Merge pull request #3188 from mashehu/fix-run-prettier

Fix run_prettier on rendered template

nf_core/pipelines/create/create.py

@@ -368,7 +368,7 @@ def render_template(self) -> None:
                     log.debug(f"Dumping pipeline template yml to pipeline config file '{config_fn.name}'")
 
         # Run prettier on files
-        run_prettier_on_file(self.outdir)
+        run_prettier_on_file([str(f) for f in self.outdir.glob("**/*")])
 
     def fix_linting(self):
         """

nf_core/pipelines/lint_utils.py

@@ -2,9 +2,10 @@
 import logging
 import subprocess
 from pathlib import Path
-from typing import List
+from typing import List, Union
 
 import rich
+import yaml
 from rich.console import Console
 from rich.table import Table
 
@@ -69,7 +70,7 @@ def print_fixes(lint_obj):
         )
 
 
-def run_prettier_on_file(file):
+def run_prettier_on_file(file: Union[Path, str, List[str]]) -> None:
     """Run the pre-commit hook prettier on a file.
 
     Args:
@@ -80,12 +81,15 @@ def run_prettier_on_file(file):
     """
 
     nf_core_pre_commit_config = Path(nf_core.__file__).parent / ".pre-commit-prettier-config.yaml"
+    args = ["pre-commit", "run", "--config", str(nf_core_pre_commit_config), "prettier"]
+    if isinstance(file, List):
+        args.extend(["--files", *file])
+    else:
+        args.extend(["--files", str(file)])
+
     try:
-        subprocess.run(
-            ["pre-commit", "run", "--config", nf_core_pre_commit_config, "prettier", "--files", file],
-            capture_output=True,
-            check=True,
-        )
+        subprocess.run(args, capture_output=True, check=True)
+        log.debug(f"${subprocess.STDOUT}")
     except subprocess.CalledProcessError as e:
         if ": SyntaxError: " in e.stdout.decode():
             log.critical(f"Can't format {file} because it has a syntax error.\n{e.stdout.decode()}")
@@ -111,6 +115,18 @@ def dump_json_with_prettier(file_name, file_content):
     run_prettier_on_file(file_name)
 
 
+def dump_yaml_with_prettier(file_name: Union[Path, str], file_content: dict) -> None:
+    """Dump a YAML file and run prettier on it.
+
+    Args:
+        file_name (Path | str): A file identifier as a string or pathlib.Path.
+        file_content (dict): Content to dump into the YAML file
+    """
+    with open(file_name, "w") as fh:
+        yaml.safe_dump(file_content, fh)
+    run_prettier_on_file(file_name)
+
+
 def ignore_file(lint_name: str, file_path: Path, dir_path: Path) -> List[List[str]]:
     """Ignore a file and add the result to the ignored list. Return the passed, failed, ignored and ignore_configs lists."""
 

nf_core/pipelines/sync.py

@@ -21,6 +21,7 @@
 import nf_core.pipelines.create.create
 import nf_core.pipelines.list
 import nf_core.utils
+from nf_core.pipelines.lint_utils import dump_yaml_with_prettier
 
 log = logging.getLogger(__name__)
 
@@ -290,8 +291,7 @@ def make_template_pipeline(self):
                 self.config_yml.template.outdir = "."
                 # Update nf-core version
                 self.config_yml.nf_core_version = nf_core.__version__
-                with open(self.config_yml_path, "w") as config_path:
-                    yaml.safe_dump(self.config_yml.model_dump(), config_path)
+                dump_yaml_with_prettier(self.config_yml_path, self.config_yml.model_dump())
 
         except Exception as err:
             # Reset to where you were to prevent git getting messed up.