Remove unused imports

nf_core/__main__.py

@@ -2,9 +2,7 @@
 """ nf-core: Helper tools for use with nf-core Nextflow pipelines. """
 import logging
 import os
-import re
 import sys
-from email.policy import default
 
 import rich.console
 import rich.logging

nf_core/bump_version.py

@@ -6,7 +6,6 @@
 import logging
 import os
 import re
-import sys
 
 import rich.console
 

nf_core/launch.py

@@ -12,7 +12,6 @@
 import webbrowser
 
 import questionary
-import requests
 from rich.console import Console
 from rich.markdown import Markdown
 from rich.prompt import Confirm

nf_core/licences.py

@@ -6,7 +6,6 @@
 import json
 import logging
 import os
-import re
 
 import requests
 import rich.console

nf_core/lint/actions_schema_validation.py

@@ -1,7 +1,6 @@
 #!/usr/bin/env python
 
 import glob
-import json
 import logging
 import os
 

nf_core/lint/modules_json.py

@@ -1,7 +1,5 @@
 #!/usr/bin/env python
 
-from logging import warn
-
 from nf_core.modules.modules_command import ModuleCommand
 from nf_core.modules.modules_json import ModulesJson
 

nf_core/lint/schema_description.py

@@ -1,7 +1,5 @@
 #!/usr/bin/env python
 
-from logging import warn
-
 import nf_core.schema
 
 

nf_core/lint/schema_lint.py

@@ -2,8 +2,6 @@
 
 import logging
 
-import jsonschema
-
 import nf_core.schema
 
 

nf_core/modules/bump_versions.py

@@ -7,7 +7,6 @@
 from __future__ import print_function
 
 import logging
-import os
 import re
 
 import questionary

nf_core/modules/info.py

@@ -2,7 +2,6 @@
 import os
 
 import questionary
-import requests
 import yaml
 from rich import box
 from rich.console import Group
@@ -15,7 +14,7 @@
 
 from .module_utils import get_repo_type
 from .modules_command import ModuleCommand
-from .modules_repo import NF_CORE_MODULES_REMOTE, ModulesRepo
+from .modules_repo import NF_CORE_MODULES_REMOTE
 
 log = logging.getLogger(__name__)
 

nf_core/modules/lint/main_nf.py

@@ -7,7 +7,6 @@
 import re
 
 import requests
-from galaxy.tool_util.deps.mulled.util import build_target
 
 import nf_core
 import nf_core.modules.module_utils

nf_core/modules/lint/meta_yml.py

@@ -1,7 +1,5 @@
 #!/usr/bin/env python
 
-from operator import imod
-
 import yaml
 
 

nf_core/modules/lint/module_changes.py

@@ -3,9 +3,6 @@
 """
 import os
 
-import requests
-import rich
-
 
 def module_changes(module_lint_object, module):
     """

nf_core/modules/lint/module_version.py

@@ -3,13 +3,8 @@
 Verify that a module has a correct entry in the modules.json file
 """
 
-import json
 import logging
 import os
-import re
-import sys
-
-import questionary
 
 import nf_core
 import nf_core.modules.module_utils

nf_core/refgenie.py

@@ -9,14 +9,14 @@
 from pathlib import Path
 from textwrap import dedent
 
-# import refgenconf
-from warnings import warn
-
 import rich
-from rich.logging import RichHandler
+import rich.traceback
 
 import nf_core.utils
 
+# import refgenconf
+
+
 # Set up logging
 log = logging.getLogger(__name__)
 log.setLevel(logging.INFO)
@@ -53,7 +53,7 @@ def _print_nf_config(rgc):
                 pth = rgc.seek(genome, asset)
             # Catch general exception instead of refgencof exception --> no refgenconf import needed
             except Exception as e:
-                log.warn(f"{genome}/{asset} is incomplete, ignoring...")
+                log.warning(f"{genome}/{asset} is incomplete, ignoring...")
             else:
                 genomes_str += f'      {asset.ljust(20, " ")} = "{pth}"\n'
         genomes_str += "    }\n"
@@ -150,7 +150,7 @@ def update_config(rgc):
             fh.write(refgenie_genomes)
         log.info(f"Updated nf-core genomes config: {refgenie_genomes_config_file}")
     except FileNotFoundError as e:
-        log.warn(f"Could not write to {refgenie_genomes_config_file}")
+        log.warning(f"Could not write to {refgenie_genomes_config_file}")
         return False
 
     # Add include statement to NXF_HOME/config

tests/lint/files_exist.py

@@ -2,8 +2,6 @@
 
 import os
 
-import yaml
-
 import nf_core.lint
 
 

tests/lint/files_unchanged.py

@@ -1,8 +1,4 @@
 import os
-import shutil
-import tempfile
-
-import pytest
 
 import nf_core.lint
 

tests/lint/merge_markers.py

@@ -2,8 +2,6 @@
 
 import os
 
-import yaml
-
 import nf_core.lint
 
 

tests/lint/modules_json.py

@@ -1,6 +1,3 @@
-import nf_core.lint
-
-
 def test_modules_json_pass(self):
     self.lint_obj._load()
     results = self.lint_obj.modules_json()

tests/lint/nextflow_config.py

@@ -1,10 +1,3 @@
-import os
-import shutil
-import tempfile
-import unittest
-
-import pytest
-
 import nf_core.create
 import nf_core.lint
 

tests/modules/lint.py

@@ -1,5 +1,3 @@
-import json
-
 import nf_core.modules
 
 

tests/test_cli.py

@@ -2,7 +2,6 @@
 """ Tests covering the command-line code.
 """
 
-import unittest
 from unittest import mock
 
 from click.testing import CliRunner

tests/test_launch.py

@@ -4,7 +4,6 @@
 
 import json
 import os
-import shutil
 import tempfile
 import unittest
 from unittest import mock

tests/test_licenses.py

@@ -1,16 +1,16 @@
 #!/usr/bin/env python
 """Some tests covering the pipeline creation sub command.
 """
-import json
-import os
-import tempfile
-import unittest
-
-import pytest
-from rich.console import Console
-
-import nf_core.create
-import nf_core.licences
+# import json
+# import os
+# import tempfile
+# import unittest
+#
+# import pytest
+# from rich.console import Console
+#
+# import nf_core.create
+# import nf_core.licences
 
 # TODO nf-core: Assess and strip out if no longer required for DSL2
 

tests/test_lint.py

@@ -5,13 +5,9 @@
 import json
 import os
 import shutil
-import subprocess
 import tempfile
 import unittest
-from unittest import mock
 
-import pytest
-import requests
 import yaml
 
 import nf_core.create

tests/test_refgenie.py

@@ -8,8 +8,6 @@
 import tempfile
 import unittest
 
-import nf_core.refgenie
-
 
 class TestRefgenie(unittest.TestCase):
     """Class for refgenie tests"""

tests/test_schema.py

@@ -9,7 +9,6 @@
 import unittest
 from unittest import mock
 
-import click
 import pytest
 import requests
 import yaml