Update pip build/package strategy to fix numpy compatibility (#867)

* Test with docker pip_for_gudhi:3.8.0rc3. Use minimal python version to build gudhi and upgrade to test * Typo in matrix variables * Fix minimal numpy version * Better use of ~= and some comments. Add some tests for pip packages * osx x86 and arm numpy version stable from 1.21.4 * activate pytest verbosity and fix osx. Release candidate 3 * Get Dockerfile_for_pip old_numpy_pip_build feature from gudhi-deploy submodule * Try to fix weird looking project description - cf. https://pypi.org/project/gudhi/3.8.0rc2/ * Build only python 3.6 for linux, 3.7 for windows and 3.8 for osx
GUDHI · Apr 14, 2023 · b1917ab · b1917ab
1 parent fc25535
commit b1917ab
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diff --git a/.github/workflows/pip-build-linux.yml b/.github/workflows/pip-build-linux.yml
@@ -12,23 +12,25 @@ jobs:
       - uses: actions/checkout@v3
         with:
           submodules: true
-      - name: Build wheel for Python 3.11
+      - name: Build wheel for Python 3.6
         run: |
-          mkdir build_311
-          cd build_311
-          cmake -DCMAKE_BUILD_TYPE=Release -DPYTHON_EXECUTABLE=$PYTHON311/bin/python ..
+          mkdir build_36
+          cd build_36
+          cmake -DCMAKE_BUILD_TYPE=Release -DPYTHON_EXECUTABLE=$PYTHON36/bin/python ..
           cd src/python
-          $PYTHON311/bin/python -m build -n -w
-          auditwheel show dist/*.whl
+          $PYTHON36/bin/python -m build -n -w
           auditwheel repair dist/*.whl
-          ls wheelhouse/*.whl
-      - name: Install and test wheel for Python 3.11
+      - name: Install and test wheel for Python 3.6
         run: |
-          $PYTHON311/bin/python -m pip install --user pytest build_311/src/python/wheelhouse/*.whl
-          $PYTHON311/bin/python -c "import gudhi; print(gudhi.__version__)"
-          $PYTHON311/bin/python -m pytest src/python/test/test_alpha_complex.py
+          $PYTHON36/bin/python -m pip install --user pytest build_36/src/python/dist/*.whl
+          $PYTHON36/bin/python -m pip install numpy --upgrade
+          $PYTHON36/bin/python -c "import gudhi; print(gudhi.__version__)"
+          $PYTHON36/bin/python -m pytest -v src/python/test/test_alpha_complex.py
+          $PYTHON36/bin/python -m pytest -v src/python/test/test_bottleneck_distance.py
+          $PYTHON36/bin/python -m pytest -v src/python/test/test_cubical_complex.py
+          $PYTHON36/bin/python -m pytest -v src/python/test/test_rips_complex.py
       - name: Upload linux python wheel
         uses: actions/upload-artifact@v3
         with:
           name: linux python wheel
-          path: build_311/src/python/wheelhouse/*.whl
+          path: build_36/src/python/wheelhouse/*.whl
diff --git a/.github/workflows/pip-build-osx.yml b/.github/workflows/pip-build-osx.yml
@@ -3,8 +3,8 @@ name: pip build osx
 on: [push, pull_request]
 
 env:
-  MACOSX_DEPLOYMENT_TARGET: 10.14
-  _PYTHON_HOST_PLATFORM: macosx-10.14-universal2
+  MACOSX_DEPLOYMENT_TARGET: 10.15
+  _PYTHON_HOST_PLATFORM: macosx-10.15-universal2
   ARCHFLAGS: "-arch arm64 -arch x86_64"
 
 jobs:
@@ -13,7 +13,12 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ['3.11']
+        # numpy packages for osx x86 and arm are only available from 1.21.2, but stable for both versions from 1.21.4
+        # and python 3.8+
+        python-version: ['3.8']
+        include:
+          - python-version: '3.8'
+            numpy-version: '1.21.4'
     name: Build wheels for Python ${{ matrix.python-version }}
     steps:
       - uses: actions/checkout@v3
@@ -27,6 +32,7 @@ jobs:
         run: |
           brew update || true
           brew install boost eigen gmp mpfr cgal || true
+          python -m pip install --user numpy~=${{ matrix.numpy-version }}
           python -m pip install --user -r ext/gudhi-deploy/build-requirements.txt
           python -m pip install --user delocate
           ./scripts/build_osx_universal_gmpfr.sh
@@ -46,9 +52,13 @@ jobs:
           delocate-wheel --require-archs universal2 -v dist/*.whl
       - name: Install and test python wheel
         run: |
+          python -m pip install --user  numpy --upgrade
           python -m pip install --user pytest build/src/python/dist/*.whl
           python -c "import gudhi; print(gudhi.__version__)"
-          python -m pytest src/python/test/test_alpha_complex.py
+          python -m pytest -v src/python/test/test_alpha_complex.py
+          python -m pytest -v src/python/test/test_bottleneck_distance.py
+          python -m pytest -v src/python/test/test_cubical_complex.py
+          python -m pytest -v src/python/test/test_rips_complex.py
       - name: Upload OSx python wheel
         uses: actions/upload-artifact@v3
         with:

diff --git a/.github/workflows/pip-build-windows.yml b/.github/workflows/pip-build-windows.yml
@@ -8,7 +8,10 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ['3.11']
+        python-version: ['3.7']
+        include:
+          - python-version: '3.7'
+            numpy-version: '1.15.0'
     name: Build wheels for Python ${{ matrix.python-version }}
     steps:
       - uses: actions/checkout@v3
@@ -24,6 +27,7 @@ jobs:
           vcpkg install eigen3 cgal --triplet x64-windows
           vcpkg version
           ls "C:\vcpkg\installed\x64-windows\bin\"
+          python -m pip install --user numpy~=${{ matrix.numpy-version }}
           python -m pip install --user -r .\ext\gudhi-deploy\build-requirements.txt
       - name: Build python wheel and install it
         run: |
@@ -41,9 +45,13 @@ jobs:
         run: |
           Get-Location
           dir
+          python -m pip install --user  numpy --upgrade
           python -m pip install --user pytest
           python -c "import gudhi; print(gudhi.__version__)"
-          python -m pytest ".\src\python\test\test_alpha_complex.py"
+          python -m pytest -v ".\src\python\test\test_alpha_complex.py"
+          python -m pytest -v ".\src\python\test\test_bottleneck_distance.py"
+          python -m pytest -v ".\src\python\test\test_cubical_complex.py"
+          python -m pytest -v ".\src\python\test\test_rips_complex.py"
       - name: Upload Windows python wheel
         uses: actions/upload-artifact@v3
         with:

diff --git a/.github/workflows/pip-packaging-linux.yml b/.github/workflows/pip-packaging-linux.yml
@@ -25,8 +25,12 @@ jobs:
       - 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 pip install numpy --upgrade
           $PYTHON36/bin/python -c "import gudhi; print(gudhi.__version__)"
-          $PYTHON36/bin/python -m pytest src/python/test/test_alpha_complex.py
+          $PYTHON36/bin/python -m pytest -v src/python/test/test_alpha_complex.py
+          $PYTHON36/bin/python -m pytest -v src/python/test/test_bottleneck_distance.py
+          $PYTHON36/bin/python -m pytest -v src/python/test/test_cubical_complex.py
+          $PYTHON36/bin/python -m pytest -v src/python/test/test_rips_complex.py
       - name: Build wheel for Python 3.7
         run: |
           mkdir build_37
@@ -38,8 +42,12 @@ jobs:
       - 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 pip install numpy --upgrade
           $PYTHON37/bin/python -c "import gudhi; print(gudhi.__version__)"
-          $PYTHON37/bin/python -m pytest src/python/test/test_alpha_complex.py
+          $PYTHON37/bin/python -m pytest -v src/python/test/test_alpha_complex.py
+          $PYTHON37/bin/python -m pytest -v src/python/test/test_bottleneck_distance.py
+          $PYTHON37/bin/python -m pytest -v src/python/test/test_cubical_complex.py
+          $PYTHON37/bin/python -m pytest -v src/python/test/test_rips_complex.py
       - name: Build wheel for Python 3.8
         run: |
           mkdir build_38
@@ -51,8 +59,12 @@ jobs:
       - 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 pip install numpy --upgrade
           $PYTHON38/bin/python -c "import gudhi; print(gudhi.__version__)"
-          $PYTHON38/bin/python -m pytest src/python/test/test_alpha_complex.py
+          $PYTHON38/bin/python -m pytest -v src/python/test/test_alpha_complex.py
+          $PYTHON38/bin/python -m pytest -v src/python/test/test_bottleneck_distance.py
+          $PYTHON38/bin/python -m pytest -v src/python/test/test_cubical_complex.py
+          $PYTHON38/bin/python -m pytest -v src/python/test/test_rips_complex.py
       - name: Build wheel for Python 3.9
         run: |
           mkdir build_39
@@ -64,8 +76,12 @@ jobs:
       - 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 pip install numpy --upgrade
           $PYTHON39/bin/python -c "import gudhi; print(gudhi.__version__)"
-          $PYTHON39/bin/python -m pytest src/python/test/test_alpha_complex.py
+          $PYTHON39/bin/python -m pytest -v src/python/test/test_alpha_complex.py
+          $PYTHON39/bin/python -m pytest -v src/python/test/test_bottleneck_distance.py
+          $PYTHON39/bin/python -m pytest -v src/python/test/test_cubical_complex.py
+          $PYTHON39/bin/python -m pytest -v src/python/test/test_rips_complex.py
       - name: Build wheel for Python 3.10
         run: |
           mkdir build_310
@@ -77,8 +93,12 @@ jobs:
       - name: Install and test wheel for Python 3.10
         run: |
           $PYTHON310/bin/python -m pip install --user pytest build_310/src/python/dist/*.whl
+          $PYTHON310/bin/python -m pip install numpy --upgrade
           $PYTHON310/bin/python -c "import gudhi; print(gudhi.__version__)"
-          $PYTHON310/bin/python -m pytest src/python/test/test_alpha_complex.py
+          $PYTHON310/bin/python -m pytest -v src/python/test/test_alpha_complex.py
+          $PYTHON310/bin/python -m pytest -v src/python/test/test_bottleneck_distance.py
+          $PYTHON310/bin/python -m pytest -v src/python/test/test_cubical_complex.py
+          $PYTHON310/bin/python -m pytest -v src/python/test/test_rips_complex.py
       - name: Build wheel for Python 3.11
         run: |
           mkdir build_311
@@ -90,8 +110,12 @@ jobs:
       - name: Install and test wheel for Python 3.11
         run: |
           $PYTHON311/bin/python -m pip install --user pytest build_311/src/python/dist/*.whl
+          $PYTHON311/bin/python -m pip install numpy --upgrade
           $PYTHON311/bin/python -c "import gudhi; print(gudhi.__version__)"
-          $PYTHON311/bin/python -m pytest src/python/test/test_alpha_complex.py
+          $PYTHON311/bin/python -m pytest -v src/python/test/test_alpha_complex.py
+          $PYTHON311/bin/python -m pytest -v src/python/test/test_bottleneck_distance.py
+          $PYTHON311/bin/python -m pytest -v src/python/test/test_cubical_complex.py
+          $PYTHON311/bin/python -m pytest -v src/python/test/test_rips_complex.py
       - name: Publish on PyPi
         env:
           TWINE_USERNAME: __token__

diff --git a/.github/workflows/pip-packaging-osx.yml b/.github/workflows/pip-packaging-osx.yml
@@ -15,7 +15,20 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        # numpy packages for osx x86 and arm are only available from 1.21.2, but stable for both versions from 1.21.4
+        # and python 3.8+
+        python-version: ['3.8', '3.9', '3.10', '3.11']
+        include:
+        # numpy >= 1.21.4 fort osx x86 and arm, but minimal numpy version for python 3.10 is 1.21.6 for instance
+        # numpy~=1.21.6 means any numpy=1.21.*, but also numpy>=1.21.6 (numpy~=1.21 do not work as it means any numpy==1.*)
+          - python-version: '3.8'
+            numpy-version: '1.21.4'
+          - python-version: '3.9'
+            numpy-version: '1.21.4'
+          - python-version: '3.10'
+            numpy-version: '1.21.6'
+          - python-version: '3.11'
+            numpy-version: '1.23.2'
     name: Build wheels for Python ${{ matrix.python-version }}
     steps:
       - uses: actions/checkout@v3
@@ -29,6 +42,7 @@ jobs:
         run: |
           brew update || true
           brew install boost eigen gmp mpfr cgal || true
+          python -m pip install --user numpy~=${{ matrix.numpy-version }}
           python -m pip install --user -r ext/gudhi-deploy/build-requirements.txt
           python -m pip install --user twine delocate
           ./scripts/build_osx_universal_gmpfr.sh
@@ -46,9 +60,13 @@ jobs:
           python -m build -n -w
       - name: Install and test python wheel
         run: |
+          python -m pip install --user  numpy --upgrade
           python -m pip install --user pytest build/src/python/dist/*.whl
           python -c "import gudhi; print(gudhi.__version__)"
-          python -m pytest src/python/test/test_alpha_complex.py
+          python -m pytest -v src/python/test/test_alpha_complex.py
+          python -m pytest -v src/python/test/test_bottleneck_distance.py
+          python -m pytest -v src/python/test/test_cubical_complex.py
+          python -m pytest -v src/python/test/test_rips_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
@@ -11,6 +11,19 @@ jobs:
       max-parallel: 4
       matrix:
         python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        # gudhi requires numpy >= 1.15.0, but minimal numpy version for python 3.8 is 1.17.3 for instance
+        # numpy~=1.17.3 means any numpy=1.17.*, but also numpy>=1.17.3 (numpy~=1.17 do not work as it means any numpy==1.*)
+        include:
+          - python-version: '3.7'
+            numpy-version: '1.15.0'
+          - python-version: '3.8'
+            numpy-version: '1.17.3'
+          - python-version: '3.9'
+            numpy-version: '1.19.3'
+          - python-version: '3.10'
+            numpy-version: '1.21.6'
+          - python-version: '3.11'
+            numpy-version: '1.23.2'
     name: Build wheels for Python ${{ matrix.python-version }}
     steps:
       - uses: actions/checkout@v3
@@ -26,6 +39,7 @@ jobs:
           vcpkg install eigen3 cgal --triplet x64-windows
           vcpkg version
           ls "C:\vcpkg\installed\x64-windows\bin\"
+          python -m pip install --user numpy~=${{ matrix.numpy-version }}
           python -m pip install --user -r .\ext\gudhi-deploy\build-requirements.txt
           python -m pip install --user twine
           python -m pip list
@@ -43,9 +57,13 @@ jobs:
           Get-ChildItem *.whl | ForEach-Object{python -m pip install --user $_.Name}
       - name: Test python wheel
         run: |
+          python -m pip install --user  numpy --upgrade
           python -m pip install --user pytest
           python -c "import gudhi; print(gudhi.__version__)"
-          python -m pytest ".\src\python\test\test_alpha_complex.py"
+          python -m pytest -v ".\src\python\test\test_alpha_complex.py"
+          python -m pytest -v ".\src\python\test\test_bottleneck_distance.py"
+          python -m pytest -v ".\src\python\test\test_cubical_complex.py"
+          python -m pytest -v ".\src\python\test\test_rips_complex.py"
       - name: Publish on PyPi
         env:
           TWINE_USERNAME: __token__

diff --git a/CMakeGUDHIVersion.txt b/CMakeGUDHIVersion.txt
@@ -2,7 +2,7 @@
 set (GUDHI_MAJOR_VERSION 3)
 set (GUDHI_MINOR_VERSION 8)
 # GUDHI_PATCH_VERSION can be 'ZaN' for Alpha release, 'ZbN' for Beta release, 'ZrcN' for release candidate or 'Z' for a final release.
-set (GUDHI_PATCH_VERSION 0rc2)
+set (GUDHI_PATCH_VERSION 0rc3)
 set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION})
 
 message(STATUS "GUDHI version : ${GUDHI_VERSION}")
diff --git a/ext/gudhi-deploy b/ext/gudhi-deploy
diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
@@ -293,7 +293,7 @@ if(PYTHONINTERP_FOUND)
 
     # Generate setup.py file to cythonize Gudhi - This file must be named setup.py by convention
     file(READ "introduction.rst" GUDHI_LONG_DESCRIPTION_WITH_UNPROPER_CR)
-    string(REPLACE "\n" "' \\\n        '" GUDHI_LONG_DESCRIPTION ${GUDHI_LONG_DESCRIPTION_WITH_UNPROPER_CR})
+    string(REPLACE "\n" "\\n' \\\n        '" GUDHI_LONG_DESCRIPTION ${GUDHI_LONG_DESCRIPTION_WITH_UNPROPER_CR})
     configure_file(setup.py.in "${CMAKE_CURRENT_BINARY_DIR}/setup.py" @ONLY)
 
     # Generate gudhi/__init__.py