cnvkit (0.9.13-2) unstable; urgency=medium

  * Team upload.
  * Conditionally skip tests requiring more CPUs than available.
  * Drop "Rules-Requires-Root: no" (default).
  * Fine-tune salsa-ci.yml.

 -- Santiago Vila <sanvila@debian.org>  Wed, 03 Jun 2026 23:50:00 +0200

cnvkit (0.9.13-1) unstable; urgency=medium

  * New upstream version
  * Standards-Version: 4.7.4 (routine-update)
  * debputy lint --auto-fix (routine-update)
  * Refreshed patches.
  * d/control: needs pomegranate v1.x+.
  * d/control: only build for the default version of Python, to match
    pomegranate/pytorch.
  * d/install: there is not a scripts directory anymore.
  * Cherry-picked patch from upstream to fix the tests.
  * Update watch file format version to 5.
  * Use GitHub template in watch file instead of explicit
    Source/Matching-Pattern.

 -- Michael R. Crusoe <crusoe@debian.org>  Mon, 18 May 2026 18:23:24 +0200

cnvkit (0.9.12-1) unstable; urgency=medium

  * New upstream version
  * Standards-Version: 4.7.0 (routine-update)
  * Removed spelling patch, it was applied upstream. Remaining patches
    were refreshed.
  * d/control: build-dep on the new python3-pomegranate that supports
    numpy 2.x.
  * Include patch from upstream for numpy 2.x support.
  * d/{install,rules,pybuild.testfiles}: simplify and modernize
  * Add my own patch to fix one last numpy 2.x issue: Use `np.bytes_`
    instead of `np.string_`.
  * d/patches/controldir: fix link to the Debian bug.

 -- Michael R. Crusoe <crusoe@debian.org>  Thu, 06 Feb 2025 15:23:25 +0100

cnvkit (0.9.10-2) unstable; urgency=medium

  * No-change rebuild of the package from experimental for unstable.

 -- Michael R. Crusoe <crusoe@debian.org>  Mon, 08 Apr 2024 10:42:20 +0200

cnvkit (0.9.10-2~0exp) experimental; urgency=medium

  * Test "Arch: all" upload to experimental

  * d/control: the binary package is architecture independent.
  * d/patches/spelling: forwarded upstream.
  * d/control: build the PEP-517 way with pybuild-plugin-pyproject.
  * d/control: also run the built-in tests as autopkgtests.
  * d/rules: move items into d/clean.
  * d/tests: skip-not-installable for s390x and others where python3-
    pysam isn't available.
  * d/control: add riscv64 to the arch list.

 -- Michael R. Crusoe <crusoe@debian.org>  Tue, 05 Mar 2024 10:11:04 +0100

cnvkit (0.9.10-1) unstable; urgency=medium

  * Team upload.

  [ Andreas Tille ]
  * New upstream version
  * Standards-Version: 4.6.2 (routine-update)
  * Drop Build-Depends python3-future
    Closes: #1059947
  * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
  * Use secure URI in Homepage field.

  [ Nilesh Patra ]
  * Add patch to ignore test warnings

 -- Andreas Tille <tille@debian.org>  Fri, 05 Jan 2024 16:18:13 +0100

cnvkit (0.9.9-2) unstable; urgency=medium

  * Team Upload.
  * Re-diff patches (refresh)
  * d/rules: do not run tests in parallel

 -- Nilesh Patra <nilesh@debian.org>  Fri, 15 Oct 2021 12:11:06 +0530

cnvkit (0.9.9-1) unstable; urgency=medium

  * Fix watchfile to detect new versions on github (routine-update)
  * New upstream version
  * Standards-Version: 4.6.0 (routine-update)
  * watch file standard 4 (routine-update)

 -- Michael R. Crusoe <crusoe@debian.org>  Mon, 13 Sep 2021 19:06:06 +0200

cnvkit (0.9.8-1) unstable; urgency=medium

  [ Steffen Moeller ]
  * Added symbolic link from /usr/lib/debian-med/bin/cnvkit.py
    to /usr/bin/cnvkit.py

    bcbio explicitly looks in /usr/bin, though.

  [ Michael R. Crusoe ]
  * New upstream version
  * Standards-Version: 4.5.1 (routine-update)
  * debhelper-compat 13 (routine-update)
  * debian/control: mips64el is not supported by upstream, remove it
    Closes: #962743

 -- Michael R. Crusoe <crusoe@debian.org>  Fri, 01 Jan 2021 16:17:10 +0100

cnvkit (0.9.7-1) unstable; urgency=medium

  * New upstream version
  * Standards-Version: 4.5.0 (routine-update)
  * Refreshed the patches
  * Add salsa-ci file (routine-update)
  * Rules-Requires-Root: no (routine-update)
  * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
    Repository-Browse.

 -- Michael R. Crusoe <crusoe@debian.org>  Mon, 01 Jun 2020 16:19:46 +0200

cnvkit (0.9.6-3) unstable; urgency=medium

  * Don't run the autopkgtests in parallel.

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Tue, 07 Jan 2020 11:48:23 +0100

cnvkit (0.9.6-2) unstable; urgency=medium

  * Support more architectures (Closes: #942582)
  * Tests pass with the latest python3-pandas. (Closes: #944041)

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Wed, 13 Nov 2019 18:57:24 +0100

cnvkit (0.9.6-1) unstable; urgency=medium

  * New upstream version
  * debhelper-compat 12
  * Standards-Version: 4.4.0

 -- Steffen Moeller <moeller@debian.org>  Wed, 28 Aug 2019 19:31:59 +0200

cnvkit (0.9.5-3) unstable; urgency=medium

  * Fix buster rebuilds (Closes: #925568)
    d/patches/controldir.patch

 -- Olivier Sallou <osallou@debian.org>  Wed, 27 Mar 2019 08:00:39 +0000

cnvkit (0.9.5-2) unstable; urgency=medium

  [ Jelmer Vernooĳ ]
  * Use secure copyright file specification URI.
  * Trim trailing whitespace.

  [ Michael R. Crusoe ]
  * Remove trailing whitespace in debian/rules
  * Standards-Version: 4.3.0
  * Run the included tests as autopkgtests.
  * Mark cnv_expression_correlate as a script
  * amd64 only, due to the realities of where python-pysam is available.

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Sun, 06 Jan 2019 04:12:46 -0800

cnvkit (0.9.5-1) unstable; urgency=medium

  * Team upload.
  * New upstream version
  * debhelper 11
  * Standards-Version: 4.2.0

 -- Andreas Tille <tille@debian.org>  Mon, 13 Aug 2018 13:02:24 +0200

cnvkit (0.9.3-2) unstable; urgency=medium

  * Add missing build-dep on python3-future. (Closes: #901877)
  * debian/rules: fix override_dh_auto_test-does-not-check-DEB_BUILD_OPTIONS

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Tue, 19 Jun 2018 15:05:43 -0700

cnvkit (0.9.3-1) unstable; urgency=medium

  * New upstream version.
  * Initial release. (Closes: #828176)
  * Policy 4.1.4 compliance
  * Moved to python3
  * Cleaning test tmp results

 -- Steffen Moeller <moeller@debian.org>  Fri, 15 Jun 2018 12:03:11 +0200

cnvkit (0.9.0-1) UNRELEASED; urgency=medium

  * Debianisation.

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Sat, 25 Jun 2016 10:57:17 -0700
