Use pre-commit run prettier if prettier is not available

MANIFEST.in

@@ -4,3 +4,4 @@ graft nf_core/module-template
 graft nf_core/pipeline-template
 graft nf_core/subworkflow-template
 include requirements.txt
+include .pre-commit-config.yaml

nf_core/lint/__init__.py

@@ -124,7 +124,7 @@ def run_linting(
  lint_obj._print_results(show_passed)
  module_lint_obj._print_results(show_passed)
  nf_core.lint_utils.print_joint_summary(lint_obj, module_lint_obj)
- nf_core.lint_utils.print_fixes(lint_obj, module_lint_obj)
+ nf_core.lint_utils.print_fixes(lint_obj)
 
  # Save results to Markdown file
  if md_fn is not None:

nf_core/lint_utils.py

@@ -1,5 +1,7 @@
 import logging
+import shutil
 import subprocess
+from pathlib import Path
 
 import rich
 from rich.console import Console
@@ -34,24 +36,25 @@ def print_joint_summary(lint_obj, module_lint_obj):
  console.print(table)
 
 
-def print_fixes(lint_obj, module_lint_obj):
+def print_fixes(lint_obj):
  """Prints available and applied fixes"""
 
- if len(lint_obj.could_fix):
- fix_cmd = "nf-core lint {} --fix {}".format(
- "" if lint_obj.wf_path == "." else f"--dir {lint_obj.wf_path}", " --fix ".join(lint_obj.could_fix)
- )
+ if lint_obj.could_fix:
+ lint_dir = "" if lint_obj.wf_path == "." else f"--dir {lint_obj.wf_path}"
+ fix_flags = " ".join([f"--fix {file}" for file in lint_obj.could_fix])
  console.print(
- f"\nTip: Some of these linting errors can automatically be resolved with the following command:\n\n[blue] {fix_cmd}\n"
+ "\nTip: Some of these linting errors can automatically be resolved with the following command:"
+ f"\n\n[blue] nf-core lint {lint_dir} {fix_flags}\n"
  )
  if len(lint_obj.fix):
  console.print(
- "Automatic fixes applied. Please check with 'git diff' and revert any changes you do not want with 'git checkout <file>'."
+ "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.
+ """Run Prettier on a file.
 
  Args:
  file (Path | str): A file identifier as a string or pathlib.Path.
@@ -60,12 +63,55 @@ def run_prettier_on_file(file):
  If Prettier is not installed, a warning is logged.
  """
 
+ if shutil.which("prettier"):
+ _run_prettier_on_file(file)
+ elif shutil.which("pre-commit"):
+ _run_pre_commit_prettier_on_file(file)
+ else:
+ log.warning(
+ "Neither Prettier nor the prettier pre-commit hook are available. At least one of them is required."
+ )
+
+
+def _run_prettier_on_file(file):
+ """Run natively installed Prettier on a file."""
+
  try:
  subprocess.run(
  ["prettier", "--write", file],
- stdout=subprocess.DEVNULL,
- stderr=subprocess.DEVNULL,
- check=False,
+ capture_output=True,
+ check=True,
+ )
+ except subprocess.CalledProcessError as e:
+ if ": SyntaxError: " in e.stderr.decode():
+ raise ValueError(f"Can't format {file} because it has a synthax error.\n{e.stderr.decode()}") from e
+ raise ValueError(
+ "There was an error running the prettier pre-commit hook.\n"
+ f"STDOUT: {e.stdout.decode()}\nSTDERR: {e.stderr.decode()}"
+ ) from e
+
+
+def _run_pre_commit_prettier_on_file(file):
+ """Runs pre-commit hook prettier on a file if pre-commit 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.
+ """
+
+ nf_core_pre_commit_config = Path(nf_core.__file__).parent.parent / ".pre-commit-config.yaml"
+ try:
+ subprocess.run(
+ ["pre-commit", "run", "--config", nf_core_pre_commit_config, "prettier", "--files", file],
+ capture_output=True,
+ check=True,
  )
- except FileNotFoundError:
- log.warning("Prettier is not installed. Please install it and run it on the pipeline to fix linting issues.")
+ except subprocess.CalledProcessError as e:
+ if ": SyntaxError: " in e.stdout.decode():
+ raise ValueError(f"Can't format {file} because it has a synthax error.\n{e.stdout.decode()}") from e
+ raise ValueError(
+ "There was an error running the prettier pre-commit hook.\n"
+ f"STDOUT: {e.stdout.decode()}\nSTDERR: {e.stderr.decode()}"
+ ) from e

requirements-dev.txt

@@ -1,7 +1,6 @@
 black
 isort
 myst_parser
-pre-commit
 pytest-cov
 pytest-datafiles
 requests-mock

requirements.txt

@@ -6,6 +6,7 @@ jinja2
 jsonschema>=3.0
 markdown>=3.3
 packaging
+pre-commit
 prompt_toolkit>=3.0.3
 pytest>=7.0.0
 pytest-workflow>=1.6.0

tests/test_lint_utils.py

@@ -0,0 +1,98 @@
+import shutil
+
+import git
+import pytest
+
+import nf_core.lint_utils
+
+JSON_WITH_SYNTAX_ERROR = "{'a':1, 1}"
+JSON_MALFORMED = "{'a':1}"
+JSON_FORMATTED = '{ "a": 1 }\n'
+
+WHICH_PRE_COMMIT = shutil.which("pre-commit")
+
+
+@pytest.fixture()
+def temp_git_repo(tmp_path_factory):
+ tmp_git_dir = tmp_path_factory.mktemp("tmp_git_dir")
+ repo = git.Repo.init(tmp_git_dir)
+ return tmp_git_dir, repo
+
+
+@pytest.fixture(name="formatted_json")
+def git_dir_with_json(temp_git_repo):
+ tmp_git_dir, repo = temp_git_repo
+ file = tmp_git_dir / "formatted.json"
+ with open(file, "w", encoding="utf-8") as f:
+ f.write(JSON_FORMATTED)
+ repo.git.add(file)
+ return file
+
+
+@pytest.fixture(name="malformed_json")
+def git_dir_with_json_malformed(temp_git_repo):
+ tmp_git_dir, repo = temp_git_repo
+ file = tmp_git_dir / "malformed.json"
+ with open(file, "w", encoding="utf-8") as f:
+ f.write(JSON_MALFORMED)
+ repo.git.add(file)
+ return file
+
+
+@pytest.fixture(name="synthax_error_json")
+def git_dir_with_json_syntax_error(temp_git_repo):
+ tmp_git_dir, repo = temp_git_repo
+ file = tmp_git_dir / "synthax-error.json"
+ with open(file, "w", encoding="utf-8") as f:
+ f.write(JSON_WITH_SYNTAX_ERROR)
+ repo.git.add(file)
+ return file
+
+
+@pytest.fixture
+def ensure_prettier_is_not_found(monkeypatch):
+ def dont_find_prettier(x):
+ if x == "pre-commit":
+ which_x = WHICH_PRE_COMMIT
+ elif x == "prettier":
+ which_x = None
+ else:
+ raise ValueError(f"This mock is only inteded to hide prettier form tests. {x}")
+ return which_x
+
+ monkeypatch.setattr("nf_core.lint_utils.shutil.which", dont_find_prettier)
+
+
+@pytest.mark.skipif(shutil.which("prettier") is None, reason="Can't test prettier if it is not available.")
+def test_run_prettier_on_formatted_file(formatted_json):
+ nf_core.lint_utils.run_prettier_on_file(formatted_json)
+ assert formatted_json.read_text() == JSON_FORMATTED
+
+
+def test_run_pre_commit_prettier_on_formatted_file(formatted_json, ensure_prettier_is_not_found):
+ nf_core.lint_utils.run_prettier_on_file(formatted_json)
+ assert formatted_json.read_text() == JSON_FORMATTED
+
+
+@pytest.mark.skipif(shutil.which("prettier") is None, reason="Can't test prettier if it is not available.")
+def test_run_prettier_on_malformed_file(malformed_json):
+ nf_core.lint_utils.run_prettier_on_file(malformed_json)
+ assert malformed_json.read_text() == JSON_FORMATTED
+
+
+def test_run_prettier_pre_commit_on_malformed_file(malformed_json, ensure_prettier_is_not_found):
+ nf_core.lint_utils.run_prettier_on_file(malformed_json)
+ assert malformed_json.read_text() == JSON_FORMATTED
+
+
+@pytest.mark.skipif(shutil.which("prettier") is None, reason="Can't test prettier if it is not available.")
+def test_run_prettier_on_synthax_error_file(synthax_error_json):
+ with pytest.raises(ValueError) as exc_info:
+ nf_core.lint_utils.run_prettier_on_file(synthax_error_json)
+ assert exc_info.value.args[0].startswith(f"Can't format {synthax_error_json} because it has a synthax error.")
+
+
+def test_run_prettier_pre_commit_on_synthax_error_file(synthax_error_json, ensure_prettier_is_not_found):
+ with pytest.raises(ValueError) as exc_info:
+ nf_core.lint_utils.run_prettier_on_file(synthax_error_json)
+ assert exc_info.value.args[0].startswith(f"Can't format {synthax_error_json} because it has a synthax error.")