Ensure a user is configured in Git config. Required for Github Action…

…s, but may also affect normal usage.

nf_core/download.py

@@ -1726,21 +1726,29 @@ def tidy_tags_and_branches(self):
     # "Private" method to add the additional custom tags to the repository.
     def __add_additional_tags(self) -> None:
         if self.additional_tags:
+            self.ensure_git_user_config(f"nf-core download v{nf_core.__version__}", "core@nf-co.re")
+
             for additional_tag in self.additional_tags:
                 # A valid git branch or tag name can contain alphanumeric characters, underscores, hyphens, and dots.
                 # But it must not start with a dot, hyphen or underscore and also cannot contain two consecutive dots.
-                if re.match(r"^\w[\w_.-]+={1}\w[\w_.-]+$",additional_tag) and '..' not in additional_tag:
+                if re.match(r"^\w[\w_.-]+={1}\w[\w_.-]+$", additional_tag) and ".." not in additional_tag:
                     anchor, tag = additional_tag.split("=")
                     if self.repo.is_valid_object(anchor) and not self.repo.is_valid_object(tag):
                         try:
-                            self.repo.create_tag(tag,ref=anchor,message=f"Synonynmous tag to {anchor}; added by 'nf-core download'.")
-                            self.repo.create_head(tag,anchor)  # should heads be created as well?
+                            self.repo.create_tag(
+                                tag, ref=anchor, message=f"Synonynmous tag to {anchor}; added by 'nf-core download'."
+                            )
+                            self.repo.create_head(tag, anchor)  # should heads be created as well?
                         except (GitCommandError, InvalidGitRepositoryError) as e:
                             log.error(f"[red]Additional tag(s) could not be applied:[/]\n{e}\n")
                     else:
-                        log.error(f"[red]Adding the additional tag '{tag}' to '{anchor}' failed.[/]\n Mind that '{anchor}' must be a valid git reference that resolves to a commit, while '{tag}' must not exist hitherto.")
+                        log.error(
+                            f"[red]Adding the additional tag '{tag}' to '{anchor}' failed.[/]\n Mind that '{anchor}' must be a valid git reference that resolves to a commit, while '{tag}' must not exist hitherto."
+                        )
                 else:
-                    log.error(f"[red]Could not apply invalid '-a' / '--additional-tag' specification[/]: '{additional_tag}'")
+                    log.error(
+                        f"[red]Could not apply invalid '-a' / '--additional-tag' specification[/]: '{additional_tag}'"
+                    )
 
     def bare_clone(self, destination):
         if self.repo:

nf_core/synced_repo.py

@@ -116,6 +116,10 @@ def __init__(self, remote_url=None, branch=None, no_pull=False, hide_progress=Fa
 
         self.remote_url = remote_url
 
+        self.repo = None
+        # ToDo: SyncedRepo doesn't have this method and both the ModulesRepo and
+        # the WorkflowRepo define their own including custom init methods. This needs
+        # fixing, but is beyond the scope of this PR.
         self.setup_local_repo(remote_url, branch, hide_progress)
 
         config_fn, repo_config = load_tools_config(self.local_repo_dir)
@@ -326,6 +330,18 @@ def component_files_identical(self, component_name, base_path, commit, component
         self.checkout_branch()
         return files_identical
 
+    def ensure_git_user_config(self, default_name: str, default_email: str) -> None:
+        with self.repo.config_reader() as git_config:
+            user_name = git_config.get_value("user", "name", default=None)
+            user_email = git_config.get_value("user", "email", default=None)
+
+        if not user_name or not user_email:
+            with self.repo.config_writer() as git_config:
+                if not user_name:
+                    git_config.set_value("user", "name", default_name)
+                if not user_email:
+                    git_config.set_value("user", "email", default_email)
+
     def get_component_git_log(self, component_name, component_type, depth=None):
         """
         Fetches the commit history the of requested module/subworkflow since a given date. The default value is

tests/test_download.py

@@ -21,7 +21,6 @@
 
 
 class DownloadTest(unittest.TestCase):
-
     @pytest.fixture(autouse=True)
     def use_caplog(self, caplog):
         self._caplog = caplog
@@ -36,7 +35,7 @@ def logged_messages(self) -> list[str]:
 
     def __contains__(self, item: str) -> bool:
         """Allows to check for log messages easily using the in operator inside a test:
-            assert 'my log message' in self
+        assert 'my log message' in self
         """
         return any(record.message == item for record in self._caplog.records if self._caplog)
 
@@ -644,15 +643,13 @@ def test_download_workflow_for_platform(self, tmp_dir, _):
             in download_obj.containers
         )  # indirect definition via $container variable.
 
-
     #
     # Test adding custom tags to Seqera Platform download
     #
     @mock.patch("nf_core.download.DownloadWorkflow.get_singularity_images")
     @with_temporary_folder
-    def test_download_workflow_for_platform_with_custom_tags(self,_, tmp_dir):
+    def test_download_workflow_for_platform_with_custom_tags(self, _, tmp_dir):
         with self._caplog.at_level(logging.INFO):
-            from git.refs.head import Head
             from git.refs.tag import TagReference
 
             download_obj = DownloadWorkflow(
@@ -661,7 +658,13 @@ def test_download_workflow_for_platform_with_custom_tags(self,_, tmp_dir):
                 compress_type="none",
                 platform=True,
                 container_system=None,
-                additional_tags=("3.7=a.tad.outdated", "3.9=cool_revision", "3.9=invalid tag","3.14.0=not_included","What is this?"),
+                additional_tags=(
+                    "3.7=a.tad.outdated",
+                    "3.9=cool_revision",
+                    "3.9=invalid tag",
+                    "3.14.0=not_included",
+                    "What is this?",
+                ),
             )
 
             download_obj.include_configs = False  # suppress prompt, because stderr.is_interactive doesn't.
@@ -696,8 +699,14 @@ def test_download_workflow_for_platform_with_custom_tags(self,_, tmp_dir):
             workflow_repo_tags = {tag.name for tag in download_obj.workflow_repo.tags}
             assert len(workflow_repo_tags) == 4
             # the invalid/malformed additional_tags should not have been added.
-            assert all(tag in workflow_repo_tags for tag in {'3.7', 'a.tad.outdated', 'cool_revision', '3.9'})
-            assert not any(tag in workflow_repo_tags for tag in {'invalid tag','not_included','What is this?'})
-
-            assert all(log in self.logged_messages for log in {"[red]Could not apply invalid '-a' / '--additional-tag' specification[/]: '3.9=invalid tag'", "[red]Adding the additional tag 'not_included' to '3.14.0' failed.[/]\n Mind that '3.14.0' must be a valid git reference that resolves to a commit, while 'not_included' must not exist hitherto.", "[red]Could not apply invalid '-a' / '--additional-tag' specification[/]: 'What is this?'"})
-
+            assert all(tag in workflow_repo_tags for tag in {"3.7", "a.tad.outdated", "cool_revision", "3.9"})
+            assert not any(tag in workflow_repo_tags for tag in {"invalid tag", "not_included", "What is this?"})
+
+            assert all(
+                log in self.logged_messages
+                for log in {
+                    "[red]Could not apply invalid '-a' / '--additional-tag' specification[/]: '3.9=invalid tag'",
+                    "[red]Adding the additional tag 'not_included' to '3.14.0' failed.[/]\n Mind that '3.14.0' must be a valid git reference that resolves to a commit, while 'not_included' must not exist hitherto.",
+                    "[red]Could not apply invalid '-a' / '--additional-tag' specification[/]: 'What is this?'",
+                }
+            )