diff --git a/.clang-format b/.clang-format deleted file mode 100644 index 59bde10c5..000000000 --- a/.clang-format +++ /dev/null @@ -1,65 +0,0 @@ ---- -Language: Cpp -# BasedOnStyle: Google -AccessModifierOffset: -2 -AlignAfterOpenBracket: true -AlignEscapedNewlinesLeft: false -AlignOperands: true -AlignTrailingComments: true -AllowAllParametersOfDeclarationOnNextLine: true -AllowShortBlocksOnASingleLine: false -AllowShortCaseLabelsOnASingleLine: false -AllowShortIfStatementsOnASingleLine: false -AllowShortLoopsOnASingleLine: true -AllowShortFunctionsOnASingleLine: All -AlwaysBreakAfterDefinitionReturnType: false -AlwaysBreakTemplateDeclarations: true -AlwaysBreakBeforeMultilineStrings: true -BreakBeforeBinaryOperators: None -BreakBeforeTernaryOperators: true -BreakConstructorInitializersBeforeComma: false -BinPackParameters: false -BinPackArguments: false -ColumnLimit: 80 -ConstructorInitializerAllOnOneLineOrOnePerLine: true -ConstructorInitializerIndentWidth: 4 -DerivePointerAlignment: true -ExperimentalAutoDetectBinPacking: false -IndentCaseLabels: true -IndentWrappedFunctionNames: false -IndentFunctionDeclarationAfterType: false -MaxEmptyLinesToKeep: 1 -KeepEmptyLinesAtTheStartOfBlocks: false -NamespaceIndentation: None -ObjCBlockIndentWidth: 2 -ObjCSpaceAfterProperty: false -ObjCSpaceBeforeProtocolList: false -PenaltyBreakBeforeFirstCallParameter: 1 -PenaltyBreakComment: 300 -PenaltyBreakString: 1000 -PenaltyBreakFirstLessLess: 120 -PenaltyExcessCharacter: 1000000 -PenaltyReturnTypeOnItsOwnLine: 200 -PointerAlignment: Left -SpacesBeforeTrailingComments: 2 -Cpp11BracedListStyle: true -Standard: Auto -IndentWidth: 2 -TabWidth: 8 -UseTab: Never -BreakBeforeBraces: Allman -SpacesInParentheses: false -SpacesInSquareBrackets: false -SpacesInAngles: false -SpaceInEmptyParentheses: false -SpacesInCStyleCastParentheses: false -SpaceAfterCStyleCast: false -SpacesInContainerLiterals: true -SpaceBeforeAssignmentOperators: true -ContinuationIndentWidth: 4 -CommentPragmas: '^ IWYU pragma:' -ForEachMacros: [ foreach, Q_FOREACH, BOOST_FOREACH ] -SpaceBeforeParens: ControlStatements -DisableFormat: false -... - diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 31fb61987..7592947e0 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -40,7 +40,7 @@ jobs: - name: Prepare ptypy run: | # Dry install to create ptypy/version.py - python setup.py install -n + pip install . - name: Lint with flake8 run: | conda install flake8 diff --git a/.gitignore b/.gitignore index 5655be7fd..70e473b91 100644 --- a/.gitignore +++ b/.gitignore @@ -12,8 +12,6 @@ dist/ doc/_img/*.png tutorial/*.png ghostdriver* -doc/version.py -ptypy/version.py .idea/ .cache/ .vscode/ @@ -29,3 +27,4 @@ ptypy/version.py *.egg-info .DS_Store .ipynb_checkpoints +.clang-format diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index de282d218..000000000 --- a/.travis.yml +++ /dev/null @@ -1,52 +0,0 @@ -cache: apt -sudo: true -language: python -python: - - 3.7 -compiler: - - gcc -before_install: - - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh; # grab miniconda - - bash miniconda.sh -b -p $HOME/miniconda # install miniconda - - export PATH="$HOME/miniconda/bin:$PATH" # add it to the path - - conda config --set always_yes yes --set changeps1 no # we want it to always do yes, and start a new console - - conda update -q conda # update this quietly - - conda install pyyaml - - conda info -a # and print the info - - - CUDA=10.1.105-1 - - CUDA_SHORT=10.1 - - UBUNTU_VERSION=ubuntu1804 - - INSTALLER=cuda-repo-${UBUNTU_VERSION}_${CUDA}_amd64.deb - - wget http://developer.download.nvidia.com/compute/cuda/repos/${UBUNTU_VERSION}/x86_64/${INSTALLER} - - sudo dpkg -i ${INSTALLER} - - wget https://developer.download.nvidia.com/compute/cuda/repos/${UBUNTU_VERSION}/x86_64/7fa2af80.pub - - sudo apt-key add 7fa2af80.pub - - sudo apt update -qq - - sudo apt install -y cuda-core-${CUDA_SHORT/./-} cuda-cudart-dev-${CUDA_SHORT/./-} cuda-cufft-dev-${CUDA_SHORT/./-} cuda-curand-dev-${CUDA_SHORT/./-} - - sudo apt clean - - CUDA_HOME=/usr/local/cuda-${CUDA_SHORT} - - LD_LIBRARY_PATH=${CUDA_HOME}/lib64:${LD_LIBRARY_PATH} - - PATH=${CUDA_HOME}/bin:${PATH} - -env: - - TEST_ENV_NAME=ptypy_core_dependencies - - TEST_ENV_NAME=ptypy_full_dependencies - -install: True - -script: - - conda env create --file ${TEST_ENV_NAME}.yml; - - source activate ${TEST_ENV_NAME}; # activate it - - conda install pytest # additional dependencies for the tests - - pip install pytest-cov - - pip install coveralls - - echo $PYTHONPATH - - conda list - - python setup.py install # install ptypy - - py.test test -v --ignore=ptypy/test/accelerate_tests --cov ptypy --cov-report term-missing # now run the tests - -after_script: - - coveralls - - diff --git a/AUTHORS b/AUTHORS index 186a462ba..d50e248f2 100644 --- a/AUTHORS +++ b/AUTHORS @@ -1,15 +1,15 @@ Main contributors: - * Pierre Thibault (p.thibault@ucl.ac.uk) - * Björn Enders (bjoern.enders@ph.tum.de) + * Pierre Thibault (pthibault@units.it) + * Bjoern Enders (benders@lbl.gov) Early versions of this package were developed by Pierre Thibault between 2007 and 2009 at Paul Scherrer Institut (Switzerland). The package was developed further by P. Thibault at the Technische Universität München -from 2009 to 2013, with important contributions from Martin Dierolf, Björn Enders, +from 2009 to 2013, with important contributions from Martin Dierolf, Bjoern Enders, and Marco Stockmar. -The complete redesign of the code has been done by Björn Enders and Pierre Thibault in +The complete redesign of the code has been done by Bjoern Enders and Pierre Thibault in 2013-2014. We would like to thank especially Martin Dierolf for his valuable feedback. diff --git a/LICENSE b/LICENSE index d6a93266f..7abfe19b8 100644 --- a/LICENSE +++ b/LICENSE @@ -1,340 +1,91 @@ -GNU GENERAL PUBLIC LICENSE - Version 2, June 1991 - - Copyright (C) 1989, 1991 Free Software Foundation, Inc., - 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The licenses for most software are designed to take away your -freedom to share and change it. By contrast, the GNU General Public -License is intended to guarantee your freedom to share and change free -software--to make sure the software is free for all its users. This -General Public License applies to most of the Free Software -Foundation's software and to any other program whose authors commit to -using it. 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If this is what you want to do, use the GNU Lesser General -Public License instead of this License. - + Academic License Agreement + ================================ + + Introduction + +This license agreement sets forth the terms and conditions under which the +authors (see AUTHORS file at https://github.com/ptycho/ptypy/) (hereafter +"LICENSOR") will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive +license for academic, non-commercial purposes only (hereafter "LICENSE") to use +the PtyPy package computer software program and associated documentation +furnished hereunder (hereafter "PROGRAM"). + + Terms and Conditions of the LICENSE + +1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the +PROGRAM for academic, non-commercial purposes, upon the terms and conditions +hereinafter set out and until termination of this license as set forth below. + +2. LICENSEE acknowledges that the PROGRAM is a research tool still in the +development stage. The PROGRAM is provided without any related services, +improvements or warranties from LICENSOR and that the LICENSE is entered into in +order to enable others to utilize the PROGRAM in their academic activities. It +is the LICENSEE’s responsibility to ensure its proper use and the correctness of +the results.” + +3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS +FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, +TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE +COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL +DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE +PROGRAM OR THE USE OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM. + +4. LICENSEE agrees that it will use the PROGRAM and any modifications, +improvements, or derivatives of PROGRAM that LICENSEE may create (collectively, +"IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy +of PROGRAM or derivatives thereof shall be distributed only under the same +license as PROGRAM. The terms "academic, non-commercial", as used in this +Agreement, mean academic or other scholarly research which (a) is not undertaken +for profit, or (b) is not intended to produce works, services, or data for +commercial use, or (c) is neither conducted, nor funded, by a person or an +entity engaged in the commercial use, application or exploitation of works +similar to the PROGRAM. + +5. LICENSEE agrees that it shall make the following acknowledgement in any +publication resulting from the use of the PROGRAM or any translation of the code +into another computing language: + + "Data processing was carried out using the PtyPy reconstruction package +(https://github.com/ptycho/ptypy)." + +Additionally, any publication using the package, or any translation of the code +into another computing language should cite the original PtyPy publication: + +B. Enders and P. Thibault, A computational framework for ptychographic +reconstructions, Proc. Royal Soc. A 472, 20160640 (2016). (doi: +10.1098/rspa.2016.0640) + +as well as the publications pertaining to the algorithms or methods employed +with the package. + +6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the +PROGRAM title or the names or logos of LICENSOR in any advertising, promotional +or sales material without prior written consent obtained from LICENSOR in each +case. + +7. Ownership of all rights, including copyright in the PROGRAM and in any +material associated therewith, shall at all times remain with LICENSOR, and +LICENSEE agrees to preserve same. LICENSEE agrees not to use any portion of the +PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, +nor to make any copies except for its internal use, without prior written +consent of LICENSOR. LICENSEE agrees to place the following copyright notice on +any such copies: + +© All rights reserved. The PtyPy team, see AUTHORS. + +8. The LICENSE shall not be construed to confer any rights upon LICENSEE by +implication or otherwise except as specifically set forth herein. + +9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK +has an international portfolio of patents and pending applications which relate +to ptychography and that the PROGRAM may be capable of being used in +circumstances which may fall within the claims of one or more of the Phase Focus +patents (see https://www.phasefocus.com/patents). The LICENSOR explicitly +declares not to indemnify the users of the software in case Phase Focus or any +other third party will open a legal action against the LICENSEE due to the use of +the program. + +10. This Agreement shall be governed by the material laws of ENGLAND and any +dispute arising out of this Agreement or use of the PROGRAM shall be brought +before the courts of England and Wales. diff --git a/README.rst b/README.rst index 1083c3160..edf712d74 100644 --- a/README.rst +++ b/README.rst @@ -1,4 +1,22 @@ -PTYPY - Ptychography Reconstruction for Python +Phase Focus Limited of Sheffield, UK, has an international portfolio +of patents and pending applications which relate to ptychography. +A current list is available `here `__. + +Phase Focus grants royalty free licences of its patent rights for +non-commercial academic research use, for reconstruction of simulated +data and for reconstruction of data obtained at synchrotrons at X-ray +wavelengths. These licenses can be applied for online by +clicking on `this link `__. + +Phase Focus asserts that the software we have made available for +download may be capable of being used in circumstances which may +fall within the claims of one or more of the Phase Focus patents. +Phase Focus advises that you apply for a licence from it before +downloading any software from this website. + +---- + +PtyPy - Ptychography Reconstruction for Python ============================================== |ptypysite| @@ -11,9 +29,9 @@ Welcome Ptychonaut! |ptypy| [#pronounciation]_ [#ptypypaper]_ is a framework for scientific ptychography compiled by -P. Thibault and B. Enders and licensed under the GPLv2 license. +P. Thibault and B. Enders and other authors (see AUTHORS). -It is the result of 7 years of experience in the field of ptychography condensed +It is the result of years of experience in the field of ptychography condensed into a versatile python package. The package covers the whole path of ptychographic analysis after the actual experiment is completed - from data management to reconstruction to visualization. @@ -27,8 +45,9 @@ distributed computing. Additionally, |ptypy| provides a rich set of utilities and helper functions, especially for input and output -To get started quickly, please find the official documentation at the project pages -`here `_ or have a look at the examples in the ``templates`` directory. +To get started quickly, please find the official documentation on +`the project pages `__ +or have a look at the examples in the ``templates`` directory. Features -------- @@ -37,7 +56,7 @@ Features * **Maximum Likelihood** [#ml]_ engine with preconditioners and regularizers. * A few more engines (RAAR, sDR, ePIE, ...). -* **Fully parallelized** (CPU only) using the Massage Passing Interface +* **Fully parallelized** using the Massage Passing Interface (`MPI `_). Simply execute your script with:: @@ -49,13 +68,13 @@ Features `ZeroMQ `_ . The reconstruction may run on a remote hpc cluster while your desktop computer displays the reconstruction progress. - * **Mixed-state** reconstructions of probe and object [#states]_ for overcoming partial coherence or related phenomena. * **On-the-fly** reconstructions (while data is being acquired) using the - the `PtyScan `_ class in the linking mode `linking mode `_ + the `PtyScan `_ + class in the `linking mode `_ Installation @@ -63,7 +82,7 @@ Installation Installation should be as simple as :: - $ sudo pip install . + $ pip install . or, as a user, :: @@ -76,10 +95,10 @@ Dependencies Ptypy depends on standard python packages: * numpy * scipy - * matplotlib * h5py + * matplotlib & pillow (optional - required for plotting) * mpi4py (optional - required for parallel computing) - * zeromq (optional - required for the offline plotting client) + * pyzmq (optional - required for the plotting client) Quicklinks @@ -94,7 +113,7 @@ Quicklinks | Have a look at the `tutorials about its special classes `_ . * | Only interested in |ptypy|'s **data file structure** and - **management**? Indulge yourself `here `_ for the structure and `here `_ for the concepts. + **management**? Indulge yourself `here `__ for the structure and `here `__ for the concepts. Contribute @@ -109,12 +128,6 @@ Support If you are having issues, please let us know. -License -------- - -The project is licensed under a GPLv2 license. - - .. |ptypy| replace:: PtyPy .. |ptypysite| image:: https://ptycho.github.io/ptypy/_static/logo_100px.png @@ -126,12 +139,12 @@ References .. [#pronounciation] Pronounced *typy*, forget the *p*, as in psychology. -.. [#ptypypaper] B.Enders and P.Thibault, *Proc. R. Soc. A* **472**, `doi `_ +.. [#ptypypaper] B.Enders and P.Thibault, *Proc. R. Soc. A* **472**, `doi `__ -.. [#states] P.Thibault and A.Menzel, *Nature* **494**, 68 (2013), `doi `_ +.. [#states] P.Thibault and A.Menzel, *Nature* **494**, 68 (2013), `doi `__ -.. [#dm] P.Thibault, M.Dierolf *et al.*, *Science* **321**, 7 (2009), `doi `_ +.. [#dm] P.Thibault, M.Dierolf *et al.*, *Science* **321**, 7 (2009), `doi `__ -.. [#ml] P.Thibault and M.Guizar-Sicairos, *New J. of Phys.* **14**, 6 (2012), `doi `_ +.. [#ml] P.Thibault and M.Guizar-Sicairos, *New J. of Phys.* **14**, 6 (2012), `doi `__ .. [#power] K.Giewekemeyer *et al.*, **PNAS 108**, 2 (2007), `suppl. material `__, `doi `__ diff --git a/doc/index.rst b/doc/index.rst index c99c71264..317f5cf50 100644 --- a/doc/index.rst +++ b/doc/index.rst @@ -3,11 +3,11 @@ Welcome Ptychonaut! |ptypy| [#Enders2016]_ is a framework for scientific ptychography compiled by -P.Thibault and B. Enders and licensed under the GPLv2 license. +P.Thibault, B. Enders, and others (see AUTHORS). -It comprises 8 years of experience in the field of ptychography condensed -to a versatile python package. The package covers the whole path of -ptychographic analysis after the actual experiment +It is the result of years of experience in the field of ptychography condensed +into a versatile python package. The package covers the whole path of +ptychographic analysis after the actual experiment is completed - from data management to reconstruction to visualization. The main idea of ptypy is: *"Flexibility and Scalabality through abstraction"*. diff --git a/ptypy/__init__.py b/ptypy/__init__.py index 33da60ac8..0ca662fb7 100644 --- a/ptypy/__init__.py +++ b/ptypy/__init__.py @@ -10,7 +10,7 @@ @article{ ... } :copyright: Copyright 2018 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. :version: %(version)s :status: %(devrel)s """ % {'version': version, 'devrel': 'release' if release else 'development', 'short': short_version} diff --git a/ptypy/accelerate/base/engines/ML_serial.py b/ptypy/accelerate/base/engines/ML_serial.py index b779a6667..248110326 100644 --- a/ptypy/accelerate/base/engines/ML_serial.py +++ b/ptypy/accelerate/base/engines/ML_serial.py @@ -9,7 +9,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np import time diff --git a/ptypy/accelerate/base/engines/projectional_serial.py b/ptypy/accelerate/base/engines/projectional_serial.py index 0816c7049..313a2e9c5 100644 --- a/ptypy/accelerate/base/engines/projectional_serial.py +++ b/ptypy/accelerate/base/engines/projectional_serial.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np import time diff --git a/ptypy/accelerate/base/engines/projectional_serial_stream.py b/ptypy/accelerate/base/engines/projectional_serial_stream.py index 1d5784700..d3164b497 100644 --- a/ptypy/accelerate/base/engines/projectional_serial_stream.py +++ b/ptypy/accelerate/base/engines/projectional_serial_stream.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ # from .. import core diff --git a/ptypy/accelerate/base/engines/stochastic.py b/ptypy/accelerate/base/engines/stochastic.py index f3b7f897e..3d2927ccf 100644 --- a/ptypy/accelerate/base/engines/stochastic.py +++ b/ptypy/accelerate/base/engines/stochastic.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np import time diff --git a/ptypy/accelerate/cuda_pycuda/engines/ML_pycuda.py b/ptypy/accelerate/cuda_pycuda/engines/ML_pycuda.py index 2022a2bdf..7e1320357 100644 --- a/ptypy/accelerate/cuda_pycuda/engines/ML_pycuda.py +++ b/ptypy/accelerate/cuda_pycuda/engines/ML_pycuda.py @@ -9,7 +9,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np from pycuda import gpuarray diff --git a/ptypy/accelerate/cuda_pycuda/engines/projectional_pycuda.py b/ptypy/accelerate/cuda_pycuda/engines/projectional_pycuda.py index aa88a380f..c02445265 100644 --- a/ptypy/accelerate/cuda_pycuda/engines/projectional_pycuda.py +++ b/ptypy/accelerate/cuda_pycuda/engines/projectional_pycuda.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np diff --git a/ptypy/accelerate/cuda_pycuda/engines/projectional_pycuda_stream.py b/ptypy/accelerate/cuda_pycuda/engines/projectional_pycuda_stream.py index c6e5adda8..e9204f80b 100644 --- a/ptypy/accelerate/cuda_pycuda/engines/projectional_pycuda_stream.py +++ b/ptypy/accelerate/cuda_pycuda/engines/projectional_pycuda_stream.py @@ -10,7 +10,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np diff --git a/ptypy/accelerate/cuda_pycuda/engines/stochastic.py b/ptypy/accelerate/cuda_pycuda/engines/stochastic.py index 3ac819725..a3363e161 100644 --- a/ptypy/accelerate/cuda_pycuda/engines/stochastic.py +++ b/ptypy/accelerate/cuda_pycuda/engines/stochastic.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np diff --git a/ptypy/accelerate/ocl_pyopencl/engines/DM_ocl.py b/ptypy/accelerate/ocl_pyopencl/engines/DM_ocl.py index 2a3604c2a..bee434f39 100644 --- a/ptypy/accelerate/ocl_pyopencl/engines/DM_ocl.py +++ b/ptypy/accelerate/ocl_pyopencl/engines/DM_ocl.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np diff --git a/ptypy/accelerate/ocl_pyopencl/engines/DM_ocl_npy.py b/ptypy/accelerate/ocl_pyopencl/engines/DM_ocl_npy.py index 3539f7c15..178a93147 100644 --- a/ptypy/accelerate/ocl_pyopencl/engines/DM_ocl_npy.py +++ b/ptypy/accelerate/ocl_pyopencl/engines/DM_ocl_npy.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import os.path diff --git a/ptypy/core/__init__.py b/ptypy/core/__init__.py index 38d47f3d5..6a27a91f3 100644 --- a/ptypy/core/__init__.py +++ b/ptypy/core/__init__.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ from .classes import * from .ptycho import * diff --git a/ptypy/core/classes.py b/ptypy/core/classes.py index aee749811..c55ee8bbe 100644 --- a/ptypy/core/classes.py +++ b/ptypy/core/classes.py @@ -29,7 +29,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np diff --git a/ptypy/core/data.py b/ptypy/core/data.py index 89b725b80..636857bca 100644 --- a/ptypy/core/data.py +++ b/ptypy/core/data.py @@ -15,7 +15,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np import os diff --git a/ptypy/core/geometry.py b/ptypy/core/geometry.py index 05a2b630e..8f2e26790 100644 --- a/ptypy/core/geometry.py +++ b/ptypy/core/geometry.py @@ -4,7 +4,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np from scipy import fftpack diff --git a/ptypy/core/illumination.py b/ptypy/core/illumination.py index cb0c7fb15..4cee7a693 100644 --- a/ptypy/core/illumination.py +++ b/ptypy/core/illumination.py @@ -7,7 +7,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np diff --git a/ptypy/core/manager.py b/ptypy/core/manager.py index 8acbc7b86..0db01562d 100644 --- a/ptypy/core/manager.py +++ b/ptypy/core/manager.py @@ -11,7 +11,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np import time diff --git a/ptypy/core/paths.py b/ptypy/core/paths.py index caf86d292..1c6787a13 100644 --- a/ptypy/core/paths.py +++ b/ptypy/core/paths.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import sys import os diff --git a/ptypy/core/ptycho.py b/ptypy/core/ptycho.py index 0cd49405c..543fa00a2 100644 --- a/ptypy/core/ptycho.py +++ b/ptypy/core/ptycho.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np import time diff --git a/ptypy/core/sample.py b/ptypy/core/sample.py index a2577bfd9..6f5702424 100644 --- a/ptypy/core/sample.py +++ b/ptypy/core/sample.py @@ -7,7 +7,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np diff --git a/ptypy/core/xy.py b/ptypy/core/xy.py index 9661b2c0c..f5c2e6f8f 100644 --- a/ptypy/core/xy.py +++ b/ptypy/core/xy.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np import warnings diff --git a/ptypy/custom/DMOPR.py b/ptypy/custom/DMOPR.py index 706198fb4..298db0b06 100644 --- a/ptypy/custom/DMOPR.py +++ b/ptypy/custom/DMOPR.py @@ -6,7 +6,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np from ptypy import utils as u diff --git a/ptypy/custom/MLOPR.py b/ptypy/custom/MLOPR.py index 000bb73bf..81cd563b0 100644 --- a/ptypy/custom/MLOPR.py +++ b/ptypy/custom/MLOPR.py @@ -8,7 +8,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np import time diff --git a/ptypy/custom/ePIE_parallel.py b/ptypy/custom/ePIE_parallel.py index 1fb3754d5..f92b1b9d0 100644 --- a/ptypy/custom/ePIE_parallel.py +++ b/ptypy/custom/ePIE_parallel.py @@ -20,7 +20,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np import time diff --git a/ptypy/debug/__init__.py b/ptypy/debug/__init__.py index 9431effbe..4e9c3991f 100644 --- a/ptypy/debug/__init__.py +++ b/ptypy/debug/__init__.py @@ -8,7 +8,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ from .embedded_shell import ipshell diff --git a/ptypy/debug/embedded_shell.py b/ptypy/debug/embedded_shell.py index 9593cd214..c67bd99fa 100644 --- a/ptypy/debug/embedded_shell.py +++ b/ptypy/debug/embedded_shell.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ from ..utils import log diff --git a/ptypy/debug/ipython_kernel.py b/ptypy/debug/ipython_kernel.py index 6efdd7309..27bbbecc6 100644 --- a/ptypy/debug/ipython_kernel.py +++ b/ptypy/debug/ipython_kernel.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import os, threading diff --git a/ptypy/engines/Bragg3d_engines.py b/ptypy/engines/Bragg3d_engines.py index 87ecfe519..6e7cb3407 100644 --- a/ptypy/engines/Bragg3d_engines.py +++ b/ptypy/engines/Bragg3d_engines.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ from .projectional import DM from . import register diff --git a/ptypy/engines/ML.py b/ptypy/engines/ML.py index 8a3c68a36..fe08995ce 100644 --- a/ptypy/engines/ML.py +++ b/ptypy/engines/ML.py @@ -9,7 +9,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np import time diff --git a/ptypy/engines/__init__.py b/ptypy/engines/__init__.py index 96fe8146d..c88eb5266 100644 --- a/ptypy/engines/__init__.py +++ b/ptypy/engines/__init__.py @@ -8,7 +8,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ from .utils import * diff --git a/ptypy/engines/base.py b/ptypy/engines/base.py index bf6d32e3f..78f1f6e04 100644 --- a/ptypy/engines/base.py +++ b/ptypy/engines/base.py @@ -6,7 +6,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np import time diff --git a/ptypy/engines/posref.py b/ptypy/engines/posref.py index 8528a3cc0..6d4460c4a 100644 --- a/ptypy/engines/posref.py +++ b/ptypy/engines/posref.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ from ..core import View from .. import utils as u @@ -319,4 +319,4 @@ def citation_dictionary(self): "year" : 2012, "page" : 64, "doi" : '10.1016/j.ultramic.2012.06.001', - "comment" : 'Position Refinement using annealing algorithm'} \ No newline at end of file + "comment" : 'Position Refinement using annealing algorithm'} diff --git a/ptypy/engines/projectional.py b/ptypy/engines/projectional.py index 89dddd675..ba72aa2db 100644 --- a/ptypy/engines/projectional.py +++ b/ptypy/engines/projectional.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np import time diff --git a/ptypy/engines/stochastic.py b/ptypy/engines/stochastic.py index c1c64c378..04a48f8c0 100644 --- a/ptypy/engines/stochastic.py +++ b/ptypy/engines/stochastic.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np import time diff --git a/ptypy/engines/utils.py b/ptypy/engines/utils.py index 6c47e123e..dd580d4e8 100644 --- a/ptypy/engines/utils.py +++ b/ptypy/engines/utils.py @@ -6,7 +6,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np from .. import utils as u diff --git a/ptypy/experiment/AMO_LCLS.py b/ptypy/experiment/AMO_LCLS.py index 43e5dc05c..333cef237 100644 --- a/ptypy/experiment/AMO_LCLS.py +++ b/ptypy/experiment/AMO_LCLS.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np diff --git a/ptypy/experiment/DiProI_FERMI.py b/ptypy/experiment/DiProI_FERMI.py index c15d6459c..43452fad4 100644 --- a/ptypy/experiment/DiProI_FERMI.py +++ b/ptypy/experiment/DiProI_FERMI.py @@ -7,7 +7,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ diff --git a/ptypy/experiment/ID16Anfp.py b/ptypy/experiment/ID16Anfp.py index bd1f3d8e6..ab81eb93f 100644 --- a/ptypy/experiment/ID16Anfp.py +++ b/ptypy/experiment/ID16Anfp.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np diff --git a/ptypy/experiment/UCL.py b/ptypy/experiment/UCL.py index 155747e7d..35ed1e95b 100644 --- a/ptypy/experiment/UCL.py +++ b/ptypy/experiment/UCL.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np import os diff --git a/ptypy/experiment/__init__.py b/ptypy/experiment/__init__.py index 4838e9186..825ee2438 100644 --- a/ptypy/experiment/__init__.py +++ b/ptypy/experiment/__init__.py @@ -14,7 +14,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ from importlib import import_module from .. import defaults_tree diff --git a/ptypy/experiment/diamond_nexus.py b/ptypy/experiment/diamond_nexus.py index f00cac086..318887756 100644 --- a/ptypy/experiment/diamond_nexus.py +++ b/ptypy/experiment/diamond_nexus.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import h5py as h5 diff --git a/ptypy/experiment/hdf5_loader.py b/ptypy/experiment/hdf5_loader.py index 6a47b7857..475eca053 100644 --- a/ptypy/experiment/hdf5_loader.py +++ b/ptypy/experiment/hdf5_loader.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import h5py as h5 @@ -998,4 +998,4 @@ def get_corrected_intensities(self, weights, intensities, index, indexed_frame_s intensities = np.pad(intensities, tuple(self.pad.reshape(2,2)), mode='constant') weights = np.pad(weights, tuple(self.pad.reshape(2,2)), mode='constant') - return weights, intensities \ No newline at end of file + return weights, intensities diff --git a/ptypy/experiment/legacy/DLS.py b/ptypy/experiment/legacy/DLS.py index 676e3ffe7..b63791b44 100644 --- a/ptypy/experiment/legacy/DLS.py +++ b/ptypy/experiment/legacy/DLS.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np diff --git a/ptypy/experiment/legacy/DLS_mapping.py b/ptypy/experiment/legacy/DLS_mapping.py index 66e378b5f..35ca4dcb7 100644 --- a/ptypy/experiment/legacy/DLS_mapping.py +++ b/ptypy/experiment/legacy/DLS_mapping.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np diff --git a/ptypy/experiment/legacy/I08.py b/ptypy/experiment/legacy/I08.py index 52ebbf8e1..345a14f01 100644 --- a/ptypy/experiment/legacy/I08.py +++ b/ptypy/experiment/legacy/I08.py @@ -7,7 +7,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np diff --git a/ptypy/experiment/legacy/I13_ffp.py b/ptypy/experiment/legacy/I13_ffp.py index 68713b063..a508281e3 100644 --- a/ptypy/experiment/legacy/I13_ffp.py +++ b/ptypy/experiment/legacy/I13_ffp.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np import os diff --git a/ptypy/experiment/legacy/I13_nfp.py b/ptypy/experiment/legacy/I13_nfp.py index dafb63621..a41228efe 100644 --- a/ptypy/experiment/legacy/I13_nfp.py +++ b/ptypy/experiment/legacy/I13_nfp.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np import os diff --git a/ptypy/experiment/plugin.py b/ptypy/experiment/plugin.py index 45f8be669..62345ff11 100644 --- a/ptypy/experiment/plugin.py +++ b/ptypy/experiment/plugin.py @@ -6,7 +6,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ diff --git a/ptypy/experiment/savu.py b/ptypy/experiment/savu.py index edcd5b27b..dae70481b 100644 --- a/ptypy/experiment/savu.py +++ b/ptypy/experiment/savu.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ from .. import utils as u diff --git a/ptypy/experiment/spec.py b/ptypy/experiment/spec.py index 142d3a3da..7043c85c0 100644 --- a/ptypy/experiment/spec.py +++ b/ptypy/experiment/spec.py @@ -6,7 +6,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import dateutil import dateutil.parser diff --git a/ptypy/io/__init__.py b/ptypy/io/__init__.py index e81674c3a..37ffa9bd9 100644 --- a/ptypy/io/__init__.py +++ b/ptypy/io/__init__.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ from .h5rw import * from .json_rw import * diff --git a/ptypy/io/h5rw.py b/ptypy/io/h5rw.py index c786c2d88..109fc4ee3 100644 --- a/ptypy/io/h5rw.py +++ b/ptypy/io/h5rw.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import h5py import numpy as np diff --git a/ptypy/io/interaction.py b/ptypy/io/interaction.py index 07c3da537..1eb63012d 100644 --- a/ptypy/io/interaction.py +++ b/ptypy/io/interaction.py @@ -7,7 +7,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import zmq diff --git a/ptypy/io/json_rw.py b/ptypy/io/json_rw.py index 0185bdeb3..6e4a4a1b3 100644 --- a/ptypy/io/json_rw.py +++ b/ptypy/io/json_rw.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import json diff --git a/ptypy/simulations/__init__.py b/ptypy/simulations/__init__.py index f32e110dd..317c2b212 100644 --- a/ptypy/simulations/__init__.py +++ b/ptypy/simulations/__init__.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ from .ptysim_utils import * from . import detector diff --git a/ptypy/simulations/detector.py b/ptypy/simulations/detector.py index 4228b1579..7b2fb6254 100644 --- a/ptypy/simulations/detector.py +++ b/ptypy/simulations/detector.py @@ -10,7 +10,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np from scipy import ndimage as ndi diff --git a/ptypy/simulations/ptysim_utils.py b/ptypy/simulations/ptysim_utils.py index 1fbc5d0d4..41a80331b 100644 --- a/ptypy/simulations/ptysim_utils.py +++ b/ptypy/simulations/ptysim_utils.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np import os diff --git a/ptypy/simulations/simscan.py b/ptypy/simulations/simscan.py index 796cefed4..1785ff7b9 100644 --- a/ptypy/simulations/simscan.py +++ b/ptypy/simulations/simscan.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np import os diff --git a/ptypy/utils/__init__.py b/ptypy/utils/__init__.py index e8e8b13b0..4667488dd 100644 --- a/ptypy/utils/__init__.py +++ b/ptypy/utils/__init__.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ from .misc import * from .math_utils import * diff --git a/ptypy/utils/array_utils.py b/ptypy/utils/array_utils.py index a6dc3ede9..af6aedfd1 100644 --- a/ptypy/utils/array_utils.py +++ b/ptypy/utils/array_utils.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np diff --git a/ptypy/utils/citations.py b/ptypy/utils/citations.py index fe4638624..138502333 100644 --- a/ptypy/utils/citations.py +++ b/ptypy/utils/citations.py @@ -4,7 +4,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ class JournalArticle(object): diff --git a/ptypy/utils/descriptor.py b/ptypy/utils/descriptor.py index e997beb5e..554dc65b2 100644 --- a/ptypy/utils/descriptor.py +++ b/ptypy/utils/descriptor.py @@ -10,7 +10,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import ast diff --git a/ptypy/utils/math_utils.py b/ptypy/utils/math_utils.py index 8faae2ecd..88cf49a6d 100644 --- a/ptypy/utils/math_utils.py +++ b/ptypy/utils/math_utils.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np from scipy.special import erf diff --git a/ptypy/utils/misc.py b/ptypy/utils/misc.py index eae31e89f..53741c54c 100644 --- a/ptypy/utils/misc.py +++ b/ptypy/utils/misc.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import os import numpy as np diff --git a/ptypy/utils/parallel.py b/ptypy/utils/parallel.py index 933cca306..6d30c7fd1 100644 --- a/ptypy/utils/parallel.py +++ b/ptypy/utils/parallel.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np diff --git a/ptypy/utils/parameters.py b/ptypy/utils/parameters.py index 96630355e..810125e03 100644 --- a/ptypy/utils/parameters.py +++ b/ptypy/utils/parameters.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import os diff --git a/ptypy/utils/plot_client.py b/ptypy/utils/plot_client.py index e6297a3af..63fbe568a 100644 --- a/ptypy/utils/plot_client.py +++ b/ptypy/utils/plot_client.py @@ -4,7 +4,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import time diff --git a/ptypy/utils/plot_utils.py b/ptypy/utils/plot_utils.py index 882a2ed20..4458d7ac0 100644 --- a/ptypy/utils/plot_utils.py +++ b/ptypy/utils/plot_utils.py @@ -4,7 +4,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np import time diff --git a/ptypy/utils/scripts.py b/ptypy/utils/scripts.py index 268894434..c49cb269d 100644 --- a/ptypy/utils/scripts.py +++ b/ptypy/utils/scripts.py @@ -4,7 +4,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import numpy as np from . import parallel diff --git a/ptypy/utils/test_utils.py b/ptypy/utils/test_utils.py index 73aa0ff77..b7476fbd7 100644 --- a/ptypy/utils/test_utils.py +++ b/ptypy/utils/test_utils.py @@ -5,7 +5,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ # SC: indentation error, commented out for now #path = inspect.stack()[0][1] diff --git a/ptypy/utils/verbose.py b/ptypy/utils/verbose.py index d069444c7..5c674cb09 100644 --- a/ptypy/utils/verbose.py +++ b/ptypy/utils/verbose.py @@ -15,7 +15,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import time import sys @@ -326,4 +326,4 @@ def __exit__(self, type, value, traceback): if self.active: self.duration = perf_counter() - self.time self.duration = parallel.MPImax([self.duration]) - self.readout = f'{self.duration:.3f} seconds' \ No newline at end of file + self.readout = f'{self.duration:.3f} seconds' diff --git a/ptypy/version.py b/ptypy/version.py new file mode 100644 index 000000000..e52b76757 --- /dev/null +++ b/ptypy/version.py @@ -0,0 +1,17 @@ + +short_version = '0.6.0' +version = '0.6.0' +release = True + +if not release: + version += '.dev' + import subprocess + try: + git_commit = subprocess.Popen(["git","log","-1","--pretty=oneline","--abbrev-commit"], + stdout=subprocess.PIPE, + stderr=subprocess.DEVNULL).communicate()[0].split()[0] + except: + pass + else: + version += git_commit.strip().decode() + diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 000000000..dcfadf665 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,71 @@ +[build-system] +requires = ["setuptools>=61.0"] +build-backend = "setuptools.build_meta" + +[project] +name = "PtyPy" +authors = [ + { name="Bjoern Enders", email="benders@lbl.gov"}, + { name="Pierre Thibault", email="pthibault@units.it" }, + { name="Benedikt Daurer", email="benedikt.daurer@diamond.ac.uk" }, +] +description = "Ptychography Reconstruction for Python" +readme = "README.rst" +requires-python = ">=3.7" +classifiers = [ + "Programming Language :: Python :: 3", + "Development Status :: 3 - Alpha", + "Intended Audience :: Science/Research", + "License :: Other/Proprietary License", + "Topic :: Scientific/Engineering", + "Topic :: Software Development", + "Operating System :: POSIX :: Linux" +] +dynamic = ["version"] +dependencies = [ +# "python >= 3.7", + "numpy", + "scipy", + "h5py", +] + +[project.optional-dependencies] +full = ["mpi4py","matplotlib","pyzmq","pillow", "pyfftw"] + + +#[project.scripts] +#"ptypy.plot" = 'scripts/ptypy.plot' +#"ptypy.inspect" = 'scripts/ptypy.inspect' +#"ptypy.plotclient" = 'scripts/ptypy.plotclient' +#"ptypy.new" = 'scripts/ptypy.new' +#"ptypy.csv2cp" = 'scripts/ptypy.csv2cp' +#"ptypy.run" ='scripts/ptypy.run' + +[project.urls] +"Homepage" = "https://github.com/ptycho/ptypy" +"Bug Tracker" = "https://github.com/ptycho/ptypy/issues" +"Documentation" = "https://ptycho.github.io/ptypy" + +[tool.pytest.ini_options] +testpaths = [ + "test/core_tests", + "test/engine_tests", + "test/io_tests", + "test/ptyscan_tests", + "test/template_tests", + "test/util_tests", +] + +# this is all BETA according to setuptools +[tool.setuptools.dynamic] +version = {attr = "ptypy.version.version"} + +[tool.setuptools.package-dir] +ptypy = "ptypy" + +#[tool.setuptools.packages.find] +#where = ["ptypy"] + +[tool.setuptools.package-data] +ptypy = ["resources/*",] +"ptypy.accelerate.cuda_pycuda.cuda" = ["*.cu"] \ No newline at end of file diff --git a/release_notes.md b/release_notes.md index 8ee1bc645..e7f5d55e2 100644 --- a/release_notes.md +++ b/release_notes.md @@ -1,3 +1,17 @@ +# PtyPy 0.6 release notes + +Public release of ptypy! After having to use a private repository +for many years, we finally have a license agreement that allows +PtyPy to go public. + +## Build changes + +In accordance with PEP 621, we are moving away +from `setup.py` for the main build of PtyPy and +adopt the new community standard for building +packages with `pyproject.toml`. + + # PtyPy 0.5 release notes We're excited to bring you a new release, with new engines, GPU accelerations and diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index ee4a5cac1..000000000 --- a/setup.cfg +++ /dev/null @@ -1,10 +0,0 @@ -[build_sphinx] -source-dir = doc -build-dir = doc/build -all_files = 1 - -[upload_sphinx] -upload-dir = doc/build/html - -[tool:pytest] -testpaths = test/core_tests test/engine_tests test/io_tests test/ptyscan_tests test/template_tests test/util_tests diff --git a/setup.py b/setup.py index 98b469622..6005472ae 100644 --- a/setup.py +++ b/setup.py @@ -1,81 +1,20 @@ #!/usr/bin/env python -# we should aim to remove the distutils dependency import setuptools -from distutils.core import setup -import sys -CLASSIFIERS = """\ -Development Status :: 3 - Alpha -Intended Audience :: Science/Research -License :: OSI Approved -Programming Language :: Python -Topic :: Scientific/Engineering -Topic :: Software Development -Operating System :: Unix -""" - - -MAJOR = 0 -MINOR = 5 -MICRO = 0 -ISRELEASED = False -VERSION = '%d.%d.%d' % (MAJOR, MINOR, MICRO) - - -# import os -# if os.path.exists('MANIFEST'): os.remove('MANIFEST') - -DEBUG = False - -def write_version_py(filename='ptypy/version.py'): - cnt = """ -# THIS FILE IS GENERATED FROM ptypy/setup.py -short_version='%(version)s' -version='%(version)s' -release=%(isrelease)s - -if not release: - version += '.dev' - import subprocess - try: - git_commit = subprocess.Popen(["git","log","-1","--pretty=oneline","--abbrev-commit"], - stdout=subprocess.PIPE, - stderr=subprocess.DEVNULL).communicate()[0].split()[0] - except: - pass - else: - version += git_commit.strip().decode() - -""" - a = open(filename, 'w') - try: - a.write(cnt % {'version': VERSION, 'isrelease': str(ISRELEASED)}) - finally: - a.close() - - -if __name__ == '__main__': - write_version_py() - write_version_py('doc/version.py') - try: - exec(open('ptypy/version.py').read()) - vers = version # noqa: F821 - except: - vers = VERSION - -exclude_packages = ["test.*", "test"] -package_list = setuptools.find_packages(exclude=exclude_packages) -setup( - name='Python Ptychography toolbox', - version=VERSION, - author='Pierre Thibault, Bjoern Enders, Martin Dierolf and others', - description='Ptychographic reconstruction toolbox', - long_description=open('README.rst', 'r').read(), - package_dir={'ptypy': 'ptypy'}, - packages=package_list, - package_data={'ptypy': ['resources/*',], - 'ptypy.accelerate.cuda_pycuda.cuda': ['*.cu']}, +# exclude_packages = ["test.*", "test"] +# package_list = setuptools.find_packages(exclude=exclude_packages) +# print(package_list) +setuptools.setup( + #name='Python Ptychography toolbox', + #version=VERSION, + #author='Pierre Thibault, Bjoern Enders, Martin Dierolf and others', + #description='', + #long_description=open('README.rst', 'r').read(), + # package_dir={'ptypy': 'ptypy'}, + # packages=package_list, + # package_data={'ptypy': ['resources/*',], + # 'ptypy.accelerate.cuda_pycuda.cuda': ['*.cu']}, scripts=['scripts/ptypy.plot', 'scripts/ptypy.inspect', 'scripts/ptypy.plotclient', diff --git a/test/accelerate_tests/base_tests/engine_tests.py b/test/accelerate_tests/base_tests/engine_tests.py index 2b9379511..dbfc1e9f6 100644 --- a/test/accelerate_tests/base_tests/engine_tests.py +++ b/test/accelerate_tests/base_tests/engine_tests.py @@ -3,7 +3,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import unittest diff --git a/test/accelerate_tests/cuda_pycuda_tests/engine_tests.py b/test/accelerate_tests/cuda_pycuda_tests/engine_tests.py index 71542d4f9..20b950c61 100644 --- a/test/accelerate_tests/cuda_pycuda_tests/engine_tests.py +++ b/test/accelerate_tests/cuda_pycuda_tests/engine_tests.py @@ -3,7 +3,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import unittest diff --git a/test/core_tests/classes_test.py b/test/core_tests/classes_test.py index 250ee7e2e..b54004fa1 100644 --- a/test/core_tests/classes_test.py +++ b/test/core_tests/classes_test.py @@ -28,7 +28,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ # Modules diff --git a/test/engine_tests/DMOPR_test.py b/test/engine_tests/DMOPR_test.py index 66c2fe3ab..a43779bcb 100644 --- a/test/engine_tests/DMOPR_test.py +++ b/test/engine_tests/DMOPR_test.py @@ -3,7 +3,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import unittest diff --git a/test/engine_tests/DM_test.py b/test/engine_tests/DM_test.py index db10f8154..9e2b88732 100644 --- a/test/engine_tests/DM_test.py +++ b/test/engine_tests/DM_test.py @@ -3,7 +3,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import unittest diff --git a/test/engine_tests/MLOPR_test.py b/test/engine_tests/MLOPR_test.py index 1c0ff79af..375a80237 100644 --- a/test/engine_tests/MLOPR_test.py +++ b/test/engine_tests/MLOPR_test.py @@ -3,7 +3,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import unittest diff --git a/test/engine_tests/ML_old_test.py b/test/engine_tests/ML_old_test.py index f52db08ea..ad6e16bfc 100644 --- a/test/engine_tests/ML_old_test.py +++ b/test/engine_tests/ML_old_test.py @@ -3,7 +3,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import unittest diff --git a/test/engine_tests/ML_test.py b/test/engine_tests/ML_test.py index d06571d7d..24a479b47 100644 --- a/test/engine_tests/ML_test.py +++ b/test/engine_tests/ML_test.py @@ -3,7 +3,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import unittest diff --git a/test/engine_tests/dummy_test.py b/test/engine_tests/dummy_test.py index 294c0bdf0..003347037 100644 --- a/test/engine_tests/dummy_test.py +++ b/test/engine_tests/dummy_test.py @@ -3,7 +3,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import unittest diff --git a/test/engine_tests/engine_utils_test.py b/test/engine_tests/engine_utils_test.py index 4e8f977ce..52910b524 100644 --- a/test/engine_tests/engine_utils_test.py +++ b/test/engine_tests/engine_utils_test.py @@ -3,7 +3,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import unittest diff --git a/test/ptyscan_tests/dls_test.py b/test/ptyscan_tests/dls_test.py index b8e689ff6..af71a7c59 100644 --- a/test/ptyscan_tests/dls_test.py +++ b/test/ptyscan_tests/dls_test.py @@ -3,7 +3,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import unittest @@ -27,4 +27,4 @@ def test_dls(self): tu.PtyscanTestRunner(DlsScan,r) if __name__ == "__main__": - unittest.main() \ No newline at end of file + unittest.main() diff --git a/test/ptyscan_tests/i08_test.py b/test/ptyscan_tests/i08_test.py index ca309e9c5..9d5a7a856 100644 --- a/test/ptyscan_tests/i08_test.py +++ b/test/ptyscan_tests/i08_test.py @@ -3,7 +3,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import unittest @@ -26,4 +26,4 @@ def test_I08(self): tu.PtyscanTestRunner(I08Scan,r) if __name__ == "__main__": - unittest.main() \ No newline at end of file + unittest.main() diff --git a/test/ptyscan_tests/savu_test.py b/test/ptyscan_tests/savu_test.py index b4f7571bb..dacc451b3 100644 --- a/test/ptyscan_tests/savu_test.py +++ b/test/ptyscan_tests/savu_test.py @@ -3,7 +3,7 @@ This file is part of the PTYPY package. :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. """ import unittest @@ -25,4 +25,4 @@ def test_savu(self): tu.PtyscanTestRunner(Savu,r) if __name__ == "__main__": - unittest.main() \ No newline at end of file + unittest.main() diff --git a/test/utils.py b/test/utils.py index 14ae745b3..7380035ef 100644 --- a/test/utils.py +++ b/test/utils.py @@ -5,7 +5,7 @@ module:: utils .. moduleauthor:: Aaron Parsons :copyright: Copyright 2014 by the PTYPY team, see AUTHORS. - :license: GPLv2, see LICENSE for details. + :license: see LICENSE for details. :platform: Unix :synopsis: utilities for the test framework """