         self.make_pipeline_logo()