Modules: If something is wrong with the local repo cache, offer to de…

…lete it and try again

Closes nf-core#1850

CHANGELOG.md

@@ -24,6 +24,7 @@
 - Schema: Remove `allOf` if no definition groups are left.
 - Use contextlib to temporarily change working directories ([#1819](https://github.com/nf-core/tools/pull/1819))
 - More helpful error messages if `nf-core download` can't parse a singularity image download
+- Modules: If something is wrong with the local repo cache, offer to delete it and try again ([#1850](https://github.com/nf-core/tools/pull/1850))
 
 ### Modules
 

nf_core/modules/modules_repo.py

@@ -5,6 +5,7 @@
 from pathlib import Path
 
 import git
+import rich
 import rich.progress
 from git.exc import GitCommandError
 
@@ -150,55 +151,64 @@ def setup_local_repo(self, remote, branch, hide_progress=True):
  Sets self.repo
  """
  self.local_repo_dir = os.path.join(NFCORE_DIR, self.fullname)
- if not os.path.exists(self.local_repo_dir):
- try:
- pbar = rich.progress.Progress(
- "[bold blue]{task.description}",
- rich.progress.BarColumn(bar_width=None),
- "[bold yellow]{task.fields[state]}",
- transient=True,
- disable=hide_progress,
- )
- with pbar:
- self.repo = git.Repo.clone_from(
- remote,
- self.local_repo_dir,
- progress=RemoteProgressbar(pbar, self.fullname, self.remote_url, "Cloning"),
+ try:
+ if not os.path.exists(self.local_repo_dir):
+ try:
+ pbar = rich.progress.Progress(
+ "[bold blue]{task.description}",
+ rich.progress.BarColumn(bar_width=None),
+ "[bold yellow]{task.fields[state]}",
+ transient=True,
+ disable=hide_progress,
  )
- ModulesRepo.update_local_repo_status(self.fullname, True)
- except GitCommandError:
- raise LookupError(f"Failed to clone from the remote: `{remote}`")
- # Verify that the requested branch exists by checking it out
- self.setup_branch(branch)
- else:
- self.repo = git.Repo(self.local_repo_dir)
-
- if ModulesRepo.no_pull_global:
- ModulesRepo.update_local_repo_status(self.fullname, True)
- # If the repo is already cloned, fetch the latest changes from the remote
- if not ModulesRepo.local_repo_synced(self.fullname):
- pbar = rich.progress.Progress(
- "[bold blue]{task.description}",
- rich.progress.BarColumn(bar_width=None),
- "[bold yellow]{task.fields[state]}",
- transient=True,
- disable=hide_progress,
- )
- with pbar:
- self.repo.remotes.origin.fetch(
- progress=RemoteProgressbar(pbar, self.fullname, self.remote_url, "Pulling")
+ with pbar:
+ self.repo = git.Repo.clone_from(
+ remote,
+ self.local_repo_dir,
+ progress=RemoteProgressbar(pbar, self.fullname, self.remote_url, "Cloning"),
+ )
+ ModulesRepo.update_local_repo_status(self.fullname, True)
+ except GitCommandError:
+ raise LookupError(f"Failed to clone from the remote: `{remote}`")
+ # Verify that the requested branch exists by checking it out
+ self.setup_branch(branch)
+ else:
+ self.repo = git.Repo(self.local_repo_dir)
+
+ if ModulesRepo.no_pull_global:
+ ModulesRepo.update_local_repo_status(self.fullname, True)
+ # If the repo is already cloned, fetch the latest changes from the remote
+ if not ModulesRepo.local_repo_synced(self.fullname):
+ pbar = rich.progress.Progress(
+ "[bold blue]{task.description}",
+ rich.progress.BarColumn(bar_width=None),
+ "[bold yellow]{task.fields[state]}",
+ transient=True,
+ disable=hide_progress,
  )
- ModulesRepo.update_local_repo_status(self.fullname, True)
-
- # Before verifying the branch, fetch the changes
- # Verify that the requested branch exists by checking it out
- self.setup_branch(branch)
-
- # Now merge the changes
- tracking_branch = self.repo.active_branch.tracking_branch()
- if tracking_branch is None:
- raise LookupError(f"There is no remote tracking branch '{self.branch}' in '{self.remote_url}'")
- self.repo.git.merge(tracking_branch.name)
+ with pbar:
+ self.repo.remotes.origin.fetch(
+ progress=RemoteProgressbar(pbar, self.fullname, self.remote_url, "Pulling")
+ )
+ ModulesRepo.update_local_repo_status(self.fullname, True)
+
+ # Before verifying the branch, fetch the changes
+ # Verify that the requested branch exists by checking it out
+ self.setup_branch(branch)
+
+ # Now merge the changes
+ tracking_branch = self.repo.active_branch.tracking_branch()
+ if tracking_branch is None:
+ raise LookupError(f"There is no remote tracking branch '{self.branch}' in '{self.remote_url}'")
+ self.repo.git.merge(tracking_branch.name)
+ except GitCommandError as e:
+ log.error(f"[red]Could not set up local cache of modules repository:[/]\n{e}\n")
+ if rich.prompt.Confirm.ask(f"[violet]Delete local cache '{self.local_repo_dir}' and try again?"):
+ log.info(f"Removing '{self.local_repo_dir}'")
+ shutil.rmtree(self.local_repo_dir)
+ self.setup_local_repo(remote, branch, hide_progress)
+ else:
+ raise LookupError("Exiting due to error with local modules git repo")
 
  def setup_branch(self, branch):
  """