├── .gitignore ├── LICENSE ├── R ├── authz_to_conf.R ├── munge_user_db.R └── svn_dump.sh ├── README.md ├── admin-docs ├── BETA.Rmd ├── Core_team_transition.Rmd ├── configure.md ├── find_unknowns.sh ├── presentations │ ├── Bioc2017-git_with_the_program.pdf │ └── Bioc2017-implementation_details.pdf └── usage.md ├── best_practices.md ├── doc ├── README.md ├── faq.md ├── images │ ├── create_repo.png │ ├── github-bioc-relationship.png │ └── setup_repo.png ├── scenario-1-svn-to-github.md ├── scenario-10-bug-fix-in-release-and-devel.md ├── scenario-11-maintain-without-github.md ├── scenario-12-modify-on-local-repository.md ├── scenario-2-push-to-github-gitbioc.md ├── scenario-3-pull-from-gitbioc-push-github.md ├── scenario-4-push-to-release-branch.md ├── scenario-5-resolve-conflicts.md ├── scenario-6-abandon-changes.md ├── scenario-7-add-collaborators.md ├── scenario-8-new-package-workflow.md ├── scenario-9-sync-existing-github-gitbioc.md └── workflows │ ├── bioconductor-github-infrastructure.md │ ├── maintainer-workflow.md │ ├── new-package-workflow.md │ └── updating-after-release.md ├── hooks └── repo-specific │ ├── README.md │ ├── post-receive-hook │ ├── pre-receive-hook-dataexp-workflow │ ├── pre-receive-hook-software │ ├── prepare_test.sh │ ├── prevent_bad_version_numbers.py │ ├── prevent_duplicate_commits.py │ ├── prevent_large_files.py │ ├── prevent_merge_markers.py │ ├── rss_feed.py │ └── test_prevent_bad_version_numbers.py ├── misc ├── detect_bad_version.py └── detect_duplicate_commits.py ├── run.py ├── settings.ini ├── setup.py └── src ├── __init__.py ├── git_api ├── __init__.py └── git_api.py ├── git_bioconductor_repository.py ├── git_experiment_repository.py ├── git_manifest_repository.py ├── helper ├── __init__.py └── helper.py ├── local_svn_dump.py ├── release_process.py ├── run_transition.py ├── svn_dump_update.py └── update_temp_git_repo.py /.gitignore: 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