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Set version 3.5.0

This commit is contained in:
Atsushi Togo 2024-09-13 15:09:53 +09:00
parent 5bfbc419a7
commit 704de3e4d0
7 changed files with 9 additions and 355 deletions
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4
doc/changelog.md
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@ -2,6 +2,10 @@
# Change Log
## Sep-13-2024: Version 3.5
- Maintenance release.
## Aug-23-2024: Version 3.4
- Update for spglib v2.5 and for following the change in phonopy.

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doc/conf.py
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@ -58,9 +58,9 @@ copyright = "2015, Atsushi Togo"
# built documents.
#
# The short X.Y version.
version = "3.4"
version = "3.5"
# The full version, including alpha/beta/rc tags.
release = "3.4.0"
release = "3.5.0"
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.

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doc/index.md
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@ -30,11 +30,8 @@ Papers that may introduce phono3py:
[JPCM.35.353001](https://iopscience.iop.org/article/10.1088/1361-648X/acd831)
(open access)
## Documentation
```{toctree}
:maxdepth: 1
:hidden:
install
workflow
examples

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phono3py/version.py
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@ -34,4 +34,4 @@
# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
__version__ = "3.4.0"
__version__ = "3.5.0"

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pyproject.toml
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@ -16,7 +16,7 @@ dependencies = [
"matplotlib>=2.2.2",
"h5py>=3.0",
"spglib>=2.3",
"phonopy>=2.27,<2.28",
"phonopy>=2.28,<2.29",
]
license = { file = "LICENSE" }

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setup-legacy.cfg
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@ -1,7 +0,0 @@
[options]
package_dir=
=.
packages=find:
[options.packages.find]
where=.

340
setup-legacy.py
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"""Phono3py setup.py.
Cmake handles automatic finding of library.
Custom settings should be written in site.cfg.
To fully customize using site.cfg,
set PHONO3PY_USE_CMAKE=false to avoid running cmake.
"""
import os
import pathlib
import shutil
import subprocess
import numpy
import setuptools
if (
"PHONO3PY_USE_CMAKE" in os.environ
and os.environ["PHONO3PY_USE_CMAKE"].lower() == "false"
):
use_cmake = False
else:
use_cmake = True
def _run_cmake(build_dir):
build_dir.mkdir()
args = [
"cmake",
"-S",
".",
"-B",
"_build",
"-DPHONONCALC=on",
"-DPHPHCALC=on",
"-DCMAKE_INSTALL_PREFIX=.",
]
if (
"PHPHCALC_USE_MTBLAS" in os.environ
and os.environ["PHPHCALC_USE_MTBLAS"].lower() == "true"
):
args.append("-DPHPHCALC_USE_MTBLAS=on")
# if "CONDA_PREFIX" in os.environ:
# args.append("-DUSE_CONDA_PATH=on")
# if "CC" in os.environ:
# args.append(f'-DCMAKE_C_COMPILER={os.environ["CC"]}')
cmake_output = subprocess.check_output(args)
print(cmake_output.decode("utf-8"))
subprocess.check_call(["cmake", "--build", "_build", "-v"])
return cmake_output
def _clean_cmake(build_dir):
if build_dir.exists():
shutil.rmtree(build_dir)
def _get_params_from_site_cfg():
"""Read extra_compile_args and extra_link_args.
Examples
--------
# For macOS
extra_compile_args = -fopenmp=libomp
extra_link_args = -lomp -lopenblas
# For linux
extra_compile_args = -fopenmp
extra_link_args = -lgomp -lopenblas -lpthread
"""
params = {
"define_macros": [],
"extra_link_args": [],
"extra_compile_args": [],
"extra_objects": [],
"include_dirs": [],
}
use_mkl_lapacke = False
use_threaded_blas = False
site_cfg_file = pathlib.Path.cwd() / "site.cfg"
if not site_cfg_file.exists():
return params
with open(site_cfg_file) as f:
lines = [line.strip().split("=", maxsplit=1) for line in f]
for line in lines:
if len(line) < 2:
continue
key = line[0].strip()
val = line[1].strip()
if key not in params:
continue
if key == "define_macros":
pair = val.split(maxsplit=1)
if pair[1].lower() == "none":
pair[1] = None
params[key].append(tuple(pair))
else:
if "mkl" in val:
use_mkl_lapacke = True
if "openblas" in val:
use_threaded_blas = True
params[key] += val.split()
if use_mkl_lapacke:
params["define_macros"].append(("MKL_LAPACKE", None))
if use_threaded_blas:
params["define_macros"].append(("MULTITHREADED_BLAS", None))
if "THM_EPSILON" not in [macro[0] for macro in params["define_macros"]]:
params["define_macros"].append(("THM_EPSILON", "1e-10"))
print("=============================================")
print("Parameters found in site.cfg")
for key, val in params.items():
print(f"{key}: {val}")
print("=============================================")
return params
def _get_extensions(build_dir):
"""Return python extension setting.
User customization by site.cfg file
-----------------------------------
See _get_params_from_site_cfg().
Automatic search using cmake
----------------------------
Invoked by environment variable unless PHONO3PY_USE_CMAKE=false.
"""
params = _get_params_from_site_cfg()
extra_objects_ph3py = []
extra_objects_phcalc = []
if not use_cmake or not shutil.which("cmake"):
print("** Setup without using cmake **")
sources_ph3py = [
"c/_phono3py.c",
"c/bzgrid.c",
"c/collision_matrix.c",
"c/fc3.c",
"c/grgrid.c",
"c/imag_self_energy_with_g.c",
"c/interaction.c",
"c/isotope.c",
"c/lagrid.c",
"c/lapack_wrapper.c",
"c/phono3py.c",
"c/phonoc_utils.c",
"c/pp_collision.c",
"c/real_self_energy.c",
"c/real_to_reciprocal.c",
"c/reciprocal_to_normal.c",
"c/snf3x3.c",
"c/tetrahedron_method.c",
"c/triplet.c",
"c/triplet_grid.c",
"c/triplet_iw.c",
]
sources_phcalc = [
"c/_phononcalc.c",
"c/dynmat.c",
"c/lapack_wrapper.c",
"c/phonon.c",
"c/phononcalc.c",
]
else:
print("** Setup using cmake **")
use_mkl_lapacke = False
found_extra_link_args = []
found_extra_compile_args = []
sources_ph3py = ["c/_phono3py.c"]
sources_phcalc = ["c/_phononcalc.c"]
cmake_output = _run_cmake(build_dir)
found_flags = {}
found_libs = {}
for line in cmake_output.decode("utf-8").split("\n"):
for key in ["BLAS", "LAPACK", "OpenMP"]:
if f"{key} libs" in line and len(line.split()) > 3:
found_libs[key] = line.split()[3].split(";")
if f"{key} flags" in line and len(line.split()) > 3:
found_flags[key] = line.split()[3].split(";")
for _, value in found_libs.items():
found_extra_link_args += value
for element in value:
if "libmkl" in element:
use_mkl_lapacke = True
for _, value in found_flags.items():
found_extra_compile_args += value
if use_mkl_lapacke:
params["define_macros"].append(("MKL_LAPACKE", None))
libph3py = list((pathlib.Path.cwd() / "_build").glob("*ph3py.*"))
if libph3py:
print("=============================================")
print(f"Phono3py library: {libph3py[0]}")
print("=============================================")
extra_objects_ph3py += [str(libph3py[0])]
libphcalc = list((pathlib.Path.cwd() / "_build").glob("*phcalc.*"))
if libphcalc:
print("=============================================")
print(f"Phonon library: {libphcalc[0]}")
print("=============================================")
extra_objects_phcalc += [str(libphcalc[0])]
params["extra_link_args"] += found_extra_link_args
params["extra_compile_args"] += found_extra_compile_args
print("=============================================")
print("Parameters found by cmake")
print("extra_compile_args: ", found_extra_compile_args)
print("extra_link_args: ", found_extra_link_args)
print("define_macros: ", params["define_macros"])
print("=============================================")
print()
extensions = []
params["define_macros"].append(("NPY_NO_DEPRECATED_API", "NPY_1_7_API_VERSION"))
params["include_dirs"] += ["c", numpy.get_include()]
extensions.append(
setuptools.Extension(
"phono3py._phono3py",
sources=sources_ph3py,
extra_link_args=params["extra_link_args"],
include_dirs=params["include_dirs"],
extra_compile_args=params["extra_compile_args"],
extra_objects=params["extra_objects"] + extra_objects_ph3py,
define_macros=params["define_macros"],
)
)
extensions.append(
setuptools.Extension(
"phono3py._phononcalc",
sources=sources_phcalc,
extra_link_args=params["extra_link_args"],
include_dirs=params["include_dirs"],
extra_compile_args=params["extra_compile_args"],
extra_objects=params["extra_objects"] + extra_objects_phcalc,
define_macros=params["define_macros"],
)
)
return extensions
def _get_version() -> str:
git_num = None
version_nums = [None, None, None]
with open("phono3py/version.py") as w:
for line in w:
if "__version__" in line:
for i, num in enumerate(line.split()[2].strip('"').split(".")):
version_nums[i] = num
break
# To deploy to pypi by travis-CI
if os.path.isfile("__nanoversion__.txt"):
nanoversion = 0
with open("__nanoversion__.txt") as nv:
try:
for line in nv:
nanoversion = int(line.strip())
break
except ValueError:
nanoversion = 0
if nanoversion != 0:
version_nums.append(nanoversion)
elif git_num:
version_nums.append(git_num)
if None in version_nums:
print("Failed to get version number in setup.py.")
raise
version = ".".join(["%s" % n for n in version_nums[:3]])
if len(version_nums) > 3:
version += "-%s" % version_nums[3]
return version
def main(build_dir):
"""Run setuptools."""
version = _get_version()
packages_phono3py = [
"phono3py",
"phono3py.conductivity",
"phono3py.cui",
"phono3py.interface",
"phono3py.other",
"phono3py.phonon",
"phono3py.phonon3",
"phono3py.sscha",
]
scripts_phono3py = [
"scripts/phono3py",
"scripts/phono3py-load",
"scripts/phono3py-kaccum",
"scripts/phono3py-kdeplot",
"scripts/phono3py-coleigplot",
]
setuptools.setup(
name="phono3py",
version=version,
description="This is the phono3py module.",
author="Atsushi Togo",
author_email="atz.togo@gmail.com",
url="http://phonopy.github.io/phono3py/",
packages=packages_phono3py,
python_requires=">=3.8",
install_requires=[
"numpy>=1.17.0",
"scipy",
"PyYAML>=5.3",
"matplotlib>=2.2.2",
"h5py>=3.0",
"spglib>=2.0",
"phonopy>=2.25,<2.26",
],
provides=["phono3py"],
scripts=scripts_phono3py,
ext_modules=_get_extensions(build_dir),
)
_clean_cmake(build_dir)
if __name__ == "__main__":
build_dir = pathlib.Path.cwd() / "_build"
main(build_dir)