Relicense Sire from GPLv3+ to LGPLv3+

.github/pull_request_template.md

@@ -6,7 +6,7 @@ This pull request fixes issue #?
 
 * I confirm that I have merged the latest version of `devel` into this branch before issuing this pull request (e.g. by running `git pull origin devel`): [y/n]
 * I confirm that I have added a changelog entry to the changelog (we will add a link to this PR as part of the review): [y/n]
-* I confirm that I have permission to release this code under the GPL3 license: [y/n]
+* I confirm that I have permission to release this code under the LGPLv3+ license: [y/n]
 
 ## If this introduces new functionality...
 
@@ -16,7 +16,7 @@ Changes proposed in this pull request:
 * I confirm that I have added a test for any new functionality in this pull request: [y/n]
 * I confirm that I have added documentation (e.g. a new tutorial page or detailed guide) for any new functionality in this pull request: [y/n]
 * I confirm that I have added a changelog entry to the changelog (we will add a link to this PR as part of the review): [y/n]
-* I confirm that I have permission to release this code under the GPL3 license: [y/n]
+* I confirm that I have permission to release this code under the LGPLv3+ license: [y/n]
 
 ## Suggested reviewers:
 @chryswoods, @lohedges

CONTRIBUTING.md

@@ -16,8 +16,8 @@ Ways you can help include:
 
 When contributing, please keep in mind our [Code of Conduct](https://sire.openbiosim.org/code_of_conduct.html).
 
-Please also ensure that your contribution is compatible with our license. sire is licensed under the GPLv3 or later. 
-Please ensure your contribution is similarly licensed (i.e. GPLv3 or later for the C++ code, MIT, BSD, Apache or GPLv3 or 
+Please also ensure that your contribution is compatible with our license. sire is licensed under the LGPLv3 or later. 
+Please ensure your contribution is similarly licensed (i.e. LGPLv3 or later for the C++ code, MIT, BSD, Apache or LGPLv3 or 
 later for the Python code). Please ensure that your employer (if you are writing code as an employee) gives permission 
 for you to contribute your code.
 

LICENSE

@@ -1,3 +1,178 @@
+Sire is licensed under the GNU Lesser General Public License, version 3
+or (at your option) any later version. The LGPL is a set of additional
+permissions on top of the GNU General Public License, version 3, so the
+full text of both licenses is included below.
+
+------------------------------------------------------------------------
+
+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+  "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+  An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+  A "Combined Work" is a work produced by combining or linking an
+Application with the Library.  The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
+  The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+  The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+  1. Exception to Section 3 of the GNU GPL.
+
+  You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+  2. Conveying Modified Versions.
+
+  If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
+facility is invoked), then you may convey a copy of the modified
+version:
+
+   a) under this License, provided that you make a good faith effort to
+   ensure that, in the event an Application does not supply the
+   function or data, the facility still operates, and performs
+   whatever part of its purpose remains meaningful, or
+
+   b) under the GNU GPL, with none of the additional permissions of
+   this License applicable to that copy.
+
+  3. Object Code Incorporating Material from Library Header Files.
+
+  The object code form of an Application may incorporate material from
+a header file that is part of the Library.  You may convey such object
+code under terms of your choice, provided that, if the incorporated
+material is not limited to numerical parameters, data structure
+layouts and accessors, or small macros, inline functions and templates
+(ten or fewer lines in length), you do both of the following:
+
+   a) Give prominent notice with each copy of the object code that the
+   Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the object code with a copy of the GNU GPL and this license
+   document.
+
+  4. Combined Works.
+
+  You may convey a Combined Work under terms of your choice that,
+taken together, effectively do not restrict modification of the
+portions of the Library contained in the Combined Work and reverse
+engineering for debugging such modifications, if you also do each of
+the following:
+
+   a) Give prominent notice with each copy of the Combined Work that
+   the Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the Combined Work with a copy of the GNU GPL and this license
+   document.
+
+   c) For a Combined Work that displays copyright notices during
+   execution, include the copyright notice for the Library among
+   these notices, as well as a reference directing the user to the
+   copies of the GNU GPL and this license document.
+
+   d) Do one of the following:
+
+       0) Convey the Minimal Corresponding Source under the terms of this
+       License, and the Corresponding Application Code in a form
+       suitable for, and under terms that permit, the user to
+       recombine or relink the Application with a modified version of
+       the Linked Version to produce a modified Combined Work, in the
+       manner specified by section 6 of the GNU GPL for conveying
+       Corresponding Source.
+
+       1) Use a suitable shared library mechanism for linking with the
+       Library.  A suitable mechanism is one that (a) uses at run time
+       a copy of the Library already present on the user's computer
+       system, and (b) will operate properly with a modified version
+       of the Library that is interface-compatible with the Linked
+       Version.
+
+   e) Provide Installation Information, but only if you would otherwise
+   be required to provide such information under section 6 of the
+   GNU GPL, and only to the extent that such information is
+   necessary to install and execute a modified version of the
+   Combined Work produced by recombining or relinking the
+   Application with a modified version of the Linked Version. (If
+   you use option 4d0, the Installation Information must accompany
+   the Minimal Corresponding Source and Corresponding Application
+   Code. If you use option 4d1, you must provide the Installation
+   Information in the manner specified by section 6 of the GNU GPL
+   for conveying Corresponding Source.)
+
+  5. Combined Libraries.
+
+  You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+   a) Accompany the combined library with a copy of the same work based
+   on the Library, uncombined with any other library facilities,
+   conveyed under the terms of this License.
+
+   b) Give prominent notice with the combined library that part of it
+   is a work based on the Library, and explaining where to find the
+   accompanying uncombined form of the same work.
+
+  6. Revised Versions of the GNU Lesser General Public License.
+
+  The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+  Each version is given a distinguishing version number. If the
+Library as you received it specifies that a certain numbered version
+of the GNU Lesser General Public License "or any later version"
+applies to it, you have the option of following the terms and
+conditions either of that published version or of any later version
+published by the Free Software Foundation. If the Library as you
+received it does not specify a version number of the GNU Lesser
+General Public License, you may choose any version of the GNU Lesser
+General Public License ever published by the Free Software Foundation.
+
+  If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.
+
+------------------------------------------------------------------------
+
                     GNU GENERAL PUBLIC LICENSE
                        Version 3, 29 June 2007
 
@@ -671,4 +846,4 @@ into proprietary programs.  If your program is a subroutine library, you
 may consider it more useful to permit linking proprietary applications with
 the library.  If this is what you want to do, use the GNU Lesser General
 Public License instead of this License.  But first, please read
-<https://www.gnu.org/licenses/why-not-lgpl.html>.
+<https://www.gnu.org/licenses/why-not-lgpl.html>.

actions/generate_recipe.py

@@ -35,7 +35,6 @@
 }
 
 RUN_DEPS = {
-    "gsl",
     "libnetcdf",
     "openmm",
     "pandas",
@@ -402,7 +401,7 @@ def generate_recipe(data, features, git_remote, git_branch, git_version, git_num
     # About
     lines.append("about:")
     lines.append("  homepage: https://github.com/openbiosim/sire")
-    lines.append("  license: GPL-3.0-or-later")
+    lines.append("  license: LGPL-3.0-or-later")
     lines.append("  license_file: LICENSE")
     lines.append('  summary: "An advanced molecular modelling framework."')
     lines.append("  repository: https://github.com/openbiosim/sire")

corelib/CMakeLists.txt

@@ -689,7 +689,7 @@ set(CMAKE_AUTOMOC OFF)
 set(CMAKE_INCLUDE_CURRENT_DIR ON)
 
 set (SIRE_FOUND_TBB FALSE)
-set (SIRE_FOUND_GSL FALSE)
+set (SIRE_FOUND_EIGEN FALSE)
 set (SIRE_FOUND_BOOST FALSE)
 set (SIRE_FOUND_BLASLAPACK FALSE)
 set (SIRE_FOUND_QT FALSE)
@@ -771,18 +771,17 @@ if (NOT ${SIRE_FOUND_BOOST})
   endif()
 endif()
 
-if (NOT ${SIRE_FOUND_GSL})
-  # Sire depends on >= GSL 1.6
-  find_package(GSL 1.6 QUIET REQUIRED)
-
-  message( STATUS "GSL paths ${GSL_LINK_DIRECTORIES} "
-                  "${GSL_LIBRARIES} | ${GSL_INCLUDE_DIR}" )
-
-  list(APPEND SIREMATHS_EXTRA_LIBRARIES ${GSL_LIBRARIES})
-
-  include_directories( BEFORE ${GSL_INCLUDE_DIR})
-
-  save_sire_variable( "SIRE_GSL_INCLUDE_PATH" "${GSL_INCLUDE_DIR}" )
+if (NOT ${SIRE_FOUND_EIGEN})
+  # Sire depends on Eigen (header-only) for small dense linear algebra.
+  # The acceptable version range is pinned in pixi.toml, not here, since
+  # Eigen's CMake package version compatibility is same-major-version only
+  # and its major version has jumped around across releases.
+  #
+  # Modern Eigen3Config.cmake only exports the Eigen3::Eigen imported
+  # target (not an EIGEN3_INCLUDE_DIR variable), so consumers link
+  # against that target rather than adding an include directory here -
+  # see corelib/src/libs/SireMaths/CMakeLists.txt.
+  find_package(Eigen3 QUIET REQUIRED NO_MODULE)
 endif()
 
 set( SIRE_USE_BLAS OFF )
@@ -987,11 +986,6 @@ install (DIRECTORY ${CMAKE_SOURCE_DIR}/templates
          USE_SOURCE_PERMISSIONS
         )
 
-install (DIRECTORY ${CMAKE_SOURCE_DIR}/share/build
-         DESTINATION ${SIRE_SHARE}
-         USE_SOURCE_PERMISSIONS
-        )
-
 # These commands are used to create an 'uninstall' target
 # (this is copied from the vtk.org wiki)
 configure_file(

corelib/build/INSTALL

@@ -95,17 +95,6 @@ with these scripts, use "--help", e.g.
 
 :-> ~/sire.app/bin/waterswap --help
 
-E. DISTRIBUTING YOUR BINARY
-
-To package your installation of Sire up into a self-extracting
-executable, type
-
-:-> ~/sire.app/bin/package_sire
-
-This will build a "sire.run" package that can be used to install Sire
-on any machine that uses the same operating system, C and C++ library
-as that on which you compiled the binary.
-
 To get further help, please get in touch with the authors
 via the Sire mailing lists, or via the email links on the
 Sire website, https://sire.openbiosim.org

corelib/build/README

@@ -14,7 +14,7 @@ build/python) in which you are encouraged to compile Sire.
 
 Full install instructions are provided in the INSTALL file.
 
-Sire is provided freely under the GPL (see the COPYING file) and
+Sire is provided freely under the LGPL (see the LICENSE file) and
 comes with NO WARRANTY and NO GUARANTEES. Sire is an
 experimental code and you should not rely on it for
 any commercial work.