fix: explicitly specify how the root and ambiguous states are handled… #3110

Job	Run time
mypy	52s
pathogen-repo-ci (dengue)	3m 14s
check-docs	36s
pathogen-repo-ci (lassa)	7m 52s
pathogen-repo-ci-v0 (avian-flu)	1m 26s
pyright	17s
pathogen-repo-ci (measles)	2m 3s
pathogen-repo-ci-v0 (ebola)	1m 30s
pathogen-repo-ci (mpox)	1m 49s
pathogen-repo-ci (seasonal-cov)	3m 2s
test (python=3.9 biopython=1.80)	13m 12s
pathogen-repo-ci (zika)	1m 41s
pathogen-repo-ci-v0 (mumps)	1m 30s
pathogen-repo-ci-v0 (ncov)	1m 45s
test (python=3.9 biopython=1.82)	13m 50s
pathogen-repo-ci-v0 (rsv)	9m 3s
test (python=3.9 biopython=latest)	13m 4s
pathogen-repo-ci-v0 (seasonal-flu)	1m 43s
test (python=3.10 biopython=1.80)	13m 10s
pathogen-repo-ci-v0 (tb)	1m 52s
test (python=3.10 biopython=1.82)	13m 10s
test (python=3.10 biopython=latest)	13m 37s
test (python=3.11 biopython=1.80)	14m 11s
test (python=3.11 biopython=1.82)	13m 20s
test (python=3.11 biopython=latest)	13m 30s
test (python=3.12 biopython=1.82)	20m 28s
test (python=3.12 biopython=latest)	20m 54s
build-docs / build	2m 30s
codecov	15s
release	0s
rebuild-docker-image	0s
	3h 25m 26s

Provide feedback