riseproject-dev · Oct 6, 2026 · Oct 9, 2026 · Oct 10, 2026
diff --git 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
@@ -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
@@ -0,0 +1,216 @@
+From 0000000000000000000000000000000000000000 Mon Sep 17 00:00:00 2001
+From: Ludovic Henry <git@ludovic.dev>
+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.<component> 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.