Merge branch 'develop' into data

pybamm-team · May 25, 2024 · 92f988a · 92f988a
2 parents ebd59a3 + 6ba81b7
commit 92f988a
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diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml
@@ -100,7 +100,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-13]
+        os: [ubuntu-latest, macos-12]
     steps:
       - uses: actions/checkout@v4
         name: Check out PyBaMM repository
@@ -113,6 +113,15 @@ jobs:
       - name: Clone pybind11 repo (no history)
         run: git clone --depth 1 --branch v2.11.1 https://github.com/pybind/pybind11.git
 
+      # sometimes gfortran cannot be found, so reinstall gcc just to be sure
+      - name: Install SuiteSparse and SUNDIALS on macOS
+        if: matrix.os == 'macos-12'
+        run: |
+          brew install graphviz libomp
+          brew reinstall gcc
+          python -m pip install cmake wget
+          python scripts/install_KLU_Sundials.py
+
       - name: Build wheels on Linux
         run: pipx run cibuildwheel --output-dir wheelhouse
         if: matrix.os == 'ubuntu-latest'
@@ -126,50 +135,11 @@ jobs:
           CIBW_TEST_COMMAND: python -c "import pybamm; pybamm.IDAKLUSolver()"
 
       - name: Build wheels on macOS amd64
-        if: matrix.os == 'macos-13'
+        if: matrix.os == 'macos-12'
         run: pipx run cibuildwheel --output-dir wheelhouse
         env:
-          MACOSX_DEPLOYMENT_TARGET: 11.0
-          # Sourced from
-          # License: BSD-3-Clause
-          # https://github.com/scipy/scipy/blob/f2d4775e7762fad984f8f0acd8227c725ff21630/tools/wheels/cibw_before_build_macos.sh#L23-L49
-          CIBW_BEFORE_ALL_MACOS: |
-            set -e -x
-
-            # download gfortran with proper macos minimum version (11.0)
-            curl -L https://github.com/isuruf/gcc/releases/download/gcc-11.3.0-2/gfortran-darwin-x86_64-native.tar.gz -o gfortran.tar.gz
-
-            GFORTRAN_SHA256=$(shasum --algorithm 256 gfortran.tar.gz)
-            KNOWN_SHA256="981367dd0ad4335613e91bbee453d60b6669f5d7e976d18c7bdb7f1966f26ae4  gfortran.tar.gz"
-            if [ "$GFORTRAN_SHA256" != "$KNOWN_SHA256" ]; then
-              echo "SHA256 mismatch for gfortran.tar.gz"
-              echo "expected: $KNOWN_SHA256"
-              echo "got: $GFORTRAN_SHA256"
-              exit 1
-            fi
-
-            mkdir -p gfortran_installed/
-            tar -xv -C gfortran_installed/ -f gfortran.tar.gz
-
-            export FC=$(pwd)/gfortran_installed/gfortran-darwin-x86_64-native/bin/gfortran
-            export PATH=$(pwd)/gfortran_installed/gfortran-darwin-x86_64-native/bin:$PATH
-
-            # link libgfortran.5.dylib, libgfortran.dylib, libquadmath.0.dylib, libquadmath.dylib, libgcc_s.1.dylib, libgcc_s.1.1.dylib
-            # and place them in $HOME/.local/lib, and then change rpath
-            # to $HOME/.local/lib
-
-            mkdir -p $HOME/.local/lib
-            lib_dir=$(pwd)/gfortran_installed/gfortran-darwin-x86_64-native/lib
-            for lib in libgfortran.5.dylib libgfortran.dylib libquadmath.0.dylib libquadmath.dylib libgcc_s.1.dylib libgcc_s.1.1.dylib; do
-              cp $lib_dir/$lib $HOME/.local/lib/
-              install_name_tool -id $HOME/.local/lib/$lib $HOME/.local/lib/$lib
-            done
-
-            export SDKROOT=${SDKROOT:-$(xcrun --show-sdk-path)}
-
-            python -m pip install cmake wget
-            python scripts/install_KLU_Sundials.py
-          CIBW_BEFORE_BUILD_MACOS: python -m pip install --upgrade pip cmake casadi setuptools wheel delocate
+          CIBW_BEFORE_BUILD_MACOS: >
+            python -m pip install --upgrade cmake casadi setuptools wheel
           CIBW_REPAIR_WHEEL_COMMAND_MACOS: delocate-listdeps {wheel} && delocate-wheel -v -w {dest_dir} {wheel}
           CIBW_TEST_COMMAND: python -c "import pybamm; pybamm.IDAKLUSolver()"
 
@@ -193,57 +163,18 @@ jobs:
       - name: Clone pybind11 repo (no history)
         run: git clone --depth 1 --branch v2.11.1 https://github.com/pybind/pybind11.git
 
-      - name: Build wheels on macOS arm64
+      - name: Install SuiteSparse and SUNDIALS on macOS
         run: |
-          python -m pip install cibuildwheel
-          python -m cibuildwheel --output-dir wheelhouse
-        env:
-          MACOSX_DEPLOYMENT_TARGET: 11.0
-          # Sourced from
-          # License: BSD-3-Clause
-          # https://github.com/scipy/scipy/blob/f2d4775e7762fad984f8f0acd8227c725ff21630/tools/wheels/cibw_before_build_macos.sh#L23-L49
-          CIBW_BEFORE_ALL_MACOS: |
-            set -e -x
-
-            # download gfortran with proper macos minimum version (11.0)
-            curl -L https://github.com/isuruf/gcc/releases/download/gcc-11.3.0-2/gfortran-darwin-arm64-native.tar.gz -o gfortran.tar.gz
-
-            GFORTRAN_SHA256=$(shasum --algorithm 256 gfortran.tar.gz)
-            KNOWN_SHA256="84364eee32ba843d883fb8124867e2bf61a0cd73b6416d9897ceff7b85a24604  gfortran.tar.gz"
-            if [ "$GFORTRAN_SHA256" != "$KNOWN_SHA256" ]; then
-              echo "SHA256 mismatch for gfortran.tar.gz"
-              echo "expected: $KNOWN_SHA256"
-              echo "got: $GFORTRAN_SHA256"
-              exit 1
-            fi
-
-            mkdir -p gfortran_installed/
-            tar -xv -C gfortran_installed/ -f gfortran.tar.gz
-
-            export FC=$(pwd)/gfortran_installed/gfortran-darwin-arm64-native/bin/gfortran
-            export PATH=$(pwd)/gfortran_installed/gfortran-darwin-arm64-native/bin:$PATH
+          brew install graphviz libomp
+          brew reinstall gcc
+          python -m pip install cmake pipx
+          python scripts/install_KLU_Sundials.py
 
-            # link libgfortran.5.dylib, libgfortran.dylib, libquadmath.0.dylib, libquadmath.dylib, libgcc_s.1.1.dylib
-            # and place them in $HOME/.local/lib, and then change rpath
-            # note: libgcc_s.1.dylib not present for arm64, skip for now
-            # to $HOME/.local/lib
-
-            mkdir -p $HOME/.local/lib
-            lib_dir=$(pwd)/gfortran_installed/gfortran-darwin-arm64-native/lib
-            for lib in libgfortran.5.dylib libgfortran.dylib libquadmath.0.dylib libquadmath.dylib libgcc_s.1.1.dylib; do
-              cp $lib_dir/$lib $HOME/.local/lib/
-              install_name_tool -id $HOME/.local/lib/$lib $HOME/.local/lib/$lib
-            done
-
-            export SDKROOT=${SDKROOT:-$(xcrun --show-sdk-path)}
-
-            python -m pip install cmake wget
-            python scripts/install_KLU_Sundials.py
-          CIBW_BEFORE_BUILD_MACOS: python -m pip install --upgrade pip cmake casadi setuptools wheel delocate
-          # Use higher macOS target for now: https://github.com/casadi/casadi/issues/3698
-          CIBW_REPAIR_WHEEL_COMMAND_MACOS: |
-            delocate-listdeps {wheel} && delocate-wheel -v -w {dest_dir} {wheel} --require-target-macos-version 11.1
-            for file in {dest_dir}/*.whl; do mv "$file" "${file//macosx_11_1/macosx_11_0}"; done
+      - name: Build wheels on macOS arm64
+        run: python -m pipx run cibuildwheel --output-dir wheelhouse
+        env:
+          CIBW_BEFORE_BUILD: python -m pip install cmake casadi setuptools wheel delocate
+          CIBW_REPAIR_WHEEL_COMMAND: delocate-listdeps {wheel} && delocate-wheel -v -w {dest_dir} {wheel}
           CIBW_TEST_COMMAND: python -c "import pybamm; pybamm.IDAKLUSolver()"
 
       - name: Upload wheels for macOS arm64

diff --git a/.github/workflows/run_periodic_tests.yml b/.github/workflows/run_periodic_tests.yml
@@ -57,7 +57,7 @@ jobs:
         # sometimes gfortran cannot be found, so reinstall gcc just to be sure
         run: |
           brew analytics off
-          brew install graphviz
+          brew install graphviz libomp
           brew reinstall gcc
 
       - name: Install Windows system dependencies

diff --git a/.github/workflows/test_on_push.yml b/.github/workflows/test_on_push.yml
@@ -74,7 +74,7 @@ jobs:
         # sometimes gfortran cannot be found, so reinstall gcc just to be sure
         run: |
           brew analytics off
-          brew install graphviz
+          brew install graphviz libomp
           brew reinstall gcc
 
       - name: Install Windows system dependencies
@@ -209,7 +209,7 @@ jobs:
         # sometimes gfortran cannot be found, so reinstall gcc just to be sure
         run: |
           brew analytics off
-          brew install graphviz
+          brew install graphviz libomp
           brew reinstall gcc
 
       - name: Install Windows system dependencies

diff --git a/.gitignore b/.gitignore
@@ -137,7 +137,3 @@ results/
 
 # tests
 test_callback.log
-
-# openmp downloads
-install_KLU_Sundials/openmp-*
-install_KLU_Sundials/usr/
diff --git a/docs/source/user_guide/installation/install-from-source.rst b/docs/source/user_guide/installation/install-from-source.rst
@@ -43,11 +43,11 @@ You can install the above with
 
 	Where ``X`` is the version sub-number.
 
-.. tab:: macOS
+.. tab:: MacOS
 
 	.. code:: bash
 
-		brew install python openblas gcc gfortran graphviz cmake pandoc
+		brew install python openblas gcc gfortran graphviz libomp cmake pandoc
 
 .. note::
 
@@ -82,9 +82,8 @@ If you are running windows, you can simply skip this section and jump to :ref:`p
 	  # in the PyBaMM/ directory
 	  nox -s pybamm-requires
 
-This will download, compile and install the SuiteSparse and SUNDIALS (with OpenMP) libraries
-and the ``pybind11`` headers.
-SuiteSparse and SUNDIALS are installed in ``~/.local`` by default.
+This will download, compile and install the SuiteSparse and SUNDIALS libraries.
+Both libraries are installed in ``~/.local``.
 
 For users requiring more control over the installation process, the ``pybamm-requires`` session supports additional command-line arguments:
 
@@ -111,7 +110,7 @@ If you'd rather do things yourself,
 
 1. Make sure you have CMake installed
 2. Compile and install SuiteSparse (PyBaMM only requires the ``KLU`` component).
-3. Compile and install SUNDIALS with `OpenMP support <https://mac.r-project.org/openmp/>`_.
+3. Compile and install SUNDIALS.
 4. Clone the pybind11 repository in the ``PyBaMM/`` directory (make sure the directory is named ``pybind11``).
 
 
@@ -316,12 +315,12 @@ source files to your current directory.
 ``ValueError: Integrator name ida does not exist``, or
 ``ValueError: Integrator name cvode does not exist``.
 
-**Solution:** This could mean that you have not linked to
-SUNDIALS correctly, check the instructions given above and make
+**Solution:** This could mean that you have not installed
+``scikits.odes`` correctly, check the instructions given above and make
 sure each command was successful.
 
 One possibility is that you have not set your ``LD_LIBRARY_PATH`` to
-point to the SUNDIALS library, type ``echo $LD_LIBRARY_PATH`` and make
+point to the sundials library, type ``echo $LD_LIBRARY_PATH`` and make
 sure one of the directories printed out corresponds to where the
 SUNDIALS libraries are located.