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Replace distutils imports #1557

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merged 6 commits into from
Oct 10, 2021
Merged

Replace distutils imports #1557

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d2b7bc1
Replace distutils imports
dweindl Oct 8, 2021
9fb97a3
pyproject.toml for model?
dweindl Oct 8, 2021
a3db951
import setuptools._distutils.ccompiler
dweindl Oct 8, 2021
87bec48
Revert "pyproject.toml for model?"
dweindl Oct 9, 2021
5c2865f
Merge branch 'develop' into maint_1553_distutils
dweindl Oct 9, 2021
89bf3b7
Merge branch 'develop' into maint_1553_distutils
Oct 9, 2021
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25 changes: 12 additions & 13 deletions python/amici/custom_commands.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,6 @@
from setuptools.command.install import install
from setuptools.command.install_lib import install_lib
from setuptools.command.sdist import sdist
from distutils import log

# typehints
Library = Tuple[str, Dict[str, List[str]]]
Expand All @@ -24,7 +23,7 @@
class AmiciInstall(install):
"""Custom install to handle extra arguments"""

log.debug("running AmiciInstall")
print("running AmiciInstall")

# Passing --no-clibs allows to install the Python-only part of AMICI
user_options = install.user_options + [
Expand Down Expand Up @@ -81,7 +80,7 @@ class AmiciBuildCLib(build_clib):
"""Custom build_clib"""

def run(self):
log.debug("running AmiciBuildCLib")
print("running AmiciBuildCLib")

# Always force recompilation. The way setuptools/distutils check for
# whether sources require recompilation is not reliable and may lead
Expand All @@ -91,7 +90,7 @@ def run(self):
build_clib.run(self)

def build_libraries(self, libraries: List[Library]):
log.debug("running AmiciBuildCLib.build_libraries")
print("running AmiciBuildCLib.build_libraries")

no_clibs = 'develop' in self.distribution.command_obj \
and self.get_finalized_command('develop').no_clibs
Expand Down Expand Up @@ -139,7 +138,7 @@ def finalize_options(self):
develop.finalize_options(self)

def run(self):
log.debug("running AmiciDevelop")
print("running AmiciDevelop")

if not self.no_clibs:
self.get_finalized_command('build_clib').run()
Expand All @@ -156,7 +155,7 @@ def run(self):
Returns:

"""
log.debug("running AmiciInstallLib")
print("running AmiciInstallLib")

if 'ENABLE_AMICI_DEBUGGING' in os.environ \
and os.environ['ENABLE_AMICI_DEBUGGING'] == 'TRUE' \
Expand Down Expand Up @@ -187,7 +186,7 @@ def run(self):
the wheel
"""

log.debug("running AmiciBuildExt")
print("running AmiciBuildExt")

no_clibs = 'develop' in self.distribution.command_obj \
and self.get_finalized_command('develop').no_clibs
Expand Down Expand Up @@ -220,13 +219,13 @@ def run(self):
f"Found unexpected number of files: {libfilenames}"
src = libfilenames[0]
dest = os.path.join(target_dir, os.path.basename(src))
log.info(f"copying {src} -> {dest}")
print(f"copying {src} -> {dest}")
copyfile(src, dest)

swig_outdir = os.path.join(os.path.abspath(build_dir), "amici")
generate_swig_interface_files(swig_outdir=swig_outdir)
swig_py_module_path = os.path.join(swig_outdir, 'amici.py')
log.debug("updating typehints")
print("updating typehints")
fix_typehints(swig_py_module_path, swig_py_module_path)

# Always force recompilation. The way setuptools/distutils check for
Expand All @@ -244,7 +243,7 @@ class AmiciSDist(sdist):
def run(self):
"""Setuptools entry-point"""

log.debug("running AmiciSDist")
print("running AmiciSDist")

save_git_version()

Expand All @@ -266,7 +265,7 @@ def save_git_version():
'--always', '--tags']
subprocess.run(cmd, stdout=f)
except Exception as e:
log.warn(e)
print(e)


def set_compiler_specific_library_options(
Expand Down Expand Up @@ -298,7 +297,7 @@ def set_compiler_specific_library_options(
for field in ['cflags', 'sources', 'macros']:
try:
lib[1][field] += lib[1][f'{field}_{compiler_type}']
log.info(f"Changed {field} for {lib[0]} with {compiler_type} "
print(f"Changed {field} for {lib[0]} with {compiler_type} "
f"to {lib[1][field]}")
except KeyError:
# No compiler-specific options set
Expand All @@ -322,7 +321,7 @@ def set_compiler_specific_extension_options(
new_value = getattr(ext, attr) + \
getattr(ext, f'{attr}_{compiler_type}')
setattr(ext, attr, new_value)
log.info(f"Changed {attr} for {compiler_type} to {new_value}")
print(f"Changed {attr} for {compiler_type} to {new_value}")
except AttributeError:
# No compiler-specific options set
pass
Expand Down
6 changes: 3 additions & 3 deletions python/amici/setup.template.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,9 +30,9 @@ def build_extension(self, ext):
# except for Windows, where this seems to be incompatible with
# providing swig files. Not investigated further...
if sys.platform != 'win32':
import distutils.ccompiler
import setuptools._distutils.ccompiler
self.compiler.compile = compile_parallel.__get__(
self.compiler, distutils.ccompiler.CCompiler)
self.compiler, setuptools._distutils.ccompiler.CCompiler)

build_ext.build_extension(self, ext)

Expand Down Expand Up @@ -64,7 +64,7 @@ def get_amici_libs() -> List[str]:


def get_extension() -> Extension:
"""Get distutils extension object for this AMICI model package"""
"""Get setuptools extension object for this AMICI model package"""

cxx_flags = []
linker_flags = []
Expand Down
27 changes: 13 additions & 14 deletions python/amici/setuptools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,6 @@
import shlex
import subprocess

from distutils import log
from .swig import find_swig, get_swig_version

try:
Expand Down Expand Up @@ -143,7 +142,7 @@ def get_hdf5_config() -> PackageInfo:
hdf5_include_dir_found = os.path.isfile(
os.path.join(hdf5_include_dir_hint, 'hdf5.h'))
if hdf5_include_dir_found:
log.info('hdf5.h found in %s' % hdf5_include_dir_hint)
print(f"hdf5.h found in {hdf5_include_dir_hint}")
h5pkgcfg['include_dirs'] = [hdf5_include_dir_hint]
break

Expand All @@ -153,7 +152,7 @@ def get_hdf5_config() -> PackageInfo:
hdf5_library_dir_found = os.path.isfile(
os.path.join(hdf5_library_dir_hint, lib_filename))
if hdf5_library_dir_found:
log.info(f'{lib_filename} found in {hdf5_library_dir_hint}')
print(f'{lib_filename} found in {hdf5_library_dir_hint}')
h5pkgcfg['library_dirs'] = [hdf5_library_dir_hint]
break
if hdf5_library_dir_found:
Expand Down Expand Up @@ -192,8 +191,8 @@ def add_coverage_flags_if_required(cxx_flags: List[str],
"""
if 'ENABLE_GCOV_COVERAGE' in os.environ and \
os.environ['ENABLE_GCOV_COVERAGE'].upper() == 'TRUE':
log.info("ENABLE_GCOV_COVERAGE was set to TRUE."
" Building AMICI with coverage symbols.")
print("ENABLE_GCOV_COVERAGE was set to TRUE."
" Building AMICI with coverage symbols.")
cxx_flags.extend(['-g', '-O0', '--coverage'])
linker_flags.extend(['--coverage', '-g'])

Expand All @@ -212,8 +211,8 @@ def add_debug_flags_if_required(cxx_flags: List[str],
"""
if 'ENABLE_AMICI_DEBUGGING' in os.environ \
and os.environ['ENABLE_AMICI_DEBUGGING'] == 'TRUE':
log.info("ENABLE_AMICI_DEBUGGING was set to TRUE."
" Building AMICI with debug symbols.")
print("ENABLE_AMICI_DEBUGGING was set to TRUE."
" Building AMICI with debug symbols.")
cxx_flags.extend(['-g', '-O0', '-UNDEBUG'])
linker_flags.extend(['-g'])

Expand All @@ -237,7 +236,7 @@ def generate_swig_interface_files(swig_outdir: str = None,
f'-Iamici{os.sep}include',
]

log.info(f"Found SWIG version {swig_version}")
print(f"Found SWIG version {swig_version}")

# Are HDF5 includes available to generate the wrapper?
if with_hdf5 is None:
Expand All @@ -258,7 +257,7 @@ def generate_swig_interface_files(swig_outdir: str = None,
'-o', os.path.join("amici", "amici_wrap.cxx"),
os.path.join("amici", "swig", "amici.i")]

log.info(f"Running SWIG: {' '.join(swig_cmd)}")
print(f"Running SWIG: {' '.join(swig_cmd)}")
sp = subprocess.run(swig_cmd, stdout=subprocess.PIPE,
stderr=sys.stdout.buffer)
if not sp.returncode == 0:
Expand All @@ -271,15 +270,15 @@ def add_openmp_flags(cxx_flags: List, ldflags: List) -> None:

# Enable OpenMP support for Linux / OSX:
if sys.platform == 'linux':
log.info("Adding OpenMP flags...")
print("Adding OpenMP flags...")
cxx_flags.insert(0, "-fopenmp")
ldflags.insert(0, "-fopenmp")
elif sys.platform == 'darwin':
if os.path.exists('/usr/local/lib/libomp.a'):
log.info("Adding OpenMP flags...")
print("Adding OpenMP flags...")
cxx_flags[0:0] = ["-Xpreprocessor", "-fopenmp"]
ldflags[0:0] = ["-Xpreprocessor", "-fopenmp", "-lomp"]
else:
log.info("Not adding OpenMP flags, because /usr/local/lib/libomp.a"
" does not exist. To enable, run `brew install libomp` "
"or add flags manually.")
print("Not adding OpenMP flags, because /usr/local/lib/libomp.a"
" does not exist. To enable, run `brew install libomp` "
"or add flags manually.")
1 change: 1 addition & 0 deletions python/sdist/setup.cfg
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Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,7 @@ install_requires =
pkgconfig
wurlitzer
toposort
setuptools>=48
include_package_data = True
zip_safe = False

Expand Down