Merge pull request #2150 from awgymer/schema-docs-fix-output

Schema docs fix output
nf-core · Jan 10, 2023 · 681ccf3 · 681ccf3
2 parents 5a7a98a + 1350a1b
commit 681ccf3
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Showing 2 changed files with 21 additions and 9 deletions.
diff --git a/nf_core/__main__.py b/nf_core/__main__.py
@@ -1446,8 +1446,7 @@ def docs(schema_path, output, format, force, columns):
     # Assume we're in a pipeline dir root if schema path not set
     schema_obj.get_schema_path(schema_path)
     schema_obj.load_schema()
-    if not output:
-        stdout.print(schema_obj.print_documentation(output, format, force, columns.split(",")))
+    schema_obj.print_documentation(output, format, force, columns.split(","))
 
 
 # nf-core bump-version

diff --git a/nf_core/schema.py b/nf_core/schema.py
@@ -6,17 +6,20 @@
 import json
 import logging
 import os
+import tempfile
 import webbrowser
 
 import jinja2
 import jsonschema
 import markdown
+import rich.console
 import yaml
 from rich.prompt import Confirm
+from rich.syntax import Syntax
 
 import nf_core.list
 import nf_core.utils
-from nf_core.lint_utils import dump_json_with_prettier
+from nf_core.lint_utils import dump_json_with_prettier, run_prettier_on_file
 
 log = logging.getLogger(__name__)
 
@@ -464,13 +467,21 @@ def print_documentation(
         if format == "html":
             output = self.markdown_to_html(output)
 
-        # Print to file
-        if output_fn:
+        with tempfile.NamedTemporaryFile(mode="w+") as fh:
+            fh.write(output)
+            run_prettier_on_file(fh.name)
+            fh.seek(0)
+            prettified_docs = fh.read()
+
+        if not output_fn:
+            console = rich.console.Console()
+            console.print("\n", Syntax(prettified_docs, format), "\n")
+        else:
             if os.path.exists(output_fn) and not force:
                 log.error(f"File '{output_fn}' exists! Please delete first, or use '--force'")
                 return
-            with open(output_fn, "w") as file:
-                file.write(output)
+            with open(output_fn, "w") as fh:
+                fh.write(prettified_docs)
                 log.info(f"Documentation written to '{output_fn}'")
 
         # Return as a string
@@ -495,9 +506,11 @@ def schema_to_markdown(self, columns):
                     if column == "parameter":
                         out += f"| `{p_key}` "
                     elif column == "description":
-                        out += f"| {param.get('description', '')} "
+                        desc = param.get("description", "").replace("\n", "<br>")
+                        out += f"| {desc} "
                         if param.get("help_text", "") != "":
-                            out += f"<details><summary>Help</summary><small>{param['help_text']}</small></details>"
+                            help_txt = param["help_text"].replace("\n", "<br>")
+                            out += f"<details><summary>Help</summary><small>{help_txt}</small></details>"
                     elif column == "type":
                         out += f"| `{param.get('type', '')}` "
                     else: