PR improvements

Author: irm-codebase

copier.yaml

@@ -30,7 +30,7 @@ _skip_if_exists:
   - AUTHORS
   - CITATION.cff
   - INTERFACE.yaml
-  # Special cases
+  # Special cases: these files should not be user-modified, even though they are in user-modifiable directories
   - "!config/README.md"
   - "!tests/clio_test.py"
 _templates_suffix: .jinja

template/workflow/Snakefile

@@ -22,6 +22,8 @@ include: "rules/automatic.smk"
 include: "rules/dummy.smk"
 
 # Add additional files to be delivered alongside the workflow here.
+# This is needed e.g. for python code files that are never
+# explicitly used as a script or input in a snakemake rule.
 # e.g.: workflow.source_path("scripts/_utils.py")
 
 rule all: