Merge branch 'dev' into add-force_pr-to-sync

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.2.2
+    rev: v0.3.1
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
@@ -9,6 +9,8 @@ repos:
     rev: "v3.1.0"
     hooks:
       - id: prettier
+        additional_dependencies:
+          - prettier@3.2.5
 
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
     rev: "2.7.3"

CHANGELOG.md

@@ -13,6 +13,7 @@
 - Update CI to use nf-core/setup-nextflow v2
 - Changelog bot: handle also patch version before dev suffix ([#2820](https://github.com/nf-core/tools/pull/2820))
 - Add `force_pr` flag to sync, to force a PR even though there are no changes committed ([#2822](https://github.com/nf-core/tools/pull/2822))
+- update prettier to 3.2.5 ([#2830](https://github.com/nf-core/tools/pull/2830))
 - Update GitHub Actions ([#2827](https://github.com/nf-core/tools/pull/2827))
 
 ## [v2.13.1 - Tin Puppy Patch](https://github.com/nf-core/tools/releases/tag/2.13) - [2024-02-29]

nf_core/__init__.py

@@ -1,4 +1,4 @@
-""" Main nf_core module file.
+"""Main nf_core module file.
 
 Shouldn't do much, as everything is under subcommands.
 """

nf_core/__main__.py

@@ -1,5 +1,6 @@
 #!/usr/bin/env python
-""" nf-core: Helper tools for use with nf-core Nextflow pipelines. """
+"""nf-core: Helper tools for use with nf-core Nextflow pipelines."""
+
 import logging
 import os
 import sys

nf_core/components/components_test.py

@@ -2,7 +2,6 @@
 The ComponentsTest class handles the generation and testing of nf-test snapshots.
 """
 
-
 import logging
 import os
 import re
@@ -91,9 +90,9 @@ def run(self) -> None:
         """Run build steps"""
         self.check_inputs()
         os.environ["NFT_DIFF"] = "pdiff"  # set nf-test differ to pdiff to get a better diff output
-        os.environ[
-            "NFT_DIFF_ARGS"
-        ] = "--line-numbers --expand-tabs=2"  # taken from https://code.askimed.com/nf-test/docs/assertions/snapshots/#snapshot-differences
+        os.environ["NFT_DIFF_ARGS"] = (
+            "--line-numbers --expand-tabs=2"  # taken from https://code.askimed.com/nf-test/docs/assertions/snapshots/#snapshot-differences
+        )
         with nf_core.utils.set_wd(Path(self.dir)):
             self.check_snapshot_stability()
         if len(self.errors) > 0:

nf_core/components/create.py

@@ -2,7 +2,6 @@
 The ComponentCreate class handles generating of module and subworkflow templates
 """
 
-
 import glob
 import json
 import logging

nf_core/components/lint/__init__.py

@@ -3,7 +3,6 @@
 in nf-core pipelines
 """
 
-
 import logging
 import operator
 import os

nf_core/components/nfcore_component.py

@@ -1,6 +1,7 @@
 """
 The NFCoreComponent class holds information and utility functions for a single module or subworkflow
 """
+
 import logging
 import re
 from pathlib import Path

nf_core/create.py

@@ -1,6 +1,7 @@
 """Creates a nf-core pipeline matching the current
 organization's specification based on a template.
 """
+
 import configparser
 import logging
 import os

nf_core/launch.py

@@ -1,5 +1,4 @@
-""" Launch a pipeline, interactively collecting params """
-
+"""Launch a pipeline, interactively collecting params"""
 
 import copy
 import json

nf_core/licences.py

@@ -1,6 +1,5 @@
 """Lists software licences for a given workflow."""
 
-
 import json
 import logging
 import os

nf_core/lint/nextflow_config.py

@@ -245,10 +245,9 @@ def nextflow_config(self):
                 raise AssertionError()
         except (AssertionError, IndexError):
             failed.append(
-                "Config variable ``manifest.homePage`` did not begin with https://github.com/nf-core/:\n    {}".format(
-                    manifest_homepage
-                )
+                f"Config variable ``manifest.homePage`` did not begin with https://github.com/nf-core/:\n    {manifest_homepage}"
             )
+
         else:
             passed.append("Config variable ``manifest.homePage`` began with https://github.com/nf-core/")
 

nf_core/list.py

@@ -1,6 +1,5 @@
 """Lists available nf-core pipelines and versions."""
 
-
 import json
 import logging
 import os

nf_core/modules/bump_versions.py

@@ -3,7 +3,6 @@
 or for a single module
 """
 
-
 import logging
 import os
 import re

nf_core/modules/lint/__init__.py

@@ -6,7 +6,6 @@
 nf-core modules lint
 """
 
-
 import logging
 import os
 

nf_core/modules/lint/module_changes.py

@@ -1,6 +1,7 @@
 """
 Check whether the content of a module has changed compared to the original repository
 """
+
 import shutil
 import tempfile
 from pathlib import Path

nf_core/modules/lint/module_tests.py

@@ -1,6 +1,7 @@
 """
 Lint the tests of a module in nf-core/modules
 """
+
 import json
 import logging
 from pathlib import Path

nf_core/params_file.py

@@ -1,5 +1,4 @@
-""" Create a YAML parameter file """
-
+"""Create a YAML parameter file"""
 
 import json
 import logging

nf_core/pipeline-template/.pre-commit-config.yaml

@@ -3,6 +3,9 @@ repos:
     rev: "v3.1.0"
     hooks:
       - id: prettier
+        additional_dependencies:
+          - prettier@3.2.5
+
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
     rev: "2.7.3"
     hooks:

nf_core/schema.py

@@ -1,5 +1,4 @@
-""" Code to deal with pipeline JSON Schema """
-
+"""Code to deal with pipeline JSON Schema"""
 
 import copy
 import json
@@ -84,16 +83,13 @@ def load_lint_schema(self):
             self.get_schema_defaults()
             self.validate_default_params()
             if len(self.invalid_nextflow_config_default_parameters) > 0:
+                params = "\n --".join(
+                    [f"{param}: {msg}" for param, msg in self.invalid_nextflow_config_default_parameters.items()]
+                )
                 log.info(
-                    "[red][✗] Invalid default parameters found:\n  --{}\n\nNOTE: Use null in config for no default.".format(
-                        "\n  --".join(
-                            [
-                                f"{param}: {msg}"
-                                for param, msg in self.invalid_nextflow_config_default_parameters.items()
-                            ]
-                        )
-                    )
+                    f"[red][✗] Invalid default parameters found:\n {params} \n\nNOTE: Use null in config for no default."
                 )
+
             else:
                 log.info(f"[green][✓] Pipeline schema looks valid[/] [dim](found {num_params} params)")
         except json.decoder.JSONDecodeError as e:
@@ -282,9 +278,9 @@ def validate_default_params(self):
                 if param in self.pipeline_params:
                     self.validate_config_default_parameter(param, group_properties[param], self.pipeline_params[param])
                 else:
-                    self.invalid_nextflow_config_default_parameters[
-                        param
-                    ] = "Not in pipeline parameters. Check `nextflow.config`."
+                    self.invalid_nextflow_config_default_parameters[param] = (
+                        "Not in pipeline parameters. Check `nextflow.config`."
+                    )
 
         # Go over ungrouped params if any exist
         ungrouped_properties = self.schema.get("properties")
@@ -297,9 +293,9 @@ def validate_default_params(self):
                         param, ungrouped_properties[param], self.pipeline_params[param]
                     )
                 else:
-                    self.invalid_nextflow_config_default_parameters[
-                        param
-                    ] = "Not in pipeline parameters. Check `nextflow.config`."
+                    self.invalid_nextflow_config_default_parameters[param] = (
+                        "Not in pipeline parameters. Check `nextflow.config`."
+                    )
 
     def validate_config_default_parameter(self, param, schema_param, config_default):
         """
@@ -314,9 +310,9 @@ def validate_config_default_parameter(self, param, schema_param, config_default)
         ):
             # Check that we are not deferring the execution of this parameter in the schema default with squiggly brakcets
             if schema_param["type"] != "string" or "{" not in schema_param["default"]:
-                self.invalid_nextflow_config_default_parameters[
-                    param
-                ] = f"Schema default (`{schema_param['default']}`) does not match the config default (`{config_default}`)"
+                self.invalid_nextflow_config_default_parameters[param] = (
+                    f"Schema default (`{schema_param['default']}`) does not match the config default (`{config_default}`)"
+                )
                 return
 
         # if default is null, we're good
@@ -326,28 +322,28 @@ def validate_config_default_parameter(self, param, schema_param, config_default)
         # Check variable types in nextflow.config
         if schema_param["type"] == "string":
             if str(config_default) in ["false", "true", "''"]:
-                self.invalid_nextflow_config_default_parameters[
-                    param
-                ] = f"String should not be set to `{config_default}`"
+                self.invalid_nextflow_config_default_parameters[param] = (
+                    f"String should not be set to `{config_default}`"
+                )
         if schema_param["type"] == "boolean":
             if str(config_default) not in ["false", "true"]:
-                self.invalid_nextflow_config_default_parameters[
-                    param
-                ] = f"Booleans should only be true or false, not `{config_default}`"
+                self.invalid_nextflow_config_default_parameters[param] = (
+                    f"Booleans should only be true or false, not `{config_default}`"
+                )
         if schema_param["type"] == "integer":
             try:
                 int(config_default)
             except ValueError:
-                self.invalid_nextflow_config_default_parameters[
-                    param
-                ] = f"Does not look like an integer: `{config_default}`"
+                self.invalid_nextflow_config_default_parameters[param] = (
+                    f"Does not look like an integer: `{config_default}`"
+                )
         if schema_param["type"] == "number":
             try:
                 float(config_default)
             except ValueError:
-                self.invalid_nextflow_config_default_parameters[
-                    param
-                ] = f"Does not look like a number (float): `{config_default}`"
+                self.invalid_nextflow_config_default_parameters[param] = (
+                    f"Does not look like a number (float): `{config_default}`"
+                )
 
     def validate_schema(self, schema=None):
         """
@@ -647,17 +643,13 @@ def build_schema(self, pipeline_dir, no_prompts, web_only, url):
                     # Extra help for people running offline
                     if "Could not connect" in e.args[0]:
                         log.info(
-                            "If you're working offline, now copy your schema ({}) and paste at https://nf-co.re/pipeline_schema_builder".format(
-                                self.schema_filename
-                            )
+                            f"If you're working offline, now copy your schema ({self.schema_filename}) and paste at https://nf-co.re/pipeline_schema_builder"
                         )
                         log.info("When you're finished, you can paste the edited schema back into the same file")
                     if self.web_schema_build_web_url:
                         log.info(
                             "To save your work, open {}\n"
-                            "Click the blue 'Finished' button, copy the schema and paste into this file: {}".format(
-                                self.web_schema_build_web_url, self.schema_filename
-                            )
+                            f"Click the blue 'Finished' button, copy the schema and paste into this file: { self.web_schema_build_web_url, self.schema_filename}"
                         )
                     return False
 

nf_core/subworkflows/lint/__init__.py

@@ -6,7 +6,6 @@
 nf-core subworkflows lint
 """
 
-
 import logging
 import os
 

nf_core/subworkflows/lint/subworkflow_changes.py

@@ -1,6 +1,7 @@
 """
 Check whether the content of a subworkflow has changed compared to the original repository
 """
+
 from pathlib import Path
 
 import nf_core.modules.modules_repo

nf_core/subworkflows/lint/subworkflow_tests.py

@@ -1,6 +1,7 @@
 """
 Lint the tests of a subworkflow in nf-core/modules
 """
+
 import json
 import logging
 from pathlib import Path

nf_core/utils.py

@@ -1,6 +1,7 @@
 """
 Common utility functions for the nf-core python package.
 """
+
 import concurrent.futures
 import datetime
 import errno

tests/components/generate_snapshot.py

@@ -1,4 +1,5 @@
 """Test generate a snapshot"""
+
 import json
 from pathlib import Path
 from unittest.mock import MagicMock

tests/components/snapshot_test.py

@@ -1,4 +1,5 @@
 """Test the 'modules test' or 'subworkflows test' command which runs nf-test test."""
+
 import shutil
 from pathlib import Path
 

tests/test_bump_version.py

@@ -1,5 +1,5 @@
-"""Some tests covering the bump_version code.
-"""
+"""Some tests covering the bump_version code."""
+
 import os
 
 import yaml

tests/test_cli.py

@@ -1,4 +1,4 @@
-""" Tests covering the command-line code.
+"""Tests covering the command-line code.
 
 Most tests check the cli arguments are passed along and that some action is
 taken.

tests/test_components.py

@@ -1,5 +1,4 @@
-""" Tests covering the modules commands
-"""
+"""Tests covering the modules commands"""
 
 import os
 import shutil

tests/test_create.py

@@ -1,5 +1,5 @@
-"""Some tests covering the pipeline creation sub command.
-"""
+"""Some tests covering the pipeline creation sub command."""
+
 import os
 import unittest
 from pathlib import Path

tests/test_download.py

@@ -1,5 +1,4 @@
-"""Tests for the download subcommand of nf-core tools
-"""
+"""Tests for the download subcommand of nf-core tools"""
 
 import os
 import re

tests/test_launch.py

@@ -1,5 +1,4 @@
-""" Tests covering the pipeline launch code.
-"""
+"""Tests covering the pipeline launch code."""
 
 import json
 import os

tests/test_licenses.py

@@ -1,5 +1,4 @@
-"""Some tests covering the pipeline creation sub command.
-"""
+"""Some tests covering the pipeline creation sub command."""
 # import json
 # import os
 # import tempfile