├── .env.example ├── .github └── workflows │ ├── publish_python.yml │ └── pytest_workflow.yml ├── .gitignore ├── .pre-commit-config.yaml ├── LICENSE.md ├── README.md ├── examples ├── MAG_upload │ ├── ENA_backup.json │ └── registered_MAGs_test.tsv └── input_example.tsv ├── genomeuploader ├── __init__.py ├── config.py ├── constants.py ├── ena.py ├── ena_submit.py ├── exceptions.py ├── genome_upload.py └── taxon_finder.py ├── pyproject.toml ├── pytest.ini └── tests ├── conftest.py ├── fixtures ├── ERR6769700_bin.1.fa.gz ├── ERR6769701_bin.1.fa.gz ├── ERR6769769_bin.1.fa.gz ├── bin_upload │ └── bin_backup.json ├── input_fixture.tsv ├── input_with_registered_fixture.tsv └── responses │ ├── private_run.json │ ├── private_run_from_assembly.xml │ ├── private_sample.xml │ ├── private_study.xml │ ├── private_study_runs.json │ ├── public_run.json │ ├── public_run_from_assembly.xml │ ├── public_sample.json │ ├── public_study.json │ └── public_study_runs.json ├── test_ena.py ├── 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