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Modules: If something is wrong with the local repo cache, offer to delete it and try again #1851

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merged 1 commit into from
Oct 1, 2022
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Modules: If something is wrong with the local repo cache, offer to delete it and try again #1851

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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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/issues/1850))

### Modules

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106 changes: 58 additions & 48 deletions nf_core/modules/modules_repo.py
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Expand Up @@ -5,8 +5,9 @@
from pathlib import Path

import git
import rich
import rich.progress
from git.exc import GitCommandError
from git.exc import GitCommandError, InvalidGitRepositoryError

import nf_core.modules.module_utils
import nf_core.modules.modules_json
Expand Down Expand Up @@ -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, InvalidGitRepositoryError) 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):
"""
Expand Down