merge and resolve conflicts for upstream/fix_windows_pip_package_3.4.1

6 files changed, 89 insertions, 21 deletions

diff --git a/.github/workflows/pip-build-linux.yml b/.github/workflows/pip-build-linux.yml
index 726ed0d5..12979a86 100644
--- a/.github/workflows/pip-build-linux.yml
+++ b/.github/workflows/pip-build-linux.yml
@@ -4,7 +4,7 @@ on: [push, pull_request]
 
 jobs:
   build:
-    name: build pip wheels
+    name: build pip wheel
     runs-on: ubuntu-latest
     # cf. https://github.com/GUDHI/gudhi-deploy/blob/main/Dockerfile_for_pip
     container: gudhi/pip_for_gudhi
@@ -12,11 +12,15 @@ jobs:
       - uses: actions/checkout@v1
         with:
           submodules: true
-      - name: Build wheels for Python 3.9
+      - name: Build wheel for Python 3.9
         run: |
           mkdir build_39
           cd build_39
           cmake -DCMAKE_BUILD_TYPE=Release -DPYTHON_EXECUTABLE=$PYTHON39/bin/python ..
           cd src/python
           $PYTHON39/bin/python setup.py bdist_wheel
-          auditwheel repair dist/*.whl
\ No newline at end of file
+          auditwheel repair dist/*.whl
+      - name: Install and test wheel for Python 3.9
+        run: |
+          $PYTHON39/bin/python -m pip install --user pytest build_39/src/python/dist/*.whl
+          $PYTHON39/bin/python -m pytest src/python/test/test_alpha_complex.py
diff --git a/.github/workflows/pip-build-osx.yml b/.github/workflows/pip-build-osx.yml
index 732e26af..1626bb77 100644
--- a/.github/workflows/pip-build-osx.yml
+++ b/.github/workflows/pip-build-osx.yml
@@ -32,3 +32,7 @@ jobs:
           cmake -DCMAKE_BUILD_TYPE=Release -DPython_ADDITIONAL_VERSIONS=3 ..
           cd src/python
           python setup.py bdist_wheel
+      - name: Install and test python wheel
+        run: |
+          python -m pip install --user pytest build/src/python/dist/*.whl
+          python -m pytest src/python/test/test_alpha_complex.py
diff --git a/.github/workflows/pip-build-windows.yml b/.github/workflows/pip-build-windows.yml
index d07e8c46..0080f4d5 100644
--- a/.github/workflows/pip-build-windows.yml
+++ b/.github/workflows/pip-build-windows.yml
@@ -20,18 +20,36 @@ jobs:
           architecture: x64
       - name: Install dependencies
         run: |
-          vcpkg update
-          vcpkg upgrade --no-dry-run
-          type c:/vcpkg/ports/cgal/portfile.cmake
-          vcpkg install eigen3 cgal --triplet x64-windows
+          cd c:/vcpkg
+          git fetch --all --tags
+          git checkout 2020.11-1
+          bootstrap-vcpkg.bat
+          set VCPKG_BUILD_TYPE=release
+          vcpkg install eigen3 mpfr boost-accumulators boost-algorithm boost-bimap boost-callable-traits boost-concept-check boost-container boost-core boost-detail boost-filesystem boost-functional boost-fusion boost-geometry boost-graph boost-heap boost-intrusive boost-iostreams boost-iterator boost-lambda boost-logic boost-math boost-mpl boost-multi-index boost-multiprecision boost-numeric-conversion boost-optional boost-parameter boost-pool boost-preprocessor boost-property-map boost-property-tree boost-ptr-container boost-random boost-range boost-serialization boost-spirit boost-thread boost-tuple boost-type-traits boost-units boost-utility boost-variant --triplet x64-windows
+          vcpkg version
+          ls C:/vcpkg/installed/x64-windows/bin
+          Invoke-WebRequest https://github.com/CGAL/cgal/releases/download/v5.2.1/CGAL-5.2.1.zip -OutFile CGAL-5.2.1.zip
+          Expand-Archive -Path CGAL-5.2.1.zip -DestinationPath .
+          cd CGAL-5.2.1
+          cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_TOOLCHAIN_FILE=c:/vcpkg/scripts/buildsystems/vcpkg.cmake -DVCPKG_TARGET_TRIPLET=x64-windows -DGMP_INCLUDE_DIR=c:/vcpkg/installed/x64-windows/include -DGMP_LIBRARIES=c:/vcpkg/installed/x64-windows/bin/mpir.dll .
+          cd ${{ github.workspace }}
           python -m pip install --user -r ext/gudhi-deploy/build-requirements.txt
           python -m pip list
       - name: Build python wheel
         run: |
           mkdir build
           cd build
-          cmake -DCMAKE_BUILD_TYPE=Release -DGMP_INCLUDE_DIR="c:/vcpkg/installed/x64-windows/include" -DGMP_LIBRARIES="c:/vcpkg/installed/x64-windows/lib/mpir.lib" -DGMP_LIBRARIES_DIR="c:/vcpkg/installed/x64-windows/lib" -DCMAKE_TOOLCHAIN_FILE=C:/vcpkg/scripts/buildsystems/vcpkg.cmake -DVCPKG_TARGET_TRIPLET=x64-windows -DPython_ADDITIONAL_VERSIONS=3 ..
+          cmake -DCGAL_DIR=c:/vcpkg/CGAL-5.2.1 -DCMAKE_BUILD_TYPE=Release -DCMAKE_TOOLCHAIN_FILE=c:/vcpkg/scripts/buildsystems/vcpkg.cmake -DVCPKG_TARGET_TRIPLET=x64-windows -DGMP_INCLUDE_DIR=c:/vcpkg/installed/x64-windows/include -DGMP_LIBRARIES=c:/vcpkg/installed/x64-windows/bin/mpir.dll ..
           cd src/python
           cp c:/vcpkg/installed/x64-windows/bin/mpfr.dll gudhi/
           cp c:/vcpkg/installed/x64-windows/bin/mpir.dll gudhi/
-          python setup.py bdist_wheel
\ No newline at end of file
+          python setup.py bdist_wheel
+          ls dist
+      - name: Install and test python wheel
+        run: |
+          cd ${{ github.workspace }}
+          cd build/src/python/dist/
+          Get-ChildItem *.whl | ForEach-Object{python -m pip install --user $_.Name}
+          cd ${{ github.workspace }}
+          python -m pip install --user pytest
+          python -m pytest src/python/test/test_alpha_complex.py
diff --git a/.github/workflows/pip-packaging-linux.yml b/.github/workflows/pip-packaging-linux.yml
index 95e8f034..0fa2c083 100644
--- a/.github/workflows/pip-packaging-linux.yml
+++ b/.github/workflows/pip-packaging-linux.yml
@@ -6,7 +6,7 @@ on:
 
 jobs:
   build:
-    name: build pip wheels
+    name: build pip wheel
     runs-on: ubuntu-latest
     # cf. https://github.com/GUDHI/gudhi-deploy/blob/main/Dockerfile_for_pip
     container: gudhi/pip_for_gudhi
@@ -14,7 +14,7 @@ jobs:
       - uses: actions/checkout@v1
         with:
           submodules: true
-      - name: Build wheels for Python 3.5
+      - name: Build wheel for Python 3.5
         run: |
           mkdir build_35
           cd build_35
@@ -22,7 +22,11 @@ jobs:
           cd src/python
           $PYTHON35/bin/python setup.py bdist_wheel
           auditwheel repair dist/*.whl
-      - name: Build wheels for Python 3.6
+      - name: Install and test wheel for Python 3.5
+        run: |
+          $PYTHON35/bin/python -m pip install --user pytest build_35/src/python/dist/*.whl
+          $PYTHON35/bin/python -m pytest src/python/test/test_alpha_complex.py
+      - name: Build wheel for Python 3.6
         run: |
           mkdir build_36
           cd build_36
@@ -30,7 +34,11 @@ jobs:
           cd src/python
           $PYTHON36/bin/python setup.py bdist_wheel
           auditwheel repair dist/*.whl
-      - name: Build wheels for Python 3.7
+      - name: Install and test wheel for Python 3.6
+        run: |
+          $PYTHON36/bin/python -m pip install --user pytest build_36/src/python/dist/*.whl
+          $PYTHON36/bin/python -m pytest src/python/test/test_alpha_complex.py
+      - name: Build wheel for Python 3.7
         run: |
           mkdir build_37
           cd build_37
@@ -38,7 +46,11 @@ jobs:
           cd src/python
           $PYTHON37/bin/python setup.py bdist_wheel
           auditwheel repair dist/*.whl
-      - name: Build wheels for Python 3.8
+      - name: Install and test wheel for Python 3.7
+        run: |
+          $PYTHON37/bin/python -m pip install --user pytest build_37/src/python/dist/*.whl
+          $PYTHON37/bin/python -m pytest src/python/test/test_alpha_complex.py
+      - name: Build wheel for Python 3.8
         run: |
           mkdir build_38
           cd build_38
@@ -46,7 +58,11 @@ jobs:
           cd src/python
           $PYTHON38/bin/python setup.py bdist_wheel
           auditwheel repair dist/*.whl
-      - name: Build wheels for Python 3.9
+      - name: Install and test wheel for Python 3.8
+        run: |
+          $PYTHON38/bin/python -m pip install --user pytest build_38/src/python/dist/*.whl
+          $PYTHON38/bin/python -m pytest src/python/test/test_alpha_complex.py
+      - name: Build wheel for Python 3.9
         run: |
           mkdir build_39
           cd build_39
@@ -54,6 +70,10 @@ jobs:
           cd src/python
           $PYTHON39/bin/python setup.py bdist_wheel
           auditwheel repair dist/*.whl
+      - name: Install and test wheel for Python 3.9
+        run: |
+          $PYTHON39/bin/python -m pip install --user pytest build_39/src/python/dist/*.whl
+          $PYTHON39/bin/python -m pytest src/python/test/test_alpha_complex.py
       - name: Publish on PyPi
         env:
           TWINE_USERNAME: __token__
@@ -63,4 +83,4 @@ jobs:
           $PYTHON39/bin/python -m twine upload build_36/src/python/wheelhouse/*
           $PYTHON39/bin/python -m twine upload build_37/src/python/wheelhouse/*
           $PYTHON39/bin/python -m twine upload build_38/src/python/wheelhouse/*
-          $PYTHON39/bin/python -m twine upload build_39/src/python/wheelhouse/*
\ No newline at end of file
+          $PYTHON39/bin/python -m twine upload build_39/src/python/wheelhouse/*
diff --git a/.github/workflows/pip-packaging-osx.yml b/.github/workflows/pip-packaging-osx.yml
index 56309b88..120c15b6 100644
--- a/.github/workflows/pip-packaging-osx.yml
+++ b/.github/workflows/pip-packaging-osx.yml
@@ -34,6 +34,10 @@ jobs:
           cmake -DCMAKE_BUILD_TYPE=Release -DPython_ADDITIONAL_VERSIONS=3 ..
           cd src/python
           python setup.py bdist_wheel
+      - name: Install and test python wheel
+        run: |
+          python -m pip install --user pytest build/src/python/dist/*.whl
+          python -m pytest src/python/test/test_alpha_complex.py
       - name: Publish on PyPi
         env:
           TWINE_USERNAME: __token__
diff --git a/.github/workflows/pip-packaging-windows.yml b/.github/workflows/pip-packaging-windows.yml
index a428eaba..f387c5ff 100644
--- a/.github/workflows/pip-packaging-windows.yml
+++ b/.github/workflows/pip-packaging-windows.yml
@@ -22,10 +22,19 @@ jobs:
           architecture: x64
       - name: Install dependencies
         run: |
-          vcpkg update
-          vcpkg upgrade --no-dry-run
-          type c:/vcpkg/ports/cgal/portfile.cmake
-          vcpkg install eigen3 cgal --triplet x64-windows
+          cd c:/vcpkg
+          git fetch --all --tags
+          git checkout 2020.11-1
+          bootstrap-vcpkg.bat
+          set VCPKG_BUILD_TYPE=release
+          vcpkg install eigen3 mpfr boost-accumulators boost-algorithm boost-bimap boost-callable-traits boost-concept-check boost-container boost-core boost-detail boost-filesystem boost-functional boost-fusion boost-geometry boost-graph boost-heap boost-intrusive boost-iostreams boost-iterator boost-lambda boost-logic boost-math boost-mpl boost-multi-index boost-multiprecision boost-numeric-conversion boost-optional boost-parameter boost-pool boost-preprocessor boost-property-map boost-property-tree boost-ptr-container boost-random boost-range boost-serialization boost-spirit boost-thread boost-tuple boost-type-traits boost-units boost-utility boost-variant --triplet x64-windows
+          vcpkg version
+          ls C:/vcpkg/installed/x64-windows/bin
+          Invoke-WebRequest https://github.com/CGAL/cgal/releases/download/v5.2.1/CGAL-5.2.1.zip -OutFile CGAL-5.2.1.zip
+          Expand-Archive -Path CGAL-5.2.1.zip -DestinationPath .
+          cd CGAL-5.2.1
+          cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_TOOLCHAIN_FILE=c:/vcpkg/scripts/buildsystems/vcpkg.cmake -DVCPKG_TARGET_TRIPLET=x64-windows -DGMP_INCLUDE_DIR=c:/vcpkg/installed/x64-windows/include -DGMP_LIBRARIES=c:/vcpkg/installed/x64-windows/bin/mpir.dll .
+          cd ${{ github.workspace }}
           python -m pip install --user -r ext/gudhi-deploy/build-requirements.txt
           python -m pip install --user twine
           python -m pip list
@@ -33,11 +42,20 @@ jobs:
         run: |
           mkdir build
           cd build
-          cmake -DCMAKE_BUILD_TYPE=Release -DGMP_INCLUDE_DIR="c:/vcpkg/installed/x64-windows/include" -DGMP_LIBRARIES="c:/vcpkg/installed/x64-windows/lib/mpir.lib" -DGMP_LIBRARIES_DIR="c:/vcpkg/installed/x64-windows/lib" -DCMAKE_TOOLCHAIN_FILE=C:/vcpkg/scripts/buildsystems/vcpkg.cmake -DVCPKG_TARGET_TRIPLET=x64-windows -DPython_ADDITIONAL_VERSIONS=3 ..
+          cmake -DCGAL_DIR=c:/vcpkg/CGAL-5.2.1 -DCMAKE_BUILD_TYPE=Release -DCMAKE_TOOLCHAIN_FILE=c:/vcpkg/scripts/buildsystems/vcpkg.cmake -DVCPKG_TARGET_TRIPLET=x64-windows -DGMP_INCLUDE_DIR=c:/vcpkg/installed/x64-windows/include -DGMP_LIBRARIES=c:/vcpkg/installed/x64-windows/bin/mpir.dll ..
           cd src/python
           cp c:/vcpkg/installed/x64-windows/bin/mpfr.dll gudhi/
           cp c:/vcpkg/installed/x64-windows/bin/mpir.dll gudhi/
           python setup.py bdist_wheel
+          ls dist
+      - name: Install and test python wheel
+        run: |
+          cd ${{ github.workspace }}
+          cd build/src/python/dist/
+          Get-ChildItem *.whl | ForEach-Object{python -m pip install --user $_.Name}
+          cd ${{ github.workspace }}
+          python -m pip install --user pytest
+          python -m pytest src/python/test/test_alpha_complex.py
       - name: Publish on PyPi
         env:
           TWINE_USERNAME: __token__