morphio 3.3.2__tar.gz → 3.3.4__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (457) hide show
  1. {MorphIO-3.3.2 → MorphIO-3.3.4}/.github/workflows/check-sdist.yml +4 -4
  2. {MorphIO-3.3.2 → MorphIO-3.3.4}/.github/workflows/clang_format_check.yaml +3 -1
  3. {MorphIO-3.3.2 → MorphIO-3.3.4}/.github/workflows/coverage_test.yaml +1 -1
  4. {MorphIO-3.3.2 → MorphIO-3.3.4}/.github/workflows/docstring_check.yaml +1 -1
  5. {MorphIO-3.3.2 → MorphIO-3.3.4}/.github/workflows/publish-sdist-wheels.yml +51 -14
  6. {MorphIO-3.3.2 → MorphIO-3.3.4}/.github/workflows/run-tests.yml +17 -8
  7. {MorphIO-3.3.2 → MorphIO-3.3.4}/.gitignore +1 -0
  8. {MorphIO-3.3.2 → MorphIO-3.3.4}/.gitmodules +4 -1
  9. {MorphIO-3.3.2 → MorphIO-3.3.4}/.readthedocs.yaml +12 -2
  10. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/CMakeLists.txt +0 -6
  11. MorphIO-3.3.4/3rdparty/GSL_LITE/CMakeLists.txt +197 -0
  12. MorphIO-3.3.4/3rdparty/GSL_LITE/cmake/gsl-lite-config-version.cmake.in +24 -0
  13. MorphIO-3.3.4/3rdparty/GSL_LITE/cmake/gsl-lite-config.cmake.in +7 -0
  14. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/GSL_LITE/gsl-lite.natvis +4 -1
  15. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/GSL_LITE/include/gsl/gsl +3 -1
  16. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/GSL_LITE/include/gsl/gsl-lite-vc6.hpp +24 -22
  17. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/GSL_LITE/include/gsl/gsl-lite.h +3 -5
  18. MorphIO-3.3.4/3rdparty/GSL_LITE/include/gsl/gsl-lite.hpp +5418 -0
  19. MorphIO-3.3.4/3rdparty/GSL_LITE/include/gsl-lite/gsl-lite.hpp +30 -0
  20. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/GSL_LITE/include/gsl.h +3 -5
  21. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/GSL_LITE/include/gsl.hpp +4 -4
  22. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/CMake/HighFiveConfig.cmake.in +10 -13
  23. MorphIO-3.3.4/3rdparty/HighFive/CMake/HighFiveTargetDeps.cmake +85 -0
  24. MorphIO-3.3.4/3rdparty/HighFive/CMake/config/CompilerFlagsHelpers.cmake +59 -0
  25. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/CMake/config/ReleaseDebugAutoFlags.cmake +6 -10
  26. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/CMakeLists.txt +33 -28
  27. {MorphIO-3.3.2/doc/source → MorphIO-3.3.4/3rdparty/HighFive/doc}/Doxyfile +186 -105
  28. {MorphIO-3.3.2/doc/source → MorphIO-3.3.4/3rdparty/HighFive/doc}/DoxygenLayout.xml +54 -7
  29. MorphIO-3.3.4/3rdparty/HighFive/doc/doxygen-awesome-css/doxygen-awesome.css +2135 -0
  30. MorphIO-3.3.4/3rdparty/HighFive/doc/doxygen-awesome-css/update_doxygen_awesome.sh +47 -0
  31. MorphIO-3.3.4/3rdparty/HighFive/doc/environment.yaml +12 -0
  32. MorphIO-3.3.4/3rdparty/HighFive/doc/poster/example1_hdf5.cpp +53 -0
  33. MorphIO-3.3.4/3rdparty/HighFive/doc/poster/example1_highfive.cpp +17 -0
  34. MorphIO-3.3.4/3rdparty/HighFive/doc/poster/example3.cpp +29 -0
  35. MorphIO-3.3.4/3rdparty/HighFive/doc/poster/example6.cpp +51 -0
  36. MorphIO-3.3.4/3rdparty/HighFive/doc/poster/example_boost.cpp +23 -0
  37. MorphIO-3.3.4/3rdparty/HighFive/doc/poster/example_boost_ublas.cpp +47 -0
  38. MorphIO-3.3.4/3rdparty/HighFive/doc/poster/example_eigen.cpp +35 -0
  39. MorphIO-3.3.4/3rdparty/HighFive/doc/poster/example_props.cpp +24 -0
  40. MorphIO-3.3.4/3rdparty/HighFive/doc/poster/examples.js +37 -0
  41. MorphIO-3.3.4/3rdparty/HighFive/doc/poster/godbolt.org.ico +0 -0
  42. MorphIO-3.3.4/3rdparty/HighFive/doc/poster/index.html +229 -0
  43. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/H5Attribute.hpp +11 -7
  44. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/H5DataSet.hpp +14 -14
  45. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/H5DataSpace.hpp +17 -64
  46. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/H5DataType.hpp +48 -22
  47. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/H5Easy.hpp +96 -83
  48. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/H5Exception.hpp +46 -26
  49. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/H5File.hpp +25 -9
  50. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/H5FileDriver.hpp +6 -5
  51. MorphIO-3.3.4/3rdparty/HighFive/include/highfive/H5Group.hpp +62 -0
  52. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/H5Object.hpp +13 -6
  53. MorphIO-3.3.4/3rdparty/HighFive/include/highfive/H5PropertyList.hpp +307 -0
  54. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/H5Reference.hpp +1 -2
  55. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/H5Selection.hpp +5 -6
  56. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/H5Utility.hpp +7 -7
  57. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/bits/H5Annotate_traits.hpp +5 -7
  58. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/bits/H5Annotate_traits_misc.hpp +38 -43
  59. MorphIO-3.3.4/3rdparty/HighFive/include/highfive/bits/H5Attribute_misc.hpp +118 -0
  60. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/bits/H5ConverterEigen_misc.hpp +27 -44
  61. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/bits/H5Converter_misc.hpp +54 -73
  62. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/bits/H5DataSet_misc.hpp +8 -22
  63. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/bits/H5DataType_misc.hpp +147 -116
  64. MorphIO-3.3.4/3rdparty/HighFive/include/highfive/bits/H5Dataspace_misc.hpp +170 -0
  65. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/bits/H5Exception_misc.hpp +6 -11
  66. MorphIO-3.3.4/3rdparty/HighFive/include/highfive/bits/H5FileDriver_misc.hpp +23 -0
  67. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/bits/H5File_misc.hpp +39 -14
  68. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/bits/H5Iterables_misc.hpp +11 -9
  69. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/bits/H5Node_traits.hpp +73 -39
  70. MorphIO-3.3.4/3rdparty/HighFive/include/highfive/bits/H5Node_traits_misc.hpp +358 -0
  71. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/bits/H5Object_misc.hpp +25 -24
  72. MorphIO-3.3.4/3rdparty/HighFive/include/highfive/bits/H5Path_traits.hpp +35 -0
  73. MorphIO-3.3.4/3rdparty/HighFive/include/highfive/bits/H5Path_traits_misc.hpp +46 -0
  74. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/bits/H5PropertyList_misc.hpp +34 -43
  75. MorphIO-3.3.4/3rdparty/HighFive/include/highfive/bits/H5ReadWrite_misc.hpp +105 -0
  76. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/bits/H5Reference_misc.hpp +8 -5
  77. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/bits/H5Selection_misc.hpp +3 -2
  78. MorphIO-3.3.4/3rdparty/HighFive/include/highfive/bits/H5Slice_traits.hpp +334 -0
  79. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/bits/H5Slice_traits_misc.hpp +65 -49
  80. MorphIO-3.3.4/3rdparty/HighFive/include/highfive/bits/H5Utils.hpp +303 -0
  81. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/bits/H5_definitions.hpp +1 -2
  82. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/h5easy_bits/H5Easy_Eigen.hpp +17 -21
  83. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/h5easy_bits/H5Easy_misc.hpp +22 -59
  84. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/h5easy_bits/H5Easy_opencv.hpp +6 -11
  85. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/h5easy_bits/H5Easy_public.hpp +17 -35
  86. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/h5easy_bits/H5Easy_scalar.hpp +5 -5
  87. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/h5easy_bits/H5Easy_vector.hpp +17 -14
  88. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/include/highfive/h5easy_bits/H5Easy_xtensor.hpp +7 -9
  89. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/lexertl14/include/lexertl/dot.hpp +3 -3
  90. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/lexertl14/include/lexertl/generator.hpp +4 -3
  91. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/lexertl14/include/lexertl/match_results.hpp +5 -0
  92. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/lexertl14/include/lexertl/parser/tokeniser/blocks.hpp +36 -1
  93. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/lexertl14/include/lexertl/parser/tokeniser/scripts.hpp +51 -38
  94. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/lexertl14/include/lexertl/parser/tokeniser/table.inc +9 -0
  95. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/lexertl14/include/lexertl/parser/tokeniser/unicode.hpp +118 -111
  96. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/lexertl14/include/lexertl/rules.hpp +2 -2
  97. MorphIO-3.3.4/CHANGELOG.md +79 -0
  98. {MorphIO-3.3.2 → MorphIO-3.3.4}/CMakeLists.txt +14 -0
  99. MorphIO-3.3.4/MANIFEST.in +32 -0
  100. {MorphIO-3.3.2 → MorphIO-3.3.4}/MorphIO.egg-info/PKG-INFO +9 -9
  101. {MorphIO-3.3.2 → MorphIO-3.3.4}/MorphIO.egg-info/SOURCES.txt +59 -163
  102. {MorphIO-3.3.2 → MorphIO-3.3.4}/PKG-INFO +9 -9
  103. {MorphIO-3.3.2 → MorphIO-3.3.4}/README.rst +6 -7
  104. MorphIO-3.3.4/binds/python/CMakeLists.txt +17 -0
  105. {MorphIO-3.3.2 → MorphIO-3.3.4}/binds/python/bind_immutable.cpp +33 -6
  106. {MorphIO-3.3.2 → MorphIO-3.3.4}/binds/python/bind_mutable.cpp +10 -0
  107. {MorphIO-3.3.2 → MorphIO-3.3.4}/binds/python/bind_vasculature.cpp +42 -0
  108. {MorphIO-3.3.2 → MorphIO-3.3.4}/binds/python/bindings_utils.cpp +3 -2
  109. MorphIO-3.3.4/binds/python/pybind11/CMakeLists.txt +299 -0
  110. MorphIO-3.3.4/binds/python/pybind11/LICENSE +29 -0
  111. {MorphIO-3.3.2/3rdparty → MorphIO-3.3.4/binds/python}/pybind11/include/pybind11/attr.h +288 -103
  112. MorphIO-3.3.4/binds/python/pybind11/include/pybind11/buffer_info.h +193 -0
  113. MorphIO-3.3.4/binds/python/pybind11/include/pybind11/cast.h +1665 -0
  114. MorphIO-3.3.4/binds/python/pybind11/include/pybind11/chrono.h +225 -0
  115. {MorphIO-3.3.2/3rdparty → MorphIO-3.3.4/binds/python}/pybind11/include/pybind11/complex.h +24 -15
  116. {MorphIO-3.3.2/3rdparty → MorphIO-3.3.4/binds/python}/pybind11/include/pybind11/detail/class.h +250 -147
  117. MorphIO-3.3.4/binds/python/pybind11/include/pybind11/detail/common.h +1169 -0
  118. MorphIO-3.3.4/binds/python/pybind11/include/pybind11/detail/descr.h +158 -0
  119. {MorphIO-3.3.2/3rdparty → MorphIO-3.3.4/binds/python}/pybind11/include/pybind11/detail/init.h +197 -104
  120. MorphIO-3.3.4/binds/python/pybind11/include/pybind11/detail/internals.h +562 -0
  121. MorphIO-3.3.4/binds/python/pybind11/include/pybind11/detail/type_caster_base.h +1010 -0
  122. {MorphIO-3.3.2/3rdparty → MorphIO-3.3.4/binds/python}/pybind11/include/pybind11/detail/typeid.h +23 -13
  123. MorphIO-3.3.4/binds/python/pybind11/include/pybind11/eigen.h +708 -0
  124. MorphIO-3.3.4/binds/python/pybind11/include/pybind11/embed.h +277 -0
  125. MorphIO-3.3.4/binds/python/pybind11/include/pybind11/eval.h +156 -0
  126. MorphIO-3.3.4/binds/python/pybind11/include/pybind11/functional.h +130 -0
  127. MorphIO-3.3.4/binds/python/pybind11/include/pybind11/gil.h +202 -0
  128. MorphIO-3.3.4/binds/python/pybind11/include/pybind11/iostream.h +265 -0
  129. MorphIO-3.3.4/binds/python/pybind11/include/pybind11/numpy.h +1984 -0
  130. MorphIO-3.3.4/binds/python/pybind11/include/pybind11/operators.h +201 -0
  131. MorphIO-3.3.4/binds/python/pybind11/include/pybind11/options.h +76 -0
  132. MorphIO-3.3.4/binds/python/pybind11/include/pybind11/pybind11.h +2864 -0
  133. MorphIO-3.3.4/binds/python/pybind11/include/pybind11/pytypes.h +2392 -0
  134. MorphIO-3.3.4/binds/python/pybind11/include/pybind11/stl/filesystem.h +116 -0
  135. {MorphIO-3.3.2/3rdparty → MorphIO-3.3.4/binds/python}/pybind11/include/pybind11/stl.h +165 -126
  136. MorphIO-3.3.4/binds/python/pybind11/include/pybind11/stl_bind.h +785 -0
  137. {MorphIO-3.3.2/3rdparty → MorphIO-3.3.4/binds/python}/pybind11/tools/FindCatch.cmake +19 -4
  138. {MorphIO-3.3.2/3rdparty → MorphIO-3.3.4/binds/python}/pybind11/tools/FindEigen3.cmake +18 -13
  139. MorphIO-3.3.4/binds/python/pybind11/tools/FindPythonLibsNew.cmake +281 -0
  140. MorphIO-3.3.4/binds/python/pybind11/tools/pybind11Common.cmake +385 -0
  141. MorphIO-3.3.4/binds/python/pybind11/tools/pybind11NewTools.cmake +254 -0
  142. MorphIO-3.3.4/binds/python/pybind11/tools/pybind11Tools.cmake +227 -0
  143. {MorphIO-3.3.2 → MorphIO-3.3.4}/include/morphio/dendritic_spine.h +5 -4
  144. {MorphIO-3.3.2 → MorphIO-3.3.4}/include/morphio/endoplasmic_reticulum.h +11 -4
  145. {MorphIO-3.3.2 → MorphIO-3.3.4}/include/morphio/enums.h +2 -1
  146. {MorphIO-3.3.2 → MorphIO-3.3.4}/include/morphio/errorMessages.h +28 -49
  147. {MorphIO-3.3.2 → MorphIO-3.3.4}/include/morphio/exceptions.h +1 -1
  148. {MorphIO-3.3.2 → MorphIO-3.3.4}/include/morphio/glial_cell.h +3 -1
  149. {MorphIO-3.3.2 → MorphIO-3.3.4}/include/morphio/mito_section.h +10 -2
  150. {MorphIO-3.3.2 → MorphIO-3.3.4}/include/morphio/mitochondria.h +7 -3
  151. {MorphIO-3.3.2 → MorphIO-3.3.4}/include/morphio/morphology.h +15 -8
  152. {MorphIO-3.3.2 → MorphIO-3.3.4}/include/morphio/mut/dendritic_spine.h +6 -3
  153. {MorphIO-3.3.2 → MorphIO-3.3.4}/include/morphio/mut/endoplasmic_reticulum.h +9 -7
  154. {MorphIO-3.3.2 → MorphIO-3.3.4}/include/morphio/mut/glial_cell.h +4 -3
  155. {MorphIO-3.3.2 → MorphIO-3.3.4}/include/morphio/mut/mito_section.h +13 -6
  156. {MorphIO-3.3.2 → MorphIO-3.3.4}/include/morphio/mut/mitochondria.h +9 -10
  157. {MorphIO-3.3.2 → MorphIO-3.3.4}/include/morphio/mut/modifiers.h +3 -2
  158. MorphIO-3.3.4/include/morphio/mut/morphology.h +240 -0
  159. {MorphIO-3.3.2 → MorphIO-3.3.4}/include/morphio/mut/section.h +27 -16
  160. MorphIO-3.3.4/include/morphio/mut/soma.h +70 -0
  161. {MorphIO-3.3.2 → MorphIO-3.3.4}/include/morphio/properties.h +7 -0
  162. {MorphIO-3.3.2 → MorphIO-3.3.4}/include/morphio/section.h +44 -23
  163. MorphIO-3.3.4/include/morphio/section_base.h +149 -0
  164. {MorphIO-3.3.2 → MorphIO-3.3.4}/include/morphio/section_iterators.hpp +20 -3
  165. {MorphIO-3.3.2 → MorphIO-3.3.4}/include/morphio/soma.h +16 -29
  166. {MorphIO-3.3.2 → MorphIO-3.3.4}/include/morphio/types.h +2 -13
  167. {MorphIO-3.3.2 → MorphIO-3.3.4}/include/morphio/vasc/iterators.hpp +2 -1
  168. {MorphIO-3.3.2 → MorphIO-3.3.4}/include/morphio/vasc/properties.h +2 -1
  169. {MorphIO-3.3.2 → MorphIO-3.3.4}/include/morphio/vasc/section.h +5 -4
  170. {MorphIO-3.3.2 → MorphIO-3.3.4}/include/morphio/vasc/vasculature.h +22 -3
  171. MorphIO-3.3.4/include/morphio/vector_types.h +31 -0
  172. MorphIO-3.3.4/include/morphio/version.h +18 -0
  173. {MorphIO-3.3.2 → MorphIO-3.3.4}/morphio/__init__.py +2 -1
  174. MorphIO-3.3.4/pyproject.toml +2 -0
  175. {MorphIO-3.3.2 → MorphIO-3.3.4}/setup.py +3 -2
  176. {MorphIO-3.3.2 → MorphIO-3.3.4}/src/CMakeLists.txt +1 -1
  177. {MorphIO-3.3.2 → MorphIO-3.3.4}/src/dendritic_spine.cpp +6 -2
  178. {MorphIO-3.3.2 → MorphIO-3.3.4}/src/endoplasmic_reticulum.cpp +4 -5
  179. {MorphIO-3.3.2 → MorphIO-3.3.4}/src/errorMessages.cpp +36 -14
  180. {MorphIO-3.3.2 → MorphIO-3.3.4}/src/glial_cell.cpp +3 -1
  181. {MorphIO-3.3.2 → MorphIO-3.3.4}/src/mito_section.cpp +4 -2
  182. {MorphIO-3.3.2 → MorphIO-3.3.4}/src/mitochondria.cpp +3 -3
  183. MorphIO-3.3.4/src/morphology.cpp +271 -0
  184. {MorphIO-3.3.2 → MorphIO-3.3.4}/src/mut/dendritic_spine.cpp +2 -1
  185. {MorphIO-3.3.2 → MorphIO-3.3.4}/src/mut/endoplasmic_reticulum.cpp +18 -21
  186. {MorphIO-3.3.2 → MorphIO-3.3.4}/src/mut/glial_cell.cpp +2 -1
  187. {MorphIO-3.3.2 → MorphIO-3.3.4}/src/mut/mito_section.cpp +32 -30
  188. {MorphIO-3.3.2 → MorphIO-3.3.4}/src/mut/mitochondria.cpp +30 -35
  189. {MorphIO-3.3.2 → MorphIO-3.3.4}/src/mut/modifiers.cpp +16 -7
  190. {MorphIO-3.3.2 → MorphIO-3.3.4}/src/mut/morphology.cpp +116 -94
  191. {MorphIO-3.3.2 → MorphIO-3.3.4}/src/mut/section.cpp +53 -27
  192. MorphIO-3.3.4/src/mut/soma.cpp +29 -0
  193. {MorphIO-3.3.2 → MorphIO-3.3.4}/src/mut/writers.cpp +72 -23
  194. MorphIO-3.3.4/src/point_utils.cpp +75 -0
  195. MorphIO-3.3.4/src/point_utils.h +23 -0
  196. {MorphIO-3.3.2 → MorphIO-3.3.4}/src/properties.cpp +32 -18
  197. MorphIO-3.3.2/src/readers/lex.cpp → MorphIO-3.3.4/src/readers/NeurolucidaLexer.inc +116 -103
  198. {MorphIO-3.3.2 → MorphIO-3.3.4}/src/readers/morphologyASC.cpp +13 -25
  199. {MorphIO-3.3.2 → MorphIO-3.3.4}/src/readers/morphologyASC.h +3 -1
  200. {MorphIO-3.3.2 → MorphIO-3.3.4}/src/readers/morphologyHDF5.cpp +14 -17
  201. {MorphIO-3.3.2 → MorphIO-3.3.4}/src/readers/morphologyHDF5.h +0 -4
  202. {MorphIO-3.3.2 → MorphIO-3.3.4}/src/readers/morphologySWC.cpp +102 -61
  203. {MorphIO-3.3.2 → MorphIO-3.3.4}/src/readers/morphologySWC.h +3 -3
  204. {MorphIO-3.3.2 → MorphIO-3.3.4}/src/readers/vasculatureHDF5.cpp +7 -1
  205. MorphIO-3.3.4/src/section.cpp +33 -0
  206. {MorphIO-3.3.2 → MorphIO-3.3.4}/src/shared_utils.hpp +9 -10
  207. {MorphIO-3.3.2 → MorphIO-3.3.4}/src/soma.cpp +6 -5
  208. {MorphIO-3.3.2 → MorphIO-3.3.4}/src/vasc/properties.cpp +27 -14
  209. {MorphIO-3.3.2 → MorphIO-3.3.4}/src/vasc/section.cpp +50 -32
  210. {MorphIO-3.3.2 → MorphIO-3.3.4}/src/vasc/vasculature.cpp +26 -7
  211. MorphIO-3.3.2/.travis.yml +0 -60
  212. MorphIO-3.3.2/3rdparty/GSL_LITE/CMakeLists.txt +0 -86
  213. MorphIO-3.3.2/3rdparty/GSL_LITE/cmake/PackageConfig.cmake.in +0 -4
  214. MorphIO-3.3.2/3rdparty/GSL_LITE/include/gsl/gsl-lite.hpp +0 -2802
  215. MorphIO-3.3.2/3rdparty/HighFive/CMake/HighFiveTargetDeps.cmake +0 -79
  216. MorphIO-3.3.2/3rdparty/HighFive/CMake/config/CompilerFlagsHelpers.cmake +0 -133
  217. MorphIO-3.3.2/3rdparty/HighFive/CMake/portability/BlueGenePortability.cmake +0 -39
  218. MorphIO-3.3.2/3rdparty/HighFive/CMake/portability/CheckCXXStandardSupport.cmake +0 -22
  219. MorphIO-3.3.2/3rdparty/HighFive/doc/Doxyfile +0 -2495
  220. MorphIO-3.3.2/3rdparty/HighFive/include/highfive/H5Group.hpp +0 -39
  221. MorphIO-3.3.2/3rdparty/HighFive/include/highfive/H5PropertyList.hpp +0 -162
  222. MorphIO-3.3.2/3rdparty/HighFive/include/highfive/bits/H5Attribute_misc.hpp +0 -147
  223. MorphIO-3.3.2/3rdparty/HighFive/include/highfive/bits/H5Dataspace_misc.hpp +0 -253
  224. MorphIO-3.3.2/3rdparty/HighFive/include/highfive/bits/H5FileDriver_misc.hpp +0 -52
  225. MorphIO-3.3.2/3rdparty/HighFive/include/highfive/bits/H5Node_traits_misc.hpp +0 -295
  226. MorphIO-3.3.2/3rdparty/HighFive/include/highfive/bits/H5ReadWrite_misc.hpp +0 -79
  227. MorphIO-3.3.2/3rdparty/HighFive/include/highfive/bits/H5Slice_traits.hpp +0 -129
  228. MorphIO-3.3.2/3rdparty/HighFive/include/highfive/bits/H5Utils.hpp +0 -271
  229. MorphIO-3.3.2/3rdparty/pybind11/CMakeLists.txt +0 -157
  230. MorphIO-3.3.2/3rdparty/pybind11/include/pybind11/buffer_info.h +0 -114
  231. MorphIO-3.3.2/3rdparty/pybind11/include/pybind11/cast.h +0 -2159
  232. MorphIO-3.3.2/3rdparty/pybind11/include/pybind11/chrono.h +0 -184
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  234. MorphIO-3.3.2/3rdparty/pybind11/include/pybind11/detail/descr.h +0 -100
  235. MorphIO-3.3.2/3rdparty/pybind11/include/pybind11/detail/internals.h +0 -349
  236. MorphIO-3.3.2/3rdparty/pybind11/include/pybind11/eigen.h +0 -607
  237. MorphIO-3.3.2/3rdparty/pybind11/include/pybind11/embed.h +0 -202
  238. MorphIO-3.3.2/3rdparty/pybind11/include/pybind11/eval.h +0 -117
  239. MorphIO-3.3.2/3rdparty/pybind11/include/pybind11/functional.h +0 -101
  240. MorphIO-3.3.2/3rdparty/pybind11/include/pybind11/iostream.h +0 -209
  241. MorphIO-3.3.2/3rdparty/pybind11/include/pybind11/numpy.h +0 -1642
  242. MorphIO-3.3.2/3rdparty/pybind11/include/pybind11/operators.h +0 -168
  243. MorphIO-3.3.2/3rdparty/pybind11/include/pybind11/options.h +0 -65
  244. MorphIO-3.3.2/3rdparty/pybind11/include/pybind11/pybind11.h +0 -2183
  245. MorphIO-3.3.2/3rdparty/pybind11/include/pybind11/pytypes.h +0 -1484
  246. MorphIO-3.3.2/3rdparty/pybind11/include/pybind11/stl_bind.h +0 -649
  247. MorphIO-3.3.2/3rdparty/pybind11/tools/FindPythonLibsNew.cmake +0 -202
  248. MorphIO-3.3.2/3rdparty/pybind11/tools/check-style.sh +0 -70
  249. MorphIO-3.3.2/3rdparty/pybind11/tools/libsize.py +0 -38
  250. MorphIO-3.3.2/3rdparty/pybind11/tools/mkdoc.py +0 -379
  251. MorphIO-3.3.2/3rdparty/pybind11/tools/pybind11Config.cmake.in +0 -104
  252. MorphIO-3.3.2/3rdparty/pybind11/tools/pybind11Tools.cmake +0 -227
  253. MorphIO-3.3.2/CHANGELOG.md +0 -21
  254. MorphIO-3.3.2/MANIFEST.in +0 -21
  255. MorphIO-3.3.2/binds/python/CMakeLists.txt +0 -18
  256. MorphIO-3.3.2/ci/check_clang_format.sh +0 -27
  257. MorphIO-3.3.2/ci/check_generated_docstrings.sh +0 -49
  258. MorphIO-3.3.2/ci/coverage_test.sh +0 -26
  259. MorphIO-3.3.2/ci/cpp_test.sh +0 -23
  260. MorphIO-3.3.2/ci/python_test.sh +0 -42
  261. MorphIO-3.3.2/doc/Makefile +0 -20
  262. MorphIO-3.3.2/doc/README.md +0 -16
  263. MorphIO-3.3.2/doc/environment.yml +0 -8
  264. MorphIO-3.3.2/doc/source/_templates/doxygen_page.rst_t +0 -4
  265. MorphIO-3.3.2/doc/source/conf.py +0 -193
  266. MorphIO-3.3.2/doc/source/cpp.rst +0 -8
  267. MorphIO-3.3.2/doc/source/doxygen/.gitignore +0 -0
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  280. MorphIO-3.3.2/doc/source/markers.rst +0 -146
  281. MorphIO-3.3.2/doc/source/mitochondria.rst +0 -68
  282. MorphIO-3.3.2/doc/source/morphology.rst +0 -192
  283. MorphIO-3.3.2/doc/source/python.rst +0 -4
  284. MorphIO-3.3.2/doc/source/reticulum.rst +0 -47
  285. MorphIO-3.3.2/doc/source/specification.rst +0 -228
  286. MorphIO-3.3.2/doc/source/specification_neurolucida.rst +0 -195
  287. MorphIO-3.3.2/doc/source/warnings.rst +0 -87
  288. MorphIO-3.3.2/examples/getting_started.ipynb +0 -711
  289. MorphIO-3.3.2/examples/getting_started_mutable.ipynb +0 -219
  290. MorphIO-3.3.2/include/morphio/mut/morphology.h +0 -315
  291. MorphIO-3.3.2/include/morphio/mut/soma.h +0 -94
  292. MorphIO-3.3.2/include/morphio/section_base.h +0 -88
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  295. MorphIO-3.3.2/include/morphio/version.h +0 -12
  296. MorphIO-3.3.2/pyproject.toml +0 -2
  297. MorphIO-3.3.2/scripts/check-clang-format-all +0 -24
  298. MorphIO-3.3.2/src/morphology.cpp +0 -232
  299. MorphIO-3.3.2/src/mut/soma.cpp +0 -47
  300. MorphIO-3.3.2/src/readers/utilsHDF5.h +0 -52
  301. MorphIO-3.3.2/src/section.cpp +0 -68
  302. MorphIO-3.3.2/src/vector_utils.cpp +0 -161
  303. MorphIO-3.3.2/tests/CMakeLists.txt +0 -44
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  324. MorphIO-3.3.2/tests/data/h5/v1/metadata_group_only.h5 +0 -0
  325. MorphIO-3.3.2/tests/data/h5/v1/mitochondria.h5 +0 -0
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  327. MorphIO-3.3.2/tests/data/h5/v1/simple-broken-section-type.h5 +0 -0
  328. MorphIO-3.3.2/tests/data/h5/v1/simple-dendritric-spine.h5 +0 -0
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  330. MorphIO-3.3.2/tests/data/h5/v1/simple-two-point-soma.h5 +0 -0
  331. MorphIO-3.3.2/tests/data/h5/v1/simple.h5 +0 -0
  332. MorphIO-3.3.2/tests/data/h5/v1/single-neurite.h5 +0 -0
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  338. MorphIO-3.3.2/tests/data/h5/v2/Neuron.h5 +0 -0
  339. MorphIO-3.3.2/tests/data/h5/vasculature-broken-section-type.h5 +0 -0
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  364. MorphIO-3.3.2/tests/data/soma_cylinders.swc +0 -8
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  368. MorphIO-3.3.2/tests/data/spine.asc +0 -29
  369. MorphIO-3.3.2/tests/data/three_point_soma.swc +0 -35
  370. MorphIO-3.3.2/tests/main.cpp +0 -3
  371. MorphIO-3.3.2/tests/requirement_tests.txt +0 -4
  372. MorphIO-3.3.2/tests/test_0_API.py +0 -49
  373. MorphIO-3.3.2/tests/test_10_vasculature.py +0 -78
  374. MorphIO-3.3.2/tests/test_1_swc.py +0 -521
  375. MorphIO-3.3.2/tests/test_2_neurolucida.py +0 -675
  376. MorphIO-3.3.2/tests/test_3_h5.py +0 -83
  377. MorphIO-3.3.2/tests/test_4_immut.py +0 -211
  378. MorphIO-3.3.2/tests/test_5_mut.py +0 -682
  379. MorphIO-3.3.2/tests/test_6_writers.py +0 -313
  380. MorphIO-3.3.2/tests/test_7_modifiers.py +0 -94
  381. MorphIO-3.3.2/tests/test_8_all_morphologies.py +0 -93
  382. MorphIO-3.3.2/tests/test_9_surfaces.py +0 -68
  383. MorphIO-3.3.2/tests/test_immutable_morphology.cpp +0 -341
  384. MorphIO-3.3.2/tests/test_morphology_readers.cpp +0 -198
  385. MorphIO-3.3.2/tests/test_mutable_morphology.cpp +0 -55
  386. MorphIO-3.3.2/tests/utils.py +0 -101
  387. {MorphIO-3.3.2 → MorphIO-3.3.4}/.clang-format +0 -0
  388. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/CMake/HighFiveTargetExport.cmake +0 -0
  389. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/CMake/config/TestHelpers.cmake +0 -0
  390. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/HighFive/doc/CMakeLists.txt +0 -0
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  393. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/lexertl14/CMakeLists.txt +0 -0
  394. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/lexertl14/include/lexertl/char_traits.hpp +0 -0
  395. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/lexertl14/include/lexertl/debug.hpp +0 -0
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  425. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/lexertl14/include/lexertl/stream_shared_iterator.hpp +0 -0
  426. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/lexertl14/include/lexertl/string_token.hpp +0 -0
  427. {MorphIO-3.3.2 → MorphIO-3.3.4}/3rdparty/lexertl14/include/lexertl/utf_iterators.hpp +0 -0
  428. {MorphIO-3.3.2 → MorphIO-3.3.4}/AUTHORS.txt +0 -0
  429. {MorphIO-3.3.2 → MorphIO-3.3.4}/CMake/CodeCoverage.cmake +0 -0
  430. {MorphIO-3.3.2 → MorphIO-3.3.4}/CMake/CompilerFlags.cmake +0 -0
  431. {MorphIO-3.3.2 → MorphIO-3.3.4}/CMake/MorphIOConfig.cmake +0 -0
  432. {MorphIO-3.3.2 → MorphIO-3.3.4}/CONTRIBUTING.md +0 -0
  433. {MorphIO-3.3.2 → MorphIO-3.3.4}/COPYING +0 -0
  434. {MorphIO-3.3.2 → MorphIO-3.3.4}/COPYING.LESSER +0 -0
  435. {MorphIO-3.3.2 → MorphIO-3.3.4}/MorphIO.egg-info/dependency_links.txt +0 -0
  436. {MorphIO-3.3.2 → MorphIO-3.3.4}/MorphIO.egg-info/not-zip-safe +0 -0
  437. {MorphIO-3.3.2 → MorphIO-3.3.4}/MorphIO.egg-info/requires.txt +0 -0
  438. {MorphIO-3.3.2 → MorphIO-3.3.4}/MorphIO.egg-info/top_level.txt +0 -0
  439. {MorphIO-3.3.2 → MorphIO-3.3.4}/binds/python/bind_enums.h +0 -0
  440. {MorphIO-3.3.2 → MorphIO-3.3.4}/binds/python/bind_immutable.h +0 -0
  441. {MorphIO-3.3.2 → MorphIO-3.3.4}/binds/python/bind_misc.cpp +0 -0
  442. {MorphIO-3.3.2 → MorphIO-3.3.4}/binds/python/bind_misc.h +0 -0
  443. {MorphIO-3.3.2 → MorphIO-3.3.4}/binds/python/bind_mutable.h +0 -0
  444. {MorphIO-3.3.2 → MorphIO-3.3.4}/binds/python/bind_vasculature.h +0 -0
  445. {MorphIO-3.3.2 → MorphIO-3.3.4}/binds/python/bindings_utils.h +0 -0
  446. {MorphIO-3.3.2 → MorphIO-3.3.4}/binds/python/generated/.clang-format +0 -0
  447. {MorphIO-3.3.2 → MorphIO-3.3.4}/binds/python/generated/docstrings.h +0 -0
  448. {MorphIO-3.3.2 → MorphIO-3.3.4}/binds/python/morphio.cpp +0 -0
  449. {MorphIO-3.3.2/3rdparty → MorphIO-3.3.4/binds/python}/pybind11/include/pybind11/common.h +0 -0
  450. {MorphIO-3.3.2 → MorphIO-3.3.4}/include/morphio/mut/writers.h +0 -0
  451. {MorphIO-3.3.2 → MorphIO-3.3.4}/include/morphio/tools.h +0 -0
  452. {MorphIO-3.3.2 → MorphIO-3.3.4}/morphio/mut/__init__.py +0 -0
  453. {MorphIO-3.3.2 → MorphIO-3.3.4}/morphio/vasculature/__init__.py +0 -0
  454. {MorphIO-3.3.2 → MorphIO-3.3.4}/setup.cfg +0 -0
  455. {MorphIO-3.3.2 → MorphIO-3.3.4}/src/enums.cpp +0 -0
  456. {MorphIO-3.3.2 → MorphIO-3.3.4}/src/readers/vasculatureHDF5.h +0 -0
  457. {MorphIO-3.3.2 → MorphIO-3.3.4}/src/version.cpp.in +0 -0
@@ -10,14 +10,14 @@ jobs:
10
10
  if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository
11
11
 
12
12
  steps:
13
- - uses: actions/checkout@v2
13
+ - uses: actions/checkout@v3
14
14
  with:
15
15
  submodules: 'true'
16
16
 
17
- - name: Set up Python 3.6
18
- uses: actions/setup-python@v2
17
+ - name: Set up Python 3.8
18
+ uses: actions/setup-python@v4
19
19
  with:
20
- python-version: 3.6
20
+ python-version: 3.8
21
21
 
22
22
  - name: Build a source tarball
23
23
  run:
@@ -11,7 +11,9 @@ jobs:
11
11
 
12
12
  steps:
13
13
  - name: Fetch repository
14
- uses: actions/checkout@v1
14
+ uses: actions/checkout@v3
15
+ with:
16
+ fetch-depth: 2
15
17
  - name: Install apt
16
18
  run: sudo apt-get update -y
17
19
  - name: Install packages
@@ -15,7 +15,7 @@ jobs:
15
15
 
16
16
  steps:
17
17
  - name: Checkout repository
18
- uses: actions/checkout@v2
18
+ uses: actions/checkout@v3
19
19
  - name: Fetch repository
20
20
  run: git fetch --prune --unshallow
21
21
  - name: Get submodules
@@ -11,7 +11,7 @@ jobs:
11
11
 
12
12
  steps:
13
13
  - name: Fetch repository
14
- uses: actions/checkout@v2
14
+ uses: actions/checkout@v3
15
15
  with:
16
16
  submodules: recursive
17
17
  - name: Install packages
@@ -3,8 +3,8 @@ on: [pull_request, push]
3
3
 
4
4
  env:
5
5
  CIBW_BUILD_VERBOSITY: 3
6
- CIBW_BUILD: 'cp3?-*'
7
- CIBW_SKIP: 'cp35-* cp36-* *-manylinux_i686 *-musllinux_* *-win32'
6
+ CIBW_BUILD: 'cp*'
7
+ CIBW_SKIP: 'cp35-* cp36-* *-manylinux_i686 *-musllinux_* *-win32 cp311-win_amd64 cp311-macosx_x86_64'
8
8
  CIBW_BEFORE_TEST: pip install -r {project}/tests/requirement_tests.txt
9
9
  CIBW_TEST_COMMAND: pytest -s -v {project}/tests
10
10
 
@@ -17,14 +17,14 @@ jobs:
17
17
  runs-on: ${{ matrix.os }}
18
18
  strategy:
19
19
  matrix:
20
- os: [ubuntu-20.04, macos-latest, windows-latest]
20
+ os: [ubuntu-20.04, macos-11, windows-2022]
21
21
 
22
22
  steps:
23
- - uses: actions/checkout@v2
23
+ - uses: actions/checkout@v3
24
24
  with:
25
25
  submodules: 'true'
26
26
 
27
- - uses: actions/setup-python@v2
27
+ - uses: actions/setup-python@v4
28
28
  name: Install Python
29
29
  with:
30
30
  python-version: '3.7'
@@ -37,7 +37,42 @@ jobs:
37
37
  if: runner.os == 'Linux'
38
38
  env:
39
39
  CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
40
- CIBW_BEFORE_BUILD: 'yum update -y; yum -y install hdf5-devel'
40
+ CIBW_BEFORE_ALL: |
41
+ AEC_VERSION="1.0.4"
42
+ HDF5_VERSION="1.12.1"
43
+
44
+ yum update -y
45
+ yum -y install zlib-devel
46
+ pushd /tmp
47
+
48
+ echo "Downloading & unpacking aec ${AEC_VERSION}"
49
+ curl -fsSLO https://gitlab.dkrz.de/k202009/libaec/uploads/ea0b7d197a950b0c110da8dfdecbb71f/libaec-${AEC_VERSION}.tar.gz
50
+ tar zxf libaec-$AEC_VERSION.tar.gz
51
+
52
+ echo "Building & installing libaec"
53
+ pushd libaec-$AEC_VERSION
54
+ ./configure
55
+ make -j 2
56
+ make install
57
+ ldconfig
58
+ popd
59
+
60
+ echo "Downloading & unpacking HDF5 ${HDF5_VERSION}"
61
+ curl -fsSLO "https://www.hdfgroup.org/ftp/HDF5/releases/hdf5-${HDF5_VERSION%.*}/hdf5-$HDF5_VERSION/src/hdf5-$HDF5_VERSION.tar.gz"
62
+ tar -xzvf hdf5-$HDF5_VERSION.tar.gz
63
+
64
+ echo "Building & installing HDF5"
65
+ pushd hdf5-$HDF5_VERSION
66
+ ./configure \
67
+ --prefix=/usr \
68
+ --enable-build-mode=production \
69
+ --with-szlib \
70
+ --enable-tools=no \
71
+ --enable-tests=no
72
+ make -j 2
73
+ make install
74
+ ldconfig
75
+ popd
41
76
  run: |
42
77
  python -m cibuildwheel --output-dir dist
43
78
 
@@ -46,8 +81,10 @@ jobs:
46
81
  env:
47
82
  MACOSX_DEPLOYMENT_TARGET: '10.13'
48
83
  CIBW_BEFORE_BUILD: |
49
- brew update
50
- brew --version
84
+ #brew update
85
+ #brew --version
86
+ export HOMEBREW_NO_AUTO_UPDATE=1
87
+ export HDF5_DIR="$(brew --prefix hdf5)";
51
88
  brew install hdf5
52
89
  run: |
53
90
  python -m cibuildwheel --output-dir dist
@@ -66,14 +103,14 @@ jobs:
66
103
  C:\windows\system32\tar.exe xf hdf5-1.12.0-Std-win10_64-vs16.zip
67
104
  start /wait msiexec /a "%cd%\hdf\HDF5-1.12.0-win64.msi" /qn TARGETDIR="c:\hdf5\"
68
105
 
69
- call "C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\VC\Auxiliary\Build\vcvars64.bat" -vcvars_ver=14.0
106
+ call "C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Auxiliary\Build\vcvars64.bat" -vcvars_ver=14.1
70
107
 
71
108
  set HDF5_DIR=C:\hdf5\HDF_Group\HDF5\1.12.0\cmake
72
109
 
73
110
  python -m cibuildwheel --output-dir dist
74
111
 
75
112
  - name: Store wheel as artifact
76
- uses: actions/upload-artifact@v2
113
+ uses: actions/upload-artifact@v3
77
114
  with:
78
115
  name: dist
79
116
  path: dist/*.whl
@@ -84,12 +121,12 @@ jobs:
84
121
 
85
122
  runs-on: ubuntu-latest
86
123
  steps:
87
- - uses: actions/checkout@v2
124
+ - uses: actions/checkout@v3
88
125
  with:
89
126
  submodules: 'true'
90
127
 
91
128
  - name: Set up Python 3.7
92
- uses: actions/setup-python@v2
129
+ uses: actions/setup-python@v4
93
130
  with:
94
131
  python-version: 3.7
95
132
 
@@ -105,7 +142,7 @@ jobs:
105
142
  pytest -s -v tests
106
143
 
107
144
  - name: Store sdist as artifact
108
- uses: actions/upload-artifact@v2
145
+ uses: actions/upload-artifact@v3
109
146
  with:
110
147
  name: dist
111
148
  path: dist/*.tar.gz
@@ -119,7 +156,7 @@ jobs:
119
156
 
120
157
  steps:
121
158
  - name: Download artifacts produced during the build_wheels and build_sdist jobs
122
- uses: actions/download-artifact@v2
159
+ uses: actions/download-artifact@v3
123
160
  with:
124
161
  name: dist
125
162
  path: dist/
@@ -3,7 +3,7 @@ on: [pull_request, push]
3
3
 
4
4
  jobs:
5
5
  build:
6
- name: Run tests on ${{ matrix.os }}
6
+ name: Run tests on ${{ matrix.os }}.${{ matrix.compiler.CC }}
7
7
  runs-on: ${{ matrix.os }}
8
8
 
9
9
  # Run on external PRs, but not internal PRs as they'll be run by the push
@@ -13,17 +13,23 @@ jobs:
13
13
  matrix:
14
14
  os: [ubuntu-latest, macos-latest]
15
15
  compiler:
16
- - CC: clang
17
- CXX: clang++
18
- - CC: gcc
19
- CXX: g++
16
+ - {CC: clang, CXX: clang++}
17
+ - {CC: gcc, CXX: g++}
18
+ exclude:
19
+ - os: macos-latest
20
+ compiler: {CC: gcc, CXX: g++}
20
21
 
21
22
  steps:
22
23
  - name: Checkout repository
23
- uses: actions/checkout@v2
24
+ uses: actions/checkout@v3
24
25
  with:
25
26
  submodules: 'true'
26
27
 
28
+ - name: Setup python
29
+ uses: actions/setup-python@v4
30
+ with:
31
+ python-version: '3.10'
32
+
27
33
  - name: Install packages on Linux
28
34
  if: runner.os == 'Linux'
29
35
  run: sudo apt-get update && sudo apt-get install build-essential libhdf5-dev
@@ -31,8 +37,11 @@ jobs:
31
37
  - name: Install packages on MacOS
32
38
  if: runner.os == 'macOS'
33
39
  run: |
34
- brew update
35
- brew --version
40
+ # { work around https://github.com/actions/setup-python/issues/577
41
+ #brew update
42
+ #brew --version
43
+ export HOMEBREW_NO_AUTO_UPDATE=1
44
+ # }
36
45
  brew install cmake || true # macos image has cmake installed, but a new version may exist; ignore it if so
37
46
  brew install hdf5
38
47
 
@@ -47,3 +47,4 @@ build/
47
47
  ci/venv*
48
48
  cmake-build*
49
49
  env*
50
+ venv-clang-format/
@@ -2,7 +2,7 @@
2
2
  path = 3rdparty/HighFive
3
3
  url = https://github.com/BlueBrain/HighFive.git
4
4
  [submodule "3rdparty/pybind11"]
5
- path = 3rdparty/pybind11
5
+ path = binds/python/pybind11
6
6
  url = https://github.com/pybind/pybind11.git
7
7
  [submodule "3rdparty/GSL_LITE"]
8
8
  path = 3rdparty/GSL_LITE
@@ -10,3 +10,6 @@
10
10
  [submodule "3rdparty/lexertl14"]
11
11
  path = 3rdparty/lexertl14
12
12
  url = https://github.com/BenHanson/lexertl14
13
+ [submodule "3rdparty/Catch2"]
14
+ path = 3rdparty/Catch2
15
+ url = https://github.com/catchorg/Catch2.git
@@ -14,8 +14,18 @@ submodules:
14
14
  # doesn't find HDF5, if the hdf5 headers are available by the system, then
15
15
  # it works
16
16
  build:
17
+ os: "ubuntu-20.04"
17
18
  apt_packages:
18
19
  - libhdf5-dev
20
+ tools:
21
+ python: "3.9"
19
22
 
20
- conda:
21
- environment: doc/environment.yml
23
+ sphinx:
24
+ configuration: doc/source/conf.py
25
+
26
+ python:
27
+ install:
28
+ - method: pip
29
+ path: .
30
+ extra_requirements:
31
+ - docs
@@ -14,9 +14,3 @@ target_include_directories(gsl-lite SYSTEM INTERFACE)
14
14
 
15
15
  add_library(lexertl INTERFACE)
16
16
  target_include_directories(lexertl SYSTEM INTERFACE lexertl14/include)
17
-
18
- if(BUILD_BINDINGS)
19
- add_subdirectory(pybind11)
20
- target_include_directories(pybind11 SYSTEM INTERFACE
21
- pybind11)
22
- endif()
@@ -0,0 +1,197 @@
1
+ # Copyright 2015-2019 by Martin Moene
2
+ # Copyright 2019-2021 by Moritz Beutel
3
+ #
4
+ # https://github.com/gsl-lite/gsl-lite
5
+ #
6
+ # gsl-lite is based on GSL: Guidelines Support Library,
7
+ # https://github.com/microsoft/gsl
8
+ #
9
+ # This code is licensed under the MIT License (MIT).
10
+
11
+ cmake_minimum_required( VERSION 3.5 FATAL_ERROR )
12
+
13
+ # gsl-lite project and version, updated by script/update-version.py:
14
+
15
+ project(
16
+ gsl_lite
17
+ VERSION 0.40.0
18
+ # DESCRIPTION "A single-file header-only version of ISO C++ Guideline Support Library (GSL) for C++98, C++11 and later"
19
+ # HOMEPAGE_URL "https://github.com/gsl-lite/gsl-lite"
20
+ LANGUAGES CXX )
21
+
22
+ # Package information:
23
+
24
+ set( unit_name "gsl" )
25
+ set( package_nspace "gsl" )
26
+ set( package_name "${unit_name}-lite" )
27
+ set( package_version "${${PROJECT_NAME}_VERSION}" )
28
+
29
+ message( STATUS "Project '${PROJECT_NAME}', package '${package_name}' version: '${package_version}'" )
30
+
31
+ # Do not build tests or examples by default:
32
+
33
+ option( GSL_LITE_OPT_BUILD_TESTS "Build and perform gsl-lite tests" OFF )
34
+ option( GSL_LITE_OPT_BUILD_CUDA_TESTS "Build and perform gsl-lite CUDA tests" OFF )
35
+ option( GSL_LITE_OPT_BUILD_EXAMPLES "Build gsl-lite examples" OFF )
36
+ option( GSL_LITE_OPT_BUILD_STATIC_ANALYSIS_DEMOS "Build and perform gsl-lite static analysis demos" OFF )
37
+ option( CMAKE_EXPORT_PACKAGE_REGISTRY "Export build directory to CMake user package registry" OFF )
38
+ option( GSL_LITE_OPT_INSTALL_COMPAT_HEADER "Install MS-GSL compatibility header <gsl/gsl>" OFF )
39
+ option( GSL_LITE_OPT_INSTALL_LEGACY_HEADERS "Install legacy headers <gsl.h>, <gsl.hpp>, <gsl/gsl-lite.h>" OFF )
40
+
41
+ # If requested, build and perform tests, build examples:
42
+
43
+ if ( GSL_LITE_OPT_BUILD_TESTS )
44
+ set( ENABLE_TESTING ON )
45
+ include( CTest )
46
+ add_subdirectory( test )
47
+ endif()
48
+ if ( GSL_LITE_OPT_BUILD_CUDA_TESTS )
49
+ set( ENABLE_TESTING ON )
50
+ include( CTest )
51
+ add_subdirectory( test/cuda )
52
+ endif()
53
+
54
+ if ( GSL_LITE_OPT_BUILD_EXAMPLES )
55
+ add_subdirectory( example )
56
+ endif()
57
+
58
+ #
59
+ # Interface, installation and packaging
60
+ #
61
+
62
+ # CMake helpers:
63
+
64
+ include( GNUInstallDirs )
65
+ include( CMakePackageConfigHelpers )
66
+
67
+ # Interface library:
68
+
69
+ add_library(
70
+ ${package_name} INTERFACE )
71
+ add_library(
72
+ ${package_nspace}::${package_name} ALIAS ${package_name} )
73
+ target_include_directories(
74
+ ${package_name}
75
+ INTERFACE
76
+ "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
77
+ "$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>" )
78
+ target_sources(
79
+ ${package_name}
80
+ INTERFACE
81
+ "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/gsl-lite.natvis>" )
82
+
83
+ # Interface library for targets with versioned defaults:
84
+
85
+ # "gsl-lite-v0" target for legacy defaults:
86
+ add_library(
87
+ ${package_name}-v0 INTERFACE )
88
+ add_library(
89
+ ${package_nspace}::${package_name}-v0 ALIAS ${package_name}-v0 )
90
+ target_include_directories(
91
+ ${package_name}-v0
92
+ INTERFACE
93
+ "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
94
+ "$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>" )
95
+ target_sources(
96
+ ${package_name}-v0
97
+ INTERFACE
98
+ "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/gsl-lite.natvis>" )
99
+
100
+ # "gsl-lite-v1" target for modern defaults:
101
+ add_library(
102
+ ${package_name}-v1 INTERFACE )
103
+ add_library(
104
+ ${package_nspace}::${package_name}-v1 ALIAS ${package_name}-v1 )
105
+ target_include_directories(
106
+ ${package_name}-v1
107
+ INTERFACE
108
+ "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
109
+ "$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>" )
110
+ target_compile_definitions(
111
+ ${package_name}-v1
112
+ INTERFACE
113
+ gsl_CONFIG_DEFAULTS_VERSION=1)
114
+ target_sources(
115
+ ${package_name}-v1
116
+ INTERFACE
117
+ "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/gsl-lite.natvis>" )
118
+
119
+ # Package configuration:
120
+ # Note: package_name and package_target are used in package_config_in
121
+
122
+ set( package_folder "${package_name}" )
123
+ set( package_target "${package_name}-targets" )
124
+ set( package_config "${package_name}-config.cmake" )
125
+ set( package_config_in "${package_name}-config.cmake.in" )
126
+ set( package_config_version "${package_name}-config-version.cmake" )
127
+
128
+ configure_package_config_file(
129
+ "${CMAKE_CURRENT_SOURCE_DIR}/cmake/${package_config_in}"
130
+ "${CMAKE_CURRENT_BINARY_DIR}/${package_config}"
131
+ INSTALL_DESTINATION "${CMAKE_INSTALL_LIBDIR}/cmake/${package_folder}"
132
+ )
133
+
134
+ configure_file(
135
+ "${CMAKE_CURRENT_SOURCE_DIR}/cmake/${package_config_version}.in"
136
+ "${CMAKE_CURRENT_BINARY_DIR}/${package_config_version}" @ONLY
137
+ )
138
+
139
+ # Installation:
140
+
141
+ install(
142
+ TARGETS ${package_name} ${package_name}-v0 ${package_name}-v1
143
+ EXPORT ${package_target}
144
+ # INCLUDES DESTINATION "${...}" # already set via target_include_directories()
145
+ )
146
+
147
+ install(
148
+ EXPORT ${package_target}
149
+ NAMESPACE ${package_nspace}::
150
+ DESTINATION "${CMAKE_INSTALL_LIBDIR}/cmake/${package_folder}"
151
+ )
152
+
153
+ export(
154
+ EXPORT ${package_target}
155
+ NAMESPACE ${package_nspace}::
156
+ FILE "${CMAKE_CURRENT_BINARY_DIR}/${package_name}-targets.cmake"
157
+ )
158
+
159
+ if(CMAKE_EXPORT_PACKAGE_REGISTRY)
160
+ export(
161
+ PACKAGE ${package_name}
162
+ )
163
+ endif()
164
+
165
+ install(
166
+ FILES "${CMAKE_CURRENT_BINARY_DIR}/${package_config}"
167
+ "${CMAKE_CURRENT_BINARY_DIR}/${package_config_version}"
168
+ DESTINATION "${CMAKE_INSTALL_LIBDIR}/cmake/${package_folder}"
169
+ )
170
+
171
+ install(
172
+ FILES "include/gsl/gsl-lite.hpp"
173
+ DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/gsl/"
174
+ )
175
+ install(
176
+ FILES "include/gsl-lite/gsl-lite.hpp"
177
+ DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/gsl-lite/"
178
+ )
179
+ if(GSL_LITE_OPT_INSTALL_COMPAT_HEADER)
180
+ install(
181
+ FILES "include/gsl/gsl"
182
+ DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/gsl/"
183
+ )
184
+ endif()
185
+ if(GSL_LITE_OPT_INSTALL_LEGACY_HEADERS)
186
+ install(
187
+ FILES "include/gsl/gsl-lite.h"
188
+ DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/gsl/"
189
+ )
190
+ install(
191
+ FILES "include/gsl.h"
192
+ "include/gsl.hpp"
193
+ DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/"
194
+ )
195
+ endif()
196
+
197
+ # end of file
@@ -0,0 +1,24 @@
1
+ # Adapted from write_basic_package_version_file(... COMPATIBILITY SameMajorVersion) output
2
+ # ARCH_INDEPENDENT is only present in cmake 3.14 and onwards
3
+
4
+ set( PACKAGE_VERSION "@package_version@" )
5
+
6
+ if( PACKAGE_VERSION VERSION_LESS PACKAGE_FIND_VERSION )
7
+ set( PACKAGE_VERSION_COMPATIBLE FALSE )
8
+ else()
9
+ if( "@package_version@" MATCHES "^([0-9]+)\\." )
10
+ set( CVF_VERSION_MAJOR "${CMAKE_MATCH_1}" )
11
+ else()
12
+ set( CVF_VERSION_MAJOR "@package_version@" )
13
+ endif()
14
+
15
+ if( PACKAGE_FIND_VERSION_MAJOR STREQUAL CVF_VERSION_MAJOR )
16
+ set( PACKAGE_VERSION_COMPATIBLE TRUE )
17
+ else()
18
+ set( PACKAGE_VERSION_COMPATIBLE FALSE )
19
+ endif()
20
+
21
+ if( PACKAGE_FIND_VERSION STREQUAL PACKAGE_VERSION )
22
+ set( PACKAGE_VERSION_EXACT TRUE )
23
+ endif()
24
+ endif()
@@ -0,0 +1,7 @@
1
+ @PACKAGE_INIT@
2
+
3
+ # Only include targets once:
4
+
5
+ if( NOT TARGET @package_nspace@::@package_name@ )
6
+ include( "${CMAKE_CURRENT_LIST_DIR}/@package_target@.cmake" )
7
+ endif()
@@ -41,6 +41,9 @@
41
41
  </Type>
42
42
 
43
43
  <Type Name="gsl::not_null&lt;*&gt;">
44
- <DisplayString>value = {*ptr_}</DisplayString>
44
+ <DisplayString>{data_.ptr_}</DisplayString>
45
+ <Expand>
46
+ <ExpandedItem>data_.ptr_</ExpandedItem>
47
+ </Expand>
45
48
  </Type>
46
49
  </AutoVisualizer>
@@ -1,5 +1,5 @@
1
1
  //
2
- // gsl-lite is based on GSL: Guideline Support Library.
2
+ // gsl-lite is based on GSL: Guidelines Support Library.
3
3
  // For more information see https://github.com/martinmoene/gsl-lite
4
4
  //
5
5
  // Copyright (c) 2015 Martin Moene
@@ -22,6 +22,8 @@
22
22
  #ifndef GSL_GSL_H_INCLUDED
23
23
  #define GSL_GSL_H_INCLUDED
24
24
 
25
+ #pragma message ("gsl/gsl is deprecated since version 0.38.1, use gsl/gsl-lite.hpp instead.")
26
+
25
27
  #include "gsl-lite.hpp"
26
28
 
27
29
  #endif // GSL_GSL_H_INCLUDED
@@ -1,6 +1,6 @@
1
1
  //
2
- // gsl-lite-vc6 is based on GSL: Guideline Support Library,
3
- // For more information see https://github.com/martinmoene/gsl-lite
2
+ // gsl-lite-vc6 is based on GSL: Guidelines Support Library,
3
+ // For more information see https://github.com/gsl-lite/gsl-lite
4
4
  //
5
5
  // Copyright (c) 2015 Martin Moene
6
6
  // Copyright (c) 2015 Microsoft Corporation. All rights reserved.
@@ -33,20 +33,20 @@
33
33
 
34
34
  // Configuration:
35
35
 
36
- #ifndef gsl_FEATURE_HAVE_IMPLICIT_MACRO
37
- # define gsl_FEATURE_HAVE_IMPLICIT_MACRO 1
36
+ #ifndef gsl_FEATURE_IMPLICIT_MACRO
37
+ # define gsl_FEATURE_IMPLICIT_MACRO 1
38
38
  #endif
39
39
 
40
- #ifndef gsl_FEATURE_HAVE_OWNER_MACRO
41
- # define gsl_FEATURE_HAVE_OWNER_MACRO 1
40
+ #ifndef gsl_FEATURE_OWNER_MACRO
41
+ # define gsl_FEATURE_OWNER_MACRO 1
42
42
  #endif
43
43
 
44
- #ifndef gsl_FEATURE_HAVE_SHARED_PTR
45
- # define gsl_FEATURE_HAVE_SHARED_PTR 0
44
+ #ifndef gsl_FEATURE_SHARED_PTR
45
+ # define gsl_FEATURE_SHARED_PTR 0
46
46
  #endif
47
47
 
48
- #ifndef gsl_FEATURE_HAVE_UNIQUE_PTR
49
- # define gsl_FEATURE_HAVE_UNIQUE_PTR 0
48
+ #ifndef gsl_FEATURE_UNIQUE_PTR
49
+ # define gsl_FEATURE_UNIQUE_PTR 0
50
50
  #endif
51
51
 
52
52
  #ifndef gsl_CONFIG_THROWS_FOR_TESTING
@@ -75,35 +75,37 @@
75
75
 
76
76
  // Compiler detection:
77
77
 
78
- #if defined(_MSC_VER)
79
- # define gsl_COMPILER_MSVC_VERSION (_MSC_VER / 100 - 5 - (_MSC_VER < 1900))
78
+ #if defined(_MSC_VER ) && !defined(__clang__)
79
+ # define gsl_COMPILER_MSVC_VER (_MSC_VER )
80
+ # define gsl_COMPILER_MSVC_VERSION (_MSC_VER / 10 - 10 * ( 5 + (_MSC_VER < 1900 ) ) )
80
81
  #else
82
+ # define gsl_COMPILER_MSVC_VER 0
81
83
  # define gsl_COMPILER_MSVC_VERSION 0
82
84
  # define gsl_COMPILER_NON_MSVC 1
83
85
  #endif
84
86
 
85
- #if gsl_COMPILER_MSVC_VERSION != 6
87
+ #if gsl_COMPILER_MSVC_VERSION != 60
86
88
  # error GSL Lite: this header is for Visual C++ 6
87
89
  #endif
88
90
 
89
91
  // half-open range [lo..hi):
90
- #define gsl_BETWEEN( v, lo, hi ) ( lo <= v && v < hi )
92
+ #define gsl_BETWEEN( v, lo, hi ) ( (lo) <= (v) && (v) < (hi) )
91
93
 
92
94
  // Presence of C++ language features:
93
95
 
94
96
  // C++ feature usage:
95
97
 
96
- #if gsl_FEATURE_HAVE_IMPLICIT_MACRO
98
+ #if gsl_FEATURE_IMPLICIT_MACRO
97
99
  # define implicit
98
100
  #endif
99
101
 
100
102
  #define gsl_DIMENSION_OF( a ) ( sizeof(a) / sizeof(0[a]) )
101
103
 
102
- #if gsl_FEATURE_HAVE_SHARED_PTR
104
+ #if gsl_FEATURE_SHARED_PTR
103
105
  # include gsl_CONFIG_SHARED_PTR_INCLUDE
104
106
  #endif
105
107
 
106
- #if gsl_FEATURE_HAVE_UNIQUE_PTR
108
+ #if gsl_FEATURE_UNIQUE_PTR
107
109
  # include gsl_CONFIG_UNIQUE_PTR_INCLUDE
108
110
  #endif
109
111
 
@@ -113,10 +115,10 @@ namespace gsl {
113
115
  // GSL.owner: ownership pointers
114
116
  //
115
117
  // ToDo:
116
- #if gsl_FEATURE_HAVE_SHARED_PTR
118
+ #if gsl_FEATURE_SHARED_PTR
117
119
  using gsl_CONFIG_SHARED_PTR_DECL;
118
120
  #endif
119
- #if gsl_FEATURE_HAVE_UNIQUE_PTR
121
+ #if gsl_FEATURE_UNIQUE_PTR
120
122
  using gsl_CONFIG_UNIQUE_PTR_DECL;
121
123
  #endif
122
124
 
@@ -124,7 +126,7 @@ template< class T > struct owner { typedef T type; };
124
126
 
125
127
  #define gsl_HAVE_OWNER_TEMPLATE 0
126
128
 
127
- #if gsl_FEATURE_HAVE_OWNER_MACRO
129
+ #if gsl_FEATURE_OWNER_MACRO
128
130
  # define Owner(t) ::gsl::owner<t>::type
129
131
  #endif
130
132
 
@@ -655,7 +657,7 @@ namespace detail {
655
657
  template<class T, class SizeType, const T Sentinel>
656
658
  struct ensure
657
659
  {
658
- static span<T> sentinel( T * seq, SizeType max = std::numeric_limits<SizeType>::max() )
660
+ static span<T> sentinel( T * seq, SizeType max = (std::numeric_limits<SizeType>::max)() )
659
661
  {
660
662
  typedef T * pointer;
661
663
  typedef typename std::iterator_traits<pointer>::difference_type difference_type;
@@ -679,7 +681,7 @@ struct ensure
679
681
  //
680
682
 
681
683
  template< typename T >
682
- span<T> ensure_z( T * sz, size_t max = std::numeric_limits<size_t>::max() )
684
+ span<T> ensure_z( T * sz, size_t max = (std::numeric_limits<size_t>::max)() )
683
685
  {
684
686
  return detail::ensure<T, size_t, 0>::sentinel( sz, max );
685
687
  }