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Documentation is now generated by scons

This commit is contained in:
Sylvain Tricot 2020-03-27 17:47:50 +01:00
parent 927ac8a8a3
commit e2ec1e8bcd
15 changed files with 481 additions and 110 deletions
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1
.gitignore vendored
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@ -8,3 +8,4 @@ __pycache__
htmlcov
package/
src/msspec/results.txt
*venv/

88
doc/SConstruct Normal file
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@ -0,0 +1,88 @@
# SCons file for Sphinx
import sys
sys.path.append('./source')
import subprocess
from pathlib import Path
from sphinx.cmd.build import main as sphinx_build
import custom
doc = Environment(
# You can set these variables from the command line.
SPHINXOPTS = "",
SPHINXBUILD = "sphinx-build",
PAPER = "",
BUILDDIR = "build")
# Internal variables.
PAPEROPT_a4 = "-D latex_elements.papersize=a4paper"
#PAPEROPT_a4 = "-D latex_paper_size=a4"
#PAPEROPT_letter = "-D latex_paper_size=letter"
ALLSPHINXOPTS = f"-d {doc['BUILDDIR']}/doctrees {PAPEROPT_a4} {doc['SPHINXOPTS']} source"
# the i18n builder cannot share the environment and doctrees with the others
I18NSPHINXOPTS = "{PAPEROPT_a4} {SPHINXOPTS} source"
# create the banner of the website
banner_src = "./source/title_template.svg"
banner_tgt = "./source/title.svg"
def build_banner(env, target, source):
custom.modify_banner(str(source[0]), str(target[0]))
banner = doc.Command(banner_tgt, banner_src, Action(build_banner, "Creating the website banner..."))
doc.Alias('banner', banner)
# convert *.svg and *.gif to *.png
# first find all of them
src_dir = Path('./source')
svg_pictures = list(src_dir.glob('**/*.svg'))
gif_pictures = list(src_dir.glob('**/*.gif'))
# conversion
pictures = []
for f in svg_pictures + banner:
pictures += doc.Command(str(f).replace('.svg', '.png'), str(f),
Action("convert -background none -density 150 $SOURCE $TARGET",
"Converting $SOURCE to PNG..."))
for f in gif_pictures:
pictures += doc.Command(str(f).replace('.gif', '.png'), str(f),
Action("convert -background none -density 150 $SOURCE[0] $TARGET",
"Converting $SOURCE to PNG..."))
doc.Alias('pictures', pictures)
Depends(pictures, banner)
# html
def html_builder(env, target, source):
return sphinx_build(f"-b html {ALLSPHINXOPTS} {doc['BUILDDIR']}/html".split())
html = doc.Command("html.target", [], Action(html_builder, "Building html..."))
Depends(html, [banner, pictures])
AlwaysBuild(html)
Clean(html, f"{doc['BUILDDIR']}/html")
doc.Alias('html', html)
# generate sitemap.xml
t = f"{doc['BUILDDIR']}/html/sitemap.xml"
cmd = f"python source/sitemap-generate.py --url https://msspec.cnrs.fr --path {doc['BUILDDIR']}/html {t}"
sitemap = doc.Command(t, [], cmd)#Action(cmd, "Generating sitemap.xml..."))
Depends(sitemap, html)
doc.Alias('html', sitemap)
# install ownership
t = f"{doc['BUILDDIR']}/html"
s = Glob('source/google*.html')
ownership = doc.Install(t, s)
Depends(ownership, html)
doc.Alias('html', ownership)
# LaTeX PDF
def latexpdf_builder(env, target, source):
rc = sphinx_build(f"-b latex {ALLSPHINXOPTS} {doc['BUILDDIR']}/latex".split())
if rc == 0:
subprocess.call(f"make -C {doc['BUILDDIR']}/latex all-pdf".split())
latexpdf = doc.Command("latexpdf.target", [], Action(latexpdf_builder, "Building LaTeX PDF..."))
Depends(latexpdf, [banner, pictures])
AlwaysBuild(latexpdf)
Clean(latexpdf, f"{doc['BUILDDIR']}/latex")
doc.Alias('latexpdf', latexpdf)

8
doc/source/conf.py
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@ -18,9 +18,10 @@ import sys, os
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
sys.path.append(os.path.abspath('./'))
sys.path.append(os.path.abspath('../../src'))
sys.path.append(os.path.abspath('../../src/msspec'))
import custom
import msspec
@ -50,7 +51,7 @@ master_doc = 'index'
# General information about the project.
project = u'MsSpec-python'
copyright = u'2016, Rennes Institute of Physics'
copyright = u'2020, Rennes Institute of Physics'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
@ -59,8 +60,7 @@ copyright = u'2016, Rennes Institute of Physics'
# The short X.Y version.
version, dev_version = custom.get_package_version()
# The full version, including alpha/beta/rc tags.
#release = custom.get_package_version()
release = '{}.post{}'.format(version, dev_version).strip('.post')
release = msspec.__version__
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.

21
doc/source/custom.py
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@ -8,20 +8,15 @@ import re
import numpy as np
from lxml import etree
print(os.getcwd())
sys.path.append('../../src')
import msspec
from msspec.calculator import MSSPEC
from msspec.misc import set_log_level
set_log_level("error")
def get_package_version():
p = subprocess.run(["git describe|sed 's/-/.post/'|cut -d'-' -f1"], shell=True, stdout=subprocess.PIPE)
full_version = p.stdout.decode('utf-8').strip()
versions = full_version.split('.post')
version = versions[0]
dev_version = ""
if len(versions) > 1:
dev_version = versions[1]
return version, dev_version
version, *dev_version = msspec.__version__.split('.post')
return version, "".join(dev_version)
def generate_download_page():
full_version = '.post'.join(get_package_version()).strip('.post')
@ -42,9 +37,9 @@ click :download:`here <{}>` to download the last version of MsSpec and
""".format(setupfile_path, docfile_path)
fd.write(content)
def modify_banner():
def modify_banner(inputfile='./title_template.svg', outputfile='./title.svg'):
version, dev_version = get_package_version()
xml = etree.parse('./title.svg')
xml = etree.parse(inputfile)
old_content = etree.tostring(xml)
svg = xml.getroot()
elements = svg.findall(".//{http://www.w3.org/2000/svg}tspan")
@ -61,7 +56,7 @@ def modify_banner():
new_content = etree.tostring(xml).decode('utf-8')
if new_content != old_content:
with open('./title.svg', 'w') as fd:
with open(outputfile, 'w') as fd:
fd.write(new_content)
def generate_parameters(spectroscopy=None):

1
doc/source/modules/calcio.rst
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@ -1,4 +1,3 @@
.. .. :orphan:
.. automodule:: calcio
:members:

1
doc/source/sitemap-generate.py
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@ -7,7 +7,6 @@ import re
from lxml import etree
import argparse
opt_defaults = {'include': ".*\.html|.*\.pdf",
'exclude': "google.*\.html",
'timezone': 'Europe/Paris'}

219
doc/source/title_template.svg Normal file
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@ -0,0 +1,219 @@
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<defs id="defs2">
<linearGradient inkscape:collect="always" id="linearGradient5962">
<stop style="stop-color:#ffffff;stop-opacity:0.85714287" offset="0" id="stop5958"/>
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Side by Side

After

Width:  |  Height:  |  Size: 61 KiB

8
src/MANIFEST.in
View File

@ -1,6 +1,4 @@
include msspec/spec/fortran/*.so
include msspec/phagen/fortran/*.so
include msspec/results.txt
include VERSION
include README.md
recursive-include msspec *.f
recursive-include msspec *.inc
recursive-include . SConstruct
include requirements.txt

11
SConstruct → src/SConstruct
View File

@ -87,8 +87,15 @@ env['BUILDERS']['F2PY'] = bld
# exports
try:
Import('local_build')
except:
local_build = False
Export('env', 'conf')
print('local_build = ', local_build)
SConscript(['src/msspec/spec/fortran/SConstruct',
'src/msspec/phagen/fortran/SConstruct'])
if not local_build:
SConscript(['msspec/spec/fortran/SConstruct',
'msspec/phagen/fortran/SConstruct'])

2
src/msspec/parameters.py
View File

@ -248,7 +248,6 @@ class BaseParameters(object):
'{}' is not an allowed attribute of {} class.
Please use one of:\n{}""".format(key, self.__class__.__name__,
data)
print(key, value)
LOGGER.error('Unknown attribute!')
raise AttributeError(err_msg)
object.__setattr__(self, key, value)
@ -1549,7 +1548,6 @@ class CalculationParameters(BaseParameters):
assert( p.value in p.allowed_values)
else:
assert( p.value is None )
print(iren_map[p.value])
self.spec_parameters.calc_iren = iren_map[p.value]
LOGGER.info("Renormalization activated with \'{}\' method".format(p.value))
except AssertionError:

5
src/msspec/phagen/fortran/SConstruct
View File

@ -1,8 +1,9 @@
try:
Import('env')
except:
SConscript(['../../../../SConstruct'])
local_build = True
Export('local_build')
SConscript(['../../../SConstruct'])
finally:
Import('env')

63
src/msspec/spec/fortran/SConstruct
View File

@ -2,18 +2,21 @@
try:
Import('env', 'conf')
except:
SConscript(['../../../../SConstruct'])
local_build = True
Export('local_build')
SConscript(['../../../SConstruct'])
finally:
Import('env', 'conf')
# Configuration:
env2 = env.Clone()
if conf.CheckPKG('lapack'):
env.ParseConfig("pkg-config lapack --libs")
env2.ParseConfig("pkg-config lapack --libs")
conf.Finish()
dir = Dir('.').get_abspath()
env.Append(FORTRANFLAGS=['-I' + dir,'-J' + dir])
env.Append(F2PY_OPTS=['-I' + dir])
env2.Append(FORTRANFLAGS=['-I' + dir,'-J' + dir])
env2.Append(F2PY_OPTS=['-I' + dir])
# define sources
dim_mod = ['memalloc/dim_mod.f']
@ -21,19 +24,15 @@ memalloc = ['memalloc/modules.f', 'memalloc/allocation.f']
cluster_gen = Glob('cluster_gen/*.f')
common_sub = Glob('common_sub/*.f')
renormalization = Glob('renormalization/*.f')
phd_se_noso_nosp_nosym = env.FilteredGlob('phd_se_noso_nosp_nosym/*.f', omit=['main.f'])
phd_mi_noso_nosp_nosym = env.FilteredGlob('phd_mi_noso_nosp_nosym/*.f', omit=['main.f'])
phd_se_noso_nosp_nosym = env2.FilteredGlob('phd_se_noso_nosp_nosym/*.f', omit=['main.f'])
phd_mi_noso_nosp_nosym = env2.FilteredGlob('phd_mi_noso_nosp_nosym/*.f', omit=['main.f'])
eig_common = Glob('eig/common/*.f')
eig_mi = env.FilteredGlob('eig/mi/*.f', omit=['main.f'])
eig_pw = env.FilteredGlob('eig/pw/*.f', omit=['main.f'])
eig_mi = env2.FilteredGlob('eig/mi/*.f', omit=['main.f'])
eig_pw = env2.FilteredGlob('eig/pw/*.f', omit=['main.f'])
#for f in eig_mi:
# print(f)
#exit()
if 'lapack' in env['LIBS']:
env.Append(F2PY_OPTS = "-llapack")
if 'lapack' in env2['LIBS']:
env2.Append(F2PY_OPTS = "-llapack")
eig_mi = [f for f in eig_mi if str(f).find('lapack') == -1]
phd_mi_noso_nosp_nosym = [f for f in phd_mi_noso_nosp_nosym if str(f).find('lapack') == -1]
@ -41,37 +40,37 @@ sources = dim_mod + memalloc + cluster_gen + common_sub + renormalization + phd
sources += phd_mi_noso_nosp_nosym + eig_common + eig_pw + eig_mi
# define objects
dim_mod_obj = env.Object(dim_mod)
memalloc_obj = env.Object(memalloc)
cluster_gen_obj = env.Object(cluster_gen)
common_sub_obj = env.Object(common_sub)
renormalization_obj = env.Object(renormalization)
phd_se_noso_nosp_nosym_obj = env.Object(phd_se_noso_nosp_nosym)
phd_mi_noso_nosp_nosym_obj = env.Object(phd_mi_noso_nosp_nosym)
eig_common_obj = env.Object(eig_common)
eig_pw_obj = env.Object(eig_pw)
eig_mi_obj = env.Object(eig_mi)
dim_mod_obj = env2.Object(dim_mod)
memalloc_obj = env2.Object(memalloc)
cluster_gen_obj = env2.Object(cluster_gen)
common_sub_obj = env2.Object(common_sub)
renormalization_obj = env2.Object(renormalization)
phd_se_noso_nosp_nosym_obj = env2.Object(phd_se_noso_nosp_nosym)
phd_mi_noso_nosp_nosym_obj = env2.Object(phd_mi_noso_nosp_nosym)
eig_common_obj = env2.Object(eig_common)
eig_pw_obj = env2.Object(eig_pw)
eig_mi_obj = env2.Object(eig_mi)
Requires(memalloc_obj, dim_mod_obj)
# define Python extensions
common_deps = dim_mod_obj + memalloc_obj + cluster_gen_obj + common_sub_obj
deps = common_deps + renormalization_obj + phd_se_noso_nosp_nosym_obj
phd_se_mod = env.F2PY('_phd_se_noso_nosp_nosym', ['phd_se_noso_nosp_nosym/main.f'] + deps)
phd_se_mod = env2.F2PY('_phd_se_noso_nosp_nosym', ['phd_se_noso_nosp_nosym/main.f'] + deps)
Requires(phd_se_mod, deps)
env.Alias('phd_se', phd_se_mod)
env2.Alias('phd_se', phd_se_mod)
deps = common_deps + renormalization_obj + phd_mi_noso_nosp_nosym_obj
phd_mi_mod = env.F2PY('_phd_mi_noso_nosp_nosym', ['phd_mi_noso_nosp_nosym/main.f'] + deps)
phd_mi_mod = env2.F2PY('_phd_mi_noso_nosp_nosym', ['phd_mi_noso_nosp_nosym/main.f'] + deps)
Requires(phd_mi_mod, deps)
env.Alias('phd_mi', phd_mi_mod)
env2.Alias('phd_mi', phd_mi_mod)
deps = common_deps + renormalization_obj + eig_common_obj + eig_mi_obj
eig_mi_mod = env.F2PY('_eig_mi', ['eig/mi/main.f'] + deps)
eig_mi_mod = env2.F2PY('_eig_mi', ['eig/mi/main.f'] + deps)
Requires(eig_mi_mod, deps)
env.Alias('eig_mi', eig_mi_mod)
env2.Alias('eig_mi', eig_mi_mod)
deps = common_deps + renormalization_obj + eig_common_obj + eig_pw_obj
eig_pw_mod = env.F2PY('_eig_pw', ['eig/pw/main.f'] + deps)
eig_pw_mod = env2.F2PY('_eig_pw', ['eig/pw/main.f'] + deps)
Requires(eig_pw_mod, deps)
env.Alias('eig_pw', eig_pw_mod)
env2.Alias('eig_pw', eig_pw_mod)

3
src/msspec/version.py
View File

@ -3,7 +3,6 @@
from setuptools_scm import get_version
from pkg_resources import parse_version, DistributionNotFound, get_distribution
from msspec.misc import LOGGER
import os
# find the version number
@ -27,5 +26,5 @@ except (LookupError, ImportError):
try:
__version__ = get_distribution(__name__.strip('.version')).version
except DistributionNotFound:
LOGGER.error("Unable to get the version number!")
print("Unable to get the version number!")

1
src/requirements.txt
View File

@ -8,3 +8,4 @@ pycairo
coverage
sphinx
setuptools_scm
wxPython

159
src/setup.py
View File

@ -1,53 +1,120 @@
# coding: utf-8
# vim: set fdm=indent ts=4 sw=4 sts=4 et tw=80 ai cc=+0 mouse=a nu : #
# vim: set fdm=indent ts=4 sw=4 sts=4 et tw=80 ai cc=+0 mouse=a nu :
from setuptools import setup, find_packages
from msspec.version import __version__
from setuptools import setup, Extension, find_packages
from distutils.file_util import copy_file
from distutils.command.build import build as _build
from setuptools.command.build_ext import build_ext as _build_ext
from setuptools.command.install import install as _install
from distutils.command.clean import clean as _clean
import subprocess
import traceback
import os
import sys
sys.path.insert(0, "msspec")
from version import __version__
SETUP_REQUIRES = ['scons', 'setuptools_scm']
with open('requirements.txt', 'r') as fd:
requirements = fd.read().strip().split('\n')
REQUIREMENTS = fd.read().strip().split('\n')
setup(name='msspec',
setup_requires=['setuptools_scm'],
version=__version__,
author='Didier Sébilleau, Sylvain Tricot',
author_email='sylvain.tricot@univ-rennes1.fr',
maintainer='Sylvain Tricot',
maintainer_email='sylvain.tricot@univ-rennes1.fr',
url='https://msspec.cnrs.fr',
description=('A multiple scattering package for sepectroscopies using '
'electrons to probe materials'),
long_description="""MsSpec is a Fortran package to compute the
cross-section of several spectroscopies involving one (or more)
electron(s) as the probe. This package provides a python interface to
control all the steps of the calculation.
subprocess.call(["pip", "install"] + SETUP_REQUIRES)
Available spectroscopies:
* Photoelectron diffraction
* Auger electron diffraction
* Low energy electron diffraction
* X-Ray absorption spectroscopy
* Auger Photoelectron coincidence spectroscopy
* Computation of the spectral radius""",
download_url='https://msspec.cnrs.fr/downloads.html',
# See https://pypi.python.org/pypi?%3Aaction=list_classifiers
classifiers=[
'Development Status :: 3 - Alpha',
'Environment :: Console',
'Intended Audience :: Science/Research',
'License :: OSI Approved :: GNU General Public License (GPL)',
'Natural Language :: English',
'Operating System :: Microsoft :: Windows :: Windows 10',
'Operating System :: POSIX :: Linux',
'Operating System :: MacOS :: MacOS X',
'Programming Language :: Fortran',
'Programming Language :: Python :: 3 :: Only',
'Topic :: Scientific/Engineering :: Physics',
],
keywords='spectroscopy atom electron photon multiple scattering',
license='GPL',
include_package_data=True,
packages=find_packages(include='msspec.*'),
install_requires=requirements
)
class BuildExtCmd(_build_ext):
def run(self):
src_dir = "."
subprocess.call(['scons'])
for ext in self.extensions:
fullname = self.get_ext_fullname(ext.name)
filename = self.get_ext_filename(fullname)
print("building ", filename)
src_filename = filename
dest_filename = os.path.join(self.build_lib, filename)
os.makedirs(os.path.dirname(dest_filename), exist_ok=True)
copy_file(src_filename, dest_filename, verbose=self.verbose,
dry_run=self.dry_run)
class BuildCmd(_build):
def run(self):
print("build_lib ", self.build_lib)
self.run_command("build_ext")
_build.run(self)
class InstallCmd(_install):
def run(self):
self.run_command("build")
_install.run(self)
class CleanCmd(_clean):
def run(self):
subprocess.call(['scons', '-c'])
_clean.run(self)
if __name__ == "__main__":
module_phagen = Extension('msspec.phagen.fortran.libphagen',['msspec/phagen/fortran/main.f'])
module_spec_phd_mi = Extension('msspec.spec.fortran._phd_mi_noso_nosp_nosym',['msspec/spec/fortran/phd_mi_noso_nosp_nosym/main.f'])
module_spec_phd_se = Extension('msspec.spec.fortran._phd_se_noso_nosp_nosym',['msspec/spec/fortran/phd_se_noso_nosp_nosym/main.f'])
module_eig_mi = Extension('msspec.spec.fortran._eig_mi',['msspec/spec/fortran/eig/mi/main.f'])
module_eig_pw = Extension('msspec.spec.fortran._eig_pw',['msspec/spec/fortran/eig/pw/main.f'])
setup(name='msspec',
version=__version__,
include_package_data=True,
ext_modules=[module_phagen, module_spec_phd_mi, module_spec_phd_se, module_eig_mi, module_eig_pw],
cmdclass={'build' : BuildCmd,
'build_ext': BuildExtCmd,
'clean' : CleanCmd,
'install' : InstallCmd,
},
packages=find_packages(include='msspec.*'),
setup_requires=SETUP_REQUIRES,
install_requires=REQUIREMENTS,
author='Didier Sébilleau, Sylvain Tricot',
author_email='sylvain.tricot@univ-rennes1.fr',
maintainer='Sylvain Tricot',
maintainer_email='sylvain.tricot@univ-rennes1.fr',
url='https://msspec.cnrs.fr',
description=('A multiple scattering package for sepectroscopies using '
'electrons to probe materials'),
long_description="""MsSpec is a Fortran package to compute the
cross-section of several spectroscopies involving one (or more)
electron(s) as the probe. This package provides a python interface to
control all the steps of the calculation.
Available spectroscopies:
* Photoelectron diffraction
* Auger electron diffraction
* Low energy electron diffraction
* X-Ray absorption spectroscopy
* Auger Photoelectron coincidence spectroscopy
* Computation of the spectral radius""",
download_url='https://msspec.cnrs.fr/downloads.html',
# See https://pypi.python.org/pypi?%3Aaction=list_classifiers
classifiers=[
'Development Status :: 3 - Alpha',
'Environment :: Console',
'Intended Audience :: Science/Research',
'License :: OSI Approved :: GNU General Public License (GPL)',
'Natural Language :: English',
'Operating System :: Microsoft :: Windows :: Windows 10',
'Operating System :: POSIX :: Linux',
'Operating System :: MacOS :: MacOS X',
'Programming Language :: Fortran',
'Programming Language :: Python :: 3 :: Only',
'Topic :: Scientific/Engineering :: Physics',
],
keywords='spectroscopy atom electron photon multiple scattering',
license='GPL',
)