fix: explicitly specify how the root and ambiguous states are handled… #3050

Job	Run time
check-docs	36s
mypy	46s
pathogen-repo-ci (dengue)	2m 44s
pathogen-repo-ci-v0 (avian-flu)	1m 2s
pathogen-repo-ci-v0 (ebola)	1m 5s
pyright	17s
pathogen-repo-ci-v0 (mumps)	56s
pathogen-repo-ci (lassa)	42s
test (python=3.8 biopython=1.80)	11m 43s
pathogen-repo-ci-v0 (ncov)	1m 17s
pathogen-repo-ci (measles)	1m 24s
pathogen-repo-ci-v0 (rsv)	8m 37s
pathogen-repo-ci (mpox)	1m 17s
test (python=3.8 biopython=1.82)	11m 38s
pathogen-repo-ci-v0 (seasonal-flu)	1m 12s
pathogen-repo-ci (seasonal-cov)	1m 46s
test (python=3.8 biopython=latest)	11m 26s
pathogen-repo-ci (zika)	59s
test (python=3.9 biopython=1.80)	11m 41s
test (python=3.9 biopython=1.82)	11m 43s
pathogen-repo-ci-v0 (tb)	1m 15s
test (python=3.9 biopython=latest)	11m 42s
test (python=3.10 biopython=1.80)	11m 44s
test (python=3.10 biopython=1.82)	11m 43s
test (python=3.10 biopython=latest)	11m 46s
test (python=3.11 biopython=1.80)	11m 44s
test (python=3.11 biopython=1.82)	11m 49s
test (python=3.11 biopython=latest)	11m 44s
test (python=3.12 biopython=1.82)	11m 42s
test (python=3.12 biopython=latest)	11m 43s
build-docs / build	2m 9s
codecov	0s
release	0s
rebuild-docker-image	0s
	3h 11m 52s

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