newstyle Find_Python, numpy2, and xtensor 0.26

.github/workflows/build.yaml

@@ -8,14 +8,13 @@ on:
 
 jobs:
   test:
-    name: ${{ matrix.os }} ${{ matrix.python-version }}
+    name: ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
 
     strategy:
       fail-fast: false
       matrix:
         os: [macos-latest, windows-latest, ubuntu-latest]
-        python-version: [3.11]
 
     steps:
       - name: Checkout
@@ -25,7 +24,6 @@ jobs:
         uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: .github/workflows/environment.yaml
-          python-version: ${{ matrix.python-version }}
 
       # this will set the system compiler;
       # I don't know how to set the conda compilers for windows

.github/workflows/build_unix.sh

@@ -1,7 +1,9 @@
 #!/bin/bash
 
-export PY_BIN="$CONDA_PREFIX/bin/python"
-cmake . \
+mkdir -p bld
+cd bld
+
+cmake .. \
     -DWITHIN_TRAVIS=ON \
     -DWITH_QPBO=OFF \
     -DWITH_HDF5=ON \
@@ -13,10 +15,8 @@ cmake . \
     -DWITH_GUROBI=OFF \
     -DBUILD_CPP_TEST=OFF \
     -DCMAKE_PREFIX_PATH="$CONDA_PREFIX" \
-    -DPython_NumPy_INCLUDE_DIRS=$(python -c "import numpy; print(numpy.get_include())") \
-    -DPYTHON_EXECUTABLE="$PY_BIN" \
-    -DCMAKE_CXX_FLAGS="-std=c++17" \
-    -DCMAKE_INSTALL_PREFIX="$CONDA_PREFIX" \
+    -DPython_EXECUTABLE="${CONDA_PREFIX}/bin/python" \
+    -DCMAKE_INSTALL_PREFIX="${CONDA_PREFIX}" \
     -DBUILD_NIFTY_PYTHON=ON
 make -j 4
 make install

.github/workflows/build_win.bat

@@ -1,15 +1,16 @@
 REM https://stackoverflow.com/questions/6832666/lnk2019-when-including-asio-headers-solution-generated-with-cmake
-cmake . -G "NMake Makefiles" ^
+mkdir bld
+cd bld
+cmake .. -G "NMake Makefiles" ^
     -DWITH_QPBO=OFF ^
-    -DWITH_HDF5=OFF ^
     -DWITH_GLPK=OFF ^
     -DWITH_CPLEX=OFF ^
     -DWITH_GUROBI=OFF ^
     -DBUILD_CPP_TEST=OFF ^
-    -DCMAKE_PREFIX_PATH="%CONDA_PREFIX%" ^
-    -DCMAKE_INSTALL_PREFIX="%CONDA_PREFIX%" ^
-    -DPython_NumPy_INCLUDE_DIRS=$(python -c "import numpy; print(numpy.get_include())") ^
-    -DCMAKE_CXX_FLAGS="/std:c++17 /EHsc" ^
+    -DCMAKE_PREFIX_PATH:PATH="%CONDA_PREFIX%" ^
+    -DCMAKE_INSTALL_PREFIX:PATH="%CONDA_PREFIX%" ^
+    -DPython_EXECUTABLE:PATH="%CONDA_PREFIX%\python.exe" ^
+    -DCMAKE_CXX_FLAGS="/EHsc" ^
     -DBUILD_NIFTY_PYTHON=ON ^
     -DWITH_HDF5=OFF ^
     -DWITH_Z5=ON ^

.github/workflows/environment.yaml

@@ -2,7 +2,7 @@ name: nifty-build-env
 channels:
   - conda-forge
 dependencies:
-  - boost-cpp>=1.63
+  - libboost-devel
   - cmake
   - compilers
   - h5py
@@ -12,4 +12,4 @@ dependencies:
   - xtensor
   - xtensor-python
   - vigra
-  - z5py
+  - z5py >=2.0.20

.pre-commit-config.yaml

@@ -0,0 +1 @@
+repos: []

CMakeLists.txt

@@ -1,8 +1,9 @@
-cmake_minimum_required(VERSION 3.1)
+cmake_minimum_required(VERSION 3.10)
 set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake/modules)
 
 project(NIFTY)
 set(${PROJECT_NAME}_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/include)
+cmake_policy(SET CMP0057 NEW)
 
 
 
@@ -158,7 +159,7 @@ endif()
 #-------------------------------------------------------------------------------------------------------------------
 # find boost
 #-------------------------------------------------------------------------------------------------------------------
-find_package(Boost 1.63.0 REQUIRED)
+find_package(Boost 1.63.0 CONFIG REQUIRED)
 
 # see this issue for discussions about the filesystem lib in CMake
 # https://gitlab.kitware.com/cmake/cmake/issues/17834

cmake/modules/PythonLibTest.cmake

@@ -1,19 +1,19 @@
 
-#message(PYTHON_VERSION_MAJOR ${PYTHON_VERSION_MAJOR})
-if(PYTHON_VERSION_MAJOR STREQUAL "2")
+#message(Python_VERSION_MAJOR ${Python_VERSION_MAJOR})
+if(Python_VERSION_MAJOR STREQUAL "2")
     #message(STATUS "222222")
     find_program(NOSETESTS_PATH NAMES
-            #"nosetests${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}"
-            #"nosetests-${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}"
-            #"nosetests${PYTHON_VERSION_MAJOR}"
-            #"nosetests-${PYTHON_VERSION_MAJOR}"
+            #"nosetests${Python_VERSION_MAJOR}.${Python_VERSION_MINOR}"
+            #"nosetests-${Python_VERSION_MAJOR}.${Python_VERSION_MINOR}"
+            #"nosetests${Python_VERSION_MAJOR}"
+            #"nosetests-${Python_VERSION_MAJOR}"
             "nosetests")
 else()
     find_program(NOSETESTS_PATH NAMES
-        #"nosetests${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}"
-        #"nosetests-${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}"
-        #"nosetests${PYTHON_VERSION_MAJOR}"
-        #"nosetests-${PYTHON_VERSION_MAJOR}"
+        #"nosetests${Python_VERSION_MAJOR}.${Python_VERSION_MINOR}"
+        #"nosetests-${Python_VERSION_MAJOR}.${Python_VERSION_MINOR}"
+        #"nosetests${Python_VERSION_MAJOR}"
+        #"nosetests-${Python_VERSION_MAJOR}"
         "nosetests3")
 endif()
 
@@ -101,4 +101,4 @@ function(add_python_test_target TARGET_NAME)
     add_dependencies(${TARGET_NAME} ${COPY_TARGET})
 
 
-endfunction()
+endfunction()

environment.yaml

@@ -1,13 +1,18 @@
-name:
-    nifty-dev
+name: nifty-dev
 channels:
-    - conda-forge
+  - conda-forge
 dependencies:
-  - boost-cpp>=1.63
-  - h5py
-  - nlohmann_json
-  - scikit-image
-  - xtensor>=0.21,<0.22
-  - xtensor-python>=0.24,<0.25
+  - python 3.12
+  - numpy
+  - xtensor >=0.26,<0.27
+  - xtensor-python >=0.28,<0.29
+  - libboost-devel
+  - libvigra
+  # Vigra Numpy is used at link time too
   - vigra
-  - z5py
+  - z5py >=2.0.20
+  # build dependencies needed for z5
+  - nlohmann_json
+  - blosc
+  - bzip2
+  - zlib

include/nifty/array/arithmetic_array.hxx

@@ -3,7 +3,7 @@
 #include <array>
 #include <vector>
 
-#include "xtensor/xtensor.hpp"
+#include "xtensor.hpp"
 #include "nifty/tools/runtime_check.hxx"
 
 namespace nifty{

include/nifty/distributed/graph_extraction.hxx

@@ -4,8 +4,8 @@
 #include <set>
 #include <boost/functional/hash.hpp>
 
-#include "xtensor/xtensor.hpp"
-#include "xtensor/xadapt.hpp"
+#include "xtensor.hpp"
+#include "xtensor/containers/xadapt.hpp"
 
 #include "z5/factory.hxx"
 #include "z5/attributes.hxx"

include/nifty/graph/agglo/cluster_policies/gasp_cluster_policy.hxx

@@ -12,7 +12,7 @@
 #include "nifty/graph/agglo/cluster_policies/cluster_policies_common.hxx"
 #include <iostream>
 #include <algorithm>    // std::max
-#include <xtensor/xview.hpp>
+#include <xtensor/views/xview.hpp>
 using namespace xt::placeholders;
 
 
@@ -633,4 +633,3 @@ namespace nifty{
         } // namespace agglo
     } // namespace nifty::graph
 } // namespace nifty
-

include/nifty/graph/label_propagation.hxx

@@ -16,11 +16,11 @@
 // #include "nifty/graph/edge_contraction_graph.hxx"
 // #include "nifty/graph/agglo/cluster_policies/cluster_policies_common.hxx"
 #include <iostream>
-#include "xtensor/xarray.hpp"
+#include "xtensor/containers/xarray.hpp"
 
 #include "nifty/parallel/threadpool.hxx"
 #include <ctime> // Random seed for shuffle
-#include <xtensor/xrandom.hpp>
+#include <xtensor/generators/xrandom.hpp>
 
 
 namespace nifty{