.env.sample
.gitignore
.pre-commit-config.yaml
README.md
pyproject.toml
uv.lock
.github/workflows/on_pr.yml
.github/workflows/on_push_main.yml
haplohub_cli/__init__.py
haplohub_cli/_version.py
haplohub_cli/cli.py
haplohub_cli/settings.py
haplohub_cli.egg-info/PKG-INFO
haplohub_cli.egg-info/SOURCES.txt
haplohub_cli.egg-info/dependency_links.txt
haplohub_cli.egg-info/entry_points.txt
haplohub_cli.egg-info/requires.txt
haplohub_cli.egg-info/top_level.txt
haplohub_cli/auth/__init__.py
haplohub_cli/auth/auth.py
haplohub_cli/auth/auth0_client.py
haplohub_cli/auth/auth_web_server.py
haplohub_cli/auth/token_storage.py
haplohub_cli/auth/tests/__init__.py
haplohub_cli/auth/tests/test_auth_web_server.py
haplohub_cli/auth/tests/test_token_storage.py
haplohub_cli/commands/__init__.py
haplohub_cli/commands/config.py
haplohub_cli/commands/file.py
haplohub_cli/commands/login.py
haplohub_cli/commands/variant.py
haplohub_cli/commands/version.py
haplohub_cli/commands/algorithm/__init__.py
haplohub_cli/commands/algorithm/result/__init__.py
haplohub_cli/commands/cohort/__init__.py
haplohub_cli/commands/cohort/biomarker.py
haplohub_cli/commands/cohort/sample.py
haplohub_cli/commands/cohort/member/__init__.py
haplohub_cli/commands/cohort/member/report.py
haplohub_cli/commands/metadata/__init__.py
haplohub_cli/config/__init__.py
haplohub_cli/config/config.py
haplohub_cli/config/config_manager.py
haplohub_cli/config/environments.py
haplohub_cli/core/__init__.py
haplohub_cli/core/checksum.py
haplohub_cli/core/network.py
haplohub_cli/core/slug.py
haplohub_cli/core/upload.py
haplohub_cli/core/api/__init__.py
haplohub_cli/core/api/client.py
haplohub_cli/core/tests/__init__.py
haplohub_cli/core/tests/test_network.py
haplohub_cli/core/tests/test_slug.py
haplohub_cli/formatters/__init__.py
haplohub_cli/formatters/algorithm.py
haplohub_cli/formatters/algorithm_result.py
haplohub_cli/formatters/biomarker.py
haplohub_cli/formatters/cohort.py
haplohub_cli/formatters/config.py
haplohub_cli/formatters/decorators.py
haplohub_cli/formatters/file.py
haplohub_cli/formatters/formatter_registry.py
haplohub_cli/formatters/generic.py
haplohub_cli/formatters/member.py
haplohub_cli/formatters/metadata.py
haplohub_cli/formatters/sample.py
haplohub_cli/formatters/utils.py
haplohub_cli/formatters/variant.py
haplohub_cli/types/__init__.py
haplohub_cli/types/variant_range.py