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Fix bug when updating modules from old version in old folder structure #1908

Merged
merged 8 commits into from
Oct 11, 2022
Merged

Fix bug when updating modules from old version in old folder structure #1908

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e529ae0
fix bug when updating modules from old version in old folder structure
mirpedrol Oct 10, 2022
ba36c76
update changelog
mirpedrol Oct 10, 2022
e85549f
fix a small mistake
mirpedrol Oct 10, 2022
b47c3f7
Merge branch 'dev' into update
mirpedrol Oct 10, 2022
641d520
[automated] Fix code linting
nf-core-bot Oct 10, 2022
24314c2
return an iterator
mirpedrol Oct 11, 2022
9b5a10e
Merge branch 'update' of https://github.com/mirpedrol/tools into update
mirpedrol Oct 11, 2022
2e07578
Merge branch 'dev' into update
mashehu Oct 11, 2022
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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 @@ -11,6 +11,7 @@
### General

- Fix error in tagging GitPod docker images during releases
- Fix bug when updating modules from old version in old folder structure
- Don't remove local copy of modules repo, only update it with fetch ([#1881](https://github.com/nf-core/tools/pull/1881))
- Add subworkflow commands create-test-yml, create and install ([#1897](https://github.com/nf-core/tools/pull/1897))
- Update subworkflows install so it installs also imported modules and subworkflows ([#1904](https://github.com/nf-core/tools/pull/1904))
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13 changes: 11 additions & 2 deletions nf_core/modules/modules_repo.py
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Expand Up @@ -430,8 +430,17 @@ def get_module_git_log(self, module_name, depth=None, since="2021-07-07T00:00:00
"""
self.checkout_branch()
module_path = os.path.join("modules", self.repo_path, module_name)
commits = self.repo.iter_commits(max_count=depth, paths=module_path)
commits = ({"git_sha": commit.hexsha, "trunc_message": commit.message.partition("\n")[0]} for commit in commits)
commits_new = self.repo.iter_commits(max_count=depth, paths=module_path)
commits_new = [
{"git_sha": commit.hexsha, "trunc_message": commit.message.partition("\n")[0]} for commit in commits_new
]
# Grab commits also from previous modules structure
module_path = os.path.join("modules", module_name)
commits_old = self.repo.iter_commits(max_count=depth, paths=module_path)
commits_old = [
{"git_sha": commit.hexsha, "trunc_message": commit.message.partition("\n")[0]} for commit in commits_old
]
commits = iter(commits_new + commits_old)
return commits

def get_subworkflow_git_log(self, subworkflow_name, depth=None, since="2021-07-07T00:00:00Z"):
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