fix(filter): allow --include/exclude-where for columns in --metadata-id-columns #4009
corneliusroemerci.yaml
on: pull_request
Matrix: pytest-cram
mypy
57s
pyright
25s
build-docs
/
build
1m 31s
check-docs
44s
check-subsample-config-schema
41s
Matrix: pathogen-repo-ci-v0
Matrix: pathogen-repo-ci
codecov
0s
rebuild-docker-image
Annotations
34 errors and 18 warnings
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test (python=3.9 biopython=1.80 numpy=latest)
Process completed with exit code 1.
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test (python=3.10 biopython=1.80 numpy=1.26.4)
Process completed with exit code 1.
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test (python=3.9 biopython=1.82 numpy=latest)
The strategy configuration was canceled because "pytest-cram._3_9_1_80" failed
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test (python=3.9 biopython=1.82 numpy=latest)
The operation was canceled.
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test (python=3.11 biopython=1.80 numpy=latest)
The strategy configuration was canceled because "pytest-cram._3_9_1_80" failed
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test (python=3.11 biopython=1.80 numpy=latest)
The operation was canceled.
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test (python=3.11 biopython=1.82 numpy=latest)
The strategy configuration was canceled because "pytest-cram._3_9_1_80" failed
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test (python=3.12 biopython=1.85 numpy=latest)
The strategy configuration was canceled because "pytest-cram._3_9_1_80" failed
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test (python=3.11 biopython=1.82 numpy=latest)
The operation was canceled.
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test (python=3.12 biopython=1.85 numpy=latest)
The operation was canceled.
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test (python=3.11 biopython=latest numpy=latest)
The strategy configuration was canceled because "pytest-cram._3_9_1_80" failed
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test (python=3.11 biopython=latest numpy=latest)
The operation was canceled.
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test (python=3.10 biopython=1.85 numpy=latest)
The strategy configuration was canceled because "pytest-cram._3_9_1_80" failed
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test (python=3.10 biopython=1.85 numpy=latest)
The operation was canceled.
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test (python=3.12 biopython=1.82 numpy=latest)
The strategy configuration was canceled because "pytest-cram._3_9_1_80" failed
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test (python=3.13 biopython=latest numpy=latest)
The strategy configuration was canceled because "pytest-cram._3_9_1_80" failed
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test (python=3.12 biopython=1.82 numpy=latest)
The operation was canceled.
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test (python=3.13 biopython=latest numpy=latest)
The operation was canceled.
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test (python=3.12 biopython=latest numpy=1.26.4)
The strategy configuration was canceled because "pytest-cram._3_9_1_80" failed
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test (python=3.12 biopython=latest numpy=1.26.4)
The operation was canceled.
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test (python=3.9 biopython=1.85 numpy=latest)
The strategy configuration was canceled because "pytest-cram._3_9_1_80" failed
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test (python=3.9 biopython=1.85 numpy=latest)
The operation was canceled.
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test (python=3.12 biopython=latest numpy=latest)
The strategy configuration was canceled because "pytest-cram._3_9_1_80" failed
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test (python=3.12 biopython=latest numpy=latest)
The operation was canceled.
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test (python=3.11 biopython=1.85 numpy=latest)
The strategy configuration was canceled because "pytest-cram._3_9_1_80" failed
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test (python=3.11 biopython=1.85 numpy=latest)
The operation was canceled.
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test (python=3.10 biopython=1.80 numpy=latest)
The strategy configuration was canceled because "pytest-cram._3_9_1_80" failed
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test (python=3.10 biopython=1.80 numpy=latest)
The operation was canceled.
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test (python=3.10 biopython=1.82 numpy=latest)
The strategy configuration was canceled because "pytest-cram._3_9_1_80" failed
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test (python=3.10 biopython=1.82 numpy=latest)
The operation was canceled.
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test (python=3.13 biopython=1.85 numpy=latest)
The strategy configuration was canceled because "pytest-cram._3_9_1_80" failed
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test (python=3.13 biopython=1.85 numpy=latest)
The operation was canceled.
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test (python=3.10 biopython=latest numpy=latest)
The strategy configuration was canceled because "pytest-cram._3_9_1_80" failed
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test (python=3.10 biopython=latest numpy=latest)
The operation was canceled.
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pyright
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
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check-subsample-config-schema
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
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mypy
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
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pathogen-repo-ci (lassa)
Failed to save: Unable to reserve cache with key 2025-10-24-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci (mumps)
Failed to save: Unable to reserve cache with key 2025-10-24-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, 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 2025-10-24-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, 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 2025-10-24-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, 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 2025-10-24-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci (wnv)
Failed to save: Unable to reserve cache with key 2025-10-24-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci-v0 (rsv)
Failed to save: Unable to reserve cache with key 2025-10-24-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, 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 2025-10-24-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci (dengue)
Failed to save: Unable to reserve cache with key 2025-10-24-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci (oropouche)
Failed to save: Unable to reserve cache with key 2025-10-24-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci (measles)
Failed to save: Unable to reserve cache with key 2025-10-24-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci (zika)
Failed to save: Unable to reserve cache with key 2025-10-24-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, 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 2025-10-24-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, 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 2025-10-24-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci (rabies)
Failed to save: Unable to reserve cache with key 2025-10-24-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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Artifacts
Produced during runtime
| Name | Size | Digest | |
|---|---|---|---|
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output-avian-flu
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98.3 KB |
sha256:0b0d8b78db52fb120b3c4428157145d31c66a2335e8cb67825f3aa32f786df56
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output-dengue
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436 KB |
sha256:46d085b515bae775c7cbcd77bfe827d905a5683b75bf17e45818597efd3e63f1
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output-lassa
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370 KB |
sha256:d01092ab717065d014ca17f756c0c396a218a20e237632c1f0f4dfdc947f1d37
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output-measles
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3.91 MB |
sha256:13ca7d001dc3efba9c524f92bd60ab950f06edeea89a0657650e78a9f020aff2
|
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output-mpox
|
14.4 MB |
sha256:0b221bcb70a008529a85aff53b6de5f61f477bdabc709ba98eefe8e16ee61496
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output-mumps
|
379 KB |
sha256:3bd65f824a0ca8a1e25437f68e2345b08437c3bc8f500f00eff20751e35ca314
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output-ncov
|
716 KB |
sha256:2d582d55cbedff1404793d05748185cb982c0d9352f145ce930a1709d27bb15c
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output-oropouche
|
588 KB |
sha256:c7bf749163cde0fd2bef2f1c2e54e8ee55e232e2647688c6c910a811c4879680
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output-rabies
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5.28 MB |
sha256:c5c0384a22b616be3f94d9cae13b7287ed2c49073783ca9bf58d0efd5763792d
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output-rsv
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1.2 MB |
sha256:b11d6ce198567f94aace05625c2aef1ec581a6d8bb8d932b329ebe414cd3626c
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output-seasonal-cov
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2.48 MB |
sha256:6fb1d2c49bd8d9cd118b964120d48132c73ff5acb491455764f9eb287021d345
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output-seasonal-flu
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60.3 KB |
sha256:7d2e99a34d6ea7770649634ac28fba00226bb4b0e9a1e274c7083e35a6d0ea3a
|
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output-vcf-input-tutorial
|
5.03 MB |
sha256:144d6b8e5c83d52bf0c3a32d5db3b3447819d186aea421566f11051f58d45549
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output-wnv
|
241 KB |
sha256:cd08b5da6ccb4166728957c3d1b5ae8dcc8afb86cff107cfe2a50be8cb14c80f
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output-yellow-fever
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2.13 MB |
sha256:045c9f52dc270d8b98aa9b67ed10d8b0bb76c32be4b6c127258f2bd2da187aca
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output-zika
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808 KB |
sha256:0ed17cc50287594956085597ce6509e0437289281732038b94ede597ad9aa02b
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