Merge pull request #1983 from fabianegli/pre-commit-run-prettier

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_utils.py

@@ -1,5 +1,6 @@
 import logging
 import subprocess
+from pathlib import Path
 
 import rich
 from rich.console import Console
@@ -53,7 +54,7 @@ def print_fixes(lint_obj):
 
 
 def run_prettier_on_file(file):
-    """Runs Prettier on a file if Prettier is installed.
+    """Run the pre-commit hook prettier on a file.
 
     Args:
         file (Path | str): A file identifier as a string or pathlib.Path.
@@ -62,12 +63,17 @@ def run_prettier_on_file(file):
         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(
-            ["prettier", "--write", file],
-            stdout=subprocess.DEVNULL,
-            stderr=subprocess.DEVNULL,
-            check=False,
+            ["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 +1,65 @@
+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
+
+
+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_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_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.")