Allow nf-core pipelines download -r to download commits
#3374
+97
−6
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files☔ View full report in Codecov by Sentry. |
muffato
force-pushed
the
download_commits
branch
from
28d0305 to
ec254d0
Compare
muffato
force-pushed
the
download_commits
branch
from
ec254d0 to
b0b9559
Compare
mirpedrol
approved these changes
Jan 7, 2025
There was a problem hiding this comment.
LGTM!
I only made a couple of clean-up code suggestions.
Also tagging @MatthiasZepper in case you want to have a quick look
Comment on lines
+88
to
+90
| pipeline = "exoseq" | ||
|
|
||
| download_obj = DownloadWorkflow(pipeline="exoseq", revision="819cbac792b76cf66c840b567ed0ee9a2f620db7") |
There was a problem hiding this comment.
Suggested change
| pipeline = "exoseq" | |
| download_obj = DownloadWorkflow(pipeline="exoseq", revision="819cbac792b76cf66c840b567ed0ee9a2f620db7") | |
| pipeline = "exoseq" | |
| revision = "819cbac792b76cf66c840b567ed0ee9a2f620db7" | |
| download_obj = DownloadWorkflow(pipeline=pipeline, revision=revision) |
| ) = nf_core.utils.get_repo_releases_branches(pipeline, wfs) | ||
| download_obj.get_revision_hash() | ||
| print(download_obj) | ||
| assert download_obj.wf_sha[download_obj.revision[0]] == "819cbac792b76cf66c840b567ed0ee9a2f620db7" |
There was a problem hiding this comment.
Suggested change
| assert download_obj.wf_sha[download_obj.revision[0]] == "819cbac792b76cf66c840b567ed0ee9a2f620db7" | |
| assert download_obj.wf_sha[download_obj.revision[0]] == revision |
| download_obj.get_revision_hash() | ||
| print(download_obj) | ||
| assert download_obj.wf_sha[download_obj.revision[0]] == "819cbac792b76cf66c840b567ed0ee9a2f620db7" | ||
| assert download_obj.outdir == "nf-core-exoseq_819cbac792b76cf66c840b567ed0ee9a2f620db7" |
There was a problem hiding this comment.
Suggested change
| assert download_obj.outdir == "nf-core-exoseq_819cbac792b76cf66c840b567ed0ee9a2f620db7" | |
| assert download_obj.outdir == f"nf-core-exoseq_{revision}" |
| assert download_obj.outdir == "nf-core-exoseq_819cbac792b76cf66c840b567ed0ee9a2f620db7" | ||
| assert ( | ||
| download_obj.wf_download_url[download_obj.revision[0]] | ||
| == "https://github.com/nf-core/exoseq/archive/819cbac792b76cf66c840b567ed0ee9a2f620db7.zip" |
There was a problem hiding this comment.
Suggested change
| == "https://github.com/nf-core/exoseq/archive/819cbac792b76cf66c840b567ed0ee9a2f620db7.zip" | |
| == f"https://github.com/nf-core/exoseq/archive/{revision}.zip" |
| wfs = nf_core.pipelines.list.Workflows() | ||
| wfs.get_remote_workflows() | ||
| # Exoseq pipeline is archived, so `dev` branch should be stable | ||
| pipeline = "exoseq" |
There was a problem hiding this comment.
same suggestions from test_get_release_hash_long_commit can also be applied here
| download_obj.wf_branches, | ||
| ) = nf_core.utils.get_repo_releases_branches(pipeline, wfs) | ||
| download_obj.get_revision_hash() | ||
| print(download_obj) |
There was a problem hiding this comment.
Suggested change
| print(download_obj) |
|
Thanks for tagging. I took a brief look and have no objections. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Supersedes #2906
This is to allow downloading a specific commit of a pipeline, instead of only a branch / tag.
As @ewels suggested in the original pull-request, I only check the commit once we know it's neither a branch nor a tag. It's a single extra query, and it won't download the whole list of possible commits.
I could reuse the tests @fellen31 wrote. Credits to them
PR checklist
CHANGELOG.mdis updateddocsis updated