Update sphinx-argparse requirement from !=0.5.0,<0.6.0,>=0.2.5 to >=0.2.5,!=0.5.0,<0.7.0 #4676
dependabot[bot]ci.yaml
on: pull_request
Matrix: pytest-cram
mypy
1m 5s
pyright
19s
check-docs
39s
check-subsample-config-schema
44s
Matrix: pathogen-repo-ci-v0
Matrix: pathogen-repo-ci
codecov
18s
rebuild-docker-image
Annotations
20 warnings
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pathogen-repo-ci-v0 (rsv)
Failed to save: Unable to reserve cache with key 2026-08-31-linux-64-augur-args-30d39f4-root-dcc80ee-bin-366cd9cd8be14df1ab8ed50352a82111082a36686b2d389fdb79a92c3fafb3e3, another job may be creating this cache.
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pathogen-repo-ci (lassa)
Failed to save: Unable to reserve cache with key 2026-08-31-linux-64-augur-args-30d39f4-root-dcc80ee-bin-366cd9cd8be14df1ab8ed50352a82111082a36686b2d389fdb79a92c3fafb3e3, another job may be creating this cache.
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pathogen-repo-ci-v0 (seasonal-flu)
Failed to save: Unable to reserve cache with key 2026-08-31-linux-64-augur-args-30d39f4-root-dcc80ee-bin-366cd9cd8be14df1ab8ed50352a82111082a36686b2d389fdb79a92c3fafb3e3, another job may be creating this cache.
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pathogen-repo-ci (mumps)
Failed to save: Unable to reserve cache with key 2026-08-31-linux-64-augur-args-30d39f4-root-dcc80ee-bin-366cd9cd8be14df1ab8ed50352a82111082a36686b2d389fdb79a92c3fafb3e3, another job may be creating this cache.
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pathogen-repo-ci-v0 (vcf-input-tutorial)
Failed to save: Unable to reserve cache with key 2026-08-31-linux-64-augur-args-30d39f4-root-dcc80ee-bin-366cd9cd8be14df1ab8ed50352a82111082a36686b2d389fdb79a92c3fafb3e3, another job may be creating this cache.
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pathogen-repo-ci-v0 (avian-flu)
Failed to save: Unable to reserve cache with key 2026-08-31-linux-64-augur-args-30d39f4-root-dcc80ee-bin-366cd9cd8be14df1ab8ed50352a82111082a36686b2d389fdb79a92c3fafb3e3, another job may be creating this cache.
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pathogen-repo-ci (yellow-fever)
Failed to save: Unable to reserve cache with key 2026-08-31-linux-64-augur-args-30d39f4-root-dcc80ee-bin-366cd9cd8be14df1ab8ed50352a82111082a36686b2d389fdb79a92c3fafb3e3, another job may be creating this cache.
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pathogen-repo-ci (dengue)
Failed to save: Unable to reserve cache with key 2026-08-31-linux-64-augur-args-30d39f4-root-dcc80ee-bin-366cd9cd8be14df1ab8ed50352a82111082a36686b2d389fdb79a92c3fafb3e3, another job may be creating this cache.
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pathogen-repo-ci-v0 (ncov)
Failed to save: Unable to reserve cache with key 2026-08-31-linux-64-augur-args-30d39f4-root-dcc80ee-bin-366cd9cd8be14df1ab8ed50352a82111082a36686b2d389fdb79a92c3fafb3e3, another job may be creating this cache.
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pathogen-repo-ci (nipah)
Failed to save: Unable to reserve cache with key 2026-08-31-linux-64-augur-args-30d39f4-root-dcc80ee-bin-366cd9cd8be14df1ab8ed50352a82111082a36686b2d389fdb79a92c3fafb3e3, another job may be creating this cache.
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pathogen-repo-ci (mpox)
Failed to save: Unable to reserve cache with key 2026-08-31-linux-64-augur-args-30d39f4-root-dcc80ee-bin-366cd9cd8be14df1ab8ed50352a82111082a36686b2d389fdb79a92c3fafb3e3, another job may be creating this cache.
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pathogen-repo-ci (oropouche)
Failed to save: Unable to reserve cache with key 2026-08-31-linux-64-augur-args-30d39f4-root-dcc80ee-bin-366cd9cd8be14df1ab8ed50352a82111082a36686b2d389fdb79a92c3fafb3e3, another job may be creating this cache.
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pathogen-repo-ci (measles)
Failed to save: Unable to reserve cache with key 2026-08-31-linux-64-augur-args-30d39f4-root-dcc80ee-bin-366cd9cd8be14df1ab8ed50352a82111082a36686b2d389fdb79a92c3fafb3e3, another job may be creating this cache.
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pathogen-repo-ci (WNV)
Failed to save: Unable to reserve cache with key 2026-08-31-linux-64-augur-args-30d39f4-root-dcc80ee-bin-366cd9cd8be14df1ab8ed50352a82111082a36686b2d389fdb79a92c3fafb3e3, another job may be creating this cache.
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pathogen-repo-ci (seasonal-cov)
Failed to save: Unable to reserve cache with key 2026-08-31-linux-64-augur-args-30d39f4-root-dcc80ee-bin-366cd9cd8be14df1ab8ed50352a82111082a36686b2d389fdb79a92c3fafb3e3, another job may be creating this cache.
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pathogen-repo-ci (norovirus)
Failed to save: Unable to reserve cache with key 2026-08-31-linux-64-augur-args-30d39f4-root-dcc80ee-bin-366cd9cd8be14df1ab8ed50352a82111082a36686b2d389fdb79a92c3fafb3e3, another job may be creating this cache.
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pathogen-repo-ci (rubella)
Failed to save: Unable to reserve cache with key 2026-08-31-linux-64-augur-args-30d39f4-root-dcc80ee-bin-366cd9cd8be14df1ab8ed50352a82111082a36686b2d389fdb79a92c3fafb3e3, another job may be creating this cache.
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pathogen-repo-ci (rabies)
Failed to save: Unable to reserve cache with key 2026-08-31-linux-64-augur-args-30d39f4-root-dcc80ee-bin-366cd9cd8be14df1ab8ed50352a82111082a36686b2d389fdb79a92c3fafb3e3, another job may be creating this cache.
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pytest-cram (python=3.14 biopython numpy)
Failed to save: Unable to reserve cache with key 2026-08-31-linux-64-augur-args-f1d7981-root-dcc80ee-bin-366cd9cd8be14df1ab8ed50352a82111082a36686b2d389fdb79a92c3fafb3e3-file-7f19b182a58d9b124966baf5507035d2f68d1548acd25246f4c7270b335c4900, another job may be creating this cache.
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pytest-cram (python=3.12 biopython numpy==1.*)
Failed to save: Unable to reserve cache with key 2026-08-31-linux-64-augur-args-e92b363-root-dcc80ee-bin-366cd9cd8be14df1ab8ed50352a82111082a36686b2d389fdb79a92c3fafb3e3-file-7f19b182a58d9b124966baf5507035d2f68d1548acd25246f4c7270b335c4900, another job may be creating this cache.
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Artifacts
Produced during runtime
| Name | Size | Digest | |
|---|---|---|---|
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coverage
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222 KB |
sha256:118885553ad32f351f4c89bb4efd543152c1cf6ae6b50815e0aba7044ac70256
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output-WNV
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977 KB |
sha256:53744316eef3d7d51dd514ec671589ec192ec350248430d4d7fc6643b1e5fc1a
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output-avian-flu
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113 KB |
sha256:10b623b89fe29fdc3577733fc5bd588a927c6f27efd104c16b17979c8e404bce
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output-dengue
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436 KB |
sha256:1dc2f6128bd3b3c345ea2eb5b77e0c5344e561b3f1accfd09e23a762e0d26e83
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output-lassa
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369 KB |
sha256:a29fbfc8921b3cf5ee82e45695815909417a175122e58c5fbcc0517b878bfda9
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output-measles
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12.3 MB |
sha256:5fe7b827d66af27ea2451632de6cdfae240bb03f52a76a14440575a5a9ba4d16
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output-mpox
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22.4 MB |
sha256:2fa7b833d4b0e4ac4e3e1c81cd4cbb25d051ff4337ea9e031620a21bdc5ce40e
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output-mumps
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379 KB |
sha256:b03c2d580c26f877f698d8aba68a2b2903497365758a5517c1c94f75ebbf47d9
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output-ncov
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862 KB |
sha256:c9cb484bbd3190b5c9a11a3b0a9a7f6a7569c83c4d3b2f95252da950f207e7dd
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output-nipah
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1.3 MB |
sha256:646c860064f74932f39fc1f7dc714ae12260a8f7db506575dd01eed17a1cd744
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output-norovirus
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3.16 MB |
sha256:15613b03af0cdad954ffe2b6a625ae34e412a90fd8d25d8819025a2c07a7002e
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output-oropouche
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639 KB |
sha256:fc19205c6f58ff5b4f24d4ee2419a31cad740de982efb2c927e7636a3a2ccd2d
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output-rabies
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5.47 MB |
sha256:8d6e90d643b4df1bdbd9039a2bf3d199368c6c93d2748af0bbfe84c22fe77b9f
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output-rsv
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665 KB |
sha256:cc37854cf16efa4fd4cbd2a4c2a7b694664459229a3bd9c0c845f9740c3a529f
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output-rubella
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1.67 MB |
sha256:91243c7e15696347632c6781b8cf40157bcb95f6491168ba42101ace77c059f5
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output-seasonal-cov
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3.4 MB |
sha256:97040013ba55c6924696646082662c02c81e5f908fff28737789e4712f9e95ab
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output-seasonal-flu
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60.4 KB |
sha256:e9b0a2aeb01b0ec7a8f6f765ed238c4ae33aa6aadac201807a25da4cda4c8eb6
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output-vcf-input-tutorial
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5.03 MB |
sha256:eadbdebc235e01c917a88c79ada0762862cf2d4c4b56e7cdebe29b8572f39e6f
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output-yellow-fever
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1.43 MB |
sha256:2518d460712a4b5223aacabecbbfc7e416b4cf80a44e1b7efa18e70e2913ab94
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output-zika
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861 KB |
sha256:896a589d7967a8261743e47a82b28d449141339390dab429ad92dca568919625
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