Merge branch 'dev' of github.com:nf-core/tools into support-update-patch

CHANGELOG.md

@@ -10,6 +10,7 @@
 - Add `CITATION.cff` [#361](https://github.com/nf-core/tools/issues/361)
 - Add Gitpod and Mamba profiles to the pipeline template ([#1673](https://github.com/nf-core/tools/pull/1673))
 - Remove call to `getGenomeAttribute` in `main.nf` when running `nf-core create` without iGenomes ([#1670](https://github.com/nf-core/tools/issues/1670))
+- Make `nf-core create` fail if Git default branch name is dev or TEMPLATE ([#1705](https://github.com/nf-core/tools/pull/1705))
 
 ### Linting
 

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/create.py

@@ -2,6 +2,7 @@
 """Creates a nf-core pipeline matching the current
 organization's specification based on a template.
 """
+import configparser
 import imghdr
 import logging
 import os
@@ -490,7 +491,24 @@ def download_pipeline_logo(self, url, img_fn):
             break
 
     def git_init_pipeline(self):
-        """Initialises the new pipeline as a Git repository and submits first commit."""
+        """Initialises the new pipeline as a Git repository and submits first commit.
+
+        Raises:
+            UserWarning: if Git default branch is set to 'dev' or 'TEMPLATE'.
+        """
+        # Check that the default branch is not dev
+        try:
+            default_branch = git.config.GitConfigParser().get_value("init", "defaultBranch")
+        except configparser.Error:
+            default_branch = None
+            log.debug("Could not read init.defaultBranch")
+        if default_branch == "dev" or default_branch == "TEMPLATE":
+            raise UserWarning(
+                f"Your Git defaultBranch is set to '{default_branch}', which is incompatible with nf-core.\n"
+                "This can be modified with the command [white on grey23] git config --global init.defaultBranch <NAME> [/]\n"
+                "Pipeline git repository is not initialised."
+            )
+        # Initialise pipeline
         log.info("Initialising pipeline git repository")
         repo = git.Repo.init(self.outdir)
         repo.git.add(A=True)

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
@@ -305,7 +304,7 @@ def test_build_schema_param_int(self):
         param = self.schema_obj.build_schema_param("12")
         assert param == {"type": "integer", "default": 12}
 
-    def test_build_schema_param_int(self):
+    def test_build_schema_param_float(self):
         """Build a new schema param from a config value (float)"""
         param = self.schema_obj.build_schema_param("12.34")
         assert param == {"type": "number", "default": 12.34}