LICENSE
README.md
pyproject.toml
src/bfxpm/__init__.py
src/bfxpm/ai_client.py
src/bfxpm/ai_config.py
src/bfxpm/main.py
src/bfxpm/safety.py
src/bfxpm/utils.py
src/bfxpm.egg-info/PKG-INFO
src/bfxpm.egg-info/SOURCES.txt
src/bfxpm.egg-info/dependency_links.txt
src/bfxpm.egg-info/entry_points.txt
src/bfxpm.egg-info/requires.txt
src/bfxpm.egg-info/top_level.txt
src/bfxpm/agents/__init__.py
src/bfxpm/agents/bio_agent.py
src/bfxpm/agents/tools.py
src/bfxpm/assets/git-essentials/CITATION.cff
src/bfxpm/assets/git-essentials/CODEOWNERS.md
src/bfxpm/assets/git-essentials/CODE_OF_CONDUCT.md
src/bfxpm/assets/git-essentials/Docker’s multi-architecture support is b.md
src/bfxpm/assets/git-essentials/LICENSE
src/bfxpm/assets/git-essentials/Makefile
src/bfxpm/assets/git-essentials/README.md
src/bfxpm/assets/git-essentials/SECURITY.md
src/bfxpm/assets/git-essentials/SUPPORT.md
src/bfxpm/assets/git-essentials/_quarto.yml
src/bfxpm/assets/git-essentials/_variables.yml
src/bfxpm/assets/git-essentials/author_manifest.qmd
src/bfxpm/assets/git-essentials/author_manifest_Rpackage.qmd
src/bfxpm/assets/git-essentials/custom.css
src/bfxpm/assets/git-essentials/dnam.puml
src/bfxpm/assets/git-essentials/docker-compose.yml
src/bfxpm/assets/git-essentials/fetch_repos.py
src/bfxpm/assets/git-essentials/git_auto_migrate_releases.sh
src/bfxpm/assets/git-essentials/git_cache.md
src/bfxpm/assets/git-essentials/git_commit.sh
src/bfxpm/assets/git-essentials/git_push.md
src/bfxpm/assets/git-essentials/git_repo_migration.sh
src/bfxpm/assets/git-essentials/github_bot.md
src/bfxpm/assets/git-essentials/gpg.md
src/bfxpm/assets/git-essentials/index.html
src/bfxpm/assets/git-essentials/migrate_all_releases.sh
src/bfxpm/assets/git-essentials/my_github_repos.html
src/bfxpm/assets/git-essentials/my_github_repos.qmd
src/bfxpm/assets/git-essentials/my_github_repos.txt
src/bfxpm/assets/git-essentials/pgp.jd.txt
src/bfxpm/assets/git-essentials/project-template-makefile.md
src/bfxpm/assets/git-essentials/rsconnect.md
src/bfxpm/assets/git-essentials/slurm_script.sbatch
src/bfxpm/assets/git-essentials/update_repo_mike.sh
src/bfxpm/assets/git-essentials/update_repo_mike2.sh
src/bfxpm/assets/git-essentials/versioning.md
src/bfxpm/assets/git-essentials/CONTRIBUTION/CONTRIBUTING.md
src/bfxpm/assets/git-essentials/ISSUE_TEMPLATE/bug_report.md
src/bfxpm/assets/git-essentials/ISSUE_TEMPLATE/custom.md
src/bfxpm/assets/git-essentials/ISSUE_TEMPLATE/feature_request.md
src/bfxpm/assets/git-essentials/scripts/git-scripts/transfer_branch.sh
src/bfxpm/assets/git-essentials/scripts/project-templates/create-project.sh
src/bfxpm/assets/git-essentials/scripts/project-templates/project-templates.mk
src/bfxpm/assets/git-essentials/workflows/docker-build.yml
src/bfxpm/assets/git-essentials/workflows/github-pages-deployment.yml
src/bfxpm/assets/git-essentials/workflows/shinyapps_deploy.yml
src/bfxpm/assets/mkdocs/mkdocs.yml
src/bfxpm/assets/mkdocs/docs/index.md
src/bfxpm/assets/mkdocs/docs/parameters.md
src/bfxpm/assets/mkdocs/docs/results.md
src/bfxpm/assets/mkdocs/docs/usage.md
src/bfxpm/commands/__init__.py
src/bfxpm/commands/ai_cmd.py
src/bfxpm/commands/clean.py
src/bfxpm/commands/deposit.py
src/bfxpm/commands/env_cmd.py
src/bfxpm/commands/fetch_cmd.py
src/bfxpm/commands/flow.py
src/bfxpm/commands/git_cmds.py
src/bfxpm/commands/init_cmd.py
src/bfxpm/commands/integrity.py
src/bfxpm/commands/map_cmd.py
src/bfxpm/commands/misc.py
src/bfxpm/commands/modify.py
src/bfxpm/commands/organize.py
src/bfxpm/commands/pipeline_cmd.py
src/bfxpm/commands/scan.py
src/bfxpm/commands/tree.py