diff --git a/CHANGELOG.md b/CHANGELOG.md index 07000cce58..d0c0f520d2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -29,7 +29,7 @@ - Bump promoted Python version from 3.7 to 3.8 ([#1971](https://github.com/nf-core/tools/pull/1971)) - Fix incorrect file deletion in `nf-core launch` when `--params_in` has the same name as `--params_out` - Updated GitHub actions ([#1998](https://github.com/nf-core/tools/pull/1998), [#2001](https://github.com/nf-core/tools/pull/2001)) -- Code maintenance ([#1818](https://github.com/nf-core/tools/pull/1818)) +- Code maintenance ([#1818](https://github.com/nf-core/tools/pull/1818), [#2032](https://github.com/nf-core/tools/pull/2032)) - Track from where modules and subworkflows are installed ([#1999](https://github.com/nf-core/tools/pull/1999)) - Substitute ModulesCommand and SubworkflowsCommand by ComponentsCommand ([#2000](https://github.com/nf-core/tools/pull/2000)) - Don't print source file + line number on logging messages (except when verbose) ([#2015](https://github.com/nf-core/tools/pull/2015)) diff --git a/nf_core/create.py b/nf_core/create.py index ed23c8487c..c7cdfc2269 100644 --- a/nf_core/create.py +++ b/nf_core/create.py @@ -26,7 +26,7 @@ log = logging.getLogger(__name__) -class PipelineCreate(object): +class PipelineCreate: """Creates a nf-core pipeline a la carte from the nf-core best-practice template. Args: diff --git a/nf_core/download.py b/nf_core/download.py index 5e7f4edb2f..2f964b3afd 100644 --- a/nf_core/download.py +++ b/nf_core/download.py @@ -64,7 +64,7 @@ def get_renderables(self): yield self.make_tasks_table([task]) -class DownloadWorkflow(object): +class DownloadWorkflow: """Downloads a nf-core workflow from GitHub to the local file system. Can also download its Singularity container image if required. diff --git a/nf_core/launch.py b/nf_core/launch.py index 03fcb6bce8..d03e112c3e 100644 --- a/nf_core/launch.py +++ b/nf_core/launch.py @@ -21,7 +21,7 @@ log = logging.getLogger(__name__) -class Launch(object): +class Launch: """Class to hold config option to launch a pipeline""" def __init__( diff --git a/nf_core/licences.py b/nf_core/licences.py index 3b188861eb..d686a56178 100644 --- a/nf_core/licences.py +++ b/nf_core/licences.py @@ -16,7 +16,7 @@ log = logging.getLogger(__name__) -class WorkflowLicences(object): +class WorkflowLicences: """A nf-core workflow licenses collection. Tries to retrieve the license information from all dependencies diff --git a/nf_core/list.py b/nf_core/list.py index b4353050e6..53307ac9bd 100644 --- a/nf_core/list.py +++ b/nf_core/list.py @@ -73,7 +73,7 @@ def get_local_wf(workflow, revision=None): return local_wf.local_path -class Workflows(object): +class Workflows: """Workflow container class. Is used to collect local and remote nf-core pipelines. Pipelines @@ -272,7 +272,7 @@ def print_json(self): ) -class RemoteWorkflow(object): +class RemoteWorkflow: """A information container for a remote workflow. Args: @@ -308,7 +308,7 @@ def __init__(self, data): ) -class LocalWorkflow(object): +class LocalWorkflow: """Class to handle local workflows pulled by nextflow""" def __init__(self, name): diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py index de50770ebb..e6786a1e7a 100644 --- a/nf_core/modules/lint/__init__.py +++ b/nf_core/modules/lint/__init__.py @@ -35,7 +35,7 @@ class ModuleLintException(Exception): pass -class LintResult(object): +class LintResult: """An object to hold the results of a lint test""" def __init__(self, mod, lint_test, message, file_path): diff --git a/nf_core/modules/modules_repo.py b/nf_core/modules/modules_repo.py index 673db73155..f9e8f31318 100644 --- a/nf_core/modules/modules_repo.py +++ b/nf_core/modules/modules_repo.py @@ -2,7 +2,6 @@ import logging import os import shutil -from importlib.resources import path from pathlib import Path import git @@ -59,7 +58,7 @@ def update(self, op_code, cur_count, max_count=None, message=""): ) -class ModulesRepo(object): +class ModulesRepo: """ An object to store details about the repository being used for modules. diff --git a/nf_core/modules/nfcore_module.py b/nf_core/modules/nfcore_module.py index 67bfc6c1c4..e8bff1f686 100644 --- a/nf_core/modules/nfcore_module.py +++ b/nf_core/modules/nfcore_module.py @@ -4,7 +4,7 @@ from pathlib import Path -class NFCoreModule(object): +class NFCoreModule: """ A class to hold the information about a nf-core module Includes functionality for linting diff --git a/nf_core/schema.py b/nf_core/schema.py index 0be825fea2..d566f2b519 100644 --- a/nf_core/schema.py +++ b/nf_core/schema.py @@ -20,7 +20,7 @@ log = logging.getLogger(__name__) -class PipelineSchema(object): +class PipelineSchema: """Class to generate a schema object with functions to handle pipeline JSON Schema""" diff --git a/nf_core/sync.py b/nf_core/sync.py index 2384ad4de7..4d0e1e88ba 100644 --- a/nf_core/sync.py +++ b/nf_core/sync.py @@ -33,7 +33,7 @@ class PullRequestException(Exception): pass -class PipelineSync(object): +class PipelineSync: """Object to hold syncing information and results. Args: diff --git a/nf_core/utils.py b/nf_core/utils.py index 117c052e0a..a7ecb19a32 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -89,7 +89,7 @@ def rich_force_colors(): return None -class Pipeline(object): +class Pipeline: """Object to hold information about a local pipeline. Args: