Merge pull request #136 from constantinpape/master

Switch CI to gh actions

.github/workflows/build.yaml

@@ -0,0 +1,59 @@
+name: build
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  test:
+    name: ${{ matrix.os }} ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macos-latest, windows-latest, ubuntu-latest]
+        python-version: [3.7, 3.8, 3.9]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Setup miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: nifty-build-env
+          auto-update-conda: true
+          channels: conda-forge
+          environment-file: .github/workflows/environment.yaml
+          python-version: ${{ matrix.python-version }}
+          auto-activate-base: false
+        env:
+          ACTIONS_ALLOW_UNSECURE_COMMANDS: true
+
+      # this will set the system compiler;
+      # I don't know how to set the conda compilers for windows
+      - name: Set windows env
+        if: matrix.os == 'windows-latest'
+        uses: ilammy/msvc-dev-cmd@v1
+
+      - name: Build linux
+        if: matrix.os == 'ubuntu-latest'
+        shell: bash -l {0}
+        run: .github/workflows/build_linux.sh
+
+      - name: Build mac
+        if: matrix.os == 'macos-latest'
+        shell: bash -l {0}
+        run: .github/workflows/build_mac.sh
+
+      - name: Build win
+        if: matrix.os == 'windows-latest'
+        shell: bash -l {0}
+        run: .github/workflows/build_win.bat
+
+      - name: Run tests
+        shell: bash -l {0}
+        run: python -m unittest discover -s src/python/test -v

.github/workflows/build_linux.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+
+export PY_BIN="$CONDA_PREFIX/bin/python"
+cmake . \
+    -DWITHIN_TRAVIS=ON \
+    -DWITH_QPBO=OFF \
+    -DWITH_HDF5=ON \
+    -DWITH_Z5=ON \
+    -DWITH_ZLIB=ON \
+    -DWITH_BLOSC=ON \
+    -DWITH_GLPK=OFF \
+    -DWITH_CPLEX=OFF \
+    -DWITH_GUROBI=OFF \
+    -DBUILD_CPP_TEST=OFF \
+    -DCMAKE_PREFIX_PATH="$CONDA_PREFIX" \
+    -DPYTHON_EXECUTABLE="$PY_BIN" \
+    -DCMAKE_CXX_FLAGS="-std=c++17" \
+    -DCMAKE_INSTALL_PREFIX="$CONDA_PREFIX" \
+    -DBUILD_NIFTY_PYTHON=ON
+make -j 4
+make install

.github/workflows/build_mac.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+
+export PY_BIN="$CONDA_PREFIX/bin/python"
+cmake . \
+    -DWITHIN_TRAVIS=ON \
+    -DWITH_QPBO=OFF \
+    -DWITH_HDF5=ON \
+    -DWITH_Z5=ON \
+    -DWITH_ZLIB=ON \
+    -DWITH_BLOSC=ON \
+    -DWITH_GLPK=OFF \
+    -DWITH_CPLEX=OFF \
+    -DWITH_GUROBI=OFF \
+    -DBUILD_CPP_TEST=OFF \
+    -DCMAKE_PREFIX_PATH="$CONDA_PREFIX" \
+    -DPYTHON_EXECUTABLE="$PY_BIN" \
+    -DCMAKE_CXX_FLAGS="-std=c++14" \
+    -DCMAKE_INSTALL_PREFIX="$CONDA_PREFIX" \
+    -DBUILD_NIFTY_PYTHON=ON
+make -j 4
+make install

.github/workflows/build_win.bat

@@ -0,0 +1,18 @@
+cmake . -G "NMake Makefiles" ^
+    -DWITH_QPBO=OFF ^
+    -DWITH_HDF5=OFF ^
+    -DWITH_Z5=OFF ^
+    -DWITH_GLPK=OFF ^
+    -DWITH_CPLEX=OFF ^
+    -DWITH_GUROBI=OFF ^
+    -DBUILD_CPP_TEST=OFF ^
+    -DCMAKE_PREFIX_PATH="%CONDA_PREFIX%" ^
+    -DCMAKE_INSTALL_PREFIX="%CONDA_PREFIX%" ^
+    -DBUILD_NIFTY_PYTHON=ON
+
+REM FIXME z5 tests still fail on windows 
+REM    -DWITH_Z5=ON ^
+REM    -DWITH_ZLIB=ON ^
+REM    -DWITH_BLOSC=ON ^
+
+cmake --build . --target INSTALL --config Release -j 4

.github/workflows/environment.yaml

@@ -0,0 +1,14 @@
+name: nifty-build-env
+channels:
+  - conda-forge
+dependencies:
+  - boost-cpp>=1.63
+  - cmake
+  - compilers
+  - h5py
+  - nlohmann_json
+  - scikit-image
+  - xtensor>=0.21,<0.22
+  - xtensor-python>=0.24,<0.25
+  - vigra
+  - z5py

CMakeLists.txt

@@ -58,6 +58,7 @@ find_package(Threads REQUIRED)
 if(MSVC)
     # Disable autolinking on MSVC.
     add_definitions(-DBOOST_ALL_NO_LIB)
+    add_definitions(-DNOMINMAX)
 endif()
 
 # from externals..
@@ -267,7 +268,10 @@ endif()
 # find z5
 #-------------------------------------------------------------------------------------------------------------------
 if(WITH_Z5)
+    find_package(z5 REQUIRED)
+    include_directories(${z5_INCLUDE_DIRS})
     add_definitions(-DWITH_Z5)
+
     option(WITH_BLOSC "Build z5 with blosc compression" ON)
     option(WITH_BZIP2 "Build z5 with bzip2 compression" ON)
     option(WITH_ZLIB "Build z5 with zlib compression" ON)

README.md

@@ -1,19 +1,12 @@
-Travis (Ubuntu builds)
+Github Workflow builds
 ---------------------------------
-Master: [![Build Status master](https://travis-ci.org/constantinpape/nifty.svg?branch=master)](https://travis-ci.org/DerThorsten/nifty)
-
-Appveyor (Windows builds)
----------------------------------
-Master: 
-[![Build status](https://ci.appveyor.com/api/projects/status/u6nfcpfhpyya5mk8/branch/master?svg=true)](https://ci.appveyor.com/project/DerThorsten/nifty-5sb8n/branch/master)
+[![Build Status](https://github.com/constantinpape/nifty/workflows/build/badge.svg)](https://github.com/constantinpape/nifty/actions)
 
 
 Nifty
 ========
 
 
-
-
 A nifty library for 2D and 3D image segmentation,
 graph based segmentation an opt.
 This library provided building blocks for segmentation

build_conda.sh

@@ -1 +1 @@
-WITH_CPLEX= CPLEX_ROOT_DIR= WITH_GUROBI= GUROBI_ROOT_DIR= conda build -c conda-forge --python=3.7 conda-recipe/
+conda build -c conda-forge --python=3.7 conda-recipe/