Verified Commit 9badffc7 authored by Chris Kerr's avatar Chris Kerr

Merge branch 'master' into 15-change-ylm-representation-to-store-magnitude-and-exp-i-phi-separately

parents 31f70a30 7ce1d26b
# 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
*
......
# SPDX-FileCopyrightText: 2016-2017 European Molecular Biology Laboratory
# SPDX-FileCopyrightText: 2017-2020 Christopher Kerr
#
# SPDX-License-Identifier: CC0-1.0
.cache/*
.tox/*
.hypothesis/*
......
# 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
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:
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# Files: src/*
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# SPDX-FileCopyrightText: 2018-2019 Christopher Kerr
#
# SPDX-License-Identifier: CC0-1.0
recursive-include src/python/cl-src *.cl
include COPYING
include 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
```
# 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
......
#!/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
......
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:
......
! -*- 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
......
/*
* 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.
*
......
/*
* 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.
*
......
/*
* 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.
*
......
/*
* 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.
*
......
/*
* 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.
*
......
/*
* 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.
*
......
# -*- 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+"
......
# -*- 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+"
......
# -*- 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
......
# -*- 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+"
......
# -*- 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+"
......
# -*- 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
......
# -*- 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
......
# -*- 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+"
......
#!/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+"
......
"""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
......
# -*- 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
......
# -*- 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
......
"""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
......
# -*- 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
......