.gitignore
Dockerfile
LICENCE
README.md
containers.conf
flow_diagram_ADI_import.png
ingestion_tracking.db
podman-containers.conf
podman_dev.sh
pyproject.toml
security_overview_privileged.md
storage.conf
.agents/skills/biomero-importer-dev/SKILL.md
.github/workflows/docker-image.yml
.github/workflows/publish-to-pypi.yml
.github/workflows/python-package.yml
biomero_importer/__init__.py
biomero_importer/_version.py
biomero_importer/api.py
biomero_importer/db_migrate.py
biomero_importer/main.py
biomero_importer.egg-info/PKG-INFO
biomero_importer.egg-info/SOURCES.txt
biomero_importer.egg-info/dependency_links.txt
biomero_importer.egg-info/requires.txt
biomero_importer.egg-info/scm_file_list.json
biomero_importer.egg-info/scm_version.json
biomero_importer.egg-info/top_level.txt
biomero_importer/migrations/alembic.ini
biomero_importer/migrations/env.py
biomero_importer/migrations/script.py.mako
biomero_importer/migrations/versions/78d3d6d84aec_add_description_to_imports.py
biomero_importer/migrations/versions/92e8f9e637a1_add_import_options_to_imports.py
biomero_importer/utils/__init__.py
biomero_importer/utils/canonical_promotion.py
biomero_importer/utils/canonical_store.py
biomero_importer/utils/importer.py
biomero_importer/utils/ingest_tracker.py
biomero_importer/utils/initialize.py
biomero_importer/utils/lifecycle.py
biomero_importer/utils/pixel_identity.py
biomero_importer/utils/register.py
biomero_importer/utils/result_zarr.py
biomero_importer/utils/upload_order_manager.py
config/sample_upload_order.txt
config/settings.yml
set_up/get_omero_info.py
tests/Barbie1.tif
tests/Barbie2.tif
tests/Barbie3.tif
tests/README.md
tests/requirements.txt
tests/setup_conda_test_env.sh
tests/system_check.py
tests/t_main.py
tests/t_settings.bak
tests/benchmarks/benchmark_shallow_a1b1.py
tests/unittests/pyetest.ini
tests/unittests/test_api.py
tests/unittests/test_canonical_promotion.py
tests/unittests/test_canonical_store.py
tests/unittests/test_ci_validation.py
tests/unittests/test_db_migrate.py
tests/unittests/test_edge_cases.py
tests/unittests/test_import_retry.py
tests/unittests/test_ingest_tracker.py
tests/unittests/test_integration.py
tests/unittests/test_lifecycle.py
tests/unittests/test_main.py
tests/unittests/test_pixel_identity.py
tests/unittests/test_podman_retry.py
tests/unittests/test_processed_data_folder.py
tests/unittests/test_result_zarr.py
tests/unittests/test_upload_order_manager.py
tests/unittests/test_zarr_import_title.py
tests/unittests/test_config/sample_groups_list.json
tests/unittests/test_config/sample_upload_order.txt
tests/unittests/test_config/settings.yml
tests/unittests/test_config/test.log