Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: relion
Upstream-Contact: scheres@mrc-lmb.cam.ac.uk
Source: https://github.com/3dem/relion.git
Files-Excluded: src/Eigen
Comment: Excluding embedded copy of Eigen

Files: *
Copyright: 2014-2025, Sjors Scheres at the MRC Laboratory of Molecular Biology
License: GPL-2+

Files: src/CPlot2D.cpp
  src/CPlot2D.h
Copyright: 2014, AMZs.
License: GPL-2+

Files: src/Healpix_2.15a/arr.h
 src/Healpix_2.15a/cxxutils.cc
 src/Healpix_2.15a/cxxutils.h
 src/Healpix_2.15a/datatypes.h
 src/Healpix_2.15a/geom_utils.h
 src/Healpix_2.15a/healpix_base.cc
 src/Healpix_2.15a/healpix_base.h
 src/Healpix_2.15a/message_error.h
 src/Healpix_2.15a/openmp_support.h
 src/Healpix_2.15a/pointing.h
 src/Healpix_2.15a/vec3.h
Copyright: 2002-2007, Max-Planck-Society
  2003, 2006, Max-Planck-Society
  2003, Max-Planck-Society
  2003-2004, Max-Planck-Society
  2003-2006, Max-Planck-Society
  2004, Max-Planck-Society
  2005-2007, Max-Planck-Society
License: GPL-2+

Files: src/jaz/d3x3/*
 src/jaz/single_particle/d3x3/*
Copyright: 2006, Joachim Kopp
License: LGPL-2.1+

Files: src/lbfgs/copyright.txt
 src/lbfgs/lbfgs.c
 src/lbfgs/lbfgs.h
 src/jaz/single_particle/lbfgs/copyright.txt
 src/jaz/single_particle/lbfgs/lbfgs.c
 src/jaz/single_particle/lbfgs/lbfgs.h
Copyright: 1990, Jorge Nocedal
  2007-2010, Naoaki Okazaki
License: Expat

Files: src/lbfgs/arithmetic_ansi.h
 src/lbfgs/arithmetic_sse_double.h
 src/lbfgs/arithmetic_sse_float.h
 src/jaz/single_particle/lbfgs/arithmetic_ansi.h
 src/jaz/single_particle/lbfgs/arithmetic_sse_double.h
 src/jaz/single_particle/lbfgs/arithmetic_sse_float.h
Copyright: 2007-2010, Naoaki Okazaki
License: Expat

Files: src/npy.hpp
Copyright: 2017, Leon Merten Lohse
License: Expat

Files: cmake/GetGitRevisionDescription.cmake
 cmake/GetGitRevisionDescription.cmake.in
Copyright: Iowa State University 2009-2010.
License: BSL-1.0

Files: tests/catch2/catch.hpp
Copyright: 2017, Two Blue Cubes Ltd.
License: BSL-1.0

Files: cmake/FindTBB.cmake
Copyright: 2015, Justus Calvin
License: Expat

Files: cmake/FindCondaPython.cmake
Copyright: 2023, Dari Kimanius
License: Expat

Files: src/funcs.cpp
Copyright: 1984, 1987, 1995, 2000, Stephen L. Moshier
License: GPL-2+

Files: src/spherical-harmonics/SphericalHarmonics.*
Copyright: 2014, IBM Corporation
           2014, Mahidol University International College
License: EPL

Files: debian/*
Copyright: 2014-2020, Q-Leap Networks GmbH <info@q-leap.de>
           © 2022 Andreas Beckmann <anbe@debian.org>
           2014-2025, Debian Med Packaging Team
License: GPL-2+

License: BSL-1.0
 Boost Software License - Version 1.0 - August 17th, 2003
 .
 Permission is hereby granted, free of charge, to any person or organization
 obtaining a copy of the software and accompanying documentation covered by
 this license (the "Software") to use, reproduce, display, distribute,
 execute, and transmit the Software, and to prepare derivative works of the
 Software, and to permit third-parties to whom the Software is furnished to
 do so, all subject to the following:
 .
 The copyright notices in the Software and this entire statement, including
 the above license grant, this restriction and the following disclaimer,
 must be included in all copies of the Software, in whole or in part, and
 all derivative works of the Software, unless such copies or derivative
 works are solely in the form of machine-executable object code generated by
 a source language processor.
 .
 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, TITLE AND NON-INFRINGEMENT. IN NO EVENT
 SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
 FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
 ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 DEALINGS IN THE SOFTWARE.

License: Expat
 Copyright (c) 1998, 1999, 2000 Thai Open Source Software Center Ltd
 .
 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 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.

License: GPL-2+
 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
 the Free Software Foundation, either version 2 of the License, or
 (at your option) any later version.
 .
 This program is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 GNU General Public License for more details.
 .
 You should have received a copy of the GNU General Public License
 along with this program.  If not, see <http://www.gnu.org/licenses/>.
 .
 On Debian systems, the full text of the GNU General Public
 License version 2 can be found in the file
 `/usr/share/common-licenses/GPL-2'.

License: LGPL-2.1+
 The full text of this license can be found in the file
 `/usr/share/common-licenses/LGPL-2.1` on your Debian system.

License: EPL
 Eclipse Public License - v 1.0
 .
 THE ACCOMPANYING PROGRAM IS PROVIDED UNDER THE TERMS OF THIS ECLIPSE
 PUBLIC LICENSE ("AGREEMENT"). ANY USE, REPRODUCTION OR DISTRIBUTION OF
 THE PROGRAM CONSTITUTES RECIPIENT'S ACCEPTANCE OF THIS AGREEMENT.
 .
 1. DEFINITIONS
 .
 "Contribution" means:
 .
    a) in the case of the initial Contributor, the initial code and
    documentation distributed under this Agreement, and
 .
    b) in the case of each subsequent Contributor:
 .
    i) changes to the Program, and
 .
    ii) additions to the Program;
 .
    where such changes and/or additions to the Program originate from
    and are distributed by that particular Contributor. A Contribution
    'originates' from a Contributor if it was added to the Program by
    such Contributor itself or anyone acting on such Contributor's
    behalf. Contributions do not include additions to the Program
    which: (i) are separate modules of software distributed in
    conjunction with the Program under their own license agreement,
    and (ii) are not derivative works of the Program.
 .
 "Contributor" means any person or entity that distributes the Program.
 .
 "Licensed Patents" mean patent claims licensable by a Contributor
 which are necessarily infringed by the use or sale of its Contribution
 alone or when combined with the Program.
 .
 "Program" means the Contributions distributed in accordance with this
 Agreement.
 .
 "Recipient" means anyone who receives the Program under this
 Agreement, including all Contributors.
 .
 2. GRANT OF RIGHTS
 .
    a) Subject to the terms of this Agreement, each Contributor hereby
    grants Recipient a non-exclusive, worldwide, royalty-free
    copyright license to reproduce, prepare derivative works of,
    publicly display, publicly perform, distribute and sublicense the
    Contribution of such Contributor, if any, and such derivative
    works, in source code and object code form.
 .
    b) Subject to the terms of this Agreement, each Contributor hereby
    grants Recipient a non-exclusive, worldwide, royalty-free patent
    license under Licensed Patents to make, use, sell, offer to sell,
    import and otherwise transfer the Contribution of such
    Contributor, if any, in source code and object code form. This
    patent license shall apply to the combination of the Contribution
    and the Program if, at the time the Contribution is added by the
    Contributor, such addition of the Contribution causes such
    combination to be covered by the Licensed Patents. The patent
    license shall not apply to any other combinations which include
    the Contribution. No hardware per se is licensed hereunder.
 .
    c) Recipient understands that although each Contributor grants the
    licenses to its Contributions set forth herein, no assurances are
    provided by any Contributor that the Program does not infringe the
    patent or other intellectual property rights of any other
    entity. Each Contributor disclaims any liability to Recipient for
    claims brought by any other entity based on infringement of
    intellectual property rights or otherwise. As a condition to
    exercising the rights and licenses granted hereunder, each
    Recipient hereby assumes sole responsibility to secure any other
    intellectual property rights needed, if any. For example, if a
    third party patent license is required to allow Recipient to
    distribute the Program, it is Recipient's responsibility to
    acquire that license before distributing the Program.
 .
    d) Each Contributor represents that to its knowledge it has
    sufficient copyright rights in its Contribution, if any, to grant
    the copyright license set forth in this Agreement.
 .
 3. REQUIREMENTS
 .
 A Contributor may choose to distribute the Program in object code form
 under its own license agreement, provided that:
 .
    a) it complies with the terms and conditions of this Agreement;
    and
 .
    b) its license agreement:
 .
    i) effectively disclaims on behalf of all Contributors all
    warranties and conditions, express and implied, including
    warranties or conditions of title and non-infringement, and
    implied warranties or conditions of merchantability and fitness
    for a particular purpose;
 .
    ii) effectively excludes on behalf of all Contributors all
    liability for damages, including direct, indirect, special,
    incidental and consequential damages, such as lost profits;
 .
    iii) states that any provisions which differ from this Agreement
    are offered by that Contributor alone and not by any other party;
    and
 .
    iv) states that source code for the Program is available from such
    Contributor, and informs licensees how to obtain it in a
    reasonable manner on or through a medium customarily used for
    software exchange.
 .
 When the Program is made available in source code form:
 .
    a) it must be made available under this Agreement; and
 .
    b) a copy of this Agreement must be included with each copy of the
    Program.
 .
 Contributors may not remove or alter any copyright notices contained
 within the Program.
 .
 Each Contributor must identify itself as the originator of its
 Contribution, if any, in a manner that reasonably allows subsequent
 Recipients to identify the originator of the Contribution.
 .
 4. COMMERCIAL DISTRIBUTION
 .
 Commercial distributors of software may accept certain
 responsibilities with respect to end users, business partners and the
 like. While this license is intended to facilitate the commercial use
 of the Program, the Contributor who includes the Program in a
 commercial product offering should do so in a manner which does not
 create potential liability for other Contributors. Therefore, if a
 Contributor includes the Program in a commercial product offering,
 such Contributor ("Commercial Contributor") hereby agrees to defend
 and indemnify every other Contributor ("Indemnified Contributor")
 against any losses, damages and costs (collectively "Losses") arising
 from claims, lawsuits and other legal actions brought by a third
 party against the Indemnified Contributor to the extent caused by the
 acts or omissions of such Commercial Contributor in connection with
 its distribution of the Program in a commercial product offering. The
 obligations in this section do not apply to any claims or Losses
 relating to any actual or alleged intellectual property
 infringement. In order to qualify, an Indemnified Contributor must:
 a) promptly notify the Commercial Contributor in writing of such
 claim, and b) allow the Commercial Contributor to control, and
 cooperate with the Commercial Contributor in, the defense and any
 related settlement negotiations. The Indemnified Contributor may
 participate in any such claim at its own expense.
 .
 For example, a Contributor might include the Program in a commercial
 product offering, Product X. That Contributor is then a Commercial
 Contributor. If that Commercial Contributor then makes performance
 claims, or offers warranties related to Product X, those performance
 claims and warranties are such Commercial Contributor's
 responsibility alone. Under this section, the Commercial Contributor
 would have to defend claims against the other Contributors related to
 those performance claims and warranties, and if a court requires any
 other Contributor to pay any damages as a result, the Commercial
 Contributor must pay those damages.
 .
 5. NO WARRANTY
 .
 EXCEPT AS EXPRESSLY SET FORTH IN THIS AGREEMENT, THE PROGRAM IS
 PROVIDED ON AN "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
 KIND, EITHER EXPRESS OR IMPLIED INCLUDING, WITHOUT LIMITATION, ANY
 WARRANTIES OR CONDITIONS OF TITLE, NON-INFRINGEMENT, MERCHANTABILITY
 OR FITNESS FOR A PARTICULAR PURPOSE. Each Recipient is solely
 responsible for determining the appropriateness of using and
 distributing the Program and assumes all risks associated with its
 exercise of rights under this Agreement , including but not limited
 to the risks and costs of program errors, compliance with applicable
 laws, damage to or loss of data, programs or equipment, and
 unavailability or interruption of operations.
 .
 6. DISCLAIMER OF LIABILITY
 .
 EXCEPT AS EXPRESSLY SET FORTH IN THIS AGREEMENT, NEITHER RECIPIENT
 NOR ANY CONTRIBUTORS SHALL HAVE ANY LIABILITY FOR ANY DIRECT,
 INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
 (INCLUDING WITHOUT LIMITATION LOST PROFITS), 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 OR DISTRIBUTION OF THE PROGRAM OR THE EXERCISE OF ANY RIGHTS
 GRANTED HEREUNDER, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
 DAMAGES.
 .
 7. GENERAL
 .
 If any provision of this Agreement is invalid or unenforceable under
 applicable law, it shall not affect the validity or enforceability of
 the remainder of the terms of this Agreement, and without further
 action by the parties hereto, such provision shall be reformed to the
 minimum extent necessary to make such provision valid and
 enforceable.
 .
 If Recipient institutes patent litigation against any entity
 (including a cross-claim or counterclaim in a lawsuit) alleging that
 the Program itself (excluding combinations of the Program with other
 software or hardware) infringes such Recipient's patent(s), then such
 Recipient's rights granted under Section 2(b) shall terminate as of
 the date such litigation is filed.
 .
 All Recipient's rights under this Agreement shall terminate if it
 fails to comply with any of the material terms or conditions of this
 Agreement and does not cure such failure in a reasonable period of
 time after becoming aware of such noncompliance. If all Recipient's
 rights under this Agreement terminate, Recipient agrees to cease use
 and distribution of the Program as soon as reasonably
 practicable. However, Recipient's obligations under this Agreement
 and any licenses granted by Recipient relating to the Program shall
 continue and survive.
 .
 Everyone is permitted to copy and distribute copies of this
 Agreement, but in order to avoid inconsistency the Agreement is
 copyrighted and may only be modified in the following manner. The
 Agreement Steward reserves the right to publish new versions
 (including revisions) of this Agreement from time to time. No one
 other than the Agreement Steward has the right to modify this
 Agreement. The Eclipse Foundation is the initial Agreement
 Steward. The Eclipse Foundation may assign the responsibility to
 serve as the Agreement Steward to a suitable separate entity. Each
 new version of the Agreement will be given a distinguishing version
 number. The Program (including Contributions) may always be
 distributed subject to the version of the Agreement under which it
 was received. In addition, after a new version of the Agreement is
 published, Contributor may elect to distribute the Program (including
 its Contributions) under the new version. Except as expressly stated
 in Sections 2(a) and 2(b) above, Recipient receives no rights or
 licenses to the intellectual property of any Contributor under this
 Agreement, whether expressly, by implication, estoppel or
 otherwise. All rights in the Program not expressly granted under this
 Agreement are reserved.
 .
 This Agreement is governed by the laws of the State of New York and
 the intellectual property laws of the United States of America. No
 party to this Agreement will bring a legal action under this
 Agreement more than one year after the cause of action arose. Each
 party waives its rights to a jury trial in any resulting litigation.
Comment:
 This license is GPL-incompatible.
