diff --git a/.github/workflows/build-mdtraj.yml b/.github/workflows/build-mdtraj.yml index fcdd82f1ac17..7a93dfd10aa6 100644 --- a/.github/workflows/build-mdtraj.yml +++ b/.github/workflows/build-mdtraj.yml @@ -84,7 +84,7 @@ jobs: CIBW_MANYLINUX_RISCV64_IMAGE: ${{ env.MANYLINUX_RISCV64_IMAGE }} CIBW_ENVIRONMENT: >- PIP_EXTRA_INDEX_URL=https://pypi.riseproject.dev/simple/ - PIP_ONLY_BINARY=numpy,scipy,pandas,tables,blosc2,numexpr,ndindex,msgpack,pydantic-core,netcdf4,cftime + PIP_ONLY_BINARY=numpy,scipy,pandas,pyarrow,tables,blosc2,numexpr,ndindex,msgpack,pydantic-core,netcdf4,cftime # Upstream's wheel job only smoke-tests; also run its CI suite against the wheel, # with its conda test env minus openmm (no riscv64 build; those tests skip). CIBW_TEST_EXTRAS: all diff --git a/docs/packages/mdtraj.yaml b/docs/packages/mdtraj.yaml index bbaf6afeb756..4436642b7542 100644 --- a/docs/packages/mdtraj.yaml +++ b/docs/packages/mdtraj.yaml @@ -19,3 +19,4 @@ versions: gpl-sources: filename: gpl-sources.tar description: gcc +- version: 1.11.2 diff --git a/patches/mdtraj/1.11.2/0001-Ship-the-licences-of-the-third-party-code-compiled-in.patch b/patches/mdtraj/1.11.2/0001-Ship-the-licences-of-the-third-party-code-compiled-in.patch new file mode 100644 index 000000000000..fe65e6e729b4 --- /dev/null +++ b/patches/mdtraj/1.11.2/0001-Ship-the-licences-of-the-third-party-code-compiled-in.patch @@ -0,0 +1,216 @@ +From 0000000000000000000000000000000000000000 Mon Sep 17 00:00:00 2001 +From: Ludovic Henry +Date: Fri, 2 Oct 2026 12:00:00 +0200 +Subject: [PATCH] Ship the licences of the third-party code compiled into the + extensions + +The wheel's extensions compile in code from five other projects under +their own permissive licences, each of which requires its notice to +travel with binary redistributions: the VMD molfile plugin library +(University of Illinois Open Source License; mdtraj.formats.dcd and the +plugin headers of mdtraj.formats.dtr), D. E. Shaw Research's dtrplugin +(BSD-3-Clause; mdtraj.formats.dtr), the xdrfile library (BSD-2-Clause; +mdtraj.formats.xtc and .trr), Jacob Frelinger's Munkres implementation +(BSD; mdtraj._lprmsd) and OpenMM's vectorization headers (MIT; the +mdtraj.geometry extensions). The notices only live in the source file +headers, so every published wheel carries mdtraj's own LGPL LICENSE alone. + +Add one LICENSE. file per component at the project root, +reproducing the notice its sources carry (the VMD sources only carry the +copyright line, so the UIUC Open Source License text is taken from the +VMD plugin library's licence page). setuptools' default license_files +glob already matches LICENSE.* at the root, so no setup.py change is +needed and the files land in dist-info/licenses/. + +Upstream-Status: To upstream [not submitted from this automated port run; needs a pull request against mdtraj/mdtraj] +--- + LICENSE.dtrplugin | 32 ++++++++++++++++++++++++++++++++ + LICENSE.munkres | 13 +++++++++++++ + LICENSE.openmm | 32 ++++++++++++++++++++++++++++++++ + LICENSE.vmd-plugins | 45 +++++++++++++++++++++++++++++++++++++++++++++ + LICENSE.xdrfile | 26 ++++++++++++++++++++++++++ + 5 files changed, 148 insertions(+) + create mode 100644 LICENSE.dtrplugin + create mode 100644 LICENSE.munkres + create mode 100644 LICENSE.openmm + create mode 100644 LICENSE.vmd-plugins + create mode 100644 LICENSE.xdrfile + +diff --git a/LICENSE.dtrplugin b/LICENSE.dtrplugin +new file mode 100644 +index 0000000..b097e44 +--- /dev/null ++++ b/LICENSE.dtrplugin +@@ -0,0 +1,32 @@ ++The D. E. Shaw Research dtrplugin compiled into mdtraj.formats.dtr ++(mdtraj/formats/dtr/src/dtrplugin.cxx) carries the following notice: ++ ++Copyright 2009, D. E. Shaw Research, LLC ++All rights reserved. ++ ++Redistribution and use in source and binary forms, with or without ++modification, are permitted provided that the following conditions are ++met: ++ ++* Redistributions of source code must retain the above copyright ++ notice, this list of conditions, and the following disclaimer. ++ ++* Redistributions in binary form must reproduce the above copyright ++ notice, this list of conditions, and the following disclaimer in the ++ documentation and/or other materials provided with the distribution. ++ ++* Neither the name of D. E. Shaw Research, LLC nor the names of its ++ contributors may be used to endorse or promote products derived from ++ this software without specific prior written permission. ++ ++THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ++"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT ++LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR ++A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT ++OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, ++SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT ++LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, ++DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY ++THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT ++(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE ++OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +diff --git a/LICENSE.munkres b/LICENSE.munkres +new file mode 100644 +index 0000000..338c6b7 +--- /dev/null ++++ b/LICENSE.munkres +@@ -0,0 +1,13 @@ ++The Munkres (Hungarian algorithm) implementation compiled into mdtraj._lprmsd ++(mdtraj/rmsd/src/Munkres.cpp, from https://github.com/jfrelinger/cython-munkres-wrapper) ++carries the following notice, reproduced as it appears in the source: ++ ++Copyright (c) 2012, Jacob Frelinger ++All rights reserved. ++ ++Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: ++ ++Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. ++Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. ++ ++THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, +diff --git a/LICENSE.openmm b/LICENSE.openmm +new file mode 100644 +index 0000000..7604496 +--- /dev/null ++++ b/LICENSE.openmm +@@ -0,0 +1,32 @@ ++The vectorization headers compiled into the mdtraj.geometry extensions ++(mdtraj/geometry/include/vectorize*.h) are taken from OpenMM and carry the ++following notice: ++ ++OpenMM ++-------------------------------------------------------------------------- ++This is part of the OpenMM molecular simulation toolkit originating from ++Simbios, the NIH National Center for Physics-Based Simulation of ++Biological Structures at Stanford, funded under the NIH Roadmap for ++Medical Research, grant U54 GM072970. See https://simtk.org. ++ ++Portions copyright (c) 2014-2018 Stanford University and the Authors. ++Authors: Peter Eastman ++Contributors: ++ ++Permission is hereby granted, free of charge, to any person obtaining a ++copy of this software and associated documentation files (the "Software"), ++to deal in the Software without restriction, including without limitation ++the rights to use, copy, modify, merge, publish, distribute, sublicense, ++and/or sell copies of the Software, and to permit persons to whom the ++Software is furnished to do so, subject to the following conditions: ++ ++The above copyright notice and this permission notice shall be included in ++all copies or substantial portions of the Software. ++ ++THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR ++IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, ++FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL ++THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, ++DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR ++OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE ++USE OR OTHER DEALINGS IN THE SOFTWARE. +diff --git a/LICENSE.vmd-plugins b/LICENSE.vmd-plugins +new file mode 100644 +index 0000000..c669ca3 +--- /dev/null ++++ b/LICENSE.vmd-plugins +@@ -0,0 +1,45 @@ ++The DCD reader/writer (mdtraj/formats/dcd) and the molfile plugin headers ++used by mdtraj/formats/dcd and mdtraj/formats/dtr are taken from the VMD ++plugin library and carry the following notice: ++ ++(C) Copyright 1995-2016 The Board of Trustees of the ++ University of Illinois ++ All Rights Reserved ++ ++The VMD plugin library is distributed under the University of Illinois ++Open Source License (https://www.ks.uiuc.edu/Research/vmd/plugins/pluginlicense.html): ++ ++University of Illinois Open Source License ++Copyright 2006 Theoretical and Computational Biophysics Group, ++All rights reserved. ++ ++Developed by: Theoretical and Computational Biophysics Group ++ University of Illinois at Urbana-Champaign ++ http://www.ks.uiuc.edu/ ++ ++Permission is hereby granted, free of charge, to any person obtaining a copy of ++this software and associated documentation files (the Software), to deal with ++the Software without restriction, including without limitation the rights to ++use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies ++of the Software, and to permit persons to whom the Software is furnished to ++do so, subject to the following conditions: ++ ++Redistributions of source code must retain the above copyright notice, ++this list of conditions and the following disclaimers. ++ ++Redistributions in binary form must reproduce the above copyright notice, ++this list of conditions and the following disclaimers in the documentation ++and/or other materials provided with the distribution. ++ ++Neither the names of Theoretical and Computational Biophysics Group, ++University of Illinois at Urbana-Champaign, nor the names of its contributors ++may be used to endorse or promote products derived from this Software without ++specific prior written permission. ++ ++THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR ++IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, ++FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL ++THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR ++OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ++ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR ++OTHER DEALINGS WITH THE SOFTWARE. +diff --git a/LICENSE.xdrfile b/LICENSE.xdrfile +new file mode 100644 +index 0000000..0d0c4a9 +--- /dev/null ++++ b/LICENSE.xdrfile +@@ -0,0 +1,26 @@ ++The xdrfile library compiled into mdtraj.formats.xtc and mdtraj.formats.trr ++(mdtraj/formats/xtc/src/xdrfile*.c) carries the following notice: ++ ++Copyright (c) 2009-2014, Erik Lindahl & David van der Spoel ++All rights reserved. ++ ++Redistribution and use in source and binary forms, with or without ++modification, are permitted provided that the following conditions are met: ++ ++1. Redistributions of source code must retain the above copyright notice, this ++list of conditions and the following disclaimer. ++ ++2. Redistributions in binary form must reproduce the above copyright notice, ++this list of conditions and the following disclaimer in the documentation ++and/or other materials provided with the distribution. ++ ++THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" ++AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE ++IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE ++DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE ++FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL ++DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR ++SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER ++CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, ++OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE ++OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.