Centralize --validation-mode and --skip-validation #2942

Job	Run time
check-docs	36s
mypy	53s
pathogen-repo-ci (dengue)	2m 49s
pathogen-repo-ci-v0 (avian-flu)	51s
pathogen-repo-ci (lassa)	42s
pathogen-repo-ci-v0 (ebola)	54s
pathogen-repo-ci (measles)	1m 19s
pathogen-repo-ci-v0 (mumps)	53s
pyright	16s
pathogen-repo-ci (mpox)	1m 14s
test (python=3.8 biopython=1.80)	11m 44s
pathogen-repo-ci-v0 (ncov)	1m 0s
pathogen-repo-ci (seasonal-cov)	1m 45s
test (python=3.8 biopython=latest)	11m 43s
pathogen-repo-ci-v0 (rsv)	8m 29s
pathogen-repo-ci (zika)	56s
test (python=3.9 biopython=1.80)	13m 12s
pathogen-repo-ci-v0 (seasonal-flu)	1m 20s
test (python=3.9 biopython=latest)	13m 4s
pathogen-repo-ci-v0 (tb)	1m 23s
test (python=3.10 biopython=1.80)	12m 26s
test (python=3.10 biopython=latest)	12m 1s
test (python=3.11 biopython=1.80)	12m 23s
test (python=3.11 biopython=latest)	12m 20s
build-docs / build	2m 1s
codecov	17s
release	0s
rebuild-docker-image	0s
	2h 6m 31s

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