Drop support for xopen v1 #3078

Job	Run time
pathogen-repo-ci (dengue)	2m 46s
pyright	21s
pathogen-repo-ci (lassa)	7m 5s
check-docs	37s
mypy	50s
pathogen-repo-ci-v0 (avian-flu)	1m 0s
pathogen-repo-ci (measles)	1m 22s
test (python=3.8 biopython=1.80)	11m 47s
pathogen-repo-ci (mpox)	1m 18s
pathogen-repo-ci-v0 (ebola)	1m 4s
test (python=3.8 biopython=1.82)	12m 17s
pathogen-repo-ci (seasonal-cov)	1m 51s
pathogen-repo-ci-v0 (mumps)	57s
test (python=3.8 biopython=latest)	12m 14s
pathogen-repo-ci (zika)	1m 2s
pathogen-repo-ci-v0 (ncov)	1m 0s
test (python=3.9 biopython=1.80)	12m 53s
pathogen-repo-ci-v0 (rsv)	8m 27s
test (python=3.9 biopython=1.82)	13m 20s
pathogen-repo-ci-v0 (seasonal-flu)	1m 24s
test (python=3.9 biopython=latest)	13m 11s
pathogen-repo-ci-v0 (tb)	1m 17s
test (python=3.10 biopython=1.80)	13m 2s
test (python=3.10 biopython=1.82)	13m 52s
test (python=3.10 biopython=latest)	12m 49s
test (python=3.11 biopython=1.80)	13m 42s
test (python=3.11 biopython=1.82)	13m 47s
test (python=3.11 biopython=latest)	12m 58s
test (python=3.12 biopython=1.82)	20m 5s
test (python=3.12 biopython=latest)	19m 37s
build-docs / build	2m 29s
codecov	11s
release	0s
rebuild-docker-image	0s
	3h 50m 35s

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