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Merge pull request #2032 from fabianegli/maintenance
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Maintenance
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fabianegli authored Nov 21, 2022
2 parents 2243440 + 17e80aa commit dd0f943
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Showing 12 changed files with 14 additions and 15 deletions.
2 changes: 1 addition & 1 deletion CHANGELOG.md
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- 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))
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2 changes: 1 addition & 1 deletion nf_core/create.py
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Expand Up @@ -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:
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2 changes: 1 addition & 1 deletion nf_core/download.py
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Expand Up @@ -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.
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2 changes: 1 addition & 1 deletion nf_core/launch.py
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Expand Up @@ -21,7 +21,7 @@
log = logging.getLogger(__name__)


class Launch(object):
class Launch:
"""Class to hold config option to launch a pipeline"""

def __init__(
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2 changes: 1 addition & 1 deletion nf_core/licences.py
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Expand Up @@ -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
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6 changes: 3 additions & 3 deletions nf_core/list.py
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Expand Up @@ -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
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)


class RemoteWorkflow(object):
class RemoteWorkflow:
"""A information container for a remote workflow.
Args:
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)


class LocalWorkflow(object):
class LocalWorkflow:
"""Class to handle local workflows pulled by nextflow"""

def __init__(self, name):
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2 changes: 1 addition & 1 deletion nf_core/modules/lint/__init__.py
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Expand Up @@ -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):
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3 changes: 1 addition & 2 deletions nf_core/modules/modules_repo.py
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Expand Up @@ -2,7 +2,6 @@
import logging
import os
import shutil
from importlib.resources import path
from pathlib import Path

import git
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)


class ModulesRepo(object):
class ModulesRepo:
"""
An object to store details about the repository being used for modules.
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2 changes: 1 addition & 1 deletion nf_core/modules/nfcore_module.py
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion nf_core/schema.py
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Expand Up @@ -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"""

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2 changes: 1 addition & 1 deletion nf_core/sync.py
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Expand Up @@ -33,7 +33,7 @@ class PullRequestException(Exception):
pass


class PipelineSync(object):
class PipelineSync:
"""Object to hold syncing information and results.
Args:
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2 changes: 1 addition & 1 deletion nf_core/utils.py
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Expand Up @@ -89,7 +89,7 @@ def rich_force_colors():
return None


class Pipeline(object):
class Pipeline:
"""Object to hold information about a local pipeline.
Args:
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