From 825d5560e8f6fa63eb54ac32ea1731be6cb082d9 Mon Sep 17 00:00:00 2001
From: dedner <a.s.dedner@warwick.ac.uk>
Date: Sun, 25 Apr 2021 20:25:58 +0100
Subject: [PATCH] use new approach in dune-common for handling python bindings
fix ci
pep 42: use implicit namespace packages which make it possible to combine subpackages using editable (source) and non editable (pypi)
only use a cmake install a python module in the SKBUILD setting - for an install from build dir pip will take take of this since it is part of the setup.py file
add a stopgap solution unti ci repo up and running again
Update requirements.
add dune packages to requires in setup.py.in
[testing]
only add dune modules that have been found as requirements in setup.py.in
removed setup.py.in since the default is provided in dune-common
adapt ci yml file to python bindings on by default
disable python bindings for clang 5 (ubuntu 18) since no numpy matching numpy version can be installed from the gitlab registry
[bug fix python bindings]
fix an issue with 'entry' being used in implicit build mode but ready==build
---
.gitlab-ci.yml | 34 ++++++++++++++++-----------------
CMakeLists.txt | 1 -
dune/python/istl/bcrsmatrix.hh | 6 +++---
pyproject.toml | 2 +-
python/CMakeLists.txt | 6 +++++-
python/dune/CMakeLists.txt | 4 ----
python/dune/__init__.py | 1 -
python/dune/istl/CMakeLists.txt | 3 +++
python/setup.py.in | 15 ---------------
setup.py | 1 +
10 files changed, 30 insertions(+), 43 deletions(-)
delete mode 100644 python/dune/__init__.py
delete mode 100644 python/setup.py.in
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index b221537e8..eef8c51df 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -19,29 +19,29 @@ variables:
# than one thread.
OMP_NUM_THREADS: 1
-debian-11-gcc-9-17-python:
+debian-11-gcc-9-17-with-checking:
image: registry.dune-project.org/docker/ci/debian:11
script: duneci-standard-test
variables:
DUNECI_TOOLCHAIN: gcc-9-17
- # so we need some variables to build the dune-py module during execution of the first python test:
- # we need to find the dune mdoule
- DUNE_CONTROL_PATH: /duneci/modules:$CI_PROJECT_DIR
- # the position for the dune-py module
- DUNE_PY_DIR: /duneci/modules/dune-py
- # during dune-py build this variable is used - do know a way to access
- # the CMAKE_FLAGS used to build the modules...
- DUNE_CMAKE_FLAGS: "-DCMAKE_CXX_COMPILER=g++-9 -DCMAKE_C_COMPILER=gcc-9 -DCMAKE_CXX_FLAGS='-std=c++17 -O2 -g -Wall -fdiagnostics-color=always' -DDUNE_ENABLE_PYTHONBINDINGS=ON -DDUNE_MAX_TEST_CORES=4 -DBUILD_SHARED_LIBS=TRUE -DDUNE_PYTHON_INSTALL_LOCATION=none -DCMAKE_POSITION_INDEPENDENT_CODE=TRUE -DCMAKE_DISABLE_FIND_PACKAGE_LATEX=TRUE -DCMAKE_DISABLE_FIND_PACKAGE_Alberta=TRUE -DCMAKE_DISABLE_FIND_PACKAGE_Vc=TRUE -DCMAKE_DISABLE_DOCUMENTATION=TRUE"
- # cmake flags we use for all dune moudle - important is that build shared libs is set (need some better way of doing this)
- DUNECI_CMAKE_FLAGS: $DUNE_CMAKE_FLAGS
- # finally set the python path to all modules
- PYTHONPATH: /duneci/modules/dune-common/build-cmake/python:$CI_PROJECT_DIR/build-cmake/python
+ DUNECI_CMAKE_FLAGS: "CC=gcc-9 CXX=g++-9 -DCMAKE_CXX_FLAGS='-std=c++17 -O2 -g -Wall -fdiagnostics-color=always -DDUNE_ISTL_WITH_CHECKING' -DDUNE_MAX_TEST_CORES=4 -DCMAKE_DISABLE_FIND_PACKAGE_LATEX=TRUE -DCMAKE_DISABLE_FIND_PACKAGE_Alberta=TRUE -DCMAKE_DISABLE_DOCUMENTATION=TRUE"
tags: [duneci]
-debian-11-gcc-9-17-with-checking:
- image: registry.dune-project.org/docker/ci/debian:11
+# no numpy version available for this image on the gitlab registry
+# disable python bindings for now
+ubuntu:18.04 clang-6-17:
+ image: registry.dune-project.org/docker/ci/ubuntu:18.04
script: duneci-standard-test
+ stage: test
variables:
- DUNECI_TOOLCHAIN: gcc-9-17
- DUNECI_CMAKE_FLAGS: "CC=gcc-9 CXX=g++-9 -DCMAKE_CXX_FLAGS='-std=c++17 -O2 -g -Wall -fdiagnostics-color=always -DDUNE_ISTL_WITH_CHECKING' -DDUNE_MAX_TEST_CORES=4 -DCMAKE_DISABLE_FIND_PACKAGE_LATEX=TRUE -DCMAKE_DISABLE_FIND_PACKAGE_Alberta=TRUE -DCMAKE_DISABLE_DOCUMENTATION=TRUE"
+ DUNECI_TOOLCHAIN: clang-6-17
+ DUNECI_CMAKE_FLAGS: "-DDUNE_ENABLE_PYTHONBINDINGS=OFF"
+ tags: [duneci]
+ubuntu:18.04 clang-5-17:
+ image: registry.dune-project.org/docker/ci/ubuntu:18.04
+ script: duneci-standard-test
+ stage: test
+ variables:
+ DUNECI_TOOLCHAIN: clang-5-17
+ DUNECI_CMAKE_FLAGS: "-DDUNE_ENABLE_PYTHONBINDINGS=OFF"
tags: [duneci]
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 942cea2a9..6d84d3193 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -30,7 +30,6 @@ add_subdirectory(doc)
# if Python bindings are enabled, include necessary sub directories.
if( DUNE_ENABLE_PYTHONBINDINGS )
add_subdirectory(python)
- dune_python_install_package(PATH python)
endif()
# finalize the dune project, e.g. generating config.h etc.
diff --git a/dune/python/istl/bcrsmatrix.hh b/dune/python/istl/bcrsmatrix.hh
index fcf180c18..b391e2969 100644
--- a/dune/python/istl/bcrsmatrix.hh
+++ b/dune/python/istl/bcrsmatrix.hh
@@ -185,7 +185,7 @@ namespace Dune
if( col >= self.M() )
throw pybind11::index_error( "No such column: " + std::to_string( col ) );
- if( self.buildMode() != BCRSMatrix::implicit )
+ if( self.buildMode() != BCRSMatrix::implicit || self.buildStage() == BCRSMatrix::built )
{
auto pos = self[ row ].find( col );
if( pos != self[ row ].end() )
@@ -212,7 +212,7 @@ namespace Dune
if( col >= self.M() )
throw pybind11::index_error( "No such column: " + std::to_string( col ) );
- if( self.buildMode() != BCRSMatrix::implicit )
+ if( self.buildMode() != BCRSMatrix::implicit || self.buildStage() == BCRSMatrix::built )
{
auto pos = self[ row ].find( col );
if( pos != self[ row ].end() )
@@ -231,7 +231,7 @@ namespace Dune
std::size_t cstart, cstop, cstep, clength;
std::get< 1 >( index ).compute( self.M(), &cstart, &cstop, &cstep, &clength );
- if( self.buildMode() == BCRSMatrix::implicit )
+ if( self.buildMode() != BCRSMatrix::implicit || self.buildStage() == BCRSMatrix::built )
{
for( auto v : value )
{
diff --git a/pyproject.toml b/pyproject.toml
index 51561aa82..7089496a5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,3 +1,3 @@
[build-system]
-requires = ['setuptools', 'wheel', 'scikit-build', 'cmake', 'ninja', 'requests', 'dune-common>=2.8.0.dev0']
+requires = ['dune-common>=2.8.0.dev0', 'numpy', 'pip', 'setuptools', 'wheel', 'scikit-build', 'cmake', 'ninja', 'requests']
build-backend = 'setuptools.build_meta'
diff --git a/python/CMakeLists.txt b/python/CMakeLists.txt
index bf6f08c04..7af28c410 100644
--- a/python/CMakeLists.txt
+++ b/python/CMakeLists.txt
@@ -1,3 +1,7 @@
add_subdirectory(dune)
-configure_file(setup.py.in setup.py)
+dune_python_install_package(
+ PATH "."
+ CMAKE_METADATA_FILE dune/istl/metadata.cmake
+ DEPENDS _istl
+)
diff --git a/python/dune/CMakeLists.txt b/python/dune/CMakeLists.txt
index 455f02598..e93d9cba6 100644
--- a/python/dune/CMakeLists.txt
+++ b/python/dune/CMakeLists.txt
@@ -1,5 +1 @@
add_subdirectory(istl)
-
-add_python_targets(dune
- __init__
-)
diff --git a/python/dune/__init__.py b/python/dune/__init__.py
deleted file mode 100644
index de40ea7ca..000000000
--- a/python/dune/__init__.py
+++ /dev/null
@@ -1 +0,0 @@
-__import__('pkg_resources').declare_namespace(__name__)
diff --git a/python/dune/istl/CMakeLists.txt b/python/dune/istl/CMakeLists.txt
index cf28165ea..37e5f9137 100644
--- a/python/dune/istl/CMakeLists.txt
+++ b/python/dune/istl/CMakeLists.txt
@@ -3,3 +3,6 @@ add_python_targets(istl
)
dune_add_pybind11_module(NAME _istl)
set_property(TARGET _istl PROPERTY LINK_LIBRARIES dunecommon APPEND)
+if(SKBUILD)
+ install(TARGETS _istl LIBRARY DESTINATION python/dune/istl)
+endif()
diff --git a/python/setup.py.in b/python/setup.py.in
deleted file mode 100644
index dd784ccf4..000000000
--- a/python/setup.py.in
+++ /dev/null
@@ -1,15 +0,0 @@
-from setuptools import setup, find_packages
-
-pkg = [m for m in "${ProjectPythonRequires}".split(' ') if "dune" not in m]
-
-setup(name="${ProjectName}",
- namespace_packages=['dune'],
- description="${ProjectDescription}",
- version="${ProjectVersionString}",
- author="${ProjectAuthor}",
- author_email="${ProjectMaintainerEmail}",
- packages = find_packages(),
- zip_safe = 0,
- package_data = {'': ['*.so']},
- install_requires = pkg
- )
diff --git a/setup.py b/setup.py
index 85afc7513..6568839f1 100644
--- a/setup.py
+++ b/setup.py
@@ -1,3 +1,4 @@
+import os, sys
try:
from dune.packagemetadata import metaData
except ImportError:
--
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