June 2020 - Neurofedora - Fedora mailing-lists

OpenVibe in NeuroFedora?
by Ankur Sinha 28 Jun '20

28 Jun '20

Hi, I was trying out the shiny new packager dashboard at: https://packager.fedorainfracloud.org I noticed that OpenVibe was orphaned by the primary maintainer and is now retired. However, it's part of the NeuroFedora packages (we have commit access) Do we want to maintain it? Anyone interested? http://openvibe.inria.fr/ https://src.fedoraproject.org/rpms/openvibe We're also happy to mentor newcomers if they'd like to help maintain the package. (A few of us are sponsors) -- Thanks, Regards, Ankur Sinha "FranciscoD" (He / Him / His) | https://fedoraproject.org/wiki/User:Ankursinha Time zone: Europe/London

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NeuroFedora @ CNS*2020 (Online, July 18-23, free to register!)
by Ankur Sinha 28 Jun '20

28 Jun '20

Hi folks, I'll present our poster on Comp-NeurFedora at CNS*2020, the annual conference for the Organization for Computational Neuroscience: https://cns2020online.sched.com/event/cm1l/p80-comp-neurofedora-a-freeopen-… The complete event is free to register, and is online. I strongly suggest everyone register and attend the conference. It'll be a great experience to learn more about computational neuroscience (the science, and the tools that are used in the field!). You can register at the OCNS website: https://www.cnsorg.org/cns-2020 We're using Sched this year (also used for Flock), and you'll receive the password when you register for the conference. Please spread the word to your colleagues, friends, labs, groups, and especially students :) (I'm on the organizing committee, so you can always e-mail me privately if you experience any issues) -- Thanks, Regards, Ankur Sinha "FranciscoD" (He / Him / His) | https://fedoraproject.org/wiki/User:Ankursinha Time zone: Europe/London

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Fwd: [ITK] ITK 5.1.0 has been released!
by Morgan Hough 25 Jun '20

25 Jun '20

---------- Forwarded message --------- From: Matt McCormick via ITK <noreply(a)discourse.itk.org> Date: Wed, Jun 10, 2020 at 12:19 Subject: [ITK] ITK 5.1.0 has been released! To: <morgan.hough(a)gmail.com> We are happy to announce the Insight Toolkit (ITK) <https://itk.org> 5.1.0 release! [image: :tada:] ITK is an open-source, cross-platform toolkit for N-dimensional scientific image processing, segmentation, and registration. ITK 5.1.0 is a feature release that improves and extends the major ITK 5.0 release. ITK 5.1.0 includes a NumPy <https://numpy.org> and Xarray <https://xarray.pydata.org> filter interface, clang-format enforced coding style, enhanced modern C++ range support, strongly-typed enum’s, and much more. A number of issues were addressed based on feedback from Release Candidate 3. Filters avoid extra copies when operating on NumPy arrays, and itk.Image is now a NumPy array-like. Remote module CI testing infrastructure has been migrated to GitHub Actions for C++ tests, Python package builds, and automated Python package deployment. Downloads *Python Packages* Install ITK Python packages <https://itkpythonpackage.readthedocs.io/en/latest/Quick_start_guide.html> with: pip install --upgrade itk or: conda -c conda-forge install itk *Guide and Textbook* - InsightSoftwareGuide-Book1-5.1.0.pdf <https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.1.0/I…> - InsightSoftwareGuide-Book2-5.1.0.pdf <https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.1.0/I…> *Library Sources* - InsightToolkit-5.1.0.tar.gz <https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.1.0/I…> - InsightToolkit-5.1.0.zip <https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.1.0/I…> *Testing Data* Unpack optional testing data in the same directory where the Library Source is unpacked. - InsightData-5.1.0.tar.gz <https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.1.0/I…> - InsightData-5.1.0.zip <https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.1.0/I…> *Checksums* - MD5SUMS <https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.1.0/M…> - SHA512SUMS <https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.1.0/S…> Features [image: ITKParabolicMorphology] Parabolic morphological filtering with the ITKParabolicMorphology <https://github.com/InsightSoftwareConsortium/ITKParabolicMorphology> remote module. To install the new Python package: pip install itk-parabolicmorphology. Jupyter notebooks are provided as examples <https://github.com/InsightSoftwareConsortium/ITKParabolicMorphology/tree/ma…>. For more information, see the Insight Journal article <http://www.insight-journal.org/browse/publication/228>, *Beare R. Morphology with parabolic structuring elements. The Insight Journal. January-June. 2008. http://www.insight-journal.org/browse/publication/228 <http://www.insight-journal.org/browse/publication/228>*. GitHub Actions for ITK Remote Module Testing, Packaging, PyPI Deployment A GitHub Action configuration <https://gist.github.com/thewtex/aab3f401b27dfd262e508cf1019853f0> is available for ITK Remote Module continuous integration (CI) testing and Python packaging on Linux, macOS, and Windows. Continuous deployment (CD) is configured to upload packages to the Python Package Index (PyPI) <https://pypi.org> when the repository is tagged. More information can be found in the ITK Python Package ReadTheDocs <https://itkpythonpackage.readthedocs.io/en/master/Build_ITK_Module_Python_p…> documentation. Pass NumPy Array’s or Xarray DataArray’s to ITK Image Filters The Pythonic, functional-like interface <https://discourse.itk.org/t/itk-5-0-beta-1-pythonic-interface/1271> to all ITK image-to-image-filters now directly supports operation on NumPy ndarray’s <https://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html>, i.e. numpy.ndarray. If a ndarray is passed as an input, a ndarray is returned as an output. For example, smoothed = itk.median_image_filter(array, radius=2) Previously, explicit conversion to / from an itk.Image was required with itk.array_from_image and itk.image_from_array. We can now also convert an itk.Image to a numpy.ndarray with the standard np.asarray call. import numpy as np import itk image = itk.imread('/path/to/image.tif') array = np.asarray(image) An itk.Image is now more NumPy array-like: shape, ndim, and dtype attributes are available; these correspond to the values when converted to a NumPy ndarray. Basic NumPy functions can be called directly on an itk.Image, i.e., min = np.min(image) max = np.max(image) mean = np.mean(image) Similar, experimental support (subject to change) is also available for Xarray DataArray’s <https://xarray.pydata.org/en/stable/generated/xarray.DataArray.html>. If an xarray.DataArray is passed as an input, an xarray.DataArray is returned as an output. Moreover, the operation preserves spatial and dimensional metadata. For example, import xarray as xr import itk image = itk.imread('/path/to/image.tif') da = itk.xarray_from_image(image) smoothed = itk.median_image_filter(da, radius=3) print(smoothed) results in: <xarray.DataArray (y: 288, x: 894)> array([[255. , 255. , 255. , ..., 255. , 255. , 255. ], [ 11.9995, 11.9995, 11.9995, ..., 11.9995, 11.9995, 11.9995], [ 11.9995, 11.9995, 11.9995, ..., 11.9995, 11.9995, 11.9995], ..., [ 11.9995, 11.9995, 11.9995, ..., 11.9995, 11.9995, 11.9995], [ 11.9995, 11.9995, 11.9995, ..., 11.9995, 11.9995, 11.9995], [ 11.9995, 11.9995, 11.9995, ..., 11.9995, 11.9995, 11.9995]], dtype=float32) Coordinates: * x (x) float64 0.0 1.0 2.0 3.0 4.0 ... 889.0 890.0 891.0 892.0 893.0 * y (y) float64 0.0 1.0 2.0 3.0 4.0 ... 283.0 284.0 285.0 286.0 287.0 Attributes: direction: [[1. 0.]\n [0. 1.]] A round trip is possible with itk.image_from_xarray. Python 3 Only ITK 5.1 will be the first Python 3-only release. Consistent with most scientific Python packages and CPython’s 2020 drop in support <https://pythonclock.org>, Python 2 support and binaries are no longer available. Python Package 64-bit Float Support In addition to the many other pixel types supported, the itk binary Python packages now include support for the double pixel type, i.e. 64-bit IEEE floating-point pixels. This improves compatibility with scikit-image <https://scikit-image.org/>, which uses this pixel type as a default. clang-format Enforced C++ Coding Style ITK has adopted a *.clang-format* <https://github.com/InsightSoftwareConsortium/ITK/blob/master/.clang-format> coding style configuration file so a consistent coding style can automatically be applied to C++ code with the clang-format <http://releases.llvm.org/download.html> binary. A consistent coding style is critical for readability and collaborative development. clang-format has been applied to the entire codebase. The Whitesmiths style of brace indentation, previously part of the ITK Coding Style Guidelines <https://itk.org/ItkSoftwareGuide.pdf>, is not supported by clang-format, so it has been replaced by a brace style consistent with VTK’s current style. A Git commit hook will automatically apply clang-format to changed C++ code. Enhanced Modern C++ Range Support In addition to the ImageBufferRange <https://itk.org/Doxygen/html/classitk_1_1Experimental_1_1ImageBufferRange.h…>, ShapedImageNeighborhoodRange <https://itk.org/Doxygen/html/classitk_1_1Experimental_1_1ShapedImageNeighbo…>, and IndexRange <https://itk.org/Doxygen/html/classitk_1_1Experimental_1_1IndexRange.html> classes introduced in ITK 5.0, ITK 5.1 adds an ImageRegionRange <https://itk.org/Doxygen/html/classitk_1_1Experimental_1_1ImageRegionRange.h…>. These range classes conform to the Standard C++ Iterator requirements so they can be used in range-based for loop’s and passed to Standard C++ algorithms. Range-based for loops provide an elegant syntax for iteration. Moreover, they are often more performant than other iteration classes available. For example, to add 42 to every pixel: ImageBufferRange<ImageType> range{ *image }; for (auto&& pixel : range) { pixel = pixel + 42; } In ITK 5.1, adoption of the range classes was extended across the toolkit, which demonstrates their use and improves toolkit performance. Point Set Registration Parallelism ITK provides a powerful registration framework for point-set registration, offering information-theoretic similarity metrics, labeled point-set metrics, and spatial transformation models that range from affine to b-spline to dense displacement fields. ITK 5.1 features enhanced parallelism in point-set metric computation, leveraging the native thread-pool and Threading Building Blocks (TBB) <https://discourse.itk.org/t/itk-5-0-alpha-2-performance/959> enhancements in ITK 5. SpatialObject’s and Strongly-Typed enum’s Improvements and refinements were made to the ITK 5 itk::SpatialObject refactoring, and modern C++ interface. In particular, ITK 5.1 transitions enumerations to strongly-typed enumerations <https://www.modernescpp.com/index.php/strongly-typed-enums>, which is flagged by modern compilers due to improved scoping and implicit conversions to int. Enum names now follow a consistent <Description>Enum naming conversion, which results in a Python interface: <Description>Enum_<EnumValue1> <Description>Enum_<EnumValue2> [...] A guide for updating to the new enum’s can be found in the Strongly Typed Enumerations <https://github.com/InsightSoftwareConsortium/ITK/blob/master/Documentation/…> section of the ITK 5 Migration Guide. DICOM Support ITK’s broadly adopted medical image support is hardened thanks to 20 years of testing and support from major open source DICOM library maintainers. In this release, many members of the community collaborated to further enhance ITK’s DICOM support for corner cases related to modality, pixel types, and vendor variations. Remote Module Updates New remote module: TubeTK <https://github.com/InsightSoftwareConsortium/ITKTubeTK>: An open-source toolkit, led by Kitware, Inc., for the segmentation, registration, and analysis of tubes and surfaces in images. A new remote module grading system <https://discourse.itk.org/t/remote-module-grading-ranking-system-needed/2750> was added to help convey the quality compliance level for the 45 remote modules. Many remote modules were updated: *AnalyzeObjectMapIO, AnisotropicDiffusionLBR, BSplineGradient, BioCell, BoneEnhancement, BoneMorphometry, Cuberille, FixedPointInverseDisplacementField, GenericLabelInterpolator, HigherOrderAccurateGradient, IOMeshSTL, IOOpenSlide, IOScanco, IOTransformDCMTK, IsotropicWavelets, LabelErodeDilate, LesionSizingToolkit, MinimalPathExtraction, Montage, MorphologicalContourInterpolation, ParabolicMorphology, PhaseSymmetry, RLEImage, RTK, SCIFIO, SimpleITKFilters, SkullStrip, SplitComponents, Strain, SubdivisionQuadEdgeMeshFilter, TextureFeatures, Thickness3D, TotalVariation,* and *TwoProjectionRegistration*. Zenodo Citation ITK has a Zenodo Citation <https://zenodo.org/badge/latestdoi/800928>: <https://zenodo.org/badge/latestdoi/800928> This citation can be used to cite a specific version of the software. If you have contributed 10 or more patches to ITK, please add your ORCID iD <https://orcid.org/> to our .zenodo.json <https://github.com/InsightSoftwareConsortium/ITK/blob/master/.zenodo.json> file for authorship association. NumFOCUS Copyright Transfer ITK’s copyright and the copyright of software held by the Insight Software Consortium <https://www.insightsoftwareconsortium.org/> have been transferred to NumFOCUS <https://numfocus.org/>. CMake <https://cmake.org>’s copyright has been transferred to Kitware <https://kitware.com>. And More Many more improvements have been made. For details, see the changelogs for the release candidates and changelog below. Congratulations Congratulations and *thank you* to everyone who contributed to this release. Of *73 authors* since v5.0.0, we would like to specially recognize the new contributors: Mathew J. Seng, Zahil Shanis, yjcchen0913, PA Rodesch, Aurélien Coussat, yinkaola, Bryce Besler, Pierre Chatelier, Rinat Mukhometzianov, Ramraj Chandradevan, Hina Shah, Gordian Kabelitz, Genevieve Buckley, Aaron Bray, nslay, Antoine Robert, James Butler, Matthew Rocklin, Gina Helfrich, and Neslisah Torosdagli, Brad T. Moore, Niklas Johansson, Flavien Bridault, Pradeep Garigipati, haaput, tabish, and Antoine Robert, Ben Wilson, Adam Rankin, PA Rodesch, Tabish Syed, vlibertiaux, Michael Jackson, Conrad Poelman, and muschellij2. *Enjoy ITK!* ITK Changes Since v5.1rc03 Bradley Lowekamp (3): Bug Fixes - Check if calculator is proper type (3e7307744e <https://github.com/InsightSoftwareConsortium/ITK/commit/3e7307744e>) - Use one calculator in ItermodesThresholder (6dc4948017 <https://github.com/InsightSoftwareConsortium/ITK/commit/6dc4948017>) - Use GDCM as private dependency in ITKIOGDCM (ca1913cee6 <https://github.com/InsightSoftwareConsortium/ITK/commit/ca1913cee6>) Conrad Poelman (1): Platform Fixes - Remove deprecated/removed std (7b2dfd28d4 <https://github.com/InsightSoftwareConsortium/ITK/commit/7b2dfd28d4>) Dženan Zukić (1): Enhancements - add the .exe executable extension to clang-format on Windows ( 343cbf9236 <https://github.com/InsightSoftwareConsortium/ITK/commit/343cbf9236>) GDCM Upstream (1): Miscellaneous Changes - efdd2cab95 (efdd2cab95 <https://github.com/InsightSoftwareConsortium/ITK/commit/efdd2cab95>) Hans J. Johnson (16): Enhancements - Remove use of deprecated, redundant interface (51792db03b <https://github.com/InsightSoftwareConsortium/ITK/commit/51792db03b>) - Prefer multiplication to division (50b91ab2cc <https://github.com/InsightSoftwareConsortium/ITK/commit/50b91ab2cc>) - Variable names updated to better indicate their pupopse (5012b7e41f <https://github.com/InsightSoftwareConsortium/ITK/commit/5012b7e41f>) - Provide new baseline for ImageRegisration4Test (623bef5c10 <https://github.com/InsightSoftwareConsortium/ITK/commit/623bef5c10>) Performance Improvements - Only compute log(fixedImageMarginalPDFValue once outside loop ( e7ef06e39a <https://github.com/InsightSoftwareConsortium/ITK/commit/e7ef06e39a>) - Avoid processing entire rows based on mathematical certainties ( 82730afa5c <https://github.com/InsightSoftwareConsortium/ITK/commit/82730afa5c>) Documentation Updates - Improve diagnostic message for exception (bebe1d6f4a <https://github.com/InsightSoftwareConsortium/ITK/commit/bebe1d6f4a>) - Fix missing \ingroup ITKIODCMTK (d7f8c463dc <https://github.com/InsightSoftwareConsortium/ITK/commit/d7f8c463dc>) - Fix typo in comment User -> Uses (d87449620f <https://github.com/InsightSoftwareConsortium/ITK/commit/d87449620f>) Platform Fixes - Suppress compiler warning about value trucation (9e137468bc <https://github.com/InsightSoftwareConsortium/ITK/commit/9e137468bc>) - Unused variable warning (c40a494c79 <https://github.com/InsightSoftwareConsortium/ITK/commit/c40a494c79>) Bug Fixes - TBB build requires consistent exception options (c4caa4cdbe <https://github.com/InsightSoftwareConsortium/ITK/commit/c4caa4cdbe>) - Pointer to temporary variable needs resetting to null. (b29dc9182e <https://github.com/InsightSoftwareConsortium/ITK/commit/b29dc9182e>) Style Changes - Reorder commands for locallity of reference (8626163a48 <https://github.com/InsightSoftwareConsortium/ITK/commit/8626163a48>) - Make alias variables to assist with clear documentation (56922b8d80 <https://github.com/InsightSoftwareConsortium/ITK/commit/56922b8d80>) - totalMassOfPDF == this->m_JointPDFSum by definition (982cfaec51 <https://github.com/InsightSoftwareConsortium/ITK/commit/982cfaec51>) Jean-Christophe Fillion-Robin (1): Platform Fixes - Fix -Wstrict-overflow warning in itkImageRegionConstIteratorWithIndex ( 93be179376 <https://github.com/InsightSoftwareConsortium/ITK/commit/93be179376>) Jon Haitz Legarreta Gorroño (5): Enhancements - Improve Thresholding module filters’ coverage. (e4507807e5 <https://github.com/InsightSoftwareConsortium/ITK/commit/e4507807e5>) - Change ivar name in `itk (e864411be3 <https://github.com/InsightSoftwareConsortium/ITK/commit/e864411be3>) - Avoid duplicated code in `itk (4217cc08a3 <https://github.com/InsightSoftwareConsortium/ITK/commit/4217cc08a3>) - Make the histogram generator set up method private (8f8b7ca7a4 <https://github.com/InsightSoftwareConsortium/ITK/commit/8f8b7ca7a4>) Bug Fixes - Fix threshold variable type/value in histogram threshold calc classes ( 5c114fec35 <https://github.com/InsightSoftwareConsortium/ITK/commit/5c114fec35>) Matt McCormick (25): Enhancements - Wrap unsigned long long for image reading writing (4febe70198 <https://github.com/InsightSoftwareConsortium/ITK/commit/4febe70198>) - Improve is_vector identification in image_from_xarray (69b90001ed <https://github.com/InsightSoftwareConsortium/ITK/commit/69b90001ed>) - Update CI testing virtual machine images (8463020847 <https://github.com/InsightSoftwareConsortium/ITK/commit/8463020847>) - Set Visual Studio toolset version in Python CI builds (8cd2bd66c7 <https://github.com/InsightSoftwareConsortium/ITK/commit/8cd2bd66c7>) - ndim, shape, and dtype attributes for itk.Image (a1763524ff <https://github.com/InsightSoftwareConsortium/ITK/commit/a1763524ff>) - Update testing data content links for 5.1.0 (d3286c9cc0 <https://github.com/InsightSoftwareConsortium/ITK/commit/d3286c9cc0>) Performance Improvements - PyBuffer importImageFilterWillOwnTheBuffer is constexpr (a306f50eff <https://github.com/InsightSoftwareConsortium/ITK/commit/a306f50eff>) Documentation Updates - Update ITKBibliography.bib link (e401d14d76 <https://github.com/InsightSoftwareConsortium/ITK/commit/e401d14d76>) - Release process updates for v5.1rc03 (e4e08332db <https://github.com/InsightSoftwareConsortium/ITK/commit/e4e08332db>) - Document how to handle operator<< link errors from enum libraries ( bced49ef65 <https://github.com/InsightSoftwareConsortium/ITK/commit/bced49ef65>) - Update .zenodo (1865c357d9 <https://github.com/InsightSoftwareConsortium/ITK/commit/1865c357d9>) Platform Fixes - Update CastXML binary for Visual Studio 2019 (ce5cf91651 <https://github.com/InsightSoftwareConsortium/ITK/commit/ce5cf91651>) - Remove unused calls in itkHashTableTest (fc88c718ed <https://github.com/InsightSoftwareConsortium/ITK/commit/fc88c718ed>) - Silence discarding return value in GE5ImageIO (da78c29634 <https://github.com/InsightSoftwareConsortium/ITK/commit/da78c29634>) - UnboundLocalError in _GetImageFromArray (97f281198c <https://github.com/InsightSoftwareConsortium/ITK/commit/97f281198c>) - Condition HDF5 HDopen on _MSC_VER definition (47a85f15a1 <https://github.com/InsightSoftwareConsortium/ITK/commit/47a85f15a1>) Bug Fixes - Correct image_view_from_array alias (26560ebc08 <https://github.com/InsightSoftwareConsortium/ITK/commit/26560ebc08>) - Reset m_Dimension in VideoFileWriter (136b8e462a <https://github.com/InsightSoftwareConsortium/ITK/commit/136b8e462a>) - Return type for PyBuffer _GetImageViewFromArray with VectorImage ( cd62423ed5 <https://github.com/InsightSoftwareConsortium/ITK/commit/cd62423ed5>) - Keep a reference to the NumPy array passed to itk.image_view_from_array (60afb52f5b <https://github.com/InsightSoftwareConsortium/ITK/commit/60afb52f5b>) - Use linspace for coords in xarray_from_image (67ddcde911 <https://github.com/InsightSoftwareConsortium/ITK/commit/67ddcde911>) - Provide initial input_type value in itkTemplate (1cf6dd01b5 <https://github.com/InsightSoftwareConsortium/ITK/commit/1cf6dd01b5>) - Keep itk.Image reference in NumPy array views (87bc23f723 <https://github.com/InsightSoftwareConsortium/ITK/commit/87bc23f723>) - Filters avoid extra copies when operating on NumPy arrays (8a8dfe5907 <https://github.com/InsightSoftwareConsortium/ITK/commit/8a8dfe5907>) - itk.CType to numpy.dtype types for Windows (7cd5889b1f <https://github.com/InsightSoftwareConsortium/ITK/commit/7cd5889b1f>) Simon Rit (2): Enhancements - update remote module RTK (319799698c <https://github.com/InsightSoftwareConsortium/ITK/commit/319799698c>) Bug Fixes - remove warning when writing 1D, 4D, 5D and 6D images read from disk ( 8932e7ccb7 <https://github.com/InsightSoftwareConsortium/ITK/commit/8932e7ccb7>) Stephen R. Aylward (2): Enhancements - Upgrade version of TubeTK (3de18fcf2e <https://github.com/InsightSoftwareConsortium/ITK/commit/3de18fcf2e>) - Added jacobian computation to ComposeScaleSkewVersorTransform (#1755) ( 2f38debfe3 <https://github.com/InsightSoftwareConsortium/ITK/commit/2f38debfe3>) VXL Maintainers (1): Miscellaneous Changes - 21e619bf69 (21e619bf69 <https://github.com/InsightSoftwareConsortium/ITK/commit/21e619bf69>) muschellij2 (2): Platform Fixes - Add CMAKE_SH definition for Eigen ExternalProject (b21c5f6001 <https://github.com/InsightSoftwareConsortium/ITK/commit/b21c5f6001>) - Fix HDF5 HDopen definition for MinGW (d997cb288f <https://github.com/InsightSoftwareConsortium/ITK/commit/d997cb288f>) ITK Examples Changes Since v5.1rc03 Dženan Zukić (1): Documentation Updates - update usage for ResampleAnImage (433c158a <https://github.com/InsightSoftwareConsortium/ITKExamples/commit/433c158a> ) Mathew Seng (6): Enhancements - Add python testing and I/O moved to Girder Python testing is now configured for this module. (dbe29b80 <https://github.com/InsightSoftwareConsortium/ITKExamples/commit/dbe29b80> ) Bug Fixes - Test expects failure, removing EXIT_FAILURE allows test to continue ( fbe2eaaf <https://github.com/InsightSoftwareConsortium/ITKExamples/commit/fbe2eaaf> ) - Change python enums to new v5 enum structure (de6e33be <https://github.com/InsightSoftwareConsortium/ITKExamples/commit/de6e33be> ) - Add exception for invalid keys that cannot be processed at runtime. ( a2fc2fbe <https://github.com/InsightSoftwareConsortium/ITKExamples/commit/a2fc2fbe> ) - Invalid vtk image being processed. Changed to use mushroom.vtk taken ITK test. (779409a4 <https://github.com/InsightSoftwareConsortium/ITKExamples/commit/779409a4> ) Style Changes - Prefer making deleted functions public Deleting a function affects fundamental aspects of the client interface of a class, and hiding them in private as if they were implementation details is unhelpful. (881346ff <https://github.com/InsightSoftwareConsortium/ITKExamples/commit/881346ff> ) Matt McCormick (10): Enhancements - Bump ITK External Project version to v5.1.0 (df2a71e2 <https://github.com/InsightSoftwareConsortium/ITKExamples/commit/df2a71e2> ) Documentation Updates - Update Sphinx date, copyright assignment (d41321f7 <https://github.com/InsightSoftwareConsortium/ITKExamples/commit/d41321f7> ) - Update links to Sphinx (7644858a <https://github.com/InsightSoftwareConsortium/ITKExamples/commit/7644858a> ) - Remove invalid label map article link (fdd95a86 <https://github.com/InsightSoftwareConsortium/ITKExamples/commit/fdd95a86> ) Platform Fixes - Update breathe for Sphinx compatibility (2216fcbe <https://github.com/InsightSoftwareConsortium/ITKExamples/commit/2216fcbe> ) - Update pyparsing for Python 3 (8032f868 <https://github.com/InsightSoftwareConsortium/ITKExamples/commit/8032f868> ) - Update doxylink for recent Sphinx (1426ac93 <https://github.com/InsightSoftwareConsortium/ITKExamples/commit/1426ac93> ) - Update breathelink for recent Sphinx (f8d6c7b0 <https://github.com/InsightSoftwareConsortium/ITKExamples/commit/f8d6c7b0> ) Bug Fixes - Correct ReadAndPrintDICOMTags output (880cee9c <https://github.com/InsightSoftwareConsortium/ITKExamples/commit/880cee9c> ) - Disable AdaptiveHistogramEqualization Python tests (7c0f4999 <https://github.com/InsightSoftwareConsortium/ITKExamples/commit/7c0f4999> ) ITK Software Guide Changes Since v5.1rc03 Jon Haitz Legarreta Gorroño (3): Enhancements - Add missing table borders in How To Create A Module chapter (7fd0894 <https://github.com/InsightSoftwareConsortium/ITKSoftwareGuide/commit/7fd0894> ) - Add section about tests for Wrapping files (fbb8615 <https://github.com/InsightSoftwareConsortium/ITKSoftwareGuide/commit/fbb8615> ) - Miscellaneous fixes in introduction and installation (a5f9673 <https://github.com/InsightSoftwareConsortium/ITKSoftwareGuide/commit/a5f9673> ) Matt McCormick (5): Enhancements - Bump ITK ExternalProject version to v5.1.0 (8d41ce7 <https://github.com/InsightSoftwareConsortium/ITKSoftwareGuide/commit/8d41ce7> ) - Add GitHub Action to build and publish Guide PDFs (68e2f9f <https://github.com/InsightSoftwareConsortium/ITKSoftwareGuide/commit/68e2f9f> ) Documentation Updates - Remove TreeContainer.tex input (6e78b83 <https://github.com/InsightSoftwareConsortium/ITKSoftwareGuide/commit/6e78b83> ) - Add GitHub Actions Build badge (f91ed71 <https://github.com/InsightSoftwareConsortium/ITKSoftwareGuide/commit/f91ed71> ) Bug Fixes - Remove CircleCI configuration (5e18abd <https://github.com/InsightSoftwareConsortium/ITKSoftwareGuide/commit/5e18abd> ) Remote Module Changes Since v5.1rc03 RTK: Antoine Robert (8): Enhancements - wrap image file reader and writer for dimension 1 (0832018a <https://github.com/SimonRit/RTK/commit/0832018a>) - wrap NumpyBridge for dimension 1 (72ed4dfb <https://github.com/SimonRit/RTK/commit/72ed4dfb>) - Add quadratic penalization to OSEM algorithm (b806c7e6 <https://github.com/SimonRit/RTK/commit/b806c7e6>) Platform Fixes - Fix wrapping when building ITK with dimension 1 (3a02b74f <https://github.com/SimonRit/RTK/commit/3a02b74f>) Bug Fixes - Use real image type as input of Hilbert filter (0d135b4d <https://github.com/SimonRit/RTK/commit/0d135b4d>) - Change member type from float to double in Zeng projectors (adb8061f <https://github.com/SimonRit/RTK/commit/adb8061f>) Style Changes - Use override instead of ITK_OVERRIDE (8db54152 <https://github.com/SimonRit/RTK/commit/8db54152>) - Use default member initialization (9ec2bc5d <https://github.com/SimonRit/RTK/commit/9ec2bc5d>) Aurélien Coussat (7): Enhancements - ProgressReporter for FDK reconstruction (4b2b1fd8 <https://github.com/SimonRit/RTK/commit/4b2b1fd8>) - filters check whether their geometry is set (40c0565d <https://github.com/SimonRit/RTK/commit/40c0565d>) - default projectors for all iterative filters (2c8ae75f <https://github.com/SimonRit/RTK/commit/2c8ae75f>) - set division threshold for SART (a0e604c7 <https://github.com/SimonRit/RTK/commit/a0e604c7>) Performance Improvements - reduced size of application tests (40f49ecc <https://github.com/SimonRit/RTK/commit/40f49ecc>) Bug Fixes - solve memory leak in rtkcheckimagequality (2a3eb595 <https://github.com/SimonRit/RTK/commit/2a3eb595>) Style Changes - fixed format in rtkIterationCommands.h (324f0609 <https://github.com/SimonRit/RTK/commit/324f0609>) Lucas Gandel (5): Enhancements - Add rtkSimulatedGeometry python application (1edbc560 <https://github.com/SimonRit/RTK/commit/1edbc560>) - Add ITK clang-format linter check (1a888880 <https://github.com/SimonRit/RTK/commit/1a888880>) - Apply clang-format to PR with tag action (974eb598 <https://github.com/SimonRit/RTK/commit/974eb598>) Platform Fixes - Set latest available itk version in setup.py (a6437840 <https://github.com/SimonRit/RTK/commit/a6437840>) Style Changes - Exclude gengetopt and lpsolve folders from clang formatting (590cf8f5 <https://github.com/SimonRit/RTK/commit/590cf8f5>) Simon Rit (14): Enhancements - use latest ITK v5.1 version for python packages (2683eed1 <https://github.com/SimonRit/RTK/commit/2683eed1>) - wrap RTK image IO (9a9d2141 <https://github.com/SimonRit/RTK/commit/9a9d2141>) Documentation Updates - change CMake variable name for RTK git tag (eeac6312 <https://github.com/SimonRit/RTK/commit/eeac6312>) Platform Fixes - remove MacOS and Windows self-hosted Cuda python packages (df54c6f7 <https://github.com/SimonRit/RTK/commit/df54c6f7>) - fix wrong header guard for rtkProgressCommands.h (e7e4c8d1 <https://github.com/SimonRit/RTK/commit/e7e4c8d1>) - fix missing ITKGDCM dependency (957d049e <https://github.com/SimonRit/RTK/commit/957d049e>) - remove warnings due to unhandled enum value (69b08d8e <https://github.com/SimonRit/RTK/commit/69b08d8e>) Bug Fixes - minimize disk space in Linux Azure pipelines to avoid saturation ( fed8944a <https://github.com/SimonRit/RTK/commit/fed8944a>) - wrong target libraries in FirstReconstruction examples (cf776249 <https://github.com/SimonRit/RTK/commit/cf776249>) - fix wrappings for 1D and double (b36a0442 <https://github.com/SimonRit/RTK/commit/b36a0442>) Style Changes - remove unused kernel parameter in Cuda forward projection (dcb015ee <https://github.com/SimonRit/RTK/commit/dcb015ee>) - fix ITK clang-format to a few RTK source files (bbcc5802 <https://github.com/SimonRit/RTK/commit/bbcc5802>) - fix ITK clang-format (84a0611c <https://github.com/SimonRit/RTK/commit/84a0611c>) Miscellaneous Changes - remove unused examples/CMakeLists.txt (a90d7738 <https://github.com/SimonRit/RTK/commit/a90d7738>) TubeTK: Stephen R. Aylward (5): Enhancements - Remove SVM and RandomForest methods and add ObjectDocuments Tests ( 4190dcba <https://github.com/InsightSoftwareConsortium/ITKTubeTK/commit/4190dcba>) - Bug Fixes - Make find_package(ITK) dependent (NOT ITK_SOURCE) (#4) (892a43bc <https://github.com/InsightSoftwareConsortium/ITKTubeTK/commit/892a43bc>) - Make find_package(ITK) dependent (NOT ITK_SOURCE) (#5) (30a909d2 <https://github.com/InsightSoftwareConsortium/ITKTubeTK/commit/30a909d2>) Miscellaneous Changes - 077e4a93 (077e4a93 <https://github.com/InsightSoftwareConsortium/ITKTubeTK/commit/077e4a93>) ------------------------------ Visit Topic <https://discourse.itk.org/t/itk-5-1-0-has-been-released/3164/1> or reply to this email to respond. To unsubscribe from these emails, click here <https://discourse.itk.org/email/unsubscribe/e3c1b641bf9af6c809a19fb6f7c37fa…> .

2 1

[Fwd] Please BuildRequire python3-setuptools explicitly
by Ankur Sinha 25 Jun '20

25 Jun '20

Hi folks, The list below isn't grouped by SIGs. I've taken care of all the packages that were listed under my name. Could everyone please go through the list and fix packages that they're primary maintainers for? It's a very simple change. You need to: - bump spec - add BuildRequires: %{py3_dist setuptools} - add new changelog entry - commit + push + build for master We can ignore the stable branches for this. When these packages are updated, we can merge master and proceed. Example commit: https://src.fedoraproject.org/rpms/python-pylatex/c/8968032a3907bda3831dd1c… Let me know if you need any help. ----- Forwarded message from Tomas Hrnciar <thrnciar(a)redhat.com> ----- > Date: Tue, 23 Jun 2020 18:26:23 +0200 > From: Tomas Hrnciar <thrnciar(a)redhat.com> > To: devel-announce(a)lists.fedoraproject.org, devel(a)lists.fedoraproject.org, > python-devel(a)lists.fedoraproject.org > Subject: Please BuildRequire python3-setuptools explicitly > > Hello everyone, > > there are plenty of Python packages in Fedora currently using setuptools at > buildtime but not all of them are BuildRequiring it explicitly. This only works > because python3-devel (transitively) depends on python3-setuptools. > > We would like to kindly ask you to add explicit BuildRequires for > python3-setuptools to packages where setuptools is used. It will help us with > testing new versions of setuptools in the future or with decoupling Python and > setuptools. Today, if we want to know if a package is using setuptools, we have > to do `fedpkg prep` and use grep to search for setuptools. Using a repoquery is > much more convenient. > > Several packages can successfully build either with or without setuptools (they > use try-except import and fallback to distutils from the standard library). > Such packages are especially dangerous when not BuildRequiring setuptools -- > they can produce different results depending on the presence of setuptools: > either an .egg-info metadata directory (w/setuptools) or .egg-info text file (w > /distutils). RPM has troubles when upgrading directories to files [1]. > > [1] https://docs.fedoraproject.org/en-US/packaging-guidelines/ > Directory_Replacement/ > > According to our grep based query on Fedora Rawhide, there are 621 known > packages using setuptools without BuildRequiring it at this point: > > Thank you very much for your help with this. > > On behalf of python-setuptools maintainers, > Tomáš Hrnčiar > > Maintainers by package: > 0ad ignatenkobrain pcpa pwalter > APLpy sergiopr skytux > COPASI sagitter > OpenMolcas jussilehtola > ProDy sagitter > PyGreSQL hhorak jmlich odubaj panovotn pkajaba pkubat praiskup > PySolFC sergiomb shlomif > R2spec pingou > ViTables tnorth zbyszek > androguard fab > ansible-review dcallagh ttrinks > artifacts fab > borgmatic heffer > btrfs-sxbackup thofmann > bumpversion duriantang jdornak > cantoolz fab > cinch greghellings > commissaire-client mbarnes smilner > compose-utils lsedlar > condor bbockelm bcotton eerlands matt matyas stevetraylen > tstclair ttheisen valtri > congruity adamwill swt2c > copr-messaging schlupov > copydeps suve > cppcheck c72578 jussilehtola sgrubb > cranc lenkaseg > crudini apevec jruzicka pbrady > cxxtest mgieseki > datanommer ralph > dblatex alexlan jchaloup mjg > dnstwist suve > dogtag-pki cipherboy dmoluguw edewata kwright mharmsen vakwetu > dolfin limb zbyszek > dot2tex thofmann > electrum jonny > expliot fab > fail2ban atkac hobbes1069 jgu orion > fedora-messaging abompard > file kdudka macermak odubaj svashisht vmihalko > flatcam dwrobel > flawfinder athoscr > flent adrian tohojo > fontdump pnemade > fontforge frixxon kevin pnemade > fonttools pnemade tagoh > freeipa-healthcheck abbra cheimes fcami mkosek pvoborni rcritten twoerner > frescobaldi limb > gajim michich > gau2grid jussilehtola > gdal alexlan devrim jmlich mmahut neteler oliver orion pali > praiskup smani volter > gedit-plugin-editorconfig ferdnyc > gfal2-python adev andreamanzi gbitzes > ginga lupinix > git-filter-repo asn > git-up mhjacks > gns3-gui kwizart > gns3-net-converter kwizart > gns3-server kwizart nucleo > gtimelog amigadave > h5py stevetraylen terjeros > hashid fab > hgview kiilerix > home-assistant-cli fab > httpie codeblock ralph > inception fab > inkscape duffy jgu limb lkundrak > ioc-writer fab > irclog2html fab > isrcsubmit amigadave > koji ausil kevin mikem puiterwijk > lammps ellio167 junghans > legendary atim > legofy lkf williamjmorenor > libCombine sagitter > libcaca hubbitus slaanesh thias > libolm xvitaly > librealsense thofmann > libreoffice caolanm dtardon erack sbergmann > libxc jussilehtola > lldb airlied daveisfera jankratochvil sergesanspaille > siddharths tstellar > llvm dmalcolm ignatenkobrain jakub jistone kyle scottt > sergesanspaille siddharths tstellar > llvm7.0 jistone petersen sergesanspaille tstellar > llvm9.0 jistone sergesanspaille tstellar > mercurial kiilerix nbecker pstodulk > mgarepo misc ngompa > minigalaxy atim > mkdocs-bootstrap cheeselee > mkdocs-cinder cheeselee > mkdocs-material cheeselee > mod_wsgi jdornak jkaluza jorton lmacken mrunge > modtools dhodovsk phracek ttomecek > modulemd-tools frostyx > moose zbyszek > mopidy-mpd girst > mozjs68 frantisekz kalev > mpi4py deji limb tomspur > mypaint avsej > mysql-connector-python hhorak hubbitus hvad mschorm > nodejs mrunge patches piotrp sgallagh zvetlik > nototools mfabian pwu > officeparser rebus > offlineimap cicku dodji notting sergesanspaille teuf > ogr2osm musuruan > opae aravuri nkorde trix > openbabel itamarjp jussilehtola rathann > oval-graph hony > past-time fab > pcapy limb > pcp agerstmayr lberk mgoodwin nathans > pcp2pdf lberk mbaldessari > pdfarranger dreua fab fschwarz > pdfposter fab > percol hubbitus > petsc sagitter > petsc4py sagitter > picard alexlan cicku gbcox ohaessler > pipsi cstratak mstuchli > pipx mhjacks > pki-core cipherboy dmoluguw edewata kwright mharmsen vakwetu > poezio fantom louizatakk > porcupine kushal > portmidi eeickmeyer mjg xavierb > protonvpn-cli jflory7 > prunerepo clime frostyx > py-bcrypt kevin limb > py3c pviktori > pyaudio chkr > pybluez limb > pycolumnize fab kushal > pyephem elwell orphan > pygobject3 johnp nacho walters > pygsl jamatos > pyhunspell mfabian till > pykka fab > pylast fab peter > pylibacl frankcrawford kevin szpak > pyodbc fjanus hhorak > pyosmium tomh > pyproj jdekloe > pyscard sjenning > pyserial stingray > pysubnettree fab > python-CommonMark jujens > python-GeoIP pingou ralph sergiomb totol > python-GridDataFormats rathann > python-OBD rathann > python-PyLEMS ankursinha > python-Pyped uggla > python-Rtree volter > python-SALib ankursinha > python-acme jhogarth nb > python-acoustid terjeros > python-agate jujens > python-aiodns fantom > python-airspeed ankursinha > python-alsa limb perex > python-aniso8601 jsedlak kparal > python-ansicolors skisela > python-apipkg fab ktdreyer thm > python-apprise lead2gold > python-apsw cicku dfateyev maci > python-arviz sergiopr > python-ase besser82 marcindulak > python-astral fab > python-astroplan sergiopr > python-astropy-healpix lupinix > python-astroquery lupinix > python-astroscrappy lupinix > python-asttokens zbyszek > python-asyncssh gsauthof > python-audioread terjeros > python-autobahn jujens > python-autopep8 mrunge ndipanov > python-babelfish jorti > python-basemap jspaleta limb > python-betamax-matchers fab > python-betamax-serializers fab > python-bigsuds xavierb > python-biopython alexlan lbazan rathann sagitter > python-bloom cottsay rmattes > python-blosc tnorth zbyszek > python-box dmsimard > python-btchip jonny xenithorb > python-cached_property adamwill immanetize > python-cachetools jeckersb > python-cachez eharney > python-carbon jsteffan piotrp > python-ccdproc lupinix > python-certbot-apache jhogarth nb > python-chai kevin pingou ralph > python-click-plugins qulogic > python-cloud-sptheme kevin ralph > python-cmigemo hubbitus > python-colorlog fab > python-colorspacious rathann > python-conda-package-handling orion > python-construct moezroy terjeros > python-contextlib2 abompard pingou ralph tjikkun > python-convertdate fab > python-cookiecutter wakko666 > python-coveralls bcl > python-crcelk fab > python-crochet abompard > python-css-parser zbyszek > python-dateparser fab limb > python-dbfread jujens > python-debrepo ktdreyer > python-decopatch zbyszek > python-descartes qulogic > python-dfdatetime fab > python-dialog itamarjp mjakubicek noodles raphgro sundaram zbyszek > python-diff-match-patch amigadave > python-dijitso zbyszek > python-dill sergiopr > python-django bkabrda churchyard jdornak mrunge rdopiera salimma > sgallagh > python-django-contact-form mrunge > python-django-formtools jpena mrunge > python-django-health-check dmsimard > python-django-registration kumarpraveen > python-django-reversion mrunge > python-django-tagging jdornak mrunge piotrp > python-django-tastypie bkabrda cquad mrunge stevetraylen > python-djangoql vkrizan > python-docx kushal124 > python-dpkt mbaldessari > python-dtfabric fab > python-duecredit ankursinha > python-dukpy zbyszek > python-dulwich fab > python-edgegrid rohanpm > python-editdistance major > python-editorconfig barracks510 > python-efel ankursinha > python-emcee sergiopr > python-emoji xvitaly > python-enthought-sphinx-theme orion > python-enzyme jorti > python-et_xmlfile jujens > python-etcd mbarnes smilner > python-faker jorti > python-fasteners mrunge > python-fastpurge rohanpm > python-feedgenerator ankursinha > python-ffc zbyszek > python-fiat fab > python-fido2 orion > python-fields cottsay > python-filetype fab > python-firkin fab > python-fisx zbyszek > python-fitsio lupinix > python-flake8-docstrings cottsay > python-flask-gravatar devrim itamarjp > python-flask-htmlmin devrim itamarjp > python-flask-paranoid devrim itamarjp > python-flask-rstpages rmarko > python-flask-security devrim itamarjp > python-flask-sphinx-themes devrim itamarjp > python-formats uggla > python-fs pnemade > python-fsleyes ankursinha > python-fsleyes-props ankursinha > python-fsleyes-widgets ankursinha > python-fslpy ankursinha > python-fuse jorti > python-fypp rathann > python-geopandas qulogic > python-gevent dcallagh ignatenkobrain orion skottler > python-giacpy sagitter > python-glances-api fab > python-gsd rathann > python-guessit jorti > python-heapdict qulogic > python-hl7 ankursinha > python-hole fab > python-html5-parser kevin > python-htmlmin jujens > python-humblewx rickardlindberg > python-hupper kevin > python-i3ipc msimacek > python-idstools jtaylor marcindulak > python-ifcfg cottsay > python-igraph bstinson limb pingou > python-img2pdf gsauthof > python-indexed_gzip ankursinha > python-inema gsauthof > python-inotify jfilak stevetraylen terjeros > python-inotify_simple praiskup > python-instant fab > python-intervaltree mikep > python-ipykernel churchyard pcpa > python-ipyparallel ellert > python-iso-639 melmorabity > python-iso3166 melmorabity > python-javalang fab > python-jep raphgro > python-jinja2-cli jujens > python-jinja2-time wakko666 > python-jnius raphgro > python-joblib besser82 ignatenkobrain sergiopr > python-journal-brief twaugh > python-jsonmodels oanson > python-jsonrpclib ihrachyshka jonny > python-junit_xml jhogarth > python-kaitaistruct rathann > python-kdcproxy rharwood > python-kerberos rcritten simo > python-kitchen kevin pingou ralph > python-kiwisolver qulogic > python-klusta ankursinha > python-landslide echevemaster > python-lark-parser totol > python-leather jujens > python-libNeuroML ankursinha > python-libnacl jonny sergiomb > python-libsass dormouse > python-libusb1 jonny > python-lmdb pspacek > python-logzero somlo > python-luftdaten fab > python-lunr cheeselee > python-m2r nforro > python-makefun zbyszek > python-mapnik tomh > python-markdown2 thm > python-matplotlib-scalebar ankursinha > python-mdp zbyszek > python-mdx_gh_links cheeselee > python-meld3 kevin stevetraylen tsao > python-metakernel ellert > python-metar jdekloe thias > python-migen somlo > python-minibelt uggla > python-mmtf rathann > python-mnemonic jonny > python-mongoquery mkrizek > python-more-executors rohanpm > python-more-itertools aarem churchyard jcaratzas > python-music21 zbyszek > python-mutagen cicku ignatenkobrain mbaldessari moezroy > python-mwclient adamwill rdieter tuxbrewr > python-myhdl filiperosset > python-mystrom fab > python-ndg_httpsclient churchyard fschwarz itamarjp noodles > python-netdata fab > python-networkmanager jdulaney > python-neurodsp major > python-nilearn ankursinha > python-nistats ankursinha > python-nitime ankursinha > python-nixio ankursinha > python-nmrglue nonamedotc > python-node-semver xvitaly > python-notario ktdreyer > python-oauth2 ignatenkobrain pjp spot sundaram > python-octave-kernel qulogic > python-odml major > python-oletools rebus robert > python-opendata-transport fab > python-openoffice sharkcz > python-opensensemap-api fab > python-paho-mqtt fab > python-pandas-datareader sergiopr > python-partd qulogic > python-paste-script andreamanzi dcallagh > python-patch-ng xvitaly > python-pathlib2 pcpa > python-patsy sergiopr > python-pbkdf2 jonny > python-pcodedmp robert > python-pdfrw fschwarz sergiopr slaanesh > python-pecan-notario ktdreyer > python-pelican firemanxbr mrunge > python-pep8-naming qulogic > python-periodictable sagitter > python-persist-queue eharney > python-petlink ankursinha > python-pexpect amcnabb fabiand ignatenkobrain radez swt2c tomspur > python-photutils sergiopr > python-pingouin ankursinha > python-pkginfo decathorpe fab pcreech17 > python-plaster-pastedeploy abompard > python-play-scraper fab > python-plumbum greghellings lorenzodalrio > python-pocketlint jkonecny vtrefny > python-polib cicku dchen diegobz dshea ivazquez moezroy suanand > python-poyo wakko666 > python-prawcore fab > python-precis_i18n michich > python-proteus sharkcz > python-psutil salimma > python-publicsuffix2 rathann > python-pulsectl pfrields > python-pvc raphgro > python-pycares fantom > python-pycha potty sharkcz > python-pycosat orion > python-pycurl jsynacek kdudka msekleta svashisht > python-pydocstyle tadej > python-pyeclib hguemar zaitcev > python-pyelectro ankursinha > python-pyemd ankursinha > python-pygeoip kevin ralph > python-pylatex ankursinha > python-pylons-sphinx-themes abompard > python-pymatreader ankursinha > python-pyotp icon > python-pypcapkit fab > python-pypet ankursinha > python-pypng kevin ralph > python-pypubsub swt2c > python-pyramid_sawing abompard > python-pyrfc3339 fschwarz itamarjp jhogarth noodles > python-pysb zbyszek > python-pysignals kni > python-pysrt jorti > python-pytelegrambotapi xvitaly > python-pytest-aiohttp fab > python-pytest-astropy-header sergiopr > python-pytest-benchmark jorti > python-pytest-cases zbyszek > python-pytest-faulthandler dkrejci lbalhar > python-pytest-fixture-config kevin > python-pytest-forked swt2c > python-pytest-harvest zbyszek > python-pytest-lazy-fixture ankursinha > python-pytest-mock jujens > python-pytest-repeat cottsay > python-pytest-shutil kevin > python-pytest-steps zbyszek > python-pytest-timeout swt2c > python-pytest-tornado qulogic > python-pytest-vcr limb > python-pytest-virtualenv kevin > python-pytest-watch jujens > python-pytest-xdist swt2c > python-pyvit fab > python-pyvo lupinix > python-queuelib fab > python-rarfile fab > python-rebulk jorti > python-recommonmark jujens > python-relatorio sharkcz > python-rencode jgu orion patches > python-reportlab sagitter > python-represent dkrejci lbalhar > python-reproject lupinix > python-requests-cache codeblock hobbes1069 > python-requests-futures fab > python-restructuredtext-lint jujens > python-retrying apevec > python-retryz eharney > python-rmtest lberk mgoodwin nathans > python-rope nonamedotc > python-rosdep cottsay rmattes thofmann > python-rpmautospec asaleh nphilipp > python-sanction kevin ralph > python-scales filabrazilska lbalhar lkundrak 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python-construct python-mutagen python-polib python-xlwt > mooninite wine-mono > mrunge mod_wsgi nodejs python-autopep8 python-django > python-django-contact-form python-django-formtools python-django-reversion > python-django-tagging python-django-tastypie python-fasteners python-pelican > python-webpy python-xvfbwrapper > mschorm mysql-connector-python > msekleta python-pycurl > msimacek python-i3ipc > mstuchli pipsi > msuchy python-testing.postgresql > musuruan ogr2osm > mvadkert rpmdeplint > nacho pygobject3 > nathans pcp python-rmtest > nb python-acme python-certbot-apache > nbecker mercurial tortoisehg > ndipanov python-autopep8 > neteler gdal > nforro python-m2r > ngompa mgarepo > nkorde opae > nonamedotc python-nmrglue python-rope spyder > noodles python-dialog python-ndg_httpsclient python-pyrfc3339 > notting offlineimap > nphilipp python-rpmautospec rpmspectool > nucleo gns3-server > oanson python-jsonmodels > obnox samba > odubaj PyGreSQL file > ohaessler picard > oliver 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puiterwijk koji > pviktori py3c > pvoborni freeipa-healthcheck > pwalter 0ad scribus > pwouters python-xml2rfc > pwu nototools > quintela qemu > qulogic python-click-plugins python-descartes python-geopandas > python-heapdict python-kiwisolver python-octave-kernel python-partd > python-pep8-naming python-pytest-tornado python-tblib python-zict > radez python-pexpect > ralph datanommer httpie python-GeoIP python-chai python-cloud-sptheme > python-contextlib2 python-kitchen python-pygeoip python-pypng python-sanction > python-sieve python-simplemediawiki python-virtualenv-clone python-xmltodict > raphgro python-dialog python-jep python-jnius python-pvc > rathann openbabel python-GridDataFormats python-OBD python-biopython > python-colorspacious python-fypp python-gsd python-kaitaistruct python-mmtf > python-publicsuffix2 python-tempdir python-xlwt python-zstandard solaar > rcritten freeipa-healthcheck python-kerberos > rdieter python-mwclient > rdopiera python-django > rebus officeparser python-oletools > rharwood python-kdcproxy > richardfearn solaar > rickardlindberg python-humblewx > rjones qemu > rmarko python-flask-rstpages > rmattes python-bloom python-rosdep > robert python-oletools python-pcodedmp > rohanpm python-edgegrid python-fastpurge python-more-executors > sagitter COPASI ProDy libCombine petsc petsc4py python-biopython > python-giacpy python-periodictable python-reportlab seqan spglib > salimma python-django python-psutil > sbergmann libreoffice > schlupov copr-messaging > scottt llvm > sergesanspaille lldb llvm llvm7.0 llvm9.0 offlineimap xtensor-python > sergiomb PySolFC python-GeoIP python-libnacl > sergiopr APLpy python-arviz python-astroplan python-dill python-emcee > python-joblib python-pandas-datareader python-patsy python-pdfrw > python-photutils python-pytest-astropy-header python-scikit-learn > python-statsmodels > sgallagh nodejs python-django > sgrubb cppcheck > sharkcz python-openoffice python-proteus python-pycha python-relatorio > python-sql scribus tryton trytond trytond-account trytond-account-be > trytond-account-de-skr03 trytond-account-invoice > trytond-account-invoice-history trytond-account-invoice-line-standalone > trytond-account-product trytond-account-statement > trytond-account-stock-anglo-saxon trytond-account-stock-continental > trytond-analytic-account trytond-analytic-invoice trytond-analytic-purchase > trytond-analytic-sale trytond-company trytond-company-work-time trytond-country > trytond-currency trytond-dashboard trytond-google-maps > trytond-ldap-authentication trytond-party trytond-party-siret trytond-product > trytond-product-cost-fifo trytond-product-cost-history > trytond-product-price-list trytond-project trytond-project-plan > trytond-project-revenue trytond-purchase > trytond-purchase-invoice-line-standalone trytond-sale trytond-sale-opportunity > trytond-sale-price-list trytond-stock trytond-stock-forecast > trytond-stock-inventory-location trytond-stock-location-sequence > trytond-stock-product-location trytond-stock-supply trytond-stock-supply-day > trytond-timesheet > shlomif PySolFC > siddharths lldb llvm > simo python-kerberos samba > simonm xrootd > sjenning pyscard yubikey-manager > skisela python-ansicolors > skottler python-gevent > skytux APLpy > slaanesh libcaca python-pdfrw > smani gdal > smilner commissaire-client python-etcd > somlo python-logzero python-migen > spot python-oauth2 texlive-base winpdb > stevetraylen condor h5py python-django-tastypie python-inotify python-meld3 > stomppy > stingray pyserial > suanand python-polib python-tinydb translate-toolkit > sundaram python-dialog python-oauth2 python-unidecode > suve copydeps dnstwist python-ssdeep > svashisht file python-pycurl > swt2c congruity python-pexpect python-pypubsub python-pytest-forked > python-pytest-timeout python-pytest-xdist python-suds > szpak pylibacl pyxattr > tachoknight swift-lang > tadej python-pydocstyle python-virtualenv-clone > tagoh fonttools > tdecacqu python-statsd > terjeros h5py python-acoustid python-audioread python-construct > python-inotify > teuf offlineimap > thias libcaca python-metar > thm python-apipkg python-markdown2 > thofmann btrfs-sxbackup dot2tex librealsense python-rosdep shyaml > thozza spyder > tibbs solaar > till pyhunspell > timj rpl > tjikkun python-contextlib2 > tnorth ViTables python-blosc python-tables > tohojo flent > tomh pyosmium python-mapnik > tomspur mpi4py python-pexpect > totol python-GeoIP python-lark-parser python-xvfbwrapper > tripledes scribus > trix opae > tsao python-meld3 > tstclair condor > tstellar lldb llvm llvm7.0 llvm9.0 > ttheisen condor > ttomecek modtools python-urwidtrees > ttrinks ansible-review > turboturtle sos-collector > tuxbrewr python-mwclient > twaugh python-journal-brief > twoerner freeipa-healthcheck > uggla python-Pyped python-formats python-minibelt python-tortilla > vakwetu dogtag-pki pki-core > valtri condor > vcrhonek yawn > vkrizan python-djangoql > vmihalko file > vmojzis sepolicy_analysis > volter gdal python-Rtree > vtrefny python-pocketlint > wakko666 python-cookiecutter python-jinja2-time python-poyo > python-tree-format > walters pygobject3 > williamjmorenor legofy > xavierb portmidi python-bigsuds > xenithorb python-btchip > xvitaly libolm python-emoji python-node-semver python-patch-ng > python-pytelegrambotapi python-wloc > zaitcev python-pyeclib > zbyszek ViTables dolfin moose python-asttokens python-blosc > python-css-parser python-decopatch python-dialog python-dijitso python-dukpy > python-ffc python-fisx python-makefun python-mdp python-music21 python-pysb > python-pytest-cases python-pytest-harvest python-pytest-steps python-soupsieve > python-tables > zvetlik nodejs > ----- End forwarded message ----- -- Thanks, Regards, Ankur Sinha "FranciscoD" (He / Him / His) | https://fedoraproject.org/wiki/User:Ankursinha Time zone: Europe/London

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Re: Please BuildRequire python3-setuptools explicitly
by Ankur Sinha 25 Jun '20

25 Jun '20

Thanks for the list. > ankursinha python-PyLEMS python-SALib python-airspeed python-duecredit > python-efel python-feedgenerator python-fsleyes python-fsleyes-props > python-fsleyes-widgets python-fslpy python-hl7 python-indexed_gzip > python-klusta python-libNeuroML python-matplotlib-scalebar python-nilearn > python-nistats python-nitime python-nixio python-petlink python-pingouin > python-pyelectro python-pyemd python-pylatex python-pymatreader python-pypet > python-pytest-lazy-fixture python-sciunit python-steps python-tasklib I've updated all of these apart from nistats which I'm waiting to retire. There are a few more neuro-sig packages in the list, but I'll wait for the primary maintainers to look into them before I start touching them. -- Thanks, Regards, Ankur Sinha "FranciscoD" (He / Him / His) | https://fedoraproject.org/wiki/User:Ankursinha Time zone: Europe/London

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Fwd: [fil.meetings] [fil.dept] UCL Neuroscience Symposium this Friday
by Morgan Hough 22 Jun '20

22 Jun '20

---------- Forwarded message --------- From: Tim Behrens <behrens(a)fmrib.ox.ac.uk> Date: Mon, Jun 22, 2020 at 00:51 Subject: Re: [fil.meetings] [fil.dept] UCL Neuroscience Symposium this Friday To: IoN.FIL BrainMeetings <ion.fil.brainmeetings(a)ucl.ac.uk> CC: fil.meetings <fil.meetings(a)ucl.ac.uk> Dear friends - If you find yourselves bereft of intellectual stimulation over the summer months due to the absence of the Brain Meeting, you will be delighted to know that your sister centre in Oxford is organising a “Summer of Neuroscience” series. This can be found by going to worldwideneuro.com and clicking on "Oxford WINeuro”. So far there are only 4 talks scheduled, but more will be appearing every day. Delighted to be the bearer of such stimulating news. T On 22 Jun 2020, at 08:43, IoN.FIL BrainMeetings < ion.fil.brainmeetings(a)ucl.ac.uk> wrote: Dear all, Now that we've come to the end of the 2019-20 Brain Meetings I'd like to take this opportunity to give a big thank you to the Committee - Gabrielle Sheehan, Elisa van der Plas and Justyna Ekert - for all their hard work behind the scenes. This year was particularly unusual of course in needing a rapid adjustment to remote talks and Zoom which they handled with considerable grace and efficiency, ensuring that there was only a brief interruption to normal service. I'm also glad to say that Gabrielle has offered to continue on to be part of next year's committee, where she will be joined by Joost Haarsma, a new postdoc in Peter Kok's group. Welcome Joost! They will be in touch in due course with details of next year's calendar which kicks off on 18th September. While there is no Brain Meeting this Friday afternoon, we would encourage everyone instead to attend the virtual UCL Neuroscience Symposium (1pm-430pm), where our very own Peter Kok is one of the keynote speakers, and Max Rollwage and Yunzhe Liu will receive their Jon Driver Prizes. So lots of things for the Centre to celebrate! Attendance is free but you need to register in advance here: https://www.eventbrite.com/e/ucl-neuroscience-symposium-2020-online-tickets… <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.event…> Best wishes Steve

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Fwd: OHBM 2020 Virtual Brainhack: June 16-18
by Morgan Hough 11 Jun '20

11 Jun '20

---------- Forwarded message --------- From: Cameron Craddock <brainhackorg(a)gmail.com> Date: Thu, Jun 11, 2020 at 10:45 Subject: OHBM 2020 Virtual Brainhack: June 16-18 To: <morgan.hough(a)gmail.com> Dear Members of the Neuroscience Community, *** Apologies for cross-posting and any inconvenience. *** This year Brainhack collaborates with OHBM Brainhack and & OHBM Open Science Special Interest Group (OS-SIG) Team to bring its first virtual Brainhack experience to the neuroscience community in which everyone can attend and contribute from their homes! For that purposes, we would like to individually raise your attention and ask for your contributions to this very exciting event as project leaders, attendees, and helpers for the various opportunities provided by the OHBM this year! The event will be held online, June 16-18 throughout 3 main hubs all around the world: Asia Pacific Hub, Europe - Middle East - Africa Hub, and Americas Hub. Each hub will run at a different time, with a common program <https://brainhack.dmanalytics2.com/click?u=https%3A%2F%2Fohbm.github.io%2Fh…> shared across the 3 hubs. You can attend any hub that you think you would like to engage in too. Registrations are still open and project submissions are still going on! The registrations are taken from here! <https://brainhack.dmanalytics2.com/click?u=http%3A%2F%2Fwww.humanbrainmappi…> The event also comes with 50 mini-grants, each worth 100 USD each to help Brainhack attendees set up for online conferencing. Apply via the link above . And as we all have a project or two that could benefit from a 3 days immersion in an environment of collaborative research, once you have registered we would love for you to submit a project here <https://brainhack.dmanalytics2.com/click?u=https%3A%2F%2Fgithub.com%2Fohbm%…> . We are also looking for volunteers to join our growing team <https://brainhack.dmanalytics2.com/click?u=https%3A%2F%2Fohbm.github.io%2Fh…> and to help us to make this event accessible and helpful for many. So you can take part in helping and running the events in hubs as signing up for any of the Website team, Host for the welcome desk, Helpdesk, Brainhack Buddies, Social Media team roles listed here <https://brainhack.dmanalytics2.com/click?u=https%3A%2F%2Fpad.inria.fr%2Fp%2…> . For more information and to learn about the already submitted projects please visit the 2020 OHBM Brainhack website <https://brainhack.dmanalytics2.com/click?u=https%3A%2F%2Fohbm.github.io%2Fh…>, the OS-SIG website <https://brainhack.dmanalytics2.com/click?u=http%3A%2F%2Fossig.netlify.com%2…> , follow @OHBMopen <https://brainhack.dmanalytics2.com/click?u=https%3A%2F%2Ftwitter.com%2Fohbm…> on Twitter or follow the OHBM WeChat official account. If you have any questions, please reach out to the organizers at ossig2019(a)inria.fr or you can contact Brainhack official email address brainhackorg(a)gmail.com. Please do not hesitate to circulate this email among your colleagues and institute members! Thank you very much all of your contributions in advance, Kind regards, On the behalf of the Brainhack Organisation & 2020 OHBM BrainhackTeams Cameron Craddock Associate Professor of Diagnostic Medicine, Dell Medical School at the University of Texas at Austin Director, Computational Neuroimaging Lab <https://brainhack.dmanalytics2.com/click?u=http%3A%2F%2Fcomputational-neuro…> Founding Chair, Organization for Human Brain Mapping Open Science Special Interest Group Co-Founder, The Neuro Bureau <https://brainhack.dmanalytics2.com/click?u=http%3A%2F%2Fneurobureau.org%2F&…> Impact Story <https://brainhack.dmanalytics2.com/click?u=https%3A%2F%2Fimpactstory.org%2F…> Google Scholar Citations <https://brainhack.dmanalytics2.com/click?u=http%3A%2F%2Fscholar.google.com%…> GitHub <https://brainhack.dmanalytics2.com/click?u=https%3A%2F%2Fgithub.com%2Fccrad…> SlideShare <https://brainhack.dmanalytics2.com/click?u=http%3A%2F%2Fwww.slideshare.net%…> Brainhack Global 2020 Organizing Committee Website: http://brainhack.org <https://brainhack.dmanalytics2.com/click?u=http%3A%2F%2Fbrainhack.org%2F&i=…> Twitter/Github: @brainhackorg Unsubscribe <https://brainhack.dmanalytics2.com/delivery-unsubscribe?d=tJLsjnVQQgePgqrhB…> [image: Direct Mail for Mac] <https://brainhack.dmanalytics2.com/about-dm?utm_source=pd-ftr&utm_medium=em…> This email is powered by Direct Mail for Mac. Learn More <https://brainhack.dmanalytics2.com/about-dm?utm_source=pd-ftr&utm_medium=em…> • Report Spam <https://brainhack.dmanalytics2.com/report-spam?d=tJLsjnVQQgePgqrhB772Dw&e=m…>

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[Fwd] Upcoming Fedora 33 Change proposal deadlines
by Ankur Sinha 11 Jun '20

11 Jun '20

Hi! Just a note of this announcement. NeuroFedora does not currently have any changes to submit. We've not made nearly enough progress on the neuro-imaging side to propose a lab image. We'll continue working on the comp-neuro packages, and add more to the image so that the F33 comp-neuro lab image has even more software in it. Does anyone have a change proposal in mind that we need to discuss? ----- Forwarded message from Ben Cotton <bcotton(a)redhat.com> ----- > Date: Wed, 10 Jun 2020 13:56:28 -0400 > Subject: Upcoming Fedora 33 Change proposal deadlines > Archived-At: <https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org…> > > This is your reminder that several Change proposal deadlines for > Fedora 33 are approaching. > > * 2020-06-24: Proposal deadline for Changes requiring infrastructure changes > * 2020-06-30: Proposal deadline for Changes requiring mass rebuild > * 2020-06-30: Proposal deadline for System-Wide Changes > * 2020-07-21: Proposal deadline for Self-Contained Changes > > For the full schedule, see > https://fedorapeople.org/groups/schedule/f-33/f-33-key-tasks.html > > -- > Ben Cotton > He / Him / His > Senior Program Manager, Fedora & CentOS Stream > Red Hat > TZ=America/Indiana/Indianapolis > _______________________________________________ > devel mailing list -- devel(a)lists.fedoraproject.org > To unsubscribe send an email to devel-leave(a)lists.fedoraproject.org > Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ > List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines > List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org ----- End forwarded message ----- -- Thanks, Regards, Ankur Sinha "FranciscoD" (He / Him / His) | https://fedoraproject.org/wiki/User:Ankursinha Time zone: Europe/London

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Neuron error
by Mohácsi Máté 11 Jun '20

11 Jun '20

Dear All, I'm encountering another neuron error (probably efel related). It started occuring on the 4th of June (maybe some update). I used the same code before and worked. The error is the following. /usr/include/c++/10/bits/stl_vector.h:1060: std::vector<_Tp, _Alloc>::const_reference std::vector<_Tp, _Alloc>::operator[](std::vector<_Tp, _Alloc>::size_type) const [with _Tp = int; _Alloc = std::allocator<int>; std::vector<_Tp, _Alloc>::const_reference = const int&; std::vector<_Tp, _Alloc>::size_type = long unsigned int]: Assertion '__builtin_expect(__n < this->size(), true)' failed. Thanks and Regards, Máté

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Updating arbor
by Antonio T. sagitter 08 Jun '20

08 Jun '20

Hi all. I have updated `arbor` to the release 0.3 If you agree, i will push this new package. Rebuilds of Arbor on Copr: https://copr.fedorainfracloud.org/coprs/sagitter/ForTesting/build/1428792/ -- --- Antonio Trande Fedora Project mailto: sagitter(a)fedoraproject.org GPG key: 0x7B30EE04E576AA84 GPG key server: https://keys.openpgp.org/

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