mdanalysis (2.10.0-1) unstable; urgency=medium

  * New upstream release
    - supports numpy 2.3. Closes: #1114702
    - Build-Depends-Indep: python3-sphinxcontrib.* for doc build:
      applehelp, bibtex, devhelp, htmlhelp, qthelp, serializinghtml
  * simplify debian/rules by removing nproc handling for tests
  * Build-Depends: python3-numpy-dev (for dh_numpy3)
  * debian patch docs_intersphinx_local.patch adds intersphinx links
    to local documentation.
    Build-Depends-Indep: python3-doc, python-gsd-doc, python-h5py-doc,
    python-matplotlib-doc, python-numpy-doc, python-dask-doc,
    python-scipy-doc, rdkit-doc

 -- Drew Parsons <dparsons@debian.org>  Wed, 22 Oct 2025 00:50:11 +0200

mdanalysis (2.9.0-12) unstable; urgency=medium

  * skip all tests, both build-time and run-time. See Bug#1108309.

 -- Drew Parsons <dparsons@debian.org>  Thu, 10 Jul 2025 11:07:57 +0200

mdanalysis (2.9.0-11) unstable; urgency=medium

  * fix order of conditional control of build-time tests

 -- Drew Parsons <dparsons@debian.org>  Wed, 09 Jul 2025 19:16:36 +0200

mdanalysis (2.9.0-10) unstable; urgency=medium

  * apply suggestion from Bug#1108309 to skip tests (build and
    runtime) if less than 2 CPUs are available
  * do not run build-time tests on hurd-i386
    or when nocheck is set in DEB_BUILD_OPTIONS

 -- Drew Parsons <dparsons@debian.org>  Wed, 09 Jul 2025 15:12:21 +0200

mdanalysis (2.9.0-9) unstable; urgency=medium

  * debian/tests/control: mark mdanalysis with Restrictions: flaky.
    mdanalysis tests are generally unreliable and fail often and
    randomly. Closes: #1108309
  * debian/tests: skip tests observed failing in debci
    migration-reference runs:
    test_dihedral_attr_warning test_AnalysisFromFunction
    test_villin_unfolded test_rmsd_frames test_file_guess_hydrogens
    test_gnm_run_step test_all_backends_give_correct_results
    test_startframe test_hbond_analysis

 -- Drew Parsons <dparsons@debian.org>  Fri, 04 Jul 2025 10:23:27 +0200

mdanalysis (2.9.0-8) unstable; urgency=medium

  * skip test_distances, since NSGrid is flaky and causes distance
    tests to often (randomly) fail, see upstream Issue #4906.
    Closes: #1104387

 -- Drew Parsons <dparsons@debian.org>  Sun, 11 May 2025 23:44:46 +0200

mdanalysis (2.9.0-7) unstable; urgency=medium

  * skip all parallel tests, including multiprocess tests.
    mdanalysis tests are flakey. Aiming to minimise the failure
    cross-section.

 -- Drew Parsons <dparsons@debian.org>  Wed, 23 Apr 2025 10:50:06 +0200

mdanalysis (2.9.0-6) unstable; urgency=medium

  * skip all openmp tests. openmp is unstable, tests often fail.

 -- Drew Parsons <dparsons@debian.org>  Tue, 22 Apr 2025 20:57:05 +0200

mdanalysis (2.9.0-5) unstable; urgency=medium

  * ppc64: skip test_timestep_copied and test_positions_share_memory
    with [ref_reader25] in coordinates/test_copying.py

 -- Drew Parsons <dparsons@debian.org>  Fri, 18 Apr 2025 20:42:23 +0200

mdanalysis (2.9.0-4) unstable; urgency=medium

  * fix parentheses in ppc64 test skips

 -- Drew Parsons <dparsons@debian.org>  Fri, 18 Apr 2025 17:35:50 +0200

mdanalysis (2.9.0-3) unstable; urgency=medium

  * skip tests failing on hppa and ppc64

 -- Drew Parsons <dparsons@debian.org>  Thu, 17 Apr 2025 23:47:22 +0200

mdanalysis (2.9.0-2) unstable; urgency=medium

  * drop PMG_TEST_FILES_DIR env var in debian/tests
  * debian patch improve_test_timeout_PR4584.diff applies upstream
    PR#4584 (diff not patch) to help improve test reliability
  * gsd causes timeouts. Explicitly disable gsd tests.
    debian patch skip_gsd_tests.patch sets HAS_GSD=False in tests.
    https://github.com/MDAnalysis/mdanalysis/issues/4209
    Closes: #1103158, #1103367

 -- Drew Parsons <dparsons@debian.org>  Thu, 17 Apr 2025 00:54:54 +0200

mdanalysis (2.9.0-1) unstable; urgency=medium

  * New upstream release
    - Build-Depends: python3-filelock
  * drop debian patch test_skip_missing_modules.patch. Deprecated by
    new upstream import checks.
  * Standards-Version: 4.7.2

 -- Drew Parsons <dparsons@debian.org>  Sat, 05 Apr 2025 19:51:52 +0200

mdanalysis (2.8.0-4) unstable; urgency=medium

  * fix running tests verbose

 -- Drew Parsons <dparsons@debian.org>  Tue, 18 Feb 2025 01:16:36 +0100

mdanalysis (2.8.0-3) unstable; urgency=medium

  * run all tests verbose

 -- Drew Parsons <dparsons@debian.org>  Mon, 17 Feb 2025 11:03:45 +0100

mdanalysis (2.8.0-2) unstable; urgency=medium

  * Depends: python3-biopython only on arches where it is available
    (biopython is optional for mdanalysis, needed for analysis.align)
  * run armel tests verbose to identify stalling distance tests
  * build i386 with -fexcess-precision=fast (better than relaxing test
    tolerance). Closes: #1095739

 -- Drew Parsons <dparsons@debian.org>  Fri, 14 Feb 2025 12:40:15 +0100

mdanalysis (2.8.0-1) unstable; urgency=medium

  * New upstream release
    - supports Numpy 2. Closes: #1094808.
    - applies debian patch xdr_type_PR4408.patch
  * drop logo exclusions (logo files no longer shipped upstream)
    Drop debian patch docs_no_logo.patch.
  * update debian/watch to latest uscan recommendations
    (without renaming for DFSG logo exclusion)
  * debian patch test_skip_missing_modules.patch skips test_hole2,
    test_psa, test_waterdynamics when mdahole2, pathsimanalysis,
    waterdynamics are not available (they are not yet packaged for
    debian)
    - and skip test_all_import[.analysis.hole2], journal.pcbi.1004568
      (duecredit test accessing pathsimanalysis)
  * run tests with --disable-pytest-warnings as recommended upstream
  * don't ignore build-time test errors.
    Apply i386 and s390x test skips in debian/tests to debian/rules.
  * delete .duecredit.p generated by tests (otherwise gets installed)
  * after dh_python3, remove leftover python3.* files (dist files not
    generated cleanly)

 -- Drew Parsons <dparsons@debian.org>  Mon, 10 Feb 2025 20:13:19 +0100

mdanalysis (2.7.0-5) unstable; urgency=medium

  * debian/tests: fix i386 test skips

 -- Drew Parsons <dparsons@debian.org>  Sat, 10 Aug 2024 19:37:15 +0200

mdanalysis (2.7.0-4) unstable; urgency=medium

  * i386: skip test_ramachandran, test_hbond_analysis,
    test_clustering_three_ensembles_two_identical

 -- Drew Parsons <dparsons@debian.org>  Sat, 10 Aug 2024 10:53:09 +0200

mdanalysis (2.7.0-3) unstable; urgency=medium

  * use debian/tests/test-mdanalysis to control debci tests
    - test over all supported python versions
    - i386: skip test_multiprocess_COG[u4]
    - s390x: skip many tests.
      Big-endian support is incomplete. See upstream Issue#1829.

 -- Drew Parsons <dparsons@debian.org>  Fri, 09 Aug 2024 11:59:17 +0200

mdanalysis (2.7.0-2) unstable; urgency=medium

  * python3-gsd is only available on little-endian systems
    (not s390x and other big-endian arches)
  * run build tests on i386 verbose (-v) to catch stalling tests
  * debian/tests: run CI verbose -v (again, to catch i386 failure)
    Closes: #1063325.

 -- Drew Parsons <dparsons@debian.org>  Thu, 08 Aug 2024 13:01:08 +0200

mdanalysis (2.7.0-1) unstable; urgency=medium

  [ Andreas Tille ]
  * New upstream version
    - supports Python 3.12. Closes: #1071800, #1061811.
  * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
  * Rules-Requires-Root: no (routine-update)
  * No tab in license text (routine-update)
  * Fix field name typo in debian/copyright (Comments ⇒ Comment).
  * Add upstream metadata

  [ Drew Parsons ]
  * Build-Depends: python3-mda-xdrlib
  * debian patch xdr_type_PR4408.patch applies upstream PR#4408
    to fix XDR types. See upstream Issue#4589.
  * remove generated timestep.cpp during clean. Closes: #1045215.
  * debian patchdoc_no_mdanalysis_sphinx.patch disables use of custom
    sphinx theme
  * Standards-Version: 4.7.0

 -- Drew Parsons <dparsons@debian.org>  Sun, 28 Jul 2024 16:38:17 +0200

mdanalysis (2.5.0+dfsg1-2) unstable; urgency=medium

  * debian patches gsd3_PR4153.diff and gsd3_PR4174.diff apply
    upstream PR#4153 and #4174 to enable support for gsd 3.

 -- Drew Parsons <dparsons@debian.org>  Fri, 28 Jul 2023 12:43:14 +0200

mdanalysis (2.5.0+dfsg1-1) unstable; urgency=medium

  * New upstream release.
    - Depends: python3-numpy (>= 1.21.0~)
    - drop Build-Depends: python3-mock (now uses unittest.mock)
  * reorder Build-Depends by order in setup.py

 -- Drew Parsons <dparsons@debian.org>  Sun, 18 Jun 2023 00:13:39 +0200

mdanalysis (2.4.2+dfsg1-1) unstable; urgency=medium

  * New upstream release.
    - fixes DensityAnalysis for numpy 1.24. Closes: #1027227,

 -- Drew Parsons <dparsons@debian.org>  Mon, 09 Jan 2023 17:54:02 +0100

mdanalysis (2.4.1+dfsg1-1) unstable; urgency=medium

  * New upstream release.
    - update Build-Depends: python3-biopython (>= 1.80)
  * mark python-mdanalysis-doc as Multi-Arch: foreign
  * Standards-Version: 4.6.2

 -- Drew Parsons <dparsons@debian.org>  Fri, 23 Dec 2022 11:52:12 +0100

mdanalysis (2.3.0+dfsg1-1) unstable; urgency=medium

  * New upstream release.
    - applies debian patch tests_floating_point.patch
  * Build-Depends: pybuild-plugin-pyproject to use pyproject.toml
    - update Build-Depends: python3-numpy (>= 1.20.0~),
      python3-networkx (>= 2.0),
      python3-scipy (>= 1.5.0),
      python3-gsd (>= 1.9.3~),
      python3-packaging,
      python3-fasteners
    - drop Build-Depends: python3-six
  * Build-Depends-Indep: python3-pybtex, python3-sphinx-rtd-theme,
    python3-sphinx-sitemap, python3-sphinxcontrib.bibtex
    - drop debian patch docs_missing_sphinx_sitemap.patch
  * Standards-Version: 4.6.1

 -- Drew Parsons <dparsons@debian.org>  Mon, 07 Nov 2022 23:10:36 +0100

mdanalysis (2.0.0+dfsg1-4) unstable; urgency=medium

  * source upload to allow python-mdanalysis-doc to migrate to testing

 -- Drew Parsons <dparsons@debian.org>  Fri, 18 Feb 2022 17:17:45 +0100

mdanalysis (2.0.0+dfsg1-3) unstable; urgency=medium

  * provide docs in python-mdanalysis-doc package
    - Build-Depends: python3-sphinx, python3-msmb-theme, libjs-mathjax
    - add debian privacy patches
      * docs_local_mathjax.patch use local mathjax.js script
      * docs_privacy.patch removes goat counter from footer

 -- Drew Parsons <dparsons@debian.org>  Sun, 13 Feb 2022 11:48:11 +0100

mdanalysis (2.0.0+dfsg1-2) unstable; urgency=medium

  * Build with -ffloat-store on i386 to workaround x87 excess
    precision causing test failures. Thanks Adrian Bunk.
  * add debian patches to enable successful build of docs
    - docs_no_logo.patch skips use of logo image files
      (upstream does not give permission to use them)
    - docs_missing_sphinx_sitemap.patch skips sphinx_sitemap
      (not yet packaged for Debian)
    - docs_sphinx_warnings_are_not_errors.patch stops treating sphinx
      warnings as errors (needed to ignore inconsistent documentation
      of analysis.density)
    - note that the doc package itself is not yet provided
  * debian patch tests_floating_point.patch fixes test of floating
    point numbers (upstream Issue#3524)
  * execute dh_numpy3 after dh_python3 to assign python3-numpy-abi
  * remove autogenerated files left after dh_auto_clean and pytest

 -- Drew Parsons <dparsons@debian.org>  Thu, 10 Feb 2022 19:36:31 +0100

mdanalysis (2.0.0+dfsg1-1) unstable; urgency=medium

  * New upstream release.
    - Build-Depends:
       python3-h5py,
       python3-numpy (>= 1.16.0~),
       python3-netcdf4 (>= 1.0~),
       python3-seaborn,
       python3-sklearn,
       python3-threadpoolctl
    - applies debian patch fix_matplotlib_PR2763.patch
  * Standards-Version: 4.6.0
  * add detailed copyright entries (GPL-2 and GPL-3) to
    debian/copyright, identified by :Copyright: tag in files.
    CODE_OF_CONDUCT.md is CCA-3.0.
  * debian/rules override_dh_clean: remove .c cython files
  * run tests with MPLBACKEND=agg to avoid Xserver (Xvfb) errors
  * Note that logo files are not used in source (+dfsg) since they are
    non-free (not free to alter and redistribute alterations)

 -- Drew Parsons <dparsons@debian.org>  Fri, 03 Sep 2021 03:12:37 +0200

mdanalysis (1.0.0+dfsg1-2) unstable; urgency=medium

  * Build-Depends: python3-all-dev (needs Python.h), cython3
    python3-hypothesis, python3-sklearn (debian/tests also)
  * python3-mdanalysis Depends: python3-duecredit,
    Recommends: python3-sklearn
  * use testsuite for build-time tests with pytest
    (over all python versions)

 -- Drew Parsons <dparsons@debian.org>  Wed, 30 Dec 2020 01:56:26 +1100

mdanalysis (1.0.0+dfsg1-1) unstable; urgency=medium

  * Initial release (Closes: #962440)
  * debian/rules: pybuild source dir PYBUILD_DIR=package
  * Build-Depends:
      python3-numpy (>=1.13.3),
      python3-biopython (>= 1.71),
      python3-networkx (>= 1.0),
      python3-griddataformats (>= 0.4.0),
      python3-six (>= 1.4.0),
      python3-mmtf (>= 1.0.0),
      python3-joblib,
      python3-scipy (>= 1.0.0),
      python3-matplotlib (>= 1.5.1),
      python3-mock,
      python3-gsd (>= 1.4.0)
  * Build-Depends: tox, python3-duecredit (to run build-time tests)
  * debian patches:
    - docs_use_built_module.patch stops doc build from using
      raw (unbuilt) source to build docs. Set PYTHONPATH to .pybuild dir.
    - fix_matplotlib_PR2763.patch applies upstream PR2763 to fix
      matplotlib API.
  * But docs are not built yet pending packaging of
    python3-sphinx-sitemap (see RFP#970811).

 -- Drew Parsons <dparsons@debian.org>  Thu, 24 Sep 2020 22:21:26 +0800