Merge branch '51-add-spdx-fsfe-reuse-metadata' into 'master'

Resolve "Add SPDX / fsfe-reuse metadata"

Closes #51

See merge request !30

.dockerignore

+# SPDX-FileCopyrightText: 2019-2020 Christopher Kerr
+#
+# SPDX-License-Identifier: CC0-1.0
+#
 # The docker image only contains dependencies so it does not need any of the files from the repo
 # therefore we ignore everything
 *

.gitignore

+# SPDX-FileCopyrightText: 2016-2017 European Molecular Biology Laboratory
+# SPDX-FileCopyrightText: 2017-2020 Christopher Kerr
+#
+# SPDX-License-Identifier: CC0-1.0
+
 .cache/*
 .tox/*
 .hypothesis/*

.gitlab-ci.yml

+# SPDX-FileCopyrightText: 2017 European Molecular Biology Laboratory (EMBL)
+# SPDX-FileCopyrightText: 2018-2020 Christopher Kerr
+#
+# SPDX-License-Identifier: LGPL-3.0-or-later
+
 variables:
   DOCKER_BASE_IMAGE: "$CI_REGISTRY_IMAGE/base"
 
@@ -25,7 +30,7 @@ test_py3:
   variables:
     PYOPENCL_COMPILER_OUTPUT: 1
   cache:
-    key: "${CI_COMMIT_REF_SLUG}-${CI_JOB_NAME}"
+    key: "${CI_JOB_NAME}"
     paths:
     - .hypothesis
     - .tox
@@ -44,7 +49,11 @@ test_py3:
 test_lint:
   stage: test
   image: python:3.7
+  cache:
+    key: "${CI_JOB_NAME}"
+    paths:
+    - .tox
   before_script:
     - pip install tox
   script:
-    - tox -e flake8
+    - tox -e flake8,reuse

.reuse/dep5

+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: GALUMPH
+Upstream-Contact: Christopher Kerr <chris.kerr@mykolab.ch>
+Source: https://git.embl.de/grp-svergun/galumph
+
+# Sample paragraph, commented out:
+#
+# Files: src/*
+# Copyright: $YEAR $NAME <$CONTACT>
+# License: ...

LICENSES/CC0-1.0.txt

+Creative Commons Legal Code
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+OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED HEREUNDER, AND DISCLAIMS
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+GNU LESSER GENERAL PUBLIC LICENSE
+
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+
+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.
+
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+Public License, and the "GNU GPL" refers to version 3 of the GNU General Public
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+
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+
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+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:
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+is used in it and that the Library and its use are covered by this License.
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+
+   4. Combined Works.
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+You may convey a Combined Work under terms of your choice that, taken together,
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+manner specified by section 6 of the GNU GPL for conveying Corresponding Source.
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+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.

MANIFEST.in

+# SPDX-FileCopyrightText: 2018-2019 Christopher Kerr
+#
+# SPDX-License-Identifier: CC0-1.0
+
 recursive-include src/python/cl-src *.cl
 include COPYING
 include README.md

README.md

 # GALUMPH #
 
+<!---
+SPDX-FileCopyrightText: 2016-2017 European Molecular Biology Laboratory (EMBL)
+SPDX-FileCopyrightText: 2018 Christopher Kerr
+
+SPDX-License-Identifier: LGPL-3.0-or-later
+-->
+
 [![pipeline status](https://git.embl.de/grp-svergun/galumph/badges/master/pipeline.svg)](https://git.embl.de/grp-svergun/galumph/commits/master)
 
 Calculate ALM (scattering amplitude decomposed into spherical harmonics) at Hyperspeed using GPU acceleration.
@@ -34,4 +41,4 @@ ff = np.array([periodictable.elements.symbol(aa.element).xray.f0(s) for aa in pd
 alm = kernel.zeros()
 kernel.add_many_atoms(alm, xyz, ff)
 Icalc = kernel.sum_intensity(alm)
-```
\ No newline at end of file
+```

dockerfile

+# SPDX-FileCopyrightText: 2019-2020 Christopher Kerr
+#
+# SPDX-License-Identifier: CC0-1.0
+#
 # Dockerfile for the 'base image'
 # This installs all the required dependencies in a docker image so that they
 # do not have to be installed every time the tests are run

setup.py

 #!/usr/bin/env python
-# -*- coding: utf-8 -*-
+
+# SPDX-FileCopyrightText: 2016-2017 European Molecular Biology Laboratory (EMBL)
+# SPDX-FileCopyrightText: 2018-2019 Christopher Kerr
+#
+# SPDX-License-Identifier: LGPL-3.0-or-later
 
 from numpy.distutils.core import setup as np_setup
 from numpy.distutils.extension import Extension as F2PyExtension

src/fortran/wignerSymbols.f

+C SPDX-FileCopyrightText: 1976 K. Schulten and R. G. Gordon
+C SPDX-FileCopyrightText: 2014-2015 Joey Dumont
+C SPDX-FileCopyrightText: 2018 Christopher Kerr
+C
+C SPDX-License-Identifier: LGPL-3.0-or-later
+C
 C The DRC3JJ subroutine was copied from the 'wignerSymbols' project by Joey Dumont,
 C and has been modified to make it a PURE subroutine and thus compatible with OpenMP.
 C The original version of the file can be found here:

src/fortran/wignerSymbols.pyf

 !    -*- f90 -*-
 
-! Copyright (c) Christopher Kerr 2018
+! SPDX-FileCopyrightText: 2018 Christopher Kerr
 !
-! This file is part of GALUMPH.
-!
-! GALUMPH is free software: you can redistribute it and/or modify it
-! under the terms of the GNU Lesser General Public License as published
-! by the Free Software Foundation, either version 3 of the License, or
-! (at your option) any later version.
-!
-! GALUMPH 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 Lesser General Public License for more details.
-!
-! You should have received a copy of the GNU Lesser General Public License
-! along with GALUMPH.  If not, see <http://www.gnu.org/licenses/>.
+! SPDX-License-Identifier: CC0-1.0
 
 python module wignerSymbols
     interface

src/opencl/alm-add-atom.cl

 /*
- * Copyright (c) European Molecular Biology Laboratory (EMBL)
+ * Copyright (c) European Molecular Biology Laboratory
+ * SPDX-FileCopyrightText: 2016 European Molecular Biology Laboratory (EMBL)
+ *
+ * SPDX-License-Identifier: LGPL-3.0-or-later
  *
  * This file is part of GALUMPH.
  *

src/opencl/intensity.cl

 /*
- * Copyright (c) European Molecular Biology Laboratory (EMBL) 2016-7
- * Copyright (c) Christopher Kerr 2018
+ * Copyright (c) European Molecular Biology Laboratory, Christopher Kerr
+ * SPDX-FileCopyrightText: 2016 European Molecular Biology Laboratory (EMBL)
+ * SPDX-FileCopyrightText: 2018 Christopher Kerr
+ *
+ * SPDX-License-Identifier: LGPL-3.0-or-later
  *
  * This file is part of GALUMPH.
  *

src/opencl/rotate-alm.cl

 /*
- * Copyright (c) 2018 Christopher Kerr
+ * Copyright (c) Christopher Kerr
+ * SPDX-FileCopyrightText: 2018 Christopher Kerr
+ *
+ * SPDX-License-Identifier: LGPL-3.0-or-later
  *
  * This file is part of GALUMPH.
  *

src/opencl/spherical-bessel.cl

 /*
- * Copyright (c) European Molecular Biology Laboratory (EMBL)
+ * Copyright (c) European Molecular Biology Laboratory, Christopher Kerr
+ * SPDX-FileCopyrightText: 2016 European Molecular Biology Laboratory (EMBL)
+ * SPDX-FileCopyrightText: 2019 Christopher Kerr
+ *
+ * SPDX-License-Identifier: LGPL-3.0-or-later
  *
  * This file is part of GALUMPH.
  *

src/opencl/spherical-harmonic.cl

 /*
- * Copyright (c) European Molecular Biology Laboratory (EMBL)
+ * Copyright (c) European Molecular Biology Laboratory, Christopher Kerr
+ * SPDX-FileCopyrightText: 2016 European Molecular Biology Laboratory (EMBL)
+ * SPDX-FileCopyrightText: 2018-2019 Christopher Kerr
+ *
+ * SPDX-License-Identifier: LGPL-3.0-or-later
  *
  * This file is part of GALUMPH.
  *

src/opencl/translate-alm.cl

 /*
- * Copyright (c) 2018 Christopher Kerr
+ * Copyright (c) Christopher Kerr
+ * SPDX-FileCopyrightText: 2018 Christopher Kerr
+ *
+ * SPDX-License-Identifier: LGPL-3.0-or-later
  *
  * This file is part of GALUMPH.
  *

src/python/__init__.py

-# -*- coding: utf-8 -*-
+# SPDX-FileCopyrightText: 2016 European Molecular Biology Laboratory (EMBL)
+# SPDX-FileCopyrightText: 2018 Christopher Kerr
+#
+# SPDX-License-Identifier: LGPL-3.0-or-later
 
 __copyright__ = "European Molecular Biology Laboratory (EMBL)"
 __license__ = "LGPLv3+"

src/python/almarray.py

-# -*- coding: utf-8 -*-
-from __future__ import absolute_import, division
+# SPDX-FileCopyrightText: 2018 Christopher Kerr
+#
+# SPDX-License-Identifier: LGPL-3.0-or-later
 
 __copyright__ = "Christopher Kerr"
 __license__ = "LGPLv3+"

src/python/atomicscattering.py

-# -*- coding: utf-8 -*-
-from __future__ import absolute_import, division
+# SPDX-FileCopyrightText: 2016 European Molecular Biology Laboratory (EMBL)
+# SPDX-FileCopyrightText: 2017-2019 Christopher Kerr
+#
+# SPDX-License-Identifier: LGPL-3.0-or-later
 
 __copyright__ = "European Molecular Biology Laboratory (EMBL)"
 __license__ = "LGPLv3+"
 
-
 import numpy as np
 import pyopencl as cl
 from pyopencl import array as cl_array

src/python/intensity.py

-# -*- coding: utf-8 -*-
-from __future__ import absolute_import, division
+# SPDX-FileCopyrightText: 2016 European Molecular Biology Laboratory (EMBL)
+# SPDX-FileCopyrightText: 2017-2018 Christopher Kerr
+#
+# SPDX-License-Identifier: LGPL-3.0-or-later
 
 __copyright__ = "Christopher Kerr"
 __license__ = "LGPLv3+"

src/python/rotalm.py

-# -*- coding: utf-8 -*-
-from __future__ import absolute_import, division
+# SPDX-FileCopyrightText: 2018 Christopher Kerr
+#
+# SPDX-License-Identifier: LGPL-3.0-or-later
 
 __copyright__ = "Christopher Kerr"
 __license__ = "LGPLv3+"

src/python/sphericalbessel.py

-# -*- coding: utf-8 -*-
-from __future__ import absolute_import, division
+# SPDX-FileCopyrightText: 2016 European Molecular Biology Laboratory (EMBL)
+# SPDX-FileCopyrightText: 2017-2019 Christopher Kerr
+#
+# SPDX-License-Identifier: LGPL-3.0-or-later
 
 __copyright__ = "European Molecular Biology Laboratory (EMBL)"
 __license__ = "LGPLv3+"
 
-
 import numpy as np
 import pyopencl as cl
 from pyopencl import array as cl_array

src/python/sphericalharmonic.py

-# -*- coding: utf-8 -*-
-from __future__ import absolute_import, division
+# SPDX-FileCopyrightText: 2016 European Molecular Biology Laboratory (EMBL)
+# SPDX-FileCopyrightText: 2017-2019 Christopher Kerr
+#
+# SPDX-License-Identifier: LGPL-3.0-or-later
 
 __copyright__ = "European Molecular Biology Laboratory (EMBL)"
 __license__ = "LGPLv3+"
 
-
 import numpy as np
 import pyopencl as cl
 import pyopencl.array as cl_array

src/python/util.py

-# -*- coding: utf-8 -*-
-
-from __future__ import division
+# SPDX-FileCopyrightText: 2018 Christopher Kerr
+#
+# SPDX-License-Identifier: LGPL-3.0-or-later
 
 __copyright__ = "Christopher Kerr"
 __license__ = "LGPLv3+"

src/python/zshift.py

-#!/usr/bin/env python3
-
-from __future__ import absolute_import, division
+# SPDX-FileCopyrightText: 2018 Christopher Kerr
+#
+# SPDX-License-Identifier: LGPL-3.0-or-later
 
 __copyright__ = "Christopher Kerr"
 __license__ = "LGPLv3+"

test/conftest.py

 """Shared pytest fixtures."""
 
+# SPDX-FileCopyrightText: 2018-2020 Christopher Kerr
+#
+# SPDX-License-Identifier: LGPL-3.0-or-later
+
 import hypothesis
 import numpy as np
 import pyopencl as cl

test/test_almarray.py

-# -*- coding: utf-8 -*-
-
-from __future__ import division
+# SPDX-FileCopyrightText: 2018 Christopher Kerr
+#
+# SPDX-License-Identifier: LGPL-3.0-or-later
 
 from hypothesis import given
 import hypothesis.strategies as st

test/test_atomic_scattering.py

-# -*- coding: utf-8 -*-
-
+# SPDX-FileCopyrightText: 2016 European Molecular Biology Laboratory (EMBL)
+# SPDX-FileCopyrightText: 2018-2020 Christopher Kerr
+#
+# SPDX-License-Identifier: LGPL-3.0-or-later
 
 from hypothesis import assume, given, settings
 import hypothesis.strategies as st

test/test_bessel.py

 """Tests for the spherical bessel functions."""
 
-from __future__ import division
+# SPDX-FileCopyrightText: 2016 European Molecular Biology Laboratory (EMBL)
+# SPDX-FileCopyrightText: 2018-2020 Christopher Kerr
+#
+# SPDX-License-Identifier: LGPL-3.0-or-later
 
 from hypothesis import assume, given, settings
 import hypothesis.strategies as st

test/test_intensity.py

-# -*- coding: utf-8 -*-
-
-from __future__ import absolute_import, division
+# SPDX-FileCopyrightText: 2016 European Molecular Biology Laboratory (EMBL)
+# SPDX-FileCopyrightText: 2018-2020 Christopher Kerr
+#
+# SPDX-License-Identifier: LGPL-3.0-or-later
 
 from hypothesis import assume, given, HealthCheck, settings
 import hypothesis.strategies as st