Refactor prettier invocation

nf_core/create.py

@@ -6,13 +6,12 @@
 import imghdr
 import logging
 import os
-import pathlib
 import random
 import re
 import shutil
-import subprocess
 import sys
 import time
+from pathlib import Path
 
 import git
 import jinja2
@@ -23,6 +22,7 @@
 import nf_core
 import nf_core.schema
 import nf_core.utils
+from nf_core.lint_utils import run_prettier_on_file
 
 log = logging.getLogger(__name__)
 
@@ -89,7 +89,7 @@ def __init__(
         self.force = force
         if outdir is None:
             outdir = os.path.join(os.getcwd(), self.template_params["name_noslash"])
-        self.outdir = outdir
+        self.outdir = Path(outdir)
 
     def create_param_dict(self, name, description, author, version, template_yaml_path, plain):
         """Creates a dictionary of parameters for the new pipeline.
@@ -236,17 +236,18 @@ def init_pipeline(self):
         if self.template_params["branded"]:
             log.info(
                 "[green bold]!!!!!! IMPORTANT !!!!!!\n\n"
-                + "[green not bold]If you are interested in adding your pipeline to the nf-core community,\n"
-                + "PLEASE COME AND TALK TO US IN THE NF-CORE SLACK BEFORE WRITING ANY CODE!\n\n"
-                + "[default]Please read: [link=https://nf-co.re/developers/adding_pipelines#join-the-community]https://nf-co.re/developers/adding_pipelines#join-the-community[/link]"
+                "[green not bold]If you are interested in adding your pipeline to the nf-core community,\n"
+                "PLEASE COME AND TALK TO US IN THE NF-CORE SLACK BEFORE WRITING ANY CODE!\n\n"
+                "[default]Please read: [link=https://nf-co.re/developers/adding_pipelines#join-the-community]"
+                "https://nf-co.re/developers/adding_pipelines#join-the-community[/link]"
             )
 
     def render_template(self):
         """Runs Jinja to create a new nf-core pipeline."""
         log.info(f"Creating new nf-core pipeline: '{self.name}'")
 
         # Check if the output directory exists
-        if os.path.exists(self.outdir):
+        if self.outdir.exists():
             if self.force:
                 log.warning(f"Output directory '{self.outdir}' exists - continuing as --force specified")
             else:
@@ -265,12 +266,13 @@ def render_template(self):
         object_attrs["nf_core_version"] = nf_core.__version__
 
         # Can't use glob.glob() as need recursive hidden dotfiles - https://stackoverflow.com/a/58126417/713980
-        template_files = list(pathlib.Path(template_dir).glob("**/*"))
-        template_files += list(pathlib.Path(template_dir).glob("*"))
+        template_files = list(Path(template_dir).glob("**/*"))
+        template_files += list(Path(template_dir).glob("*"))
         ignore_strs = [".pyc", "__pycache__", ".pyo", ".pyd", ".DS_Store", ".egg"]
+        short_name = self.template_params["short_name"]
         rename_files = {
-            "workflows/pipeline.nf": f"workflows/{self.template_params['short_name']}.nf",
-            "lib/WorkflowPipeline.groovy": f"lib/Workflow{self.template_params['short_name'][0].upper()}{self.template_params['short_name'][1:]}.groovy",
+            "workflows/pipeline.nf": f"workflows/{short_name}.nf",
+            "lib/WorkflowPipeline.groovy": f"lib/Workflow{short_name[0].upper()}{short_name[1:]}.groovy",
         }
 
         # Set the paths to skip according to customization
@@ -291,9 +293,9 @@ def render_template(self):
 
                 # Set up vars and directories
                 template_fn = os.path.relpath(template_fn_path, template_dir)
-                output_path = os.path.join(self.outdir, template_fn)
+                output_path = self.outdir / template_fn
                 if template_fn in rename_files:
-                    output_path = os.path.join(self.outdir, rename_files[template_fn])
+                    output_path = self.outdir / rename_files[template_fn]
                 os.makedirs(os.path.dirname(output_path), exist_ok=True)
 
                 try:
@@ -345,7 +347,7 @@ def update_nextflow_schema(self):
         """
         Removes unused parameters from the nextflow schema.
         """
-        schema_path = os.path.join(self.outdir, "nextflow_schema.json")
+        schema_path = self.outdir / "nextflow_schema.json"
 
         schema = nf_core.schema.PipelineSchema()
         schema.schema_filename = schema_path
@@ -354,22 +356,14 @@ def update_nextflow_schema(self):
         schema.get_wf_params()
         schema.remove_schema_notfound_configs()
         schema.save_schema(suppress_logging=True)
-
-        # The schema is not guaranteed to follow Prettier standards
-        # so we run prettier on the schema file
-        try:
-            subprocess.run(
-                ["prettier", "--write", schema_path], stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL, check=False
-            )
-        except FileNotFoundError:
-            log.warning("Prettier not found. Please install it and run it on the pipeline to fix linting issues.")
+        run_prettier_on_file(schema_path)
 
     def remove_nf_core_in_bug_report_template(self):
         """
         Remove the field mentioning nf-core documentation
         in the github bug report template
         """
-        bug_report_path = os.path.join(self.outdir, ".github", "ISSUE_TEMPLATE", "bug_report.yml")
+        bug_report_path = self.outdir / ".github" / "ISSUE_TEMPLATE" / "bug_report.yml"
 
         with open(bug_report_path, "r") as fh:
             contents = yaml.load(fh, Loader=yaml.FullLoader)
@@ -380,17 +374,7 @@ def remove_nf_core_in_bug_report_template(self):
         with open(bug_report_path, "w") as fh:
             yaml.dump(contents, fh, default_flow_style=False, sort_keys=False)
 
-        # The dumped yaml file will not follow prettier formatting rules
-        # so we run prettier on the file
-        try:
-            subprocess.run(
-                ["prettier", "--write", bug_report_path],
-                stdout=subprocess.DEVNULL,
-                stderr=subprocess.DEVNULL,
-                check=False,
-            )
-        except FileNotFoundError:
-            log.warning("Prettier not found. Please install it and run it on the pipeline to fix linting issues.")
+        run_prettier_on_file(bug_report_path)
 
     def fix_linting(self):
         """
@@ -455,34 +439,24 @@ def fix_linting(self):
         # Add the lint content to the preexisting nf-core config
         nf_core_yml = nf_core.utils.load_tools_config(self.outdir)
         nf_core_yml["lint"] = lint_config
-        with open(os.path.join(self.outdir, ".nf-core.yml"), "w") as fh:
+        with open(self.outdir / ".nf-core.yml", "w") as fh:
             yaml.dump(nf_core_yml, fh, default_flow_style=False, sort_keys=False)
 
-        # The dumped yaml file will not follow prettier formatting rules
-        # so we run prettier on the file
-        try:
-            subprocess.run(
-                ["prettier", "--write", os.path.join(self.outdir, ".nf-core.yml")],
-                stdout=subprocess.DEVNULL,
-                stderr=subprocess.DEVNULL,
-                check=False,
-            )
-        except FileNotFoundError:
-            log.warning(
-                "Prettier is not installed. Please install it and run it on the pipeline to fix linting issues."
-            )
+        run_prettier_on_file(os.path.join(self.outdir, ".nf-core.yml"))
 
     def make_pipeline_logo(self):
         """Fetch a logo for the new pipeline from the nf-core website"""
 
         logo_url = f"https://nf-co.re/logo/{self.template_params['short_name']}?theme=light"
         log.debug(f"Fetching logo from {logo_url}")
 
-        email_logo_path = f"{self.outdir}/assets/{self.template_params['name_noslash']}_logo_light.png"
+        email_logo_path = self.outdir / "assets" / f"{self.template_params['name_noslash']}_logo_light.png"
         self.download_pipeline_logo(f"{logo_url}&w=400", email_logo_path)
         for theme in ["dark", "light"]:
             readme_logo_url = f"{logo_url}?w=600&theme={theme}"
-            readme_logo_path = f"{self.outdir}/docs/images/{self.template_params['name_noslash']}_logo_{theme}.png"
+            readme_logo_path = (
+                self.outdir / "docs" / "images" / f"{self.template_params['name_noslash']}_logo_{theme}.png"
+            )
             self.download_pipeline_logo(readme_logo_url, readme_logo_path)
 
     def download_pipeline_logo(self, url, img_fn):

nf_core/lint_utils.py

@@ -1,4 +1,5 @@
 import logging
+import subprocess
 
 import rich
 from rich.console import Console
@@ -47,3 +48,24 @@ def print_fixes(lint_obj, module_lint_obj):
         console.print(
             "Automatic fixes applied. Please check with 'git diff' and revert any changes you do not want with 'git checkout <file>'."
         )
+
+
+def run_prettier_on_file(file):
+    """Runs Prettier on a file if Prettier is installed.
+
+    Args:
+        file (Path | str): A file identifier as a string or pathlib.Path.
+
+    Warns:
+        If Prettier is not installed, a warning is logged.
+    """
+
+    try:
+        subprocess.run(
+            ["prettier", "--write", file],
+            stdout=subprocess.DEVNULL,
+            stderr=subprocess.DEVNULL,
+            check=False,
+        )
+    except FileNotFoundError:
+        log.warning("Prettier is not installed. Please install it and run it on the pipeline to fix linting issues.")