Merge branch 'dev' into dev

Argonne-National-Laboratory · Oct 31, 2024 · 4fe45b2 · 4fe45b2
2 parents 514fbc3 + 92fe09e
commit 4fe45b2
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Showing 8 changed files with 43 additions and 26 deletions.
diff --git a/.github/workflows/package.yml b/.github/workflows/package.yml
@@ -5,7 +5,7 @@ on:
 jobs:
       build_wheels_linux_mac:
             env:
-                  CIBW_SKIP: cp311-* cp312-* cp313-* *-manylinux_i686 pp* *_ppc641e *_s390x *_aarch64 *musllinux* 
+                  CIBW_SKIP: cp36-* cp311-* cp312-* cp313-* *-manylinux_i686 pp* *_ppc641e *_s390x *_aarch64 *musllinux* 
                   CIBW_BEFORE_ALL_LINUX: yum -y install cmake cmake3 blas-devel lapack-devel && alternatives --install /usr/local/bin/cmake cmake /usr/bin/cmake 10 --slave /usr/local/bin/ctest ctest /usr/bin/ctest --slave /usr/local/bin/cpack cpack /usr/bin/cpack --slave /usr/local/bin/ccmake ccmake /usr/bin/ccmake --family cmake && alternatives --install /usr/local/bin/cmake cmake /usr/bin/cmake3 20 --slave /usr/local/bin/ctest ctest /usr/bin/ctest3 --slave /usr/local/bin/cpack cpack /usr/bin/cpack3 --slave /usr/local/bin/ccmake ccmake /usr/bin/ccmake3 --family cmake
                   CIBW_BEFORE_ALL_MACOS: brew install cmake openblas superlu gfortran
                   CIBW_BEFORE_BUILD: "cmake -DCMAKE_BUILD_TYPE=Release -DUSE_OPENMP=OFF . && cmake --build . && rm CMakeCache.txt && rm -rf CMakeFiles && pip install -r requirements.txt"
@@ -32,10 +32,10 @@ jobs:
                     run: python -m pip install cibuildwheel
                   - name: Build wheels
                     run: python -m cibuildwheel --output-dir wheelhouse
-                  - uses: actions/upload-artifact@v2
+                  - uses: actions/upload-artifact@v4
                     with:
                           path: ./wheelhouse/*.whl
-                          name: packages
+                          name: packages-${{matrix.os}}
 
       build_sdist:
             name: Build source distribution
@@ -50,19 +50,36 @@ jobs:
                           python-version: '3.8'
                   - name: Build source distribution
                     run: python setup.py sdist
-                  - uses: actions/upload-artifact@v2
+                  - uses: actions/upload-artifact@v4
                     with:
                           path: dist/*.tar.gz
-                          name: packages
+                          name: packages-source
 
-      upload_pypi:
+      upload_pypi_wheel:
+            needs: [build_wheels_linux_mac, build_sdist]
+            runs-on: ubuntu-latest
+            name: Upload packages to pypi
+            strategy:
+                  matrix:
+                        os: [ubuntu-latest, macos-latest]
+            steps:
+                  - uses: actions/[email protected]
+                    with:
+                          name: packages-${{matrix.os}}
+                          path: dist
+                  - uses: pypa/gh-action-pypi-publish@master
+                    with:
+                          user: __token__
+                          password: ${{ secrets.PIPY_PASSWORD }}
+
+      upload_pypi_source:
             needs: [build_wheels_linux_mac, build_sdist]
             runs-on: ubuntu-latest
             name: Upload packages to pypi
             steps:
-                  - uses: actions/download-artifact@v2
+                  - uses: actions/download-artifact@v4.1.7
                     with:
-                          name: packages
+                          name: packages-source
                           path: dist
                   - uses: pypa/gh-action-pypi-publish@master
                     with:

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -44,7 +44,7 @@ jobs:
               with:
                     submodules: recursive
             - run: brew update
-            - run: brew install cmake openblas superlu 1>/dev/null || true
+            - run: brew install cmake openblas superlu
             - uses: actions/setup-python@v4
               with:
                 python-version: '3.11'
@@ -62,9 +62,9 @@ jobs:
               with:
                     submodules: recursive
             - run: brew update
-            - run: brew install cmake openblas superlu gfortran valgrind 1>/dev/null || true
+            - run: brew install cmake openblas superlu gfortran
             - run: brew reinstall gcc
-            - run: cmake -D CMAKE_CXX_COMPILER=/usr/bin/g++ -D CMAKE_C_COMPILER=/usr/bin/gcc -D CMAKE_Fortran_COMPILER=/usr/local/bin/gfortran -D CMAKE_BUILD_TYPE=${{ matrix.btype }} -D USE_OPENMP=OFF -D BUILD_UTILS=ON .
+            - run: cmake -D CMAKE_CXX_COMPILER=/usr/bin/g++ -D CMAKE_C_COMPILER=/usr/bin/gcc -D CMAKE_Fortran_COMPILER=/opt/homebrew/bin/gfortran -D CMAKE_BUILD_TYPE=${{ matrix.btype }} -D USE_OPENMP=OFF -D BUILD_UTILS=ON .
             - run: make -j 2
             - run: test/drivers/test_drivers.sh
             - run: cd profiling && ./check_memory.sh
@@ -84,7 +84,7 @@ jobs:
              with:
                msystem: MINGW64
                update: true
-               install: git mingw-w64-x86_64-toolchain base-devel mingw-w64-x86_64-openblas mingw-w64-x86_64-cmake mingw-w64-x86_64-python-pip mingw-w64-x86_64-python-numpy mingw-w64-x86_64-python-scipy mingw-w64-x86_64-python-networkx mingw-w64-x86_64-python-matplotlib
+               install: git mingw-w64-x86_64-toolchain base-devel mingw-w64-x86_64-openblas mingw-w64-x86_64-cmake mingw-w64-x86_64-python-pip mingw-w64-x86_64-python-numpy mingw-w64-x86_64-python-scipy mingw-w64-x86_64-python-networkx mingw-w64-x86_64-python-matplotlib mingw-w64-x86_64-gcc-fortran
            - run: pip install nose2
            - run: cmake . -G"MSYS Makefiles" -D"WRAP_PYTHON=ON" -D"CMAKE_BUILD_TYPE=${{ matrix.btype }}"
            - run: make -j 2
@@ -105,7 +105,7 @@ jobs:
              with:
                msystem: MINGW64
                update: true
-               install: git mingw-w64-x86_64-toolchain base-devel mingw-w64-x86_64-openblas mingw-w64-x86_64-cmake
+               install: git mingw-w64-x86_64-toolchain base-devel mingw-w64-x86_64-openblas mingw-w64-x86_64-cmake mingw-w64-x86_64-gcc-fortran
            - run: cmake . -G"MSYS Makefiles" -D"BUILD_UTILS=ON" -D"CMAKE_BUILD_TYPE=${{ matrix.btype }}"
            - run: make -j 2
            - run: PATH=$PATH:$PWD/lib ./test/drivers/test_drivers.sh
diff --git a/.github/workflows/test_packages.yml b/.github/workflows/test_packages.yml
@@ -3,7 +3,7 @@ on: pull_request
 jobs:
       test_wheels_linux_mac:
             env:
-                  CIBW_SKIP: cp311-* cp312-* cp313-* *-manylinux_i686 pp* *_ppc641e *_s390x *_aarch64 *musllinux* 
+                  CIBW_SKIP: cp36-* cp311-* cp312-* cp313-* *-manylinux_i686 pp* *_ppc641e *_s390x *_aarch64 *musllinux* 
                   CIBW_BEFORE_ALL_LINUX: yum -y install cmake cmake3 blas-devel lapack-devel && alternatives --install /usr/local/bin/cmake cmake /usr/bin/cmake 10 --slave /usr/local/bin/ctest ctest /usr/bin/ctest --slave /usr/local/bin/cpack cpack /usr/bin/cpack --slave /usr/local/bin/ccmake ccmake /usr/bin/ccmake --family cmake && alternatives --install /usr/local/bin/cmake cmake /usr/bin/cmake3 20 --slave /usr/local/bin/ctest ctest /usr/bin/ctest3 --slave /usr/local/bin/cpack cpack /usr/bin/cpack3 --slave /usr/local/bin/ccmake ccmake /usr/bin/ccmake3 --family cmake
                   CIBW_BEFORE_ALL_MACOS: brew install cmake openblas superlu gfortran
                   CIBW_BEFORE_BUILD: "cmake -DCMAKE_BUILD_TYPE=Release -DUSE_OPENMP=OFF . && cmake --build . && rm CMakeCache.txt && rm -rf CMakeFiles && pip install -r requirements.txt"
@@ -30,10 +30,10 @@ jobs:
                     run: python -m pip install cibuildwheel
                   - name: Build wheels
                     run: python -m cibuildwheel --output-dir wheelhouse
-                  - uses: actions/upload-artifact@v2 
+                  - uses: actions/upload-artifact@v4 
                     with:
                           path: ./wheelhouse/*.whl
-                          name: packages
+                          name: packages-${{matrix.os}}
 
       test_sdist:
             name: Test source distribution on linux
@@ -48,7 +48,7 @@ jobs:
                           python-version: '3.8'
                   - name: Build source distribution
                     run: python setup.py sdist
-                  - uses: actions/upload-artifact@v2
+                  - uses: actions/upload-artifact@v4
                     with:
                           path: dist/*.tar.gz
                           name: packages
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,4 +1,4 @@
-CMAKE_MINIMUM_REQUIRED(VERSION 3.1)
+CMAKE_MINIMUM_REQUIRED(VERSION 3.5)
 project(NEML LANGUAGES CXX)
 
 ### Version ###

diff --git a/pybind11 b/pybind11
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -40,15 +40,17 @@ target_include_directories(neml PRIVATE "../include")
 target_link_libraries(neml ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES} ${SOLVER_LIBRARIES} ${OpenMP_CXX_LIBRARIES})
 generate_export_header(neml EXPORT_FILE_NAME ${PROJECT_SOURCE_DIR}/include/neml_export.h)
 generate_export_header(neml EXPORT_FILE_NAME ${PROJECT_BINARY_DIR}/include/neml_export.h)
-set_target_properties(neml PROPERTIES PUBLIC_HEADER 
-      "${PROJECT_BINARY_DIR}/include/neml_export.h;../include/neml_interface.h;../include/nemlerror.h;../include/windows.h")
+
 
 # An annoyance for building the python package
 if (PYTHON_PACKAGE)
       # Strictly we don't need this for wheels, but for source builds it's handy
       install(TARGETS neml 
             LIBRARY DESTINATION neml)
 else()
+      set_target_properties(neml PROPERTIES PUBLIC_HEADER 
+            "${PROJECT_BINARY_DIR}/include/neml_export.h;../include/neml_interface.h;../include/nemlerror.h;../include/windows.h"
+            )
       install(TARGETS neml 
             LIBRARY DESTINATION lib
             PUBLIC_HEADER DESTINATION include)

diff --git a/src/cp/slipharden.cxx b/src/cp/slipharden.cxx
@@ -392,10 +392,8 @@ void FASlipHardening::populate_hist(History & history) const
 
 void FASlipHardening::init_hist(History & history) const
 {
-  size_t i = 0;
   for (auto vn : varnames_) {
     history.get<double>(vn) = 0.0;
-    i++;
   }
 }
 
@@ -799,10 +797,8 @@ void SimpleLinearHardening::populate_hist(History & history) const
 
 void SimpleLinearHardening::init_hist(History & history) const
 {
-  size_t i = 0;
   for (auto vn : varnames_) {
     history.get<double>(vn) = 0;
-    i++;
   }
 }
 

diff --git a/test/test_nemlmath.py b/test/test_nemlmath.py
@@ -1,6 +1,8 @@
 import sys
 sys.path.append('..')
 
+import math
+
 from neml.math.nemlmath import *
 from common import *
 
@@ -396,7 +398,7 @@ def test_isclose(self):
 class TestVariousFactorial(unittest.TestCase):
   def test_factorial(self):
     for i in range(10):
-      self.assertTrue(np.isclose(np.math.factorial(i), factorial(i)))
+      self.assertTrue(np.isclose(math.factorial(i), factorial(i)))
 
 class TestEigenstuff(unittest.TestCase):
   def setUp(self):