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change license to LGPL switch (#4794)
* change license from GPLv2+ to LGPLv2.1+ * license change * package is temporarily under LGPLv3+ until we remove apache licensed dependencies: Update LICENSE files (LGPLv3+), include a copy of GPLv3 license text as referenced by LGPLv3 * Update all code references of GPLv2+ to LGPLv2.1+ * see https://www.mdanalysis.org/2023/09/22/licensing-update/#detailing-our-proposed-relicensing-process for details (we are now at step 3, where we package under LGPLv3+ until we remove our apache dependencies) * specific changes * Update main LICENSE * update the other two LICENSE files * Updating license headers for MDAnalysisTests * Update docs, README, authors, pyproject.toml, setup.py * Analysis files * Through to lib * The rest * update CHANGELOG --------- Co-authored-by: Oliver Beckstein <[email protected]> Co-authored-by: Rocco Meli <[email protected]>
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‎LICENSE

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‎README.rst

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**Source code** is hosted in a git repository at
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https://github.com/MDAnalysis/mdanalysis and is packaged under the
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GNU General Public License, version 3 or any later version. Invidiual
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source code components are provided under a mixture of GPLv3+ compatible
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licenses, including LGPLv2.1+ and GPLv2+. Please see the file LICENSE_
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for more information.
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GNU Lesser General Public License, version 3 or any later version (LGPLv3+).
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Invidiual source code components are provided under the
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GNU Lesser General Public License, version 2.1 or any later version (LGPLv2.1+).
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Please see the file LICENSE_ for more information.
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Contributing

‎package/AUTHORS

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External code
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-------------
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External code (under a GPL-compatible licence) was obtained from
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External code (under a LGPL-compatible licence) was obtained from
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various sources. The authors (as far as we know them) are listed here.
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xdrfile
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The Gromacs libxdrfile (LGPL-licensed) was used before MDAnalysis
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version 0.8.0.
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Between MDAnalysis versions 0.8.0 and 0.13.0 libxdrfile was replaced by
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libxdrfile2, our GPLv2 enhanced derivative of libxdrfile.
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libxdrfile2, our LGPLv2.1+ enhanced derivative of libxdrfile.
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Since version 0.14.0 xdr enhanecments were rebased onto Gromacs'
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xdrfile 1.1.4 code (now BSD-licensed). Our contributions remain GPLv2
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xdrfile 1.1.4 code (now BSD-licensed). Our contributions remain LGPLv2.1+
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and were split into files xtc_seek.c, trr_seek.c, xtc_seek.h, and
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trr_seek.h, for clarity (xdrfile 1.1.4 code is distributed with minor
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‎package/CHANGELOG

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DOI 10.1021/acs.jpcb.7b11988. (Issue #2039, PR #4524)
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Changes
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* Relicense code contributions from GPLv2+ to LGPLv2.1+
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and the package from GPLv3+ to LGPLv3+ (PR #4794)
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* only use distopia < 0.3.0 due to API changes (Issue #4739)
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* The `fetch_mmtf` method has been removed as the REST API service
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for MMTF files has ceased to exist (Issue #4634)

‎package/LICENSE

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‎package/MDAnalysis/__init__.py

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# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
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# (see the file AUTHORS for the full list of names)
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#
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# Released under the GNU Public Licence, v2 or any higher version
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# Released under the Lesser GNU Public Licence, v2.1 or any higher version
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#
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‎package/MDAnalysis/analysis/__init__.py

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#
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# Released under the GNU Public Licence, v2 or any higher version
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# Released under the Lesser GNU Public Licence, v2.1 or any higher version
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‎package/MDAnalysis/analysis/align.py

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# Released under the Lesser GNU Public Licence, v2.1 or any higher version
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:Author: Oliver Beckstein, Joshua Adelman
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:Year: 2010--2013
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:Copyright: GNU Public License v3
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:Copyright: Lesser GNU Public License v2.1+
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The module contains functions to fit a target structure to a reference
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‎package/MDAnalysis/analysis/atomicdistances.py

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# Released under the GNU Public Licence, v2 or any higher version
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# Released under the Lesser GNU Public Licence, v2.1 or any higher version
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This module provides a class to efficiently compute distances between
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‎package/MDAnalysis/analysis/base.py

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‎package/MDAnalysis/analysis/bat.py

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:Author: Soohaeng Yoo Willow and David Minh
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:Year: 2020
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:Copyright: GNU Public License, v2 or any higher version
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:Copyright: Lesser GNU Public License, v2.1 or any higher version
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.. versionadded:: 2.0.0
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‎package/MDAnalysis/analysis/contacts.py

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‎package/MDAnalysis/analysis/data/filenames.py

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‎package/MDAnalysis/analysis/density.py

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:Author: Oliver Beckstein
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‎package/MDAnalysis/analysis/dielectric.py

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"""
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‎package/MDAnalysis/analysis/diffusionmap.py

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‎package/MDAnalysis/analysis/dihedrals.py

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‎package/MDAnalysis/analysis/distances.py

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‎package/MDAnalysis/analysis/encore/__init__.py

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‎package/MDAnalysis/analysis/encore/clustering/ClusterCollection.py

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