mdtraj (1.10.1-2) unstable; urgency=medium * Team upload. * d/control: Remove python3-astunparse from depedencies. It is not longer needed. -- Emmanuel Arias Mon, 11 Nov 2024 15:52:34 -0300 mdtraj (1.10.1-1) unstable; urgency=medium * Team upload. * New upstream version. * Update patches according to new upstream release: - d/patches/rename-mdconvert-mdtraj.patch. - d/patches/drop_notebook_in_docs.patch. - d/patches/test_increase_timeout.patch. * Remove patches, not longer needed: - d/patches/fix_netcdf_PR1894.patch. - d/patches/remove_six_PR1908.patch. * d/control: Add python3-versioneer, pandoc, python3-nbsphinx, python3-nbsphinx-link as build dependency. - Remove python3-astuparse, it is not longer needed. * d/control: Use cython3 instead of cython3-legacy (Closes: #1082092). -- Emmanuel Arias Sat, 09 Nov 2024 21:59:21 -0300 mdtraj (1.10.0-3) unstable; urgency=medium * only remove python3-specific mdtraj/core/lib (from libtheobald.a) if the excess dir exists (it's only left over if there is more than one supported python version). Closes: #1076166. -- Drew Parsons Sun, 14 Jul 2024 12:37:33 +0200 mdtraj (1.10.0-2) unstable; urgency=medium * debian patch remove_six_PR1908.patch applies upstream PR#1908 to remove remaining references to six. -- Drew Parsons Fri, 05 Jul 2024 18:32:59 +0200 mdtraj (1.10.0-1) unstable; urgency=medium * New upstream release - drops distutils. Closes: #1065901. - drops binpos and tng formats and utils/six.py * Build-Depends: (Recommends:) python3-gsd - drop debian patch test_gsd_skip.patch * debian patch fix_netcdf_PR1894.patch applies upstream PR#1894 to fix loading of netcdf files. Build-Depends: (Recommends): python3-netcdf4 * remove python-specific path left by installation of static lib libtheobald.a. dh_python3 can't see the static libs are identical (mostly). py3.11 compiles libtheobald.o with -fwrapv, where py3.12 uses -fno-strict-overflow * build docs after dh_auto_install to avoid double-building * after dh_auto_clean, remove generated docs and lib * Standards-Version: 4.7.0 -- Drew Parsons Fri, 05 Jul 2024 02:19:44 +0200 mdtraj (1.9.9-1) unstable; urgency=medium * Team upload. * Switch to cython3-legacy. Closes: #1056815 * Fix clean target Closes: #1045994 * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Use secure URI in Homepage field. * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository-Browse. * Fix field name typo in debian/copyright (Comments ⇒ Comment). * Explicitly call dh_python3 in d/rules * d/rules: verbose * Fix capitalisation in description * Set hardening options * Manually remove copy of libtheobald.a in /usr/lib/python3.1*/dist-packages * Update python_hashbang.patch to replace all instances of /bin/env -- Andreas Tille Tue, 16 Jan 2024 11:14:21 +0100 mdtraj (1.9.7-6) unstable; urgency=medium * update debian patch test_relax_tol.patch to relax tolerance in periodic test in test_distances_t (test_distance.py). Was occasionally failing on arm64. -- Drew Parsons Wed, 01 Mar 2023 11:54:43 +0100 mdtraj (1.9.7-5) unstable; urgency=medium * debian patch python3.11_PR1758.patch adapts upstream PR1758 to fix build with python3.11. Also, skip test_image_molecules in debian/tests (segfaults). Closes: #1028995. * Standards-Version: 4.6.2 -- Drew Parsons Wed, 18 Jan 2023 16:38:41 +0100 mdtraj (1.9.7-4) unstable; urgency=medium * debian/tests: add Restrictions: needs-internet (test_examples.py pulls a random PDB sample file from www.rcsb.org) * debian patch test_increase_timeout.patch increases TIMEOUT to 180 sec in test_examples.py to allow for poor internet connections. Closes: #1009079. * Standards-Version: 4.6.1 -- Drew Parsons Wed, 01 Jun 2022 18:02:27 +0200 mdtraj (1.9.7-3) unstable; urgency=medium * python3-mdtraj Depends: python3-astunparse - drop debian patch reinstate_astor_not_astunparse_revert_a8b2b9c.patch -- Drew Parsons Sun, 03 Apr 2022 18:41:47 +0200 mdtraj (1.9.7-2) unstable; urgency=medium * rename debian patch test_order_relax_tol.patch to test_relax_tol.patch and relax tolerance in test_distances_t (test_distance.py) to improve test relability on arm64. -- Drew Parsons Sun, 02 Jan 2022 22:11:24 +0100 mdtraj (1.9.7-1) unstable; urgency=medium * New upstream release. - applies debianpatch fix_notebook_PR1687.patch * add debian patches - docs_use_local_mathjax.patch uses local mathjax installation in order to preserve privacy - drop_notebook_in_docs.patch drops use of nbconvert in docs, because of the mistune error Bug#1002372. -- Drew Parsons Sat, 01 Jan 2022 19:16:35 +0100 mdtraj (1.9.6-3) unstable; urgency=medium * debian patch fix_notebook_PR1687.patch applies upstream PR#1687 fixing notebook tests to work with latest jupyter -- Drew Parsons Fri, 12 Nov 2021 12:13:35 +0100 mdtraj (1.9.6-2) unstable; urgency=medium * allow for mathjax changes: latest.js no longer used. Closes: #997749. * call dh_numpy3 after dh_install * update debian/copyright - remove deprecated devtools/authors.py - acknowledge Robert T. McGibbon in mdtraj/formats/xtc/src -- Drew Parsons Sun, 31 Oct 2021 12:48:20 +0100 mdtraj (1.9.6-1) unstable; urgency=medium * New upstream release. * use triple-slash for mathjax reference in docs * Standards-Version: 4.6.0 -- Drew Parsons Wed, 18 Aug 2021 16:05:50 +0200 mdtraj (1.9.5-1) unstable; urgency=medium * New upstream release. * Standards-Version: 4.5.1 * debian/tests: skip nmr.ipynb, it requires SPARTA+ which is not available. Closes: #980050. -- Drew Parsons Mon, 18 Jan 2021 16:30:54 +1100 mdtraj (1.9.4+git20201015.068f29a-5) unstable; urgency=medium * debian patch rename-mdconvert-mdtraj.patch renames mdconvert to mdconvert-mdtraj to avoid filename conflict with mdconvert from the isync package. Closes: #973631. -- Drew Parsons Tue, 03 Nov 2020 16:07:00 +0800 mdtraj (1.9.4+git20201015.068f29a-4) unstable; urgency=medium * eliminate automated Testsuite: autopkgtest-pkg-python. Not compatible with incomplete built Architecture set (no armhf). -- Drew Parsons Sun, 01 Nov 2020 00:36:36 +0800 mdtraj (1.9.4+git20201015.068f29a-3) unstable; urgency=medium * set Architecture: any-amd64 arm64 i386 in debian/tests to match debian/control. Otherwise armhf failure prevents migration. -- Drew Parsons Fri, 30 Oct 2020 02:09:33 +0800 mdtraj (1.9.4+git20201015.068f29a-2) unstable; urgency=medium * add debian patches - 32bit_skip_image_molecule.patch skips test_image_molecules in test_trajectory.py on 32-bit systems to avoid segfault in image_molecule (see upstream Issue #1591) - test_order_relax_tol.patch relaxes absolute tolerance in test_order.py::test_directors_angle_from_traj to help i386 pass tests. * restrict python3-mdtraj Architecture: any-amd64 arm64 i386. mdtraj needs SSE2 or NEON. Closes: #972592. -- Drew Parsons Sat, 24 Oct 2020 12:34:12 +0800 mdtraj (1.9.4+git20201015.068f29a-1) unstable; urgency=medium * New upstream snapshot. - adds support for NEON (arm64) * Build-Depends-Indep: python3-ipykernel, python3-jupyter-client, python3-matplotlib, python3-six, python3-sklearn to build docs from examples. Closes: #972635. * set MPLCONFIGDIR to catch matplotlib output for examples in docs and fix doc access to generated image files * Remove local __pycache__ when running debian/rules clean (dh_auto_clean) * predownload .pdb files from http://www.rcsb.org/pdb/files and store in debian/external alongside doi badge (to enable doc build when internet is not available for build) * debian patch reinstate_astor_not_astunparse_revert_a8b2b9c.patch reverts upstream commit a8b2b9c to reinstate astor instead of astunparse (astunparse is not yet packaged for Debian) * create mdconvert.1, mdinspect.1 man pages using help2man -- Drew Parsons Fri, 23 Oct 2020 15:08:19 +0800 mdtraj (1.9.4-6) unstable; urgency=medium * debian patch check_sse2.patch checks if system supports SSE2 (i.e. if system is x86 or amd64) before compiling with -msse2. Closes: #972592. * debian/tests Depends: python3-matplotlib, python3-sklearn -- Drew Parsons Wed, 21 Oct 2020 17:40:20 +0800 mdtraj (1.9.4-5) unstable; urgency=medium * python3-mdtraj Depends: python3-networkx, python3-pandas * debian/tests Depends: python3-ipykernel -- Drew Parsons Wed, 21 Oct 2020 10:14:47 +0800 mdtraj (1.9.4-4) unstable; urgency=medium * python3-mdtraj [Build-]Depends: python3-tables -- Drew Parsons Wed, 21 Oct 2020 01:21:03 +0800 mdtraj (1.9.4-3) unstable; urgency=medium * python3-mdtraj Depends: python3-distutils * debian/tests Depends: python3-jupyter-client, python3-nbformat, python3-six -- Drew Parsons Tue, 20 Oct 2020 20:17:02 +0800 mdtraj (1.9.4-2) unstable; urgency=medium * Build-Depends: cython3 (>= 0.29~), python3-all-dev * build docs with default python, sphinx and Build-Depends-Indep: python3-msmb-theme, python3-nbconvert, python3-nbformat, python3-numpydoc -- Drew Parsons Tue, 20 Oct 2020 13:35:11 +0800 mdtraj (1.9.4-1) unstable; urgency=medium * Initial release (Closes: #962442) * create debian patches - build_dir_pybuild.patch adapts build scripts to allow for pybuild build dir. - python_hashbang.patch sets python hashbang to /usr/bin/python3 in place of /bin/env python - test_gsd_skip.patch skips test_gsd.py in tests (the gsd module is not available, see RFP#966019) * privacy: use local copy of DOI badge doi-10.1016_j.bpj.2015.08.015-blue.svg in docs -- Drew Parsons Mon, 24 Aug 2020 14:05:10 +0800