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]>
MDAnalysis · Nov 22, 2024 · 0a91d2c · 0a91d2c
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diff --git a/LICENSE b/LICENSE
diff --git a/README.rst b/README.rst
@@ -78,10 +78,10 @@ described in the `Installation Quick Start`_.
 
 **Source code** is hosted in a git repository at
 https://github.com/MDAnalysis/mdanalysis and is packaged under the
-GNU General Public License, version 3 or any later version. Invidiual
-source code components are provided under a mixture of GPLv3+ compatible
-licenses, including LGPLv2.1+ and GPLv2+. Please see the file LICENSE_
-for more information.
+GNU Lesser General Public License, version 3 or any later version (LGPLv3+).
+Invidiual source code components are provided under the
+GNU Lesser General Public License, version 2.1 or any later version (LGPLv2.1+).
+Please see the file LICENSE_ for more information.
 
 
 Contributing

diff --git a/package/AUTHORS b/package/AUTHORS
@@ -249,7 +249,7 @@ Chronological list of authors
 External code
 -------------
 
-External code (under a GPL-compatible licence) was obtained from
+External code (under a LGPL-compatible licence) was obtained from
 various sources. The authors (as far as we know them) are listed here.
 
 xdrfile
@@ -261,9 +261,9 @@ xdrfile
   The Gromacs libxdrfile (LGPL-licensed) was used before MDAnalysis
    version 0.8.0.
   Between MDAnalysis versions 0.8.0 and 0.13.0 libxdrfile was replaced by
-   libxdrfile2, our GPLv2 enhanced derivative of libxdrfile.
+   libxdrfile2, our LGPLv2.1+ enhanced derivative of libxdrfile.
   Since version 0.14.0 xdr enhanecments were rebased onto Gromacs'
-   xdrfile 1.1.4 code (now BSD-licensed). Our contributions remain GPLv2
+   xdrfile 1.1.4 code (now BSD-licensed). Our contributions remain LGPLv2.1+
    and were split into files xtc_seek.c, trr_seek.c, xtc_seek.h, and
    trr_seek.h, for clarity (xdrfile 1.1.4 code is distributed with minor
    modifications). Also for clarity we now name the resulting enhanced

diff --git a/package/CHANGELOG b/package/CHANGELOG
@@ -97,6 +97,8 @@ Enhancements
    DOI 10.1021/acs.jpcb.7b11988. (Issue #2039, PR #4524)
 
 Changes
+ * Relicense code contributions from GPLv2+ to LGPLv2.1+
+   and the package from GPLv3+ to LGPLv3+ (PR #4794)
  * only use distopia < 0.3.0 due to API changes (Issue #4739)
  * The `fetch_mmtf` method has been removed as the REST API service
    for MMTF files has ceased to exist (Issue #4634)

diff --git a/package/LICENSE b/package/LICENSE
diff --git a/package/MDAnalysis/__init__.py b/package/MDAnalysis/__init__.py
@@ -5,7 +5,7 @@
 # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
 # (see the file AUTHORS for the full list of names)
 #
-# Released under the GNU Public Licence, v2 or any higher version
+# Released under the Lesser GNU Public Licence, v2.1 or any higher version
 #
 # Please cite your use of MDAnalysis in published work:
 #

diff --git a/package/MDAnalysis/analysis/__init__.py b/package/MDAnalysis/analysis/__init__.py
@@ -5,7 +5,7 @@
 # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
 # (see the file AUTHORS for the full list of names)
 #
-# Released under the GNU Public Licence, v2 or any higher version
+# Released under the Lesser GNU Public Licence, v2.1 or any higher version
 #
 # Please cite your use of MDAnalysis in published work:
 #

diff --git a/package/MDAnalysis/analysis/align.py b/package/MDAnalysis/analysis/align.py
@@ -5,7 +5,7 @@
 # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
 # (see the file AUTHORS for the full list of names)
 #
-# Released under the GNU Public Licence, v2 or any higher version
+# Released under the Lesser GNU Public Licence, v2.1 or any higher version
 #
 # Please cite your use of MDAnalysis in published work:
 #
@@ -26,7 +26,7 @@
 
 :Author: Oliver Beckstein, Joshua Adelman
 :Year: 2010--2013
-:Copyright: GNU Public License v3
+:Copyright: Lesser GNU Public License v2.1+
 
 The module contains functions to fit a target structure to a reference
 structure. They use the fast QCP algorithm to calculate the root mean
@@ -1669,4 +1669,4 @@ def get_atoms_byres(g, match_mask=np.logical_not(mismatch_mask)):
                 logger.error(errmsg)
                 raise SelectionError(errmsg)
 
-    return ag1, ag2
+    return ag1, ag2
diff --git a/package/MDAnalysis/analysis/atomicdistances.py b/package/MDAnalysis/analysis/atomicdistances.py
@@ -5,7 +5,7 @@
 # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
 # (see the file AUTHORS for the full list of names)
 #
-# Released under the GNU Public Licence, v2 or any higher version
+# Released under the Lesser GNU Public Licence, v2.1 or any higher version
 #
 # Please cite your use of MDAnalysis in published work:
 #
@@ -29,7 +29,7 @@
 
 :Author: Xu Hong Chen
 :Year: 2023
-:Copyright: GNU Public License v3
+:Copyright: Lesser GNU Public License v2.1+
 
 This module provides a class to efficiently compute distances between
 two groups of atoms with an equal number of atoms over a trajectory.

diff --git a/package/MDAnalysis/analysis/base.py b/package/MDAnalysis/analysis/base.py
@@ -5,7 +5,7 @@
 # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
 # (see the file AUTHORS for the full list of names)
 #
-# Released under the GNU Public Licence, v2 or any higher version
+# Released under the Lesser GNU Public Licence, v2.1 or any higher version
 #
 # Please cite your use of MDAnalysis in published work:
 #

diff --git a/package/MDAnalysis/analysis/bat.py b/package/MDAnalysis/analysis/bat.py
@@ -5,7 +5,7 @@
 # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
 # (see the file AUTHORS for the full list of names)
 #
-# Released under the GNU Public Licence, v2 or any higher version
+# Released under the Lesser GNU Public Licence, v2.1 or any higher version
 #
 # Please cite your use of MDAnalysis in published work:
 #
@@ -25,7 +25,7 @@
 
 :Author: Soohaeng Yoo Willow and David Minh
 :Year: 2020
-:Copyright: GNU Public License, v2 or any higher version
+:Copyright: Lesser GNU Public License, v2.1 or any higher version
 
 .. versionadded:: 2.0.0
 

diff --git a/package/MDAnalysis/analysis/contacts.py b/package/MDAnalysis/analysis/contacts.py
@@ -5,7 +5,7 @@
 # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
 # (see the file AUTHORS for the full list of names)
 #
-# Released under the GNU Public Licence, v2 or any higher version
+# Released under the Lesser GNU Public Licence, v2.1 or any higher version
 #
 # Please cite your use of MDAnalysis in published work:
 #

diff --git a/package/MDAnalysis/analysis/data/filenames.py b/package/MDAnalysis/analysis/data/filenames.py
@@ -5,7 +5,7 @@
 # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
 # (see the file AUTHORS for the full list of names)
 #
-# Released under the GNU Public Licence, v2 or any higher version
+# Released under the Lesser GNU Public Licence, v2.1 or any higher version
 #
 # Please cite your use of MDAnalysis in published work:
 #

diff --git a/package/MDAnalysis/analysis/density.py b/package/MDAnalysis/analysis/density.py
@@ -5,7 +5,7 @@
 # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
 # (see the file AUTHORS for the full list of names)
 #
-# Released under the GNU Public Licence, v2 or any higher version
+# Released under the Lesser GNU Public Licence, v2.1 or any higher version
 #
 # Please cite your use of MDAnalysis in published work:
 #
@@ -30,7 +30,7 @@
 
 :Author: Oliver Beckstein
 :Year: 2011
-:Copyright: GNU Public License v3
+:Copyright: Lesser GNU Public License v2.1+
 
 The module provides classes and functions to generate and represent
 volumetric data, in particular densities.

diff --git a/package/MDAnalysis/analysis/dielectric.py b/package/MDAnalysis/analysis/dielectric.py
@@ -5,7 +5,7 @@
 # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
 # (see the file AUTHORS for the full list of names)
 #
-# Released under the GNU Public Licence, v2 or any higher version
+# Released under the Lesser GNU Public Licence, v2.1 or any higher version
 #
 # Please cite your use of MDAnalysis in published work:
 #
@@ -27,7 +27,7 @@
 
 :Authors: Mattia Felice Palermo, Philip Loche
 :Year: 2022
-:Copyright: GNU Public License v3
+:Copyright: Lesser GNU Public License v2.1+
 """
 
 import numpy as np

diff --git a/package/MDAnalysis/analysis/diffusionmap.py b/package/MDAnalysis/analysis/diffusionmap.py
@@ -5,7 +5,7 @@
 # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
 # (see the file AUTHORS for the full list of names)
 #
-# Released under the GNU Public Licence, v2 or any higher version
+# Released under the Lesser GNU Public Licence, v2.1 or any higher version
 #
 # Please cite your use of MDAnalysis in published work:
 #
@@ -26,7 +26,7 @@
 
 :Authors: Eugen Hruska, John Detlefs
 :Year: 2016
-:Copyright: GNU Public License v2
+:Copyright: Lesser GNU Public License v2.1+
 
 This module contains the non-linear dimension reduction method diffusion map.
 The eigenvectors of a diffusion matrix represent the 'collective coordinates'

diff --git a/package/MDAnalysis/analysis/dihedrals.py b/package/MDAnalysis/analysis/dihedrals.py
@@ -5,7 +5,7 @@
 # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
 # (see the file AUTHORS for the full list of names)
 #
-# Released under the GNU Public Licence, v2 or any higher version
+# Released under the Lesser GNU Public Licence, v2.1 or any higher version
 #
 # Please cite your use of MDAnalysis in published work:
 #
@@ -25,7 +25,7 @@
 
 :Author: Henry Mull
 :Year: 2018
-:Copyright: GNU Public License v2
+:Copyright: Lesser GNU Public License v2.1+
 
 .. versionadded:: 0.19.0
 

diff --git a/package/MDAnalysis/analysis/distances.py b/package/MDAnalysis/analysis/distances.py
@@ -5,7 +5,7 @@
 # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
 # (see the file AUTHORS for the full list of names)
 #
-# Released under the GNU Public Licence, v2 or any higher version
+# Released under the Lesser GNU Public Licence, v2.1 or any higher version
 #
 # Please cite your use of MDAnalysis in published work:
 #

diff --git a/package/MDAnalysis/analysis/encore/__init__.py b/package/MDAnalysis/analysis/encore/__init__.py
@@ -5,7 +5,7 @@
 # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
 # (see the file AUTHORS for the full list of names)
 #
-# Released under the GNU Public Licence, v2 or any higher version
+# Released under the Lesser GNU Public Licence, v2.1 or any higher version
 #
 # Please cite your use of MDAnalysis in published work:
 #

diff --git a/package/MDAnalysis/analysis/encore/bootstrap.py b/package/MDAnalysis/analysis/encore/bootstrap.py
@@ -5,7 +5,7 @@
 # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
 # (see the file AUTHORS for the full list of names)
 #
-# Released under the GNU Public Licence, v2 or any higher version
+# Released under the Lesser GNU Public Licence, v2.1 or any higher version
 #
 # Please cite your use of MDAnalysis in published work:
 #

diff --git a/package/MDAnalysis/analysis/encore/clustering/ClusterCollection.py b/package/MDAnalysis/analysis/encore/clustering/ClusterCollection.py
@@ -5,7 +5,7 @@
 # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
 # (see the file AUTHORS for the full list of names)
 #
-# Released under the GNU Public Licence, v2 or any higher version
+# Released under the Lesser GNU Public Licence, v2.1 or any higher version
 #
 # Please cite your use of MDAnalysis in published work:
 #

diff --git a/package/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py b/package/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py
@@ -5,7 +5,7 @@
 # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
 # (see the file AUTHORS for the full list of names)
 #
-# Released under the GNU Public Licence, v2 or any higher version
+# Released under the Lesser GNU Public Licence, v2.1 or any higher version
 #
 # Please cite your use of MDAnalysis in published work:
 #

diff --git a/package/MDAnalysis/analysis/encore/clustering/__init__.py b/package/MDAnalysis/analysis/encore/clustering/__init__.py
@@ -5,7 +5,7 @@
 # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
 # (see the file AUTHORS for the full list of names)
 #
-# Released under the GNU Public Licence, v2 or any higher version
+# Released under the Lesser GNU Public Licence, v2.1 or any higher version
 #
 # Please cite your use of MDAnalysis in published work:
 #

diff --git a/package/MDAnalysis/analysis/encore/clustering/affinityprop.pyx b/package/MDAnalysis/analysis/encore/clustering/affinityprop.pyx
@@ -5,7 +5,7 @@
 # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
 # (see the file AUTHORS for the full list of names)
 #
-# Released under the GNU Public Licence, v2 or any higher version
+# Released under the Lesser GNU Public Licence, v2.1 or any higher version
 #
 # Please cite your use of MDAnalysis in published work:
 #

diff --git a/package/MDAnalysis/analysis/encore/clustering/cluster.py b/package/MDAnalysis/analysis/encore/clustering/cluster.py
@@ -5,7 +5,7 @@
 # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
 # (see the file AUTHORS for the full list of names)
 #
-# Released under the GNU Public Licence, v2 or any higher version
+# Released under the Lesser GNU Public Licence, v2.1 or any higher version
 #
 # Please cite your use of MDAnalysis in published work:
 #

diff --git a/package/MDAnalysis/analysis/encore/clustering/include/ap.h b/package/MDAnalysis/analysis/encore/clustering/include/ap.h
@@ -5,7 +5,7 @@
   Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
   (see the file AUTHORS for the full list of names)
 
-  Released under the GNU Public Licence, v2 or any higher version
+  Released under the Lesser GNU Public Licence, v2.1 or any higher version
 
   Please cite your use of MDAnalysis in published work:
 

diff --git a/package/MDAnalysis/analysis/encore/clustering/src/ap.c b/package/MDAnalysis/analysis/encore/clustering/src/ap.c
@@ -5,7 +5,7 @@
   Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
   (see the file AUTHORS for the full list of names)
 
-  Released under the GNU Public Licence, v2 or any higher version
+  Released under the Lesser GNU Public Licence, v2.1 or any higher version
 
   Please cite your use of MDAnalysis in published work:
 

diff --git a/package/MDAnalysis/analysis/encore/confdistmatrix.py b/package/MDAnalysis/analysis/encore/confdistmatrix.py
@@ -5,7 +5,7 @@
 # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
 # (see the file AUTHORS for the full list of names)
 #
-# Released under the GNU Public Licence, v2 or any higher version
+# Released under the Lesser GNU Public Licence, v2.1 or any higher version
 #
 # Please cite your use of MDAnalysis in published work:
 #

diff --git a/package/MDAnalysis/analysis/encore/covariance.py b/package/MDAnalysis/analysis/encore/covariance.py
@@ -5,7 +5,7 @@
 # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
 # (see the file AUTHORS for the full list of names)
 #
-# Released under the GNU Public Licence, v2 or any higher version
+# Released under the Lesser GNU Public Licence, v2.1 or any higher version
 #
 # Please cite your use of MDAnalysis in published work:
 #

diff --git a/package/MDAnalysis/analysis/encore/cutils.pyx b/package/MDAnalysis/analysis/encore/cutils.pyx
@@ -5,7 +5,7 @@
 # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
 # (see the file AUTHORS for the full list of names)
 #
-# Released under the GNU Public Licence, v2 or any higher version
+# Released under the Lesser GNU Public Licence, v2.1 or any higher version
 #
 # Please cite your use of MDAnalysis in published work:
 #

diff --git a/package/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py b/package/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py
@@ -5,7 +5,7 @@
 # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
 # (see the file AUTHORS for the full list of names)
 #
-# Released under the GNU Public Licence, v2 or any higher version
+# Released under the Lesser GNU Public Licence, v2.1 or any higher version
 #
 # Please cite your use of MDAnalysis in published work:
 #

diff --git a/package/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py b/package/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py
@@ -5,7 +5,7 @@
 # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
 # (see the file AUTHORS for the full list of names)
 #
-# Released under the GNU Public Licence, v2 or any higher version
+# Released under the Lesser GNU Public Licence, v2.1 or any higher version
 #
 # Please cite your use of MDAnalysis in published work:
 #

diff --git a/package/MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h b/package/MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h
@@ -5,7 +5,7 @@
   Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
   (see the file AUTHORS for the full list of names)
 
-  Released under the GNU Public Licence, v2 or any higher version
+  Released under the Lesser GNU Public Licence, v2.1 or any higher version
 
   Please cite your use of MDAnalysis in published work:
 

diff --git a/package/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py b/package/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py
@@ -5,7 +5,7 @@
 # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
 # (see the file AUTHORS for the full list of names)
 #
-# Released under the GNU Public Licence, v2 or any higher version
+# Released under the Lesser GNU Public Licence, v2.1 or any higher version
 #
 # Please cite your use of MDAnalysis in published work:
 #

diff --git a/package/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c b/package/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c
@@ -5,7 +5,7 @@
   Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
   (see the file AUTHORS for the full list of names)
 
-  Released under the GNU Public Licence, v2 or any higher version
+  Released under the Lesser GNU Public Licence, v2.1 or any higher version
 
   Please cite your use of MDAnalysis in published work:
 

diff --git a/package/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx b/package/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx
@@ -5,7 +5,7 @@
 # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
 # (see the file AUTHORS for the full list of names)
 #
-# Released under the GNU Public Licence, v2 or any higher version
+# Released under the Lesser GNU Public Licence, v2.1 or any higher version
 #
 # Please cite your use of MDAnalysis in published work:
 #