manually fix other ruff errors

nf_core/__main__.py

@@ -934,7 +934,7 @@ def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed,
     Test modules within a pipeline or a clone of the
     nf-core/modules repository.
     """
-    from nf_core.components.lint import LintException
+    from nf_core.components.lint import LintExceptionError
     from nf_core.modules import ModuleLint
 
     try:
@@ -960,7 +960,7 @@ def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed,
         )
         if len(module_lint.failed) > 0:
             sys.exit(1)
-    except LintException as e:
+    except LintExceptionError as e:
         log.error(e)
         sys.exit(1)
     except (UserWarning, LookupError) as e:
@@ -1020,7 +1020,7 @@ def bump_versions(ctx, tool, dir, all, show_all):
     the nf-core/modules repo.
     """
     from nf_core.modules.bump_versions import ModuleVersionBumper
-    from nf_core.modules.modules_utils import ModuleException
+    from nf_core.modules.modules_utils import ModuleExceptionError
 
     try:
         version_bumper = ModuleVersionBumper(
@@ -1030,7 +1030,7 @@ def bump_versions(ctx, tool, dir, all, show_all):
             ctx.obj["modules_repo_no_pull"],
         )
         version_bumper.bump_versions(module=tool, all_modules=all, show_uptodate=show_all)
-    except ModuleException as e:
+    except ModuleExceptionError as e:
         log.error(e)
         sys.exit(1)
     except (UserWarning, LookupError) as e:
@@ -1207,7 +1207,7 @@ def subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, lo
     Test subworkflows within a pipeline or a clone of the
     nf-core/modules repository.
     """
-    from nf_core.components.lint import LintException
+    from nf_core.components.lint import LintExceptionError
     from nf_core.subworkflows import SubworkflowLint
 
     try:
@@ -1232,7 +1232,7 @@ def subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, lo
         )
         if len(subworkflow_lint.failed) > 0:
             sys.exit(1)
-    except LintException as e:
+    except LintExceptionError as e:
         log.error(e)
         sys.exit(1)
     except (UserWarning, LookupError) as e:
@@ -1647,7 +1647,7 @@ def sync(dir, from_branch, pull_request, github_repository, username, template_y
     the pipeline. It is run automatically for all pipelines when ever a
     new release of [link=https://github.com/nf-core/tools]nf-core/tools[/link] (and the included template) is made.
     """
-    from nf_core.sync import PipelineSync, PullRequestException, SyncException
+    from nf_core.sync import PipelineSync, PullRequestExceptionError, SyncExceptionError
     from nf_core.utils import is_pipeline_directory
 
     # Check if pipeline directory contains necessary files
@@ -1657,7 +1657,7 @@ def sync(dir, from_branch, pull_request, github_repository, username, template_y
     sync_obj = PipelineSync(dir, from_branch, pull_request, github_repository, username, template_yaml)
     try:
         sync_obj.sync()
-    except (SyncException, PullRequestException) as e:
+    except (SyncExceptionError, PullRequestExceptionError) as e:
         log.error(e)
         sys.exit(1)
 

nf_core/components/lint/__init__.py

@@ -26,7 +26,7 @@
 log = logging.getLogger(__name__)
 
 
-class LintException(Exception):
+class LintExceptionError(Exception):
     """Exception raised when there was an error with module or subworkflow linting"""
 
     pass

nf_core/components/nfcore_component.py

@@ -168,7 +168,7 @@ def get_inputs_from_main_nf(self):
         input_data = data.split("input:")[1].split("output:")[0]
         regex = r"(val|path)\s*(\(([^)]+)\)|\s*([^)\s,]+))"
         matches = re.finditer(regex, input_data, re.MULTILINE)
-        for matchNum, match in enumerate(matches, start=1):
+        for _, match in enumerate(matches, start=1):
             if match.group(3):
                 inputs.append(match.group(3))
             elif match.group(4):
@@ -187,7 +187,7 @@ def get_outputs_from_main_nf(self):
         output_data = data.split("output:")[1].split("when:")[0]
         regex = r"emit:\s*([^)\s,]+)"
         matches = re.finditer(regex, output_data, re.MULTILINE)
-        for matchNum, match in enumerate(matches, start=1):
+        for _, match in enumerate(matches, start=1):
             outputs.append(match.group(1))
         log.info(f"Found {len(outputs)} outputs in {self.main_nf}")
         self.outputs = outputs

nf_core/download.py

@@ -20,7 +20,7 @@
 import rich
 import rich.progress
 from git.exc import GitCommandError, InvalidGitRepositoryError
-from pkg_resources import parse_version as VersionParser
+from pkg_resources import parse_version as version_parser
 
 import nf_core
 import nf_core.list
@@ -1065,10 +1065,10 @@ def get_singularity_images(self, current_revision=""):
                                 self.singularity_pull_image(*container, library, progress)
                                 # Pulling the image was successful, no ContainerError was raised, break the library loop
                                 break
-                            except ContainerError.ImageExists:
+                            except ContainerError.ImageExistsError:
                                 # Pulling not required
                                 break
-                            except ContainerError.RegistryNotFound as e:
+                            except ContainerError.RegistryNotFoundError as e:
                                 self.container_library.remove(library)
                                 # The only library was removed
                                 if not self.container_library:
@@ -1078,13 +1078,13 @@ def get_singularity_images(self, current_revision=""):
                                 else:
                                     # Other libraries can be used
                                     continue
-                            except ContainerError.ImageNotFound as e:
+                            except ContainerError.ImageNotFoundError as e:
                                 # Try other registries
                                 if e.error_log.absolute_URI:
                                     break  # there no point in trying other registries if absolute URI was specified.
                                 else:
                                     continue
-                            except ContainerError.InvalidTag:
+                            except ContainerError.InvalidTagError:
                                 # Try other registries
                                 continue
                             except ContainerError.OtherError as e:
@@ -1523,7 +1523,7 @@ def tidy_tags_and_branches(self):
                     else:
                         # desired revisions may contain arbitrary branch names that do not correspond to valid sematic versioning patterns.
                         valid_versions = [
-                            VersionParser(v)
+                            version_parser(v)
                             for v in desired_revisions
                             if re.match(r"\d+\.\d+(?:\.\d+)*(?:[\w\-_])*", v)
                         ]
@@ -1582,7 +1582,7 @@ def __init__(self, container, registry, address, absolute_URI, out_path, singula
 
         for line in error_msg:
             if re.search(r"dial\stcp.*no\ssuch\shost", line):
-                self.error_type = self.RegistryNotFound(self)
+                self.error_type = self.RegistryNotFoundError(self)
                 break
             elif (
                 re.search(r"requested\saccess\sto\sthe\sresource\sis\sdenied", line)
@@ -1594,13 +1594,13 @@ def __init__(self, container, registry, address, absolute_URI, out_path, singula
                 #                    unauthorized: authentication required
                 # Quay.io: StatusCode: 404,  <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">\n']
                 # ghcr.io: Requesting bearer token: invalid status code from registry 400 (Bad Request)
-                self.error_type = self.ImageNotFound(self)
+                self.error_type = self.ImageNotFoundError(self)
                 break
             elif re.search(r"manifest\sunknown", line):
-                self.error_type = self.InvalidTag(self)
+                self.error_type = self.InvalidTagError(self)
                 break
             elif re.search(r"Image\sfile\salready\sexists", line):
-                self.error_type = self.ImageExists(self)
+                self.error_type = self.ImageExistsError(self)
                 break
             else:
                 continue
@@ -1614,7 +1614,7 @@ def __init__(self, container, registry, address, absolute_URI, out_path, singula
 
         raise self.error_type
 
-    class RegistryNotFound(ConnectionRefusedError):
+    class RegistryNotFoundError(ConnectionRefusedError):
         """The specified registry does not resolve to a valid IP address"""
 
         def __init__(self, error_log):
@@ -1627,7 +1627,7 @@ def __init__(self, error_log):
             )
             super().__init__(self.message, self.helpmessage, self.error_log)
 
-    class ImageNotFound(FileNotFoundError):
+    class ImageNotFoundError(FileNotFoundError):
         """The image can not be found in the registry"""
 
         def __init__(self, error_log):
@@ -1643,7 +1643,7 @@ def __init__(self, error_log):
 
             super().__init__(self.message)
 
-    class InvalidTag(AttributeError):
+    class InvalidTagError(AttributeError):
         """Image and registry are valid, but the (version) tag is not"""
 
         def __init__(self, error_log):
@@ -1652,7 +1652,7 @@ def __init__(self, error_log):
             self.helpmessage = f'Please chose a different library than {self.error_log.registry}\nor try to locate the "{self.error_log.address.split(":")[-1]}" version of "{self.error_log.container}" manually.\nPlease troubleshoot the command \n"{" ".join(self.error_log.singularity_command)}" manually.\n'
             super().__init__(self.message)
 
-    class ImageExists(FileExistsError):
+    class ImageExistsError(FileExistsError):
         """Image already exists in cache/output directory."""
 
         def __init__(self, error_log):

nf_core/modules/__init__.py

@@ -6,7 +6,7 @@
 from .list import ModuleList
 from .modules_json import ModulesJson
 from .modules_repo import ModulesRepo
-from .modules_utils import ModuleException
+from .modules_utils import ModuleExceptionError
 from .patch import ModulePatch
 from .remove import ModuleRemove
 from .update import ModuleUpdate

nf_core/modules/bump_versions.py

@@ -71,7 +71,7 @@ def bump_versions(
 
         # Verify that this is not a pipeline
         if not self.repo_type == "modules":
-            raise nf_core.modules.modules_utils.ModuleException(
+            raise nf_core.modules.modules_utils.ModuleExceptionError(
                 "This command only works on the nf-core/modules repository, not on pipelines!"
             )
 
@@ -102,12 +102,14 @@ def bump_versions(
         if module:
             self.show_up_to_date = True
             if all_modules:
-                raise nf_core.modules.modules_utils.ModuleException(
+                raise nf_core.modules.modules_utils.ModuleExceptionError(
                     "You cannot specify a tool and request all tools to be bumped."
                 )
             nfcore_modules = [m for m in nfcore_modules if m.component_name == module]
             if len(nfcore_modules) == 0:
-                raise nf_core.modules.modules_utils.ModuleException(f"Could not find the specified module: '{module}'")
+                raise nf_core.modules.modules_utils.ModuleExceptionError(
+                    f"Could not find the specified module: '{module}'"
+                )
 
         progress_bar = Progress(
             "[bold blue]{task.description}",

nf_core/modules/lint/__init__.py

@@ -15,7 +15,7 @@
 
 import nf_core.modules.modules_utils
 import nf_core.utils
-from nf_core.components.lint import ComponentLint, LintException, LintResult
+from nf_core.components.lint import ComponentLint, LintExceptionError, LintResult
 from nf_core.lint_utils import console
 
 log = logging.getLogger(__name__)
@@ -118,11 +118,11 @@ def lint(
         # Only lint the given module
         if module:
             if all_modules:
-                raise LintException("You cannot specify a tool and request all tools to be linted.")
+                raise LintExceptionError("You cannot specify a tool and request all tools to be linted.")
             local_modules = []
             remote_modules = [m for m in self.all_remote_components if m.component_name == module]
             if len(remote_modules) == 0:
-                raise LintException(f"Could not find the specified module: '{module}'")
+                raise LintExceptionError(f"Could not find the specified module: '{module}'")
         else:
             local_modules = self.all_local_components
             remote_modules = self.all_remote_components

nf_core/modules/modules_utils.py

@@ -9,7 +9,7 @@
 log = logging.getLogger(__name__)
 
 
-class ModuleException(Exception):
+class ModuleExceptionError(Exception):
     """Exception raised when there was an error with module commands"""
 
     pass
@@ -69,7 +69,7 @@ def get_installed_modules(dir: str, repo_type="modules") -> Tuple[List[str], Lis
     if os.path.exists(nfcore_modules_dir):
         for m in sorted([m for m in os.listdir(nfcore_modules_dir) if not m == "lib"]):
             if not os.path.isdir(os.path.join(nfcore_modules_dir, m)):
-                raise ModuleException(
+                raise ModuleExceptionError(
                     f"File found in '{nfcore_modules_dir}': '{m}'! This directory should only contain module directories."
                 )
             m_content = os.listdir(os.path.join(nfcore_modules_dir, m))

nf_core/subworkflows/lint/__init__.py

@@ -15,7 +15,7 @@
 
 import nf_core.modules.modules_utils
 import nf_core.utils
-from nf_core.components.lint import ComponentLint, LintException, LintResult
+from nf_core.components.lint import ComponentLint, LintExceptionError, LintResult
 from nf_core.lint_utils import console
 
 log = logging.getLogger(__name__)
@@ -113,11 +113,11 @@ def lint(
         # Only lint the given module
         if subworkflow:
             if all_subworkflows:
-                raise LintException("You cannot specify a tool and request all tools to be linted.")
+                raise LintExceptionError("You cannot specify a tool and request all tools to be linted.")
             local_subworkflows = []
             remote_subworkflows = [s for s in self.all_remote_components if s.component_name == subworkflow]
             if len(remote_subworkflows) == 0:
-                raise LintException(f"Could not find the specified subworkflow: '{subworkflow}'")
+                raise LintExceptionError(f"Could not find the specified subworkflow: '{subworkflow}'")
         else:
             local_subworkflows = self.all_local_components
             remote_subworkflows = self.all_remote_components