LICENSE.txt
README.rst
pyproject.toml
setup.cfg
setup.py
bio_pype.egg-info/PKG-INFO
bio_pype.egg-info/SOURCES.txt
bio_pype.egg-info/dependency_links.txt
bio_pype.egg-info/entry_points.txt
bio_pype.egg-info/requires.txt
bio_pype.egg-info/top_level.txt
pype/__config__.py
pype/__init__.py
pype/__version__.py
pype/argparse.py
pype/binfmisc.py
pype/commands.py
pype/exceptions.py
pype/logger.py
pype/misc.py
pype/process.py
pype/lsp/__init__.py
pype/lsp/server.py
pype/lsp/features/__init__.py
pype/lsp/handlers/__init__.py
pype/lsp/handlers/completion.py
pype/lsp/handlers/diagnostics.py
pype/lsp/handlers/hover.py
pype/lsp/utils/__init__.py
pype/lsp/utils/command_builder.py
pype/modules/__init__.py
pype/modules/compute_bio.py
pype/modules/pipelines.py
pype/modules/profiles.py
pype/modules/registry.py
pype/modules/resume.py
pype/modules/run.py
pype/modules/snippets.py
pype/modules/validate.py
pype/pype_modules/__init__.py
pype/pype_modules/repos.yaml
pype/pype_modules/pipelines/__init__.py
pype/pype_modules/profiles/__init__.py
pype/pype_modules/queues/__init__.py
pype/pype_modules/queues/dry_run.py
pype/pype_modules/queues/parallel.py
pype/pype_modules/queues/slurm.py
pype/pype_modules/snippets/__init__.py
pype/pype_modules/snippets/_benchmark_power.py
pype/pype_modules/snippets/_dowload_files.md
pype/registry/__init__.py
pype/registry/builder.py
pype/registry/commands.py
pype/registry/conflicts.py
pype/registry/database.py
pype/registry/extractors.py
pype/registry/git_utils.py
pype/registry/hashing.py
pype/registry/installer.py
pype/registry/manager.py
pype/registry/metadata.py
pype/registry/snippet_registry.py
pype/utils/__init__.py
pype/utils/arguments.py
pype/utils/carbon.py
pype/utils/compute_bio_api.py
pype/utils/containers.py
pype/utils/introspect.py
pype/utils/overlay.py
pype/utils/pipeline.py
pype/utils/profile_specs.md
pype/utils/profiles.py
pype/utils/progress.py
pype/utils/queue_base.py
pype/utils/queue_commands.py
pype/utils/queues.py
pype/utils/resource_matcher.py
pype/utils/resource_monitor.py
pype/utils/runtime.py
pype/utils/scheduler.py
pype/utils/snippets.py
pype/validation/__init__.py
pype/validation/context.py
pype/validation/core.py
pype/validation/parsers.py
pype/validation/pipeline_validator.py
pype/validation/profile_validator.py
pype/validation/snippet_validator.py
scripts/pype-activate
test/test_arguments.py
test/test_commands.py
test/test_config.py
test/test_containers.py
test/test_exceptions.py
test/test_list_arg_substitution.py
test/test_logger.py
test/test_misc.py
test/test_parallel_queue.py
test/test_pipelines.py
test/test_process.py
test/test_profile_pull.py
test/test_profiles.py
test/test_queues.py
test/test_resource_matcher.py
test/test_resource_monitor.py
test/test_snippets.py
test/test_validation.py