Merge branch 'develop' into issue-1429-simplifications

.github/workflows/build_wheels.yml

@@ -0,0 +1,75 @@
+name: Build
+
+on:
+  push:
+    branches: master
+  workflow_dispatch:
+    inputs:
+      target:
+        description: 'Deployment target. Can be "pypi" or "testpypi"'
+        default: 'pypi'
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [macOS-10.15, ubuntu-20.04]
+
+    steps:
+      - uses: actions/checkout@v2
+
+      # Used to host cibuildwheel
+      - uses: actions/setup-python@v2
+
+      - name: Install cibuildwheel
+        run: python -m pip install cibuildwheel==1.9.0
+
+      - name: Install sundials on macOS
+        if: matrix.os == 'macOS-10.15'
+        run: |
+          brew update
+          brew install sundials
+
+      - name: Clone pybind11 repo
+        run: git clone https://github.com/pybind/pybind11.git
+
+      - name: Build wheels
+        run: python -m cibuildwheel --output-dir wheelhouse
+        env:
+          CIBW_BEFORE_ALL_LINUX: "bash build_manylinux_wheels/install_sundials.sh 5.8.1 5.7.0"
+          CIBW_BEFORE_BUILD_LINUX: "python -m pip install cmake"
+
+      - uses: actions/upload-artifact@v2
+        with:
+          name: wheels
+          path: ./wheelhouse/*.whl
+
+
+  publish-pypi:
+    name: Upload wheels to PyPI
+    needs: build_wheels
+    runs-on: ubuntu-latest
+    steps:
+      - name: Download wheels
+        uses: actions/download-artifact@v1
+        with:
+          name: wheels
+
+      - name: Publish wheels on PyPI
+        if: ${{ github.events.inputs.target }} == 'pypi'
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_TOKEN }}
+          packages_dir: wheels/
+
+      - name: Publish wheels on TestPyPI
+        if: ${{ github.events.inputs.target }} == 'testpypi'
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.TESTPYPI_TOKEN }}
+          packages_dir: wheels/
+          repository_url: https://test.pypi.org/legacy/

CMakeBuild.py

@@ -94,14 +94,13 @@ def run(self):
     def move_output(self, ext):
         # Copy built module to dist/ directory
         build_temp = Path(self.build_temp).resolve()
-        source_path = build_temp / self.get_ext_filename(ext.name)
         # Get destination location
         # self.get_ext_fullpath(ext.name) -->
         # build/lib.linux-x86_64-3.5/idaklu.cpython-37m-x86_64-linux-gnu.so
         # using resolve() with python < 3.6 will result in a FileNotFoundError
         # since the location does not yet exists.
         dest_path = Path(self.get_ext_fullpath(ext.name)).resolve()
-        source_path = build_temp / self.get_ext_filename(ext.name)
+        source_path = build_temp / os.path.basename(self.get_ext_filename(ext.name))
         dest_directory = dest_path.parents[0]
         dest_directory.mkdir(parents=True, exist_ok=True)
         self.copy_file(source_path, dest_path)

build_manylinux_wheels/install_sundials.sh

@@ -1,35 +1,80 @@
 #!/bin/bash
 
-mkdir /deps
-wget https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.7.2.tar.gz .
-wget https://computing.llnl.gov/projects/sundials/download/sundials-5.3.0.tar.gz .
-tar -xf v5.7.2.tar.gz --directory /deps
-tar -xf sundials-5.3.0.tar.gz --directory /deps
-rm v5.7.2.tar.gz
-rm sundials-5.3.0.tar.gz
+# This script installs both SuiteSparse
+# (https://people.engr.tamu.edu/davis/suitesparse.html) and Sundials
+# (https://computing.llnl.gov/projects/sundials) from source. For each
+# two library:
+# - Archive downloaded and source code extrated in current working
+#   directory.
+# - Library is built and installed.
+#
+# Usage: ./install_sundials.sh suitesparse_version sundials_version
 
-SUITESPARSE_DIR=/deps/SuiteSparse-5.7.2
-SUNDIALS_DIR=/deps/sundials-5.3.0
+function prepend_python_bin_dir_to_PATH {
+    python_bin_dir_cmd="print(os.path.split(sys.executable)[0])"
+    python_bin_dir=$(python -c "import sys, os;$python_bin_dir_cmd")
+    export PATH=$python_bin_dir:$PATH
+}
 
+function download {
+    ROOT_ADDR=$1
+    FILENAME=$2
+
+    wget -q $ROOT_ADDR/$FILENAME
+}
+
+function extract {
+    tar -xf $1
+}
+
+SUITESPARSE_VERSION=$1
+SUNDIALS_VERSION=$2
+
+SUITESPARSE_ROOT_ADDR=https://github.com/LLNL/sundials/releases/download/v$SUNDIALS_VERSION
+SUNDIALS_ROOT_ADDR=https://computing.llnl.gov/projects/sundials/download
+
+SUITESPARSE_ARCHIVE_NAME=v$SUITESPARSE_VERSION.tar.gz
+SUNDIALS_ARCHIVE_NAME=sundials-$SUNDIALS_VERSION.tar.gz
+
+yum -y update
+yum -y install wget
+download $SUITESPARSE_ROOT_ADDR $SUITESPARSE_ARCHIVE_NAME
+download $SUNDIALS_ROOT_ADDR $SUNDIALS_ARCHIVE_NAME
+extract $SUITESPARSE_ARCHIVE_NAME
+extract $SUNDIALS_ARCHIVE_NAME
+
+### Compile and install SUITESPARSE ###
+# SuiteSparse is required to compile SUNDIALS's
+# KLU solver.
+
+SUITESPARSE_DIR=SuiteSparse-$SUITESPARSE_VERSION
 for dir in SuiteSparse_config AMD COLAMD BTF KLU
 do
-    cd $SUITESPARSE_DIR/$dir;
-    make library
-    make install INSTALL=/usr
-    cd ../
+    make -C $SUITESPARSE_DIR/$dir library
+    make -C $SUITESPARSE_DIR/$dir install INSTALL=/usr
 done
 
+### Compile and install SUNDIALS ###
+
+# Building cmake requires cmake >= 3.5
+python -m pip install cmake
+prepend_python_bin_dir_to_PATH
+
+# Building SUNDIALS requires a BLAS library
+yum -y install openblas-devel
+
+mkdir -p build_sundials
+cd build_sundials
 KLU_INCLUDE_DIR=/usr/include
 KLU_LIBRARY_DIR=/usr/lib
-mkdir -p /deps/build_sundials
-cd /deps/build_sundials
-cmake -DLAPACK_ENABLE=ON\
+SUNDIALS_DIR=sundials-$SUNDIALS_VERSION
+cmake -DENABLE_LAPACK=ON\
       -DSUNDIALS_INDEX_SIZE=32\
       -DEXAMPLES_ENABLE:BOOL=OFF\
-      -DKLU_ENABLE=ON\
+      -DENABLE_KLU=ON\
       -DKLU_INCLUDE_DIR=$KLU_INCLUDE_DIR\
       -DKLU_LIBRARY_DIR=$KLU_LIBRARY_DIR\
       -DCMAKE_INSTALL_PREFIX=/usr\
-      $SUNDIALS_DIR
+      ../$SUNDIALS_DIR
 make install
 

pybamm/solvers/idaklu_solver.py

@@ -8,7 +8,7 @@
 
 import importlib
 
-idaklu_spec = importlib.util.find_spec("idaklu")
+idaklu_spec = importlib.util.find_spec("pybamm.solvers.idaklu")
 if idaklu_spec is not None:
     idaklu = importlib.util.module_from_spec(idaklu_spec)
     idaklu_spec.loader.exec_module(idaklu)

setup.py

@@ -158,7 +158,10 @@ def compile_KLU():
 pybamm_data.append("./CITATIONS.txt")
 pybamm_data.append("./plotting/pybamm.mplstyle")
 
-idaklu_ext = Extension("idaklu", ["pybamm/solvers/c_solvers/idaklu.cpp"])
+idaklu_ext = Extension(
+    "pybamm.solvers.idaklu",
+    ["pybamm/solvers/c_solvers/idaklu.cpp"]
+)
 ext_modules = [idaklu_ext] if compile_KLU() else []
 
 jax_dependencies = []