python-biopython - Debian Package Tracker

general

source: python-biopython (main)
version: 1.86+dfsg-1
maintainer: Debian Med Packaging Team (archive) (DMD) (LowNMU)
uploaders: Andreas Tille [DMD] – Charles Plessy [DMD] – Étienne Mollier [DMD]
arch: all any
std-ver: 4.7.2
VCS: Git (Browse, QA)

versions [more versions can be listed by madison] [old versions available from snapshot.debian.org]

[pool directory]

o-o-stable: 1.78+dfsg-4
oldstable: 1.80+dfsg-4
stable: 1.85+dfsg-4
testing: 1.85+dfsg-5
unstable: 1.86+dfsg-1

versioned links

1.78+dfsg-4: [.dsc, use dget on this link to retrieve source package] [changelog] [copyright] [rules] [control]
1.80+dfsg-4: [.dsc, use dget on this link to retrieve source package] [changelog] [copyright] [rules] [control]
1.85+dfsg-4: [.dsc, use dget on this link to retrieve source package] [changelog] [copyright] [rules] [control]
1.85+dfsg-5: [.dsc, use dget on this link to retrieve source package] [changelog] [copyright] [rules] [control]
1.86+dfsg-1: [.dsc, use dget on this link to retrieve source package] [changelog] [copyright] [rules] [control]

binaries

python-biopython-doc
python3-biopython
python3-biopython-sql

action needed

Marked for autoremoval on 23 November due to python-igraph, rdflib: #1117766, #1117769 high

Version 1.85+dfsg-5 of python-biopython is marked for autoremoval from testing on Sun 23 Nov 2025. It depends (transitively) on python-igraph, rdflib, affected by #1117766, #1117769. You should try to prevent the removal by fixing these RC bugs.

Created: 2025-10-17 Last update: 2025-10-30 07:01

Depends on packages which need a new maintainer normal

The packages that python-biopython depends on which need a new maintainer are:

w3c-sgml-lib (#739087)
- Depends: w3c-sgml-lib

Created: 2022-03-06 Last update: 2025-10-30 06:30

debian/patches: 1 patch to forward upstream low

Among the 8 debian patches available in version 1.85+dfsg-5 of the package, we noticed the following issues:

1 patch where the metadata indicates that the patch has not yet been forwarded upstream. You should either forward the patch upstream or update the metadata to document its real status.

Created: 2024-09-14 Last update: 2025-09-14 08:30

testing migrations

excuses:
- Migration status for python-biopython (1.85+dfsg-5 to 1.86+dfsg-1): BLOCKED: Maybe temporary, maybe blocked but Britney is missing information (check below)
- Issues preventing migration:
- ∙ ∙ missing build on riscv64
- ∙ ∙ arch:riscv64 not built yet, autopkgtest delayed there
- ∙ ∙ autopkgtest for ariba/2.14.7+ds-7: amd64: Pass, arm64: Pass, ppc64el: Test triggered
- ∙ ∙ autopkgtest for augur/24.4.0-3: amd64: Pass, arm64: Pass, i386: Test triggered, ppc64el: Test triggered, s390x: Test triggered
- ∙ ∙ autopkgtest for bbmap/39.20+dfsg-2: amd64: Pass, arm64: Pass, i386: Test triggered, ppc64el: Test triggered, s390x: Test triggered
- ∙ ∙ autopkgtest for busco/5.5.0-3: amd64: Pass, arm64: Pass, i386: Test triggered
- ∙ ∙ autopkgtest for changeo/1.3.0-3: amd64: Pass, arm64: Pass, i386: Test triggered, ppc64el: Test triggered, s390x: Test triggered
- ∙ ∙ autopkgtest for cnvkit/0.9.12-1: amd64: Pass, arm64: Pass, i386: Test triggered, ppc64el: Test triggered, s390x: Test triggered
- ∙ ∙ autopkgtest for cutesv/2.1.1-1: amd64: No tests, superficial or marked flaky ♻, arm64: No tests, superficial or marked flaky ♻, i386: Test triggered (will not be considered a regression) ♻ (reference ♻), ppc64el: Test triggered, s390x: Test triggered (will not be considered a regression) ♻ (reference ♻)
- ∙ ∙ autopkgtest for gasic/0.0.r19-8: amd64: Pass, arm64: Pass, i386: Test triggered (will not be considered a regression) ♻ (reference ♻), ppc64el: Test triggered, s390x: Test triggered (will not be considered a regression) ♻ (reference ♻)
- ∙ ∙ autopkgtest for gemmi/0.7.1+ds-2: amd64: Pass, arm64: Pass, i386: Test triggered, ppc64el: Test triggered, s390x: Test triggered
- ∙ ∙ autopkgtest for graphlan/1.1.3-6: amd64: Pass, arm64: Pass, i386: Test triggered, ppc64el: Test triggered, s390x: Test triggered
- ∙ ∙ autopkgtest for gubbins/3.4-2: amd64: Pass, i386: Test triggered
- ∙ ∙ autopkgtest for insilicoseq/2.0.1-1: amd64: Pass, arm64: Pass, i386: Test triggered, ppc64el: Test triggered, s390x: Test triggered (will not be considered a regression) ♻ (reference ♻)
- ∙ ∙ autopkgtest for kaptive/2.0.8-1: amd64: Pass, arm64: Pass, i386: Test triggered, ppc64el: Test triggered, s390x: Test triggered
- ∙ ∙ autopkgtest for kleborate/2.4.1-5: amd64: Pass, arm64: Pass, ppc64el: Test triggered, s390x: Test triggered
- ∙ ∙ autopkgtest for mcaller/1.0.3+git20210624.b415090-3: amd64: Pass, arm64: Pass, i386: Test triggered, ppc64el: Test triggered, s390x: Test triggered
- ∙ ∙ autopkgtest for mdanalysis: amd64: Test triggered (failure will be ignored), arm64: Test triggered (failure will be ignored), i386: Test triggered (failure will be ignored), ppc64el: Test triggered (failure will be ignored), s390x: Test triggered (failure will be ignored)
- ∙ ∙ autopkgtest for metaphlan/4.0.4+ds-1: amd64: Pass, arm64: Test triggered, i386: Test triggered (will not be considered a regression) ♻ (reference ♻), ppc64el: Test triggered, s390x: Test triggered (will not be considered a regression) ♻ (reference ♻)
- ∙ ∙ autopkgtest for mirtop/0.4.30-1: amd64: Pass, arm64: Pass, i386: Test triggered, ppc64el: Test triggered, s390x: Test triggered (will not be considered a regression) ♻ (reference ♻)
- ∙ ∙ autopkgtest for nanofilt/2.8.0-1: amd64: Pass, arm64: Pass, i386: Test triggered, ppc64el: Test triggered, s390x: Test triggered
- ∙ ∙ autopkgtest for nanolyse/1.2.0-4: amd64: Pass, arm64: Pass, i386: Test triggered, ppc64el: Test triggered, s390x: Test triggered
- ∙ ∙ autopkgtest for ncbi-acc-download/0.2.8-3: amd64: Pass, arm64: Pass, i386: Test triggered, ppc64el: Test triggered, s390x: Test triggered
- ∙ ∙ autopkgtest for optimir/1.2-2: amd64: Pass, arm64: Pass, i386: Test triggered, ppc64el: Test triggered, s390x: Test triggered
- ∙ ∙ autopkgtest for parsnp/2.1.3+dfsg-1: amd64: Pass, arm64: Pass, i386: Test triggered, ppc64el: Test triggered, s390x: Test triggered
- ∙ ∙ autopkgtest for peptidebuilder/1.1.0-3: amd64: Pass, arm64: Pass, i386: Test triggered, ppc64el: Test triggered, s390x: Test triggered
- ∙ ∙ autopkgtest for presto/0.7.5-1: amd64: Pass, arm64: Pass, i386: Test triggered, ppc64el: Test triggered, s390x: Test triggered
- ∙ ∙ autopkgtest for python-bcbio-gff/0.7.1-2: amd64: Pass, arm64: Pass, i386: Test triggered, ppc64el: Test triggered, s390x: Test triggered
- ∙ ∙ autopkgtest for python-biopython/1.86+dfsg-1: amd64: Pass, arm64: Pass, i386: Test triggered, ppc64el: Test triggered, s390x: Test triggered
- ∙ ∙ autopkgtest for python-cai/1.0.4-2: amd64: Pass, arm64: Pass, i386: Test triggered, ppc64el: Test triggered, s390x: Test triggered
- ∙ ∙ autopkgtest for python-cgecore/1.5.6+ds-2: amd64: No tests, superficial or marked flaky ♻, arm64: No tests, superficial or marked flaky ♻, i386: Test triggered, ppc64el: Test triggered, s390x: Test triggered
- ∙ ∙ autopkgtest for python-cooler/0.10.3-1: amd64: Pass, arm64: Pass, ppc64el: Test triggered
- ∙ ∙ autopkgtest for python-gffutils/0.13-3: amd64: Pass, arm64: Pass, i386: Test triggered, ppc64el: Test triggered, s390x: Test triggered
- ∙ ∙ autopkgtest for python-nanoget/1.19.3-1: amd64: Pass, arm64: Pass, i386: Test triggered, ppc64el: Test triggered, s390x: Test triggered (will not be considered a regression) ♻ (reference ♻)
- ∙ ∙ autopkgtest for python-pauvre/0.2.3-4: amd64: Pass, arm64: Pass, i386: Test triggered, ppc64el: Test triggered, s390x: Test triggered
- ∙ ∙ autopkgtest for python-prodigy/2.4.0-2: amd64: Pass, arm64: Pass, i386: Test triggered, ppc64el: Test triggered, s390x: Test triggered
- ∙ ∙ autopkgtest for python-pyani/0.2.13-1: amd64: Pass, arm64: Pass, i386: Test triggered, ppc64el: Test triggered, s390x: Test triggered
- ∙ ∙ autopkgtest for python-pyfaidx/0.8.1.3-2: amd64: Pass, arm64: Pass, i386: Test triggered, ppc64el: Test triggered, s390x: Test triggered
- ∙ ∙ autopkgtest for python-treetime/0.11.4-1: amd64: Pass, arm64: Pass, i386: Test triggered, ppc64el: Test triggered, s390x: Test triggered
- ∙ ∙ autopkgtest for qcat/1.1.0-8: amd64: Pass, arm64: Pass, i386: Test triggered, ppc64el: Test triggered, s390x: Test triggered
- ∙ ∙ autopkgtest for recan/0.5+dfsg-1: amd64: Pass, arm64: Pass, i386: Test triggered, ppc64el: Test triggered, s390x: Test triggered
- ∙ ∙ autopkgtest for seqmagick/0.8.6-4: amd64: Pass, arm64: Pass, i386: Test triggered, ppc64el: Test triggered, s390x: Test triggered
- ∙ ∙ autopkgtest for srst2/0.2.0-13: amd64: Pass, arm64: Pass, ppc64el: Test triggered
- ∙ ∙ autopkgtest for yanagiba/1.0.0-5: amd64: Pass, arm64: Pass, i386: Test triggered, ppc64el: Test triggered, s390x: Test triggered
- ∙ ∙ Waiting for lintian test results (stalls migration) - info
- ∙ ∙ Too young, only 0 of 5 days old
- Additional info:
- ∙ ∙ Piuparts tested OK - https://piuparts.debian.org/sid/source/p/python-biopython.html
- ∙ ∙ Reproducible on amd64 - info ♻
- ∙ ∙ Reproducible on arm64 - info ♻
- Not considered

news

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[2025-10-29] Accepted python-biopython 1.86+dfsg-1 (source) into unstable (Étienne Mollier)
[2025-09-16] python-biopython 1.85+dfsg-5 MIGRATED to testing (Debian testing watch)
[2025-09-14] Accepted python-biopython 1.85+dfsg-5 (source) into unstable (Étienne Mollier)
[2025-04-15] python-biopython 1.85+dfsg-4 MIGRATED to testing (Debian testing watch)
[2025-04-11] Accepted python-biopython 1.85+dfsg-4 (source) into unstable (Santiago Vila)
[2025-04-11] Accepted python-biopython 1.85+dfsg-3 (source) into unstable (Santiago Vila)
[2025-02-13] python-biopython 1.85+dfsg-2 MIGRATED to testing (Debian testing watch)
[2025-02-06] Accepted python-biopython 1.85+dfsg-2 (source) into unstable (Michael R. Crusoe)
[2025-01-29] Accepted python-biopython 1.85+dfsg-1 (source) into unstable (Michael R. Crusoe)
[2024-11-02] python-biopython 1.84+dfsg-4 MIGRATED to testing (Debian testing watch)
[2024-10-31] Accepted python-biopython 1.84+dfsg-4 (source) into unstable (Étienne Mollier)
[2024-10-20] python-biopython 1.84+dfsg-3 MIGRATED to testing (Debian testing watch)
[2024-10-18] Accepted python-biopython 1.84+dfsg-3 (source) into unstable (Étienne Mollier)
[2024-09-25] Accepted python-biopython 1.84+dfsg-2 (source) into unstable (Étienne Mollier)
[2024-09-23] Accepted python-biopython 1.84+dfsg-1 (source) into unstable (Étienne Mollier)
[2024-09-20] python-biopython 1.83+dfsg1-5 MIGRATED to testing (Debian testing watch)
[2024-09-16] Accepted python-biopython 1.84+dfsg-1~0exp1 (source) into experimental (Étienne Mollier)
[2024-09-14] Accepted python-biopython 1.83+dfsg1-5 (source) into unstable (Michael R. Crusoe)
[2024-09-08] python-biopython 1.83+dfsg1-4 MIGRATED to testing (Debian testing watch)
[2024-09-06] Accepted python-biopython 1.83+dfsg1-4 (source) into unstable (Étienne Mollier)
[2024-05-25] python-biopython 1.83+dfsg1-3 MIGRATED to testing (Debian testing watch)
[2024-05-22] Accepted python-biopython 1.83+dfsg1-3 (source) into unstable (Étienne Mollier)
[2024-05-03] python-biopython 1.83+dfsg1-2 MIGRATED to testing (Debian testing watch)
[2024-04-17] Accepted python-biopython 1.83+dfsg1-2 (source) into unstable (Andrius Merkys)
[2024-03-21] Accepted python-biopython 1.83+dfsg1-1 (source) into unstable (Étienne Mollier)
[2024-03-10] Accepted python-biopython 1.83+dfsg-1 (source) into unstable (Étienne Mollier)
[2023-12-24] python-biopython 1.81+dfsg-3 MIGRATED to testing (Debian testing watch)
[2023-12-19] Accepted python-biopython 1.81+dfsg-3 (source) into unstable (Étienne Mollier)
[2023-11-14] python-biopython 1.81+dfsg-2 MIGRATED to testing (Debian testing watch)
[2023-11-11] Accepted python-biopython 1.81+dfsg-2 (source) into unstable (Étienne Mollier)

bugs [bug history graph]

all: 0

links

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ubuntu

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version: 1.85+dfsg-4