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Components: Handle extended set of git path prefixes #2945

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merged 5 commits into from
May 6, 2024
Merged

Components: Handle extended set of git path prefixes #2945

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90a1070
Extend repo_full_name_from_remote function to
robsyme May 1, 2024
bb49920
Update changelog
robsyme May 1, 2024
453f9ea
Ruff formatting fix
robsyme May 1, 2024
d0c17ca
[automated] Update CHANGELOG.md
nf-core-bot May 3, 2024
32fda2c
Merge branch 'dev' into handle-ssh-git-paths
mirpedrol May 6, 2024
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3 changes: 3 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,8 @@

## v2.13.2dev

- Handle more complete list of possible git URL forms (ssh:// and ftp:// prefixes specifically)

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### Template

- Remove fasta default from nextflow.config ([#2828](https://github.com/nf-core/tools/pull/2828))
Expand Down Expand Up @@ -61,6 +63,7 @@
- Update gitpod/workspace-base Docker digest to 5aeb24f ([#2929](https://github.com/nf-core/tools/pull/2929))
- Update pre-commit hook pre-commit/mirrors-mypy to v1.10.0 ([#2933](https://github.com/nf-core/tools/pull/2933))
- Update GitHub Actions ([#2939](https://github.com/nf-core/tools/pull/2939))
- Components: Handle extended set of git path prefixes ([#2945](https://github.com/nf-core/tools/pull/2945))

## [v2.13.1 - Tin Puppy Patch](https://github.com/nf-core/tools/releases/tag/2.13) - [2024-02-29]

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25 changes: 12 additions & 13 deletions nf_core/modules/modules_utils.py
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Expand Up @@ -20,20 +20,19 @@ def repo_full_name_from_remote(remote_url: str) -> str:
Extracts the path from the remote URL
See https://mirrors.edge.kernel.org/pub/software/scm/git/docs/git-clone.html#URLS for the possible URL patterns
"""
# Check whether we have a https or ssh url
if remote_url.startswith("https"):
path = urlparse(remote_url).path
# Remove the intial '/'
path = path[1:]
# Remove extension
path = os.path.splitext(path)[0]

if remote_url.startswith(("https://", "http://", "ftps://", "ftp://", "ssh://")):
# Parse URL and remove the initial '/'
path = urlparse(remote_url).path.lstrip("/")
elif "git@" in remote_url:
# Extract the part after 'git@' and parse it
path = urlparse(remote_url.split("git@")[-1]).path
else:
# Remove the initial `git@``
split_path: list = remote_url.split("@")
path = split_path[-1] if len(split_path) > 1 else split_path[0]
path = urlparse(path).path
# Remove extension
path = os.path.splitext(path)[0]
path = urlparse(remote_url).path

# Remove the file extension from the path
path, _ = os.path.splitext(path)

return path


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