Merge branch 'pip-standard-orig-python' into 'master'
The new install version based on classical setup.py See merge request obitools/obitools3!1
This commit is contained in:
13
.gitignore
vendored
Normal file
13
.gitignore
vendored
Normal file
@ -0,0 +1,13 @@
|
|||||||
|
.DS_Store
|
||||||
|
/obitools.test/
|
||||||
|
/OBITools3- 1.01.16/
|
||||||
|
/OBITools3-0.00.0/
|
||||||
|
/build/
|
||||||
|
/testpip/
|
||||||
|
/toto.obidms/
|
||||||
|
/unittests/
|
||||||
|
/setup.py.old
|
||||||
|
/3_Hornung_testseq.fastq
|
||||||
|
/sample/
|
||||||
|
/save.temp/
|
||||||
|
/obitmp/
|
||||||
17
.project
Normal file
17
.project
Normal file
@ -0,0 +1,17 @@
|
|||||||
|
<?xml version="1.0" encoding="UTF-8"?>
|
||||||
|
<projectDescription>
|
||||||
|
<name>obitools3</name>
|
||||||
|
<comment></comment>
|
||||||
|
<projects>
|
||||||
|
</projects>
|
||||||
|
<buildSpec>
|
||||||
|
<buildCommand>
|
||||||
|
<name>org.python.pydev.PyDevBuilder</name>
|
||||||
|
<arguments>
|
||||||
|
</arguments>
|
||||||
|
</buildCommand>
|
||||||
|
</buildSpec>
|
||||||
|
<natures>
|
||||||
|
<nature>org.python.pydev.pythonNature</nature>
|
||||||
|
</natures>
|
||||||
|
</projectDescription>
|
||||||
20
.pydevproject
Normal file
20
.pydevproject
Normal file
@ -0,0 +1,20 @@
|
|||||||
|
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
|
||||||
|
<?eclipse-pydev version="1.0"?><pydev_project>
|
||||||
|
|
||||||
|
|
||||||
|
<pydev_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">python3.6-obitool3</pydev_property>
|
||||||
|
|
||||||
|
|
||||||
|
<pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python interpreter</pydev_property>
|
||||||
|
|
||||||
|
|
||||||
|
<pydev_pathproperty name="org.python.pydev.PROJECT_SOURCE_PATH">
|
||||||
|
|
||||||
|
|
||||||
|
<path>/${PROJECT_DIR_NAME}/python</path>
|
||||||
|
|
||||||
|
|
||||||
|
</pydev_pathproperty>
|
||||||
|
|
||||||
|
|
||||||
|
</pydev_project>
|
||||||
33
Makefile
33
Makefile
@ -1,33 +0,0 @@
|
|||||||
ifeq ($(CC),gcc)
|
|
||||||
LFLAGS = -fopenmp
|
|
||||||
else
|
|
||||||
LFLAGS =
|
|
||||||
endif
|
|
||||||
|
|
||||||
SOURCE_DIR := src
|
|
||||||
ENV_DIR := $(abspath .)
|
|
||||||
OBJ_DIR := $(ENV_DIR)/obi_objdir
|
|
||||||
LIB_DIR := $(ENV_DIR)/obi_libdir
|
|
||||||
|
|
||||||
SOURCE_FILES = $(SOURCE_DIR)/libecoPCR/libapat/*.c $(SOURCE_DIR)/libecoPCR/libthermo/*.c $(SOURCE_DIR)/libecoPCR/*.c $(SOURCE_DIR)/libjson/*.c $(SOURCE_DIR)/*.c
|
|
||||||
OBJ_FILES = $(OBJ_DIR)/*.o
|
|
||||||
DYN_LIB_FILES = $(LIB_DIR)/libobi3.so
|
|
||||||
|
|
||||||
all: $(DYN_LIB_FILES)
|
|
||||||
|
|
||||||
$(LIB_DIR):
|
|
||||||
mkdir -p $(LIB_DIR)
|
|
||||||
|
|
||||||
$(OBJ_DIR):
|
|
||||||
mkdir -p $(OBJ_DIR)
|
|
||||||
|
|
||||||
$(DYN_LIB_FILES): $(OBJ_FILES) | $(LIB_DIR)
|
|
||||||
$(CC) -shared -o $@ $^
|
|
||||||
|
|
||||||
$(OBJ_FILES): | $(OBJ_DIR)
|
|
||||||
$(CC) $(LFLAGS) -fpic -c $(SOURCE_FILES)
|
|
||||||
mv *.o $(OBJ_DIR)
|
|
||||||
|
|
||||||
clean:
|
|
||||||
rm -rf $(LIB_DIR)
|
|
||||||
rm -rf $(OBJ_DIR)
|
|
||||||
@ -1,38 +0,0 @@
|
|||||||
'''
|
|
||||||
Created on 20 oct. 2012
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
from distutils.command.build import build as ori_build
|
|
||||||
from obidistutils.serenity.checksystem import is_mac_system
|
|
||||||
|
|
||||||
|
|
||||||
class build(ori_build):
|
|
||||||
|
|
||||||
def has_ext_modules(self):
|
|
||||||
return self.distribution.has_ext_modules()
|
|
||||||
|
|
||||||
def has_pidname(self):
|
|
||||||
return is_mac_system()
|
|
||||||
|
|
||||||
def has_doc(self):
|
|
||||||
return True
|
|
||||||
|
|
||||||
def has_littlebigman(self):
|
|
||||||
return True
|
|
||||||
|
|
||||||
try:
|
|
||||||
from obidistutils.command.build_sphinx import build_sphinx # @UnusedImport
|
|
||||||
|
|
||||||
sub_commands = [("littlebigman",has_littlebigman),
|
|
||||||
('pidname',has_pidname)
|
|
||||||
] \
|
|
||||||
+ ori_build.sub_commands + \
|
|
||||||
[('build_sphinx',has_doc)]
|
|
||||||
except ImportError:
|
|
||||||
sub_commands = [("littlebigman",has_littlebigman),
|
|
||||||
('pidname',has_pidname)
|
|
||||||
] \
|
|
||||||
+ ori_build.sub_commands
|
|
||||||
|
|
||||||
@ -1,85 +0,0 @@
|
|||||||
'''
|
|
||||||
Created on 20 oct. 2012
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
from .build_ctools import build_ctools
|
|
||||||
from .build_exe import build_exe
|
|
||||||
from distutils.errors import DistutilsSetupError
|
|
||||||
from distutils import log
|
|
||||||
import os
|
|
||||||
|
|
||||||
class build_cexe(build_ctools):
|
|
||||||
|
|
||||||
description = "build C/C++ executable distributed with Python extensions"
|
|
||||||
|
|
||||||
|
|
||||||
def initialize_options(self):
|
|
||||||
build_ctools.initialize_options(self)
|
|
||||||
self.built_files = None
|
|
||||||
|
|
||||||
|
|
||||||
def finalize_options(self):
|
|
||||||
# This might be confusing: both build-cexe and build-temp default
|
|
||||||
# to build-temp as defined by the "build" command. This is because
|
|
||||||
# I think that C libraries are really just temporary build
|
|
||||||
# by-products, at least from the point of view of building Python
|
|
||||||
# extensions -- but I want to keep my options open.
|
|
||||||
|
|
||||||
build_cexe_dir = self.build_cexe
|
|
||||||
build_ctools.finalize_options(self)
|
|
||||||
|
|
||||||
if build_cexe_dir is None:
|
|
||||||
self.build_cexe=None
|
|
||||||
|
|
||||||
self.set_undefined_options('build',
|
|
||||||
('build_scripts', 'build_cexe'))
|
|
||||||
|
|
||||||
self.set_undefined_options('build_files',
|
|
||||||
('files', 'built_files'))
|
|
||||||
|
|
||||||
self.executables = self.distribution.executables
|
|
||||||
# self.build_cexe = os.path.join(os.path.dirname(self.build_cexe),'cbinaries')
|
|
||||||
# self.mkpath(self.build_cexe)
|
|
||||||
|
|
||||||
if self.executables:
|
|
||||||
self.check_executable_list(self.executables)
|
|
||||||
|
|
||||||
|
|
||||||
# XXX same as for build_ext -- what about 'self.define' and
|
|
||||||
# 'self.undef' ?
|
|
||||||
|
|
||||||
def substitute_sources(self,exe_name,sources):
|
|
||||||
"""
|
|
||||||
Substitutes source file name starting by an @ by the actual
|
|
||||||
name of the built file (see --> build_files)
|
|
||||||
"""
|
|
||||||
sources = list(sources)
|
|
||||||
for i in range(len(sources)):
|
|
||||||
message = "%s :-> %s" % (exe_name,sources[i])
|
|
||||||
if sources[i][0]=='@':
|
|
||||||
try:
|
|
||||||
filename = self.built_files[sources[i][1:]]
|
|
||||||
except KeyError:
|
|
||||||
raise DistutilsSetupError(
|
|
||||||
'The %s filename declared in the source '
|
|
||||||
'files of the program %s have not been '
|
|
||||||
'built by the installation process' % (sources[i],
|
|
||||||
exe_name))
|
|
||||||
sources[i]=filename
|
|
||||||
log.info("%s changed to %s",message,filename)
|
|
||||||
else:
|
|
||||||
log.info("%s ok",message)
|
|
||||||
|
|
||||||
return sources
|
|
||||||
|
|
||||||
def run(self):
|
|
||||||
|
|
||||||
for cmd_name in self.get_sub_commands():
|
|
||||||
self.run_command(cmd_name)
|
|
||||||
|
|
||||||
build_exe.run(self)
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
@ -1,63 +0,0 @@
|
|||||||
'''
|
|
||||||
Created on 20 oct. 2012
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
|
|
||||||
from .build_exe import build_exe
|
|
||||||
from distutils import log
|
|
||||||
|
|
||||||
class build_ctools(build_exe):
|
|
||||||
description = "build C/C++ executable not distributed with Python extensions"
|
|
||||||
|
|
||||||
def initialize_options(self):
|
|
||||||
build_exe.initialize_options(self)
|
|
||||||
|
|
||||||
# List of built tools
|
|
||||||
self.ctools = None
|
|
||||||
self.littlebigman = None
|
|
||||||
|
|
||||||
|
|
||||||
def finalize_options(self):
|
|
||||||
# This might be confusing: both build-cexe and build-temp default
|
|
||||||
# to build-temp as defined by the "build" command. This is because
|
|
||||||
# I think that C libraries are really just temporary build
|
|
||||||
# by-products, at least from the point of view of building Python
|
|
||||||
# extensions -- but I want to keep my options open.
|
|
||||||
|
|
||||||
build_exe.finalize_options(self)
|
|
||||||
|
|
||||||
|
|
||||||
self.set_undefined_options('build',
|
|
||||||
('build_temp', 'build_cexe'))
|
|
||||||
|
|
||||||
self.set_undefined_options('littlebigman',
|
|
||||||
('littlebigman', 'littlebigman'))
|
|
||||||
|
|
||||||
self.executables = self.distribution.ctools
|
|
||||||
self.check_executable_list(self.executables)
|
|
||||||
|
|
||||||
|
|
||||||
if self.littlebigman =='-DLITTLE_END':
|
|
||||||
if self.define is None:
|
|
||||||
self.define=[('LITTLE_END',None)]
|
|
||||||
else:
|
|
||||||
self.define.append('LITTLE_END',None)
|
|
||||||
|
|
||||||
log.info('Look for CPU architecture... %s',self.define)
|
|
||||||
|
|
||||||
self.ctools = set()
|
|
||||||
|
|
||||||
def run(self):
|
|
||||||
|
|
||||||
for cmd_name in self.get_sub_commands():
|
|
||||||
self.run_command(cmd_name)
|
|
||||||
|
|
||||||
|
|
||||||
build_exe.run(self)
|
|
||||||
|
|
||||||
for e,p in self.executables: # @UnusedVariable
|
|
||||||
self.ctools.add(e)
|
|
||||||
|
|
||||||
|
|
||||||
@ -1,228 +0,0 @@
|
|||||||
'''
|
|
||||||
Created on 20 oct. 2012
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
import os
|
|
||||||
|
|
||||||
from distutils import sysconfig
|
|
||||||
from distutils.core import Command
|
|
||||||
from distutils.sysconfig import customize_compiler as customize_compiler_ori
|
|
||||||
from distutils.errors import DistutilsSetupError
|
|
||||||
from distutils import log
|
|
||||||
from distutils.ccompiler import show_compilers
|
|
||||||
|
|
||||||
def customize_compiler(compiler):
|
|
||||||
customize_compiler_ori(compiler)
|
|
||||||
compilername = compiler.compiler[0]
|
|
||||||
if ("gcc" in compilername or "g++" in compilername):
|
|
||||||
cc_cmd = ' '.join(compiler.compiler + ['-fopenmp'])
|
|
||||||
ccshared= ' '.join(x for x in sysconfig.get_config_vars("ccshared") if x is not None)
|
|
||||||
|
|
||||||
compiler.set_executables(
|
|
||||||
compiler=cc_cmd,
|
|
||||||
compiler_so=cc_cmd + ' ' + ccshared
|
|
||||||
)
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
class build_exe(Command):
|
|
||||||
|
|
||||||
description = "build an executable -- Abstract command "
|
|
||||||
|
|
||||||
user_options = [
|
|
||||||
('build-cexe', 'x',
|
|
||||||
"directory to build C/C++ libraries to"),
|
|
||||||
('build-temp', 't',
|
|
||||||
"directory to put temporary build by-products"),
|
|
||||||
('debug', 'g',
|
|
||||||
"compile with debugging information"),
|
|
||||||
('force', 'f',
|
|
||||||
"forcibly build everything (ignore file timestamps)"),
|
|
||||||
('compiler=', 'c',
|
|
||||||
"specify the compiler type"),
|
|
||||||
]
|
|
||||||
|
|
||||||
boolean_options = ['debug', 'force']
|
|
||||||
|
|
||||||
help_options = [
|
|
||||||
('help-compiler', None,
|
|
||||||
"list available compilers", show_compilers),
|
|
||||||
]
|
|
||||||
|
|
||||||
def initialize_options(self):
|
|
||||||
self.build_cexe = None
|
|
||||||
self.build_temp = None
|
|
||||||
|
|
||||||
# List of executables to build
|
|
||||||
self.executables = None
|
|
||||||
|
|
||||||
# Compilation options for all libraries
|
|
||||||
self.include_dirs = None
|
|
||||||
self.define = None
|
|
||||||
self.undef = None
|
|
||||||
self.extra_compile_args = None
|
|
||||||
self.debug = None
|
|
||||||
self.force = 0
|
|
||||||
self.compiler = None
|
|
||||||
self.sse = None
|
|
||||||
self.built_files=None
|
|
||||||
|
|
||||||
def finalize_options(self):
|
|
||||||
# This might be confusing: both build-cexe and build-temp default
|
|
||||||
# to build-temp as defined by the "build" command. This is because
|
|
||||||
# I think that C libraries are really just temporary build
|
|
||||||
# by-products, at least from the point of view of building Python
|
|
||||||
# extensions -- but I want to keep my options open.
|
|
||||||
self.set_undefined_options('build',
|
|
||||||
('build_temp', 'build_temp'),
|
|
||||||
('compiler', 'compiler'),
|
|
||||||
('debug', 'debug'),
|
|
||||||
('force', 'force'))
|
|
||||||
|
|
||||||
if self.include_dirs is None:
|
|
||||||
self.include_dirs = self.distribution.include_dirs or []
|
|
||||||
|
|
||||||
if isinstance(self.include_dirs, str):
|
|
||||||
self.include_dirs = self.include_dirs.split(os.pathsep)
|
|
||||||
|
|
||||||
self.sse = self.distribution.sse
|
|
||||||
|
|
||||||
if self.sse is not None:
|
|
||||||
if self.extra_compile_args is None:
|
|
||||||
self.extra_compile_args=['-m%s' % self.sse]
|
|
||||||
else:
|
|
||||||
self.extra_compile_args.append('-m%s' % self.sse)
|
|
||||||
|
|
||||||
|
|
||||||
# XXX same as for build_ext -- what about 'self.define' and
|
|
||||||
# 'self.undef' ?
|
|
||||||
|
|
||||||
def run(self):
|
|
||||||
|
|
||||||
if not self.executables:
|
|
||||||
return
|
|
||||||
|
|
||||||
self.mkpath(self.build_cexe)
|
|
||||||
|
|
||||||
# Yech -- this is cut 'n pasted from build_ext.py!
|
|
||||||
from distutils.ccompiler import new_compiler
|
|
||||||
self.compiler = new_compiler(compiler=self.compiler,
|
|
||||||
dry_run=self.dry_run,
|
|
||||||
force=self.force)
|
|
||||||
customize_compiler(self.compiler)
|
|
||||||
|
|
||||||
if self.include_dirs is not None:
|
|
||||||
self.compiler.set_include_dirs(self.include_dirs)
|
|
||||||
if self.define is not None:
|
|
||||||
# 'define' option is a list of (name,value) tuples
|
|
||||||
for (name,value) in self.define:
|
|
||||||
self.compiler.define_macro(name, value)
|
|
||||||
|
|
||||||
if self.undef is not None:
|
|
||||||
for macro in self.undef:
|
|
||||||
self.compiler.undefine_macro(macro)
|
|
||||||
|
|
||||||
self.build_executables(self.executables)
|
|
||||||
|
|
||||||
|
|
||||||
def check_executable_list(self, executables):
|
|
||||||
"""Ensure that the list of executables is valid.
|
|
||||||
|
|
||||||
`executable` is presumably provided as a command option 'executables'.
|
|
||||||
This method checks that it is a list of 2-tuples, where the tuples
|
|
||||||
are (executable_name, build_info_dict).
|
|
||||||
|
|
||||||
Raise DistutilsSetupError if the structure is invalid anywhere;
|
|
||||||
just returns otherwise.
|
|
||||||
"""
|
|
||||||
if not isinstance(executables, list):
|
|
||||||
raise DistutilsSetupError("'executables' option must be a list of tuples")
|
|
||||||
|
|
||||||
for exe in executables:
|
|
||||||
if not isinstance(exe, tuple) and len(exe) != 2:
|
|
||||||
raise DistutilsSetupError("each element of 'executables' must a 2-tuple")
|
|
||||||
|
|
||||||
name, build_info = exe
|
|
||||||
|
|
||||||
if not isinstance(name, str):
|
|
||||||
raise DistutilsSetupError(
|
|
||||||
"first element of each tuple in 'executables' "
|
|
||||||
"must be a string (the executables name)")
|
|
||||||
|
|
||||||
if '/' in name or (os.sep != '/' and os.sep in name):
|
|
||||||
raise DistutilsSetupError(
|
|
||||||
"bad executable name '%s': "
|
|
||||||
"may not contain directory separators" % exe[0])
|
|
||||||
|
|
||||||
if not isinstance(build_info, dict):
|
|
||||||
raise DistutilsSetupError(
|
|
||||||
"second element of each tuple in 'executables' "
|
|
||||||
"must be a dictionary (build info)")
|
|
||||||
|
|
||||||
def get_executable_names(self):
|
|
||||||
# Assume the executables list is valid -- 'check_executable_list()' is
|
|
||||||
# called from 'finalize_options()', so it should be!
|
|
||||||
if not self.executables:
|
|
||||||
return None
|
|
||||||
|
|
||||||
exe_names = []
|
|
||||||
for (exe_name, build_info) in self.executables: # @UnusedVariable
|
|
||||||
exe_names.append(exe_name)
|
|
||||||
return exe_names
|
|
||||||
|
|
||||||
|
|
||||||
def get_source_files(self):
|
|
||||||
self.check_executable_list(self.executables)
|
|
||||||
filenames = []
|
|
||||||
for (exe_name, build_info) in self.executables: # @UnusedVariable
|
|
||||||
sources = build_info.get('sources')
|
|
||||||
if sources is None or not isinstance(sources, (list, tuple)):
|
|
||||||
raise DistutilsSetupError(
|
|
||||||
"in 'executables' option (library '%s'), "
|
|
||||||
"'sources' must be present and must be "
|
|
||||||
"a list of source filenames" % exe_name)
|
|
||||||
|
|
||||||
filenames.extend(sources)
|
|
||||||
return filenames
|
|
||||||
|
|
||||||
def substitute_sources(self,exe_name,sources):
|
|
||||||
return list(sources)
|
|
||||||
|
|
||||||
def build_executables(self, executables):
|
|
||||||
for (exe_name, build_info) in executables:
|
|
||||||
sources = build_info.get('sources')
|
|
||||||
if sources is None or not isinstance(sources, (list, tuple)):
|
|
||||||
raise DistutilsSetupError(
|
|
||||||
"in 'executables' option (library '%s'), "
|
|
||||||
"'sources' must be present and must be "
|
|
||||||
"a list of source filenames" % exe_name)
|
|
||||||
|
|
||||||
sources = self.substitute_sources(exe_name,sources)
|
|
||||||
|
|
||||||
log.info("building '%s' program", exe_name)
|
|
||||||
|
|
||||||
# First, compile the source code to object files in the library
|
|
||||||
# directory. (This should probably change to putting object
|
|
||||||
# files in a temporary build directory.)
|
|
||||||
macros = build_info.get('macros')
|
|
||||||
include_dirs = build_info.get('include_dirs')
|
|
||||||
extra_args = self.extra_compile_args or []
|
|
||||||
|
|
||||||
objects = self.compiler.compile(sources,
|
|
||||||
output_dir=self.build_temp,
|
|
||||||
macros=macros,
|
|
||||||
include_dirs=include_dirs,
|
|
||||||
extra_postargs=extra_args,
|
|
||||||
debug=self.debug)
|
|
||||||
|
|
||||||
# Now "link" the object files together into a static library.
|
|
||||||
# (On Unix at least, this isn't really linking -- it just
|
|
||||||
# builds an archive. Whatever.)
|
|
||||||
self.compiler.link_executable(objects, exe_name,
|
|
||||||
output_dir=self.build_cexe,
|
|
||||||
debug=self.debug)
|
|
||||||
|
|
||||||
|
|
||||||
@ -1,143 +0,0 @@
|
|||||||
'''
|
|
||||||
Created on 13 fevr. 2014
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
from distutils import log
|
|
||||||
import os
|
|
||||||
|
|
||||||
from distutils import sysconfig
|
|
||||||
from distutils.errors import DistutilsSetupError
|
|
||||||
|
|
||||||
def _customize_compiler(compiler):
|
|
||||||
compilername = compiler.compiler[0]
|
|
||||||
if ("gcc" in compilername or "g++" in compilername):
|
|
||||||
cc_cmd = ' '.join(compiler.compiler + ['-fopenmp'])
|
|
||||||
ccshared= ' '.join(x for x in sysconfig.get_config_vars("ccshared") if x is not None)
|
|
||||||
|
|
||||||
compiler.set_executables(
|
|
||||||
compiler=cc_cmd,
|
|
||||||
compiler_so=cc_cmd + ' ' + ccshared
|
|
||||||
)
|
|
||||||
|
|
||||||
|
|
||||||
try:
|
|
||||||
from Cython.Distutils import build_ext as ori_build_ext # @UnresolvedImport
|
|
||||||
from Cython.Compiler import Options as cython_options # @UnresolvedImport
|
|
||||||
class build_ext(ori_build_ext):
|
|
||||||
|
|
||||||
|
|
||||||
def modifyDocScripts(self):
|
|
||||||
try:
|
|
||||||
os.mkdir("doc/sphinx")
|
|
||||||
except:
|
|
||||||
pass
|
|
||||||
build_dir_file=open("doc/sphinx/build_dir.txt","w")
|
|
||||||
print(self.build_lib,file=build_dir_file)
|
|
||||||
build_dir_file.close()
|
|
||||||
|
|
||||||
def initialize_options(self):
|
|
||||||
ori_build_ext.initialize_options(self) # @UndefinedVariable
|
|
||||||
self.littlebigman = None
|
|
||||||
self.built_files = None
|
|
||||||
|
|
||||||
|
|
||||||
def finalize_options(self):
|
|
||||||
super(build_ext, self).finalize_options()
|
|
||||||
|
|
||||||
|
|
||||||
self.set_undefined_options('littlebigman',
|
|
||||||
('littlebigman', 'littlebigman'))
|
|
||||||
|
|
||||||
self.set_undefined_options('build_files',
|
|
||||||
('files', 'built_files'))
|
|
||||||
|
|
||||||
self.cython_c_in_temp = 1
|
|
||||||
|
|
||||||
if self.littlebigman =='-DLITTLE_END':
|
|
||||||
if self.define is None:
|
|
||||||
self.define=[('LITTLE_END',None)]
|
|
||||||
else:
|
|
||||||
self.define.append('LITTLE_END',None)
|
|
||||||
|
|
||||||
def substitute_sources(self,exe_name,sources):
|
|
||||||
"""
|
|
||||||
Substitutes source file name starting by an @ by the actual
|
|
||||||
name of the built file (see --> build_files)
|
|
||||||
"""
|
|
||||||
sources = list(sources)
|
|
||||||
for i in range(len(sources)):
|
|
||||||
message = "%s :-> %s" % (exe_name,sources[i])
|
|
||||||
if sources[i][0]=='@':
|
|
||||||
try:
|
|
||||||
filename = self.built_files[sources[i][1:]]
|
|
||||||
except KeyError:
|
|
||||||
tmpfilename = os.path.join(self.build_temp,sources[i][1:])
|
|
||||||
if os.path.isfile (tmpfilename):
|
|
||||||
filename = tmpfilename
|
|
||||||
else:
|
|
||||||
raise DistutilsSetupError(
|
|
||||||
'The %s filename declared in the source '
|
|
||||||
'files of the program %s have not been '
|
|
||||||
'built by the installation process' % (sources[i],
|
|
||||||
exe_name))
|
|
||||||
sources[i]=filename
|
|
||||||
log.info("%s changed to %s",message,filename)
|
|
||||||
else:
|
|
||||||
log.info("%s ok",message)
|
|
||||||
|
|
||||||
return sources
|
|
||||||
|
|
||||||
def build_extensions(self):
|
|
||||||
# First, sanity-check the 'extensions' list
|
|
||||||
|
|
||||||
for ext in self.extensions:
|
|
||||||
ext.sources = self.substitute_sources(ext.name,ext.sources)
|
|
||||||
|
|
||||||
self.check_extensions_list(self.extensions)
|
|
||||||
|
|
||||||
print("pouic")
|
|
||||||
print(ext.sources)
|
|
||||||
print("pouac")
|
|
||||||
|
|
||||||
for ext in self.extensions:
|
|
||||||
log.info("%s :-> %s",ext.name,ext.sources)
|
|
||||||
ext.sources = self.cython_sources(ext.sources, ext)
|
|
||||||
self.build_extension(ext)
|
|
||||||
|
|
||||||
def build_extensions(self): # TODO what?? double? is it supposed to be build_extension?
|
|
||||||
if hasattr(self, 'compiler'):
|
|
||||||
_customize_compiler(self.compiler)
|
|
||||||
if hasattr(self, 'shlib_compiler'):
|
|
||||||
_customize_compiler(self.shlib_compiler)
|
|
||||||
|
|
||||||
ori_build_ext.build_extensions(self)
|
|
||||||
|
|
||||||
|
|
||||||
def run(self):
|
|
||||||
self.modifyDocScripts()
|
|
||||||
|
|
||||||
for cmd_name in self.get_sub_commands():
|
|
||||||
self.run_command(cmd_name)
|
|
||||||
|
|
||||||
cython_options.annotate = True
|
|
||||||
ori_build_ext.run(self) # @UndefinedVariable
|
|
||||||
|
|
||||||
|
|
||||||
def has_files(self):
|
|
||||||
return self.distribution.has_files()
|
|
||||||
|
|
||||||
def has_executables(self):
|
|
||||||
return self.distribution.has_executables()
|
|
||||||
|
|
||||||
sub_commands = [('build_files',has_files),
|
|
||||||
('build_cexe', has_executables)
|
|
||||||
] + ori_build_ext.sub_commands
|
|
||||||
|
|
||||||
except ImportError:
|
|
||||||
from distutils.command import build_ext # @UnusedImport
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
@ -1,63 +0,0 @@
|
|||||||
'''
|
|
||||||
Created on 20 oct. 2012
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
import os.path
|
|
||||||
|
|
||||||
from distutils.core import Command
|
|
||||||
from distutils import log
|
|
||||||
|
|
||||||
class build_files(Command):
|
|
||||||
|
|
||||||
def initialize_options(self):
|
|
||||||
self.files=None
|
|
||||||
self.ctools=None
|
|
||||||
self.build_temp=None
|
|
||||||
self.build_cexe=None
|
|
||||||
|
|
||||||
def finalize_options(self):
|
|
||||||
|
|
||||||
self.set_undefined_options('build_ctools',
|
|
||||||
('ctools', 'ctools'),
|
|
||||||
('build_temp','build_temp'),
|
|
||||||
('build_cexe','build_cexe'),
|
|
||||||
)
|
|
||||||
|
|
||||||
self.files = {}
|
|
||||||
|
|
||||||
def run(self):
|
|
||||||
|
|
||||||
for cmd_name in self.get_sub_commands():
|
|
||||||
self.run_command(cmd_name)
|
|
||||||
|
|
||||||
|
|
||||||
for dest,prog,command in self.distribution.files:
|
|
||||||
destfile = os.path.join(self.build_temp,dest)
|
|
||||||
if prog in self.ctools:
|
|
||||||
progfile = os.path.join(self.build_cexe,prog)
|
|
||||||
else:
|
|
||||||
progfile = prog
|
|
||||||
|
|
||||||
log.info("Building file : %s" % dest)
|
|
||||||
|
|
||||||
commandline = command % {'prog' : progfile,
|
|
||||||
'dest' : destfile}
|
|
||||||
|
|
||||||
log.info(" --> %s" % commandline)
|
|
||||||
|
|
||||||
os.system(commandline)
|
|
||||||
self.files[dest]=destfile
|
|
||||||
|
|
||||||
log.info("Done.\n")
|
|
||||||
|
|
||||||
def has_ctools(self):
|
|
||||||
return self.distribution.has_ctools()
|
|
||||||
|
|
||||||
|
|
||||||
sub_commands = [('build_ctools', has_ctools)] + \
|
|
||||||
Command.sub_commands
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
@ -1,104 +0,0 @@
|
|||||||
'''
|
|
||||||
Created on 20 oct. 2012
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
import os.path
|
|
||||||
|
|
||||||
from distutils.command.build_scripts import build_scripts as ori_build_scripts
|
|
||||||
from distutils.util import convert_path
|
|
||||||
from distutils import log, sysconfig
|
|
||||||
from distutils.dep_util import newer
|
|
||||||
from stat import ST_MODE
|
|
||||||
import re
|
|
||||||
|
|
||||||
first_line_re = re.compile('^#!.*python[0-9.]*([ \t].*)?$')
|
|
||||||
|
|
||||||
class build_scripts(ori_build_scripts):
|
|
||||||
|
|
||||||
def copy_scripts (self):
|
|
||||||
"""Copy each script listed in 'self.scripts'; if it's marked as a
|
|
||||||
Python script in the Unix way (first line matches 'first_line_re',
|
|
||||||
ie. starts with "\#!" and contains "python"), then adjust the first
|
|
||||||
line to refer to the current Python interpreter as we copy.
|
|
||||||
"""
|
|
||||||
self.mkpath(self.build_dir)
|
|
||||||
rawbuild_dir = os.path.join(os.path.dirname(self.build_dir),'raw_scripts')
|
|
||||||
self.mkpath(rawbuild_dir)
|
|
||||||
|
|
||||||
outfiles = []
|
|
||||||
for script in self.scripts:
|
|
||||||
adjust = 0
|
|
||||||
script = convert_path(script)
|
|
||||||
outfile = os.path.join(self.build_dir, os.path.splitext(os.path.basename(script))[0])
|
|
||||||
rawoutfile = os.path.join(rawbuild_dir, os.path.basename(script))
|
|
||||||
outfiles.append(outfile)
|
|
||||||
|
|
||||||
if not self.force and not newer(script, outfile):
|
|
||||||
log.debug("not copying %s (up-to-date)", script)
|
|
||||||
continue
|
|
||||||
|
|
||||||
# Always open the file but ignore failures in dry-run mode --
|
|
||||||
# that way, we'll get accurate feedback if we can read the
|
|
||||||
# script.
|
|
||||||
try:
|
|
||||||
f = open(script, "r")
|
|
||||||
except IOError:
|
|
||||||
if not self.dry_run:
|
|
||||||
raise
|
|
||||||
f = None
|
|
||||||
else:
|
|
||||||
first_line = f.readline()
|
|
||||||
if not first_line:
|
|
||||||
self.warn("%s is an empty file (skipping)" % script)
|
|
||||||
continue
|
|
||||||
|
|
||||||
match = first_line_re.match(first_line)
|
|
||||||
if match:
|
|
||||||
adjust = 1
|
|
||||||
post_interp = match.group(1) or ''
|
|
||||||
|
|
||||||
log.info("Store the raw script %s -> %s", script,rawoutfile)
|
|
||||||
self.copy_file(script, rawoutfile)
|
|
||||||
|
|
||||||
|
|
||||||
if adjust:
|
|
||||||
log.info("copying and adjusting %s -> %s", script,
|
|
||||||
self.build_dir)
|
|
||||||
if not self.dry_run:
|
|
||||||
outf = open(outfile, "w")
|
|
||||||
if not sysconfig.python_build:
|
|
||||||
outf.write("#!%s%s\n" %
|
|
||||||
(self.executable,
|
|
||||||
post_interp))
|
|
||||||
else:
|
|
||||||
outf.write("#!%s%s\n" %
|
|
||||||
(os.path.join(
|
|
||||||
sysconfig.get_config_var("BINDIR"),
|
|
||||||
"python%s%s" % (sysconfig.get_config_var("VERSION"),
|
|
||||||
sysconfig.get_config_var("EXE"))),
|
|
||||||
post_interp))
|
|
||||||
outf.writelines(f.readlines())
|
|
||||||
outf.close()
|
|
||||||
if f:
|
|
||||||
f.close()
|
|
||||||
else:
|
|
||||||
if f:
|
|
||||||
f.close()
|
|
||||||
self.copy_file(script, outfile)
|
|
||||||
|
|
||||||
if os.name == 'posix':
|
|
||||||
for F in outfiles:
|
|
||||||
if self.dry_run:
|
|
||||||
log.info("changing mode of %s", F)
|
|
||||||
else:
|
|
||||||
oldmode = os.stat(F)[ST_MODE]
|
|
||||||
oldmode = oldmode & 0o7777
|
|
||||||
|
|
||||||
newmode = (oldmode | 0o555) & 0o7777
|
|
||||||
if newmode != oldmode:
|
|
||||||
log.info("changing mode of %s from %o to %o",
|
|
||||||
F, oldmode, newmode)
|
|
||||||
os.chmod(F, newmode)
|
|
||||||
|
|
||||||
@ -1,27 +0,0 @@
|
|||||||
'''
|
|
||||||
Created on 10 mars 2015
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
try:
|
|
||||||
from sphinx.setup_command import BuildDoc as ori_build_sphinx # @UnresolvedImport
|
|
||||||
|
|
||||||
class build_sphinx(ori_build_sphinx):
|
|
||||||
'''Build Sphinx documentation in html, epub and man formats
|
|
||||||
'''
|
|
||||||
|
|
||||||
description = __doc__
|
|
||||||
|
|
||||||
def run(self):
|
|
||||||
self.builder='html'
|
|
||||||
self.finalize_options()
|
|
||||||
ori_build_sphinx.run(self)
|
|
||||||
self.builder='epub'
|
|
||||||
self.finalize_options()
|
|
||||||
ori_build_sphinx.run(self)
|
|
||||||
self.builder='man'
|
|
||||||
self.finalize_options()
|
|
||||||
ori_build_sphinx.run(self)
|
|
||||||
except ImportError:
|
|
||||||
pass
|
|
||||||
@ -1,19 +0,0 @@
|
|||||||
'''
|
|
||||||
Created on 6 oct. 2014
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
# try:
|
|
||||||
# from setuptools.command.install import install as install_ori
|
|
||||||
# except ImportError:
|
|
||||||
# from distutils.command.install import install as install_ori
|
|
||||||
|
|
||||||
from distutils.command.install import install as install_ori
|
|
||||||
|
|
||||||
class install(install_ori):
|
|
||||||
|
|
||||||
def __init__(self,dist):
|
|
||||||
install_ori.__init__(self, dist)
|
|
||||||
# self.sub_commands.insert(0, ('build',lambda self: True))
|
|
||||||
self.sub_commands.append(('install_sphinx',lambda self: self.distribution.serenity))
|
|
||||||
@ -1,47 +0,0 @@
|
|||||||
'''
|
|
||||||
Created on 20 oct. 2012
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
# try:
|
|
||||||
# from setuptools.command.install_scripts import install_scripts as ori_install_scripts
|
|
||||||
# except ImportError:
|
|
||||||
# from distutils.command.install_scripts import install_scripts as ori_install_scripts
|
|
||||||
|
|
||||||
from distutils.command.install_scripts import install_scripts as ori_install_scripts
|
|
||||||
|
|
||||||
import os.path
|
|
||||||
from distutils import log
|
|
||||||
|
|
||||||
class install_scripts(ori_install_scripts):
|
|
||||||
|
|
||||||
def initialize_options(self):
|
|
||||||
ori_install_scripts.initialize_options(self)
|
|
||||||
self.public_dir = None
|
|
||||||
|
|
||||||
|
|
||||||
def install_public_link(self):
|
|
||||||
self.mkpath(self.public_dir)
|
|
||||||
for file in self.get_outputs():
|
|
||||||
log.info("exporting file %s -> %s", file,os.path.join(self.public_dir,
|
|
||||||
os.path.split(file)[1]
|
|
||||||
))
|
|
||||||
if not self.dry_run:
|
|
||||||
dest = os.path.join(self.public_dir,
|
|
||||||
os.path.split(file)[1]
|
|
||||||
)
|
|
||||||
if os.path.exists(dest):
|
|
||||||
os.unlink(dest)
|
|
||||||
os.symlink(file,dest)
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
def run(self):
|
|
||||||
ori_install_scripts.run(self)
|
|
||||||
if self.distribution.serenity:
|
|
||||||
self.public_dir=os.path.join(self.install_dir,"../export/bin")
|
|
||||||
self.public_dir=os.path.abspath(self.public_dir)
|
|
||||||
self.install_public_link()
|
|
||||||
|
|
||||||
|
|
||||||
@ -1,61 +0,0 @@
|
|||||||
'''
|
|
||||||
Created on 10 mars 2015
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
from distutils.core import Command
|
|
||||||
import os.path
|
|
||||||
import glob
|
|
||||||
|
|
||||||
class install_sphinx(Command):
|
|
||||||
'''
|
|
||||||
Install the sphinx documentation
|
|
||||||
'''
|
|
||||||
|
|
||||||
description = "Install the sphinx documentation in serenity mode"
|
|
||||||
|
|
||||||
boolean_options = ['force', 'skip-build']
|
|
||||||
|
|
||||||
|
|
||||||
def initialize_options (self):
|
|
||||||
self.install_doc = None
|
|
||||||
self.build_dir = None
|
|
||||||
|
|
||||||
def finalize_options (self):
|
|
||||||
self.set_undefined_options('build_sphinx', ('build_dir', 'build_dir'))
|
|
||||||
self.set_undefined_options('install',
|
|
||||||
('install_scripts', 'install_doc'))
|
|
||||||
|
|
||||||
def run (self):
|
|
||||||
if self.distribution.serenity:
|
|
||||||
self.install_doc = os.path.join(self.install_doc,"../export/share")
|
|
||||||
self.install_doc=os.path.abspath(self.install_doc)
|
|
||||||
self.mkpath(self.install_doc)
|
|
||||||
self.mkpath(os.path.join(self.install_doc,'html'))
|
|
||||||
outfiles = self.copy_tree(os.path.join(self.build_dir,'html'), # @UnusedVariable
|
|
||||||
os.path.join(self.install_doc,'html'))
|
|
||||||
|
|
||||||
self.mkpath(os.path.join(self.install_doc,'man','man1'))
|
|
||||||
outfiles = self.copy_tree(os.path.join(self.build_dir,'man'), # @UnusedVariable
|
|
||||||
os.path.join(self.install_doc,'man','man1'))
|
|
||||||
|
|
||||||
for epub in glob.glob(os.path.join(self.build_dir,'epub/*.epub')):
|
|
||||||
self.copy_file(os.path.join(epub),
|
|
||||||
os.path.join(self.install_doc,os.path.split(epub)[1]))
|
|
||||||
|
|
||||||
def get_outputs(self):
|
|
||||||
directory=os.path.join(self.install_doc,'html')
|
|
||||||
files = [os.path.join(self.install_doc,'html', f)
|
|
||||||
for dp, dn, filenames in os.walk(directory) for f in filenames] # @UnusedVariable
|
|
||||||
|
|
||||||
directory=os.path.join(self.build_dir,'man')
|
|
||||||
files.append(os.path.join(self.install_doc,'man','man1', f)
|
|
||||||
for dp, dn, filenames in os.walk(directory) for f in filenames) # @UnusedVariable
|
|
||||||
|
|
||||||
directory=os.path.join(self.build_dir,'epub')
|
|
||||||
files.append(os.path.join(self.install_doc, f)
|
|
||||||
for dp, dn, filenames in os.walk(directory) # @UnusedVariable
|
|
||||||
for f in glob.glob(os.path.join(dp, '*.epub')) )
|
|
||||||
|
|
||||||
return files
|
|
||||||
|
|
||||||
@ -1,59 +0,0 @@
|
|||||||
'''
|
|
||||||
Created on 20 oct. 2012
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
import os
|
|
||||||
|
|
||||||
from obidistutils.command.build_exe import build_exe
|
|
||||||
from distutils import log
|
|
||||||
|
|
||||||
import subprocess
|
|
||||||
|
|
||||||
class littlebigman(build_exe):
|
|
||||||
|
|
||||||
description = "build the littlebigman executable testing endianness of the CPU"
|
|
||||||
|
|
||||||
|
|
||||||
def initialize_options(self):
|
|
||||||
build_exe.initialize_options(self)
|
|
||||||
|
|
||||||
self.littlebigman = None
|
|
||||||
|
|
||||||
|
|
||||||
def finalize_options(self):
|
|
||||||
# This might be confusing: both build-cexe and build-temp default
|
|
||||||
# to build-temp as defined by the "build" command. This is because
|
|
||||||
# I think that C libraries are really just temporary build
|
|
||||||
# by-products, at least from the point of view of building Python
|
|
||||||
# extensions -- but I want to keep my options open.
|
|
||||||
|
|
||||||
build_exe.finalize_options(self)
|
|
||||||
|
|
||||||
self.set_undefined_options('build',
|
|
||||||
('build_temp', 'build_cexe'))
|
|
||||||
|
|
||||||
# self.ctools = self.distribution.ctools
|
|
||||||
|
|
||||||
if os.path.isfile("distutils.ext/src/littlebigman.c"):
|
|
||||||
self.executables = [('littlebigman',{"sources":["distutils.ext/src/littlebigman.c"]})]
|
|
||||||
self.check_executable_list(self.executables)
|
|
||||||
else:
|
|
||||||
self.executables = []
|
|
||||||
|
|
||||||
|
|
||||||
def run_littlebigman(self):
|
|
||||||
p = subprocess.Popen("'%s'" % os.path.join(self.build_temp,
|
|
||||||
'littlebigman'),
|
|
||||||
shell=True,
|
|
||||||
stdout=subprocess.PIPE)
|
|
||||||
little = p.communicate()[0]
|
|
||||||
return little.decode('latin1')
|
|
||||||
|
|
||||||
def run(self):
|
|
||||||
build_exe.run(self)
|
|
||||||
self.littlebigman=self.run_littlebigman()
|
|
||||||
log.info("Your CPU is in mode : %s" % self.littlebigman)
|
|
||||||
|
|
||||||
|
|
||||||
@ -1,55 +0,0 @@
|
|||||||
'''
|
|
||||||
Created on 20 oct. 2012
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
import os
|
|
||||||
|
|
||||||
from obidistutils.command.build_exe import build_exe
|
|
||||||
from obidistutils.serenity.checksystem import is_mac_system
|
|
||||||
|
|
||||||
|
|
||||||
class pidname(build_exe):
|
|
||||||
|
|
||||||
description = "build the pidname executable returning the executable path from a PID on a mac"
|
|
||||||
|
|
||||||
|
|
||||||
def initialize_options(self):
|
|
||||||
build_exe.initialize_options(self)
|
|
||||||
|
|
||||||
self.pidname = False
|
|
||||||
|
|
||||||
|
|
||||||
def finalize_options(self):
|
|
||||||
# This might be confusing: both build-cexe and build-temp default
|
|
||||||
# to build-temp as defined by the "build" command. This is because
|
|
||||||
# I think that C libraries are really just temporary build
|
|
||||||
# by-products, at least from the point of view of building Python
|
|
||||||
# extensions -- but I want to keep my options open.
|
|
||||||
|
|
||||||
build_exe.finalize_options(self)
|
|
||||||
|
|
||||||
self.set_undefined_options('build',
|
|
||||||
('build_scripts', 'build_cexe'))
|
|
||||||
|
|
||||||
# self.ctools = self.distribution.ctools
|
|
||||||
|
|
||||||
if os.path.isfile("distutils.ext/src/pidname.c"):
|
|
||||||
self.executables = [('pidname',{"sources":["distutils.ext/src/pidname.c"]})]
|
|
||||||
self.check_executable_list(self.executables)
|
|
||||||
else:
|
|
||||||
self.executables = []
|
|
||||||
|
|
||||||
# self.build_cexe = os.path.join(os.path.dirname(self.build_cexe),'cbinaries')
|
|
||||||
# self.mkpath(self.build_cexe)
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
def run(self):
|
|
||||||
if is_mac_system():
|
|
||||||
build_exe.run(self)
|
|
||||||
self.pidname=True
|
|
||||||
else:
|
|
||||||
self.pidname=False
|
|
||||||
|
|
||||||
@ -1,42 +0,0 @@
|
|||||||
'''
|
|
||||||
Created on 10 mars 2015
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
import os.path
|
|
||||||
|
|
||||||
from distutils.command.sdist import sdist as orig_sdist
|
|
||||||
from distutils import dir_util
|
|
||||||
|
|
||||||
class sdist(orig_sdist):
|
|
||||||
|
|
||||||
def make_distribution(self):
|
|
||||||
"""Create the source distribution(s). First, we create the release
|
|
||||||
tree with 'make_release_tree()'; then, we create all required
|
|
||||||
archive files (according to 'self.formats') from the release tree.
|
|
||||||
Finally, we clean up by blowing away the release tree (unless
|
|
||||||
'self.keep_temp' is true). The list of archive files created is
|
|
||||||
stored so it can be retrieved later by 'get_archive_files()'.
|
|
||||||
"""
|
|
||||||
# Don't warn about missing meta-data here -- should be (and is!)
|
|
||||||
# done elsewhere.
|
|
||||||
base_dir = self.distribution.get_fullname()
|
|
||||||
base_name = os.path.join(self.dist_dir,base_dir)
|
|
||||||
|
|
||||||
self.make_release_tree(os.path.join('tmp',base_dir), self.filelist.files)
|
|
||||||
archive_files = [] # remember names of files we create
|
|
||||||
# tar archive must be created last to avoid overwrite and remove
|
|
||||||
if 'tar' in self.formats:
|
|
||||||
self.formats.append(self.formats.pop(self.formats.index('tar')))
|
|
||||||
|
|
||||||
for fmt in self.formats:
|
|
||||||
file = self.make_archive(base_name, fmt, root_dir='tmp',base_dir=base_dir,
|
|
||||||
owner=self.owner, group=self.group)
|
|
||||||
archive_files.append(file)
|
|
||||||
self.distribution.dist_files.append(('sdist', '', file))
|
|
||||||
|
|
||||||
self.archive_files = archive_files
|
|
||||||
|
|
||||||
if not self.keep_temp:
|
|
||||||
dir_util.remove_tree(os.path.join('tmp',base_dir), dry_run=self.dry_run)
|
|
||||||
@ -1,234 +0,0 @@
|
|||||||
'''
|
|
||||||
Created on 20 oct. 2012
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
from os import path
|
|
||||||
import os.path
|
|
||||||
import glob
|
|
||||||
import sys
|
|
||||||
|
|
||||||
try:
|
|
||||||
from setuptools.extension import Extension
|
|
||||||
except ImportError:
|
|
||||||
from distutils.extension import Extension
|
|
||||||
|
|
||||||
# from distutils.extension import Extension
|
|
||||||
|
|
||||||
from obidistutils.serenity.checkpackage import install_requirements,\
|
|
||||||
check_requirements, \
|
|
||||||
RequirementError
|
|
||||||
|
|
||||||
from obidistutils.serenity.rerun import enforce_good_python
|
|
||||||
from obidistutils.serenity.rerun import rerun_with_anothe_python
|
|
||||||
from distutils import log
|
|
||||||
|
|
||||||
from obidistutils.dist import Distribution
|
|
||||||
from obidistutils.serenity import is_serenity
|
|
||||||
|
|
||||||
|
|
||||||
def findPackage(root,base=None):
|
|
||||||
modules=[]
|
|
||||||
if base is None:
|
|
||||||
base=[]
|
|
||||||
for module in (path.basename(path.dirname(x))
|
|
||||||
for x in glob.glob(path.join(root,'*','__init__.py'))):
|
|
||||||
modules.append('.'.join(base+[module]))
|
|
||||||
modules.extend(findPackage(path.join(root,module),base+[module]))
|
|
||||||
return modules
|
|
||||||
|
|
||||||
def findCython(root,base=None,pyrexs=None):
|
|
||||||
setupdir = os.path.dirname(sys.argv[0])
|
|
||||||
pyrexs=[]
|
|
||||||
|
|
||||||
if base is None:
|
|
||||||
base=[]
|
|
||||||
for module in (path.basename(path.dirname(x))
|
|
||||||
for x in glob.glob(path.join(root,'*','__init__.py'))):
|
|
||||||
|
|
||||||
for pyrex in glob.glob(path.join(root,module,'*.pyx')):
|
|
||||||
libabspath = os.path.abspath('obi_libdir')
|
|
||||||
obiabspath = os.path.abspath('.')
|
|
||||||
pyrexs.append(Extension('.'.join(base+[module,path.splitext(path.basename(pyrex))[0]]),
|
|
||||||
[pyrex],
|
|
||||||
library_dirs=[libabspath],
|
|
||||||
include_dirs=[libabspath],
|
|
||||||
libraries=["obi3"],
|
|
||||||
runtime_library_dirs=[libabspath],
|
|
||||||
extra_link_args=["-Wl,-rpath,"+libabspath, "-L"+libabspath]
|
|
||||||
)
|
|
||||||
)
|
|
||||||
try:
|
|
||||||
cfiles = os.path.splitext(pyrex)[0]+".cfiles"
|
|
||||||
cfilesdir = os.path.dirname(cfiles)
|
|
||||||
cfiles = open(cfiles)
|
|
||||||
cfiles = [os.path.relpath(os.path.join(cfilesdir,y),setupdir).strip()
|
|
||||||
if y[0] !='@' else y.strip()
|
|
||||||
for y in cfiles]
|
|
||||||
|
|
||||||
log.info("Cython module : %s",cfiles)
|
|
||||||
incdir = set(os.path.dirname(x) for x in cfiles if x[-2:]==".h")
|
|
||||||
#cfiles = [x for x in cfiles if x[-2:]==".c"]
|
|
||||||
#pyrexs[-1].sources.extend(cfiles)
|
|
||||||
pyrexs[-1].include_dirs.extend(incdir)
|
|
||||||
pyrexs[-1].extra_compile_args.extend(['-msse2',
|
|
||||||
'-Wno-unused-function',
|
|
||||||
'-Wmissing-braces',
|
|
||||||
'-Wchar-subscripts',
|
|
||||||
'-fPIC'
|
|
||||||
])
|
|
||||||
|
|
||||||
except IOError:
|
|
||||||
pass
|
|
||||||
|
|
||||||
pyrexs.extend(findCython(path.join(root,module),base+[module]))
|
|
||||||
return pyrexs
|
|
||||||
|
|
||||||
|
|
||||||
def rootname(x):
|
|
||||||
return os.path.splitext(x.sources[0])[0]
|
|
||||||
|
|
||||||
|
|
||||||
def prepare_commands():
|
|
||||||
from obidistutils.command.build import build
|
|
||||||
from obidistutils.command.littlebigman import littlebigman
|
|
||||||
# from obidistutils.command.serenity import serenity
|
|
||||||
from obidistutils.command.build_cexe import build_cexe
|
|
||||||
from obidistutils.command.build_ext import build_ext
|
|
||||||
from obidistutils.command.build_ctools import build_ctools
|
|
||||||
from obidistutils.command.build_files import build_files
|
|
||||||
from obidistutils.command.build_scripts import build_scripts
|
|
||||||
from obidistutils.command.install_scripts import install_scripts
|
|
||||||
from obidistutils.command.install_sphinx import install_sphinx
|
|
||||||
from obidistutils.command.install import install
|
|
||||||
from obidistutils.command.pidname import pidname
|
|
||||||
from obidistutils.command.sdist import sdist
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
COMMANDS = {'build':build,
|
|
||||||
# 'serenity':serenity,
|
|
||||||
'littlebigman':littlebigman,
|
|
||||||
'pidname':pidname,
|
|
||||||
'build_ctools':build_ctools,
|
|
||||||
'build_files':build_files,
|
|
||||||
'build_cexe':build_cexe,
|
|
||||||
'build_ext': build_ext,
|
|
||||||
'build_scripts':build_scripts,
|
|
||||||
'install_scripts':install_scripts,
|
|
||||||
'install_sphinx':install_sphinx,
|
|
||||||
'install':install,
|
|
||||||
'sdist':sdist}
|
|
||||||
|
|
||||||
# try:
|
|
||||||
# from setuptools.commands import egg_info
|
|
||||||
# COMMANDS['egg_info']=egg_info
|
|
||||||
# except ImportError:
|
|
||||||
# pass
|
|
||||||
try:
|
|
||||||
from obidistutils.command.build_sphinx import build_sphinx
|
|
||||||
COMMANDS['build_sphinx']=build_sphinx
|
|
||||||
except ImportError:
|
|
||||||
pass
|
|
||||||
|
|
||||||
return COMMANDS
|
|
||||||
|
|
||||||
|
|
||||||
CTOOLS =[]
|
|
||||||
CEXES =[]
|
|
||||||
FILES =[]
|
|
||||||
|
|
||||||
def setup(**attrs):
|
|
||||||
|
|
||||||
log.set_threshold(log.INFO)
|
|
||||||
|
|
||||||
minversion = attrs.get("pythonmin",'3.7')
|
|
||||||
maxversion = attrs.get('pythonmax',None)
|
|
||||||
fork = attrs.get('fork',False)
|
|
||||||
requirementfile = attrs.get('requirements','requirements.txt')
|
|
||||||
|
|
||||||
try:
|
|
||||||
del attrs['pythonmin']
|
|
||||||
except KeyError:
|
|
||||||
pass
|
|
||||||
|
|
||||||
try:
|
|
||||||
del attrs['pythonmax']
|
|
||||||
except KeyError:
|
|
||||||
pass
|
|
||||||
|
|
||||||
try:
|
|
||||||
del attrs['fork']
|
|
||||||
except KeyError:
|
|
||||||
pass
|
|
||||||
|
|
||||||
try:
|
|
||||||
del attrs['requirements']
|
|
||||||
except KeyError:
|
|
||||||
pass
|
|
||||||
|
|
||||||
if is_serenity():
|
|
||||||
|
|
||||||
|
|
||||||
enforce_good_python(minversion, maxversion, fork)
|
|
||||||
|
|
||||||
if (install_requirements(requirementfile)):
|
|
||||||
rerun_with_anothe_python(sys.executable,minversion,maxversion,fork)
|
|
||||||
|
|
||||||
|
|
||||||
try:
|
|
||||||
check_requirements(requirementfile)
|
|
||||||
except RequirementError as e :
|
|
||||||
log.error(e)
|
|
||||||
sys.exit(1)
|
|
||||||
|
|
||||||
if 'distclass' not in attrs:
|
|
||||||
attrs['distclass']=Distribution
|
|
||||||
|
|
||||||
if 'python_src' not in attrs:
|
|
||||||
SRC = 'python'
|
|
||||||
else:
|
|
||||||
SRC = attrs['python_src']
|
|
||||||
del(attrs['python_src'])
|
|
||||||
|
|
||||||
if 'scripts' not in attrs:
|
|
||||||
attrs['scripts'] = glob.glob('%s/*.py' % SRC)
|
|
||||||
|
|
||||||
if 'package_dir' not in attrs:
|
|
||||||
attrs['package_dir'] = {'': SRC}
|
|
||||||
|
|
||||||
if 'packages' not in attrs:
|
|
||||||
attrs['packages'] = findPackage(SRC)
|
|
||||||
|
|
||||||
if 'cmdclass' not in attrs:
|
|
||||||
attrs['cmdclass'] = prepare_commands()
|
|
||||||
|
|
||||||
if 'ctools' not in attrs:
|
|
||||||
attrs['ctools'] = CTOOLS
|
|
||||||
|
|
||||||
if 'executables' not in attrs:
|
|
||||||
attrs['executables'] = CEXES
|
|
||||||
|
|
||||||
if 'files' not in attrs:
|
|
||||||
attrs['files'] = FILES
|
|
||||||
|
|
||||||
if 'sse' not in attrs:
|
|
||||||
attrs['sse']=None
|
|
||||||
|
|
||||||
if 'serenity' not in attrs:
|
|
||||||
attrs['serenity']=False
|
|
||||||
|
|
||||||
EXTENTION=findCython(SRC)
|
|
||||||
|
|
||||||
if 'ext_modules' not in attrs:
|
|
||||||
attrs['ext_modules'] = EXTENTION
|
|
||||||
|
|
||||||
# try:
|
|
||||||
# from setuptools.core import setup as ori_setup
|
|
||||||
# except ImportError:
|
|
||||||
# from distutils.core import setup as ori_setup
|
|
||||||
|
|
||||||
from distutils.core import setup as ori_setup
|
|
||||||
|
|
||||||
return ori_setup(**attrs)
|
|
||||||
@ -1,58 +0,0 @@
|
|||||||
'''
|
|
||||||
Created on 20 oct. 2012
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
try:
|
|
||||||
from setuptools.dist import Distribution as ori_Distribution
|
|
||||||
except ImportError:
|
|
||||||
from distutils.dist import Distribution as ori_Distribution
|
|
||||||
|
|
||||||
# from distutils.dist import Distribution as ori_Distribution
|
|
||||||
|
|
||||||
class Distribution(ori_Distribution):
|
|
||||||
|
|
||||||
def __init__(self,attrs=None):
|
|
||||||
self.executables = None
|
|
||||||
self.ctools = None
|
|
||||||
self.files = None
|
|
||||||
self.build_cexe = None
|
|
||||||
self.deprecated_scripts = None
|
|
||||||
self.zip_safe=False
|
|
||||||
self.sse = None
|
|
||||||
self.serenity=attrs['serenity']
|
|
||||||
|
|
||||||
ori_Distribution.__init__(self, attrs)
|
|
||||||
|
|
||||||
self.global_options.insert(0,('serenity', None, "install or build the package in a python virtualenv "
|
|
||||||
"without polluting the installed python and with many "
|
|
||||||
"checks during the installation process"
|
|
||||||
))
|
|
||||||
self.global_options.insert(0,('virtualenv', None, "if the installation is done using the serenity mode "
|
|
||||||
"this option allows for specifying the virtualenv name. "
|
|
||||||
"By default the name is PACKAGE-VERSION"
|
|
||||||
))
|
|
||||||
|
|
||||||
def run_commands(self):
|
|
||||||
"""Run each command that was seen on the setup script command line.
|
|
||||||
Uses the list of commands found and cache of command objects
|
|
||||||
created by 'get_command_obj()'.
|
|
||||||
"""
|
|
||||||
# self.run_command('littlebigman')
|
|
||||||
ori_Distribution.run_commands(self)
|
|
||||||
|
|
||||||
|
|
||||||
def has_executables(self):
|
|
||||||
return self.executables is not None and self.executables
|
|
||||||
|
|
||||||
def has_ctools(self):
|
|
||||||
return self.ctools is not None and self.ctools
|
|
||||||
|
|
||||||
def has_files(self):
|
|
||||||
return self.files is not None and self.files
|
|
||||||
|
|
||||||
def has_deprecated_scripts(self):
|
|
||||||
return self.deprecated_scripts is not None and self.deprecated_scripts
|
|
||||||
|
|
||||||
|
|
||||||
@ -1,118 +0,0 @@
|
|||||||
import sys
|
|
||||||
|
|
||||||
from distutils import util
|
|
||||||
from distutils import sysconfig
|
|
||||||
from distutils import log
|
|
||||||
from distutils.version import LooseVersion, StrictVersion
|
|
||||||
import glob
|
|
||||||
import os
|
|
||||||
import subprocess
|
|
||||||
import re
|
|
||||||
from distutils.errors import DistutilsError
|
|
||||||
import tempfile
|
|
||||||
|
|
||||||
from importlib.util import spec_from_file_location # @UnresolvedImport
|
|
||||||
import zipimport
|
|
||||||
|
|
||||||
import argparse
|
|
||||||
|
|
||||||
import base64
|
|
||||||
|
|
||||||
from .checkpython import is_python_version
|
|
||||||
|
|
||||||
|
|
||||||
from obidistutils.serenity.rerun import enforce_good_python
|
|
||||||
from obidistutils.serenity.rerun import rerun_with_anothe_python
|
|
||||||
|
|
||||||
from obidistutils.serenity.virtual import serenity_virtualenv
|
|
||||||
|
|
||||||
from obidistutils.serenity.checksystem import is_mac_system, \
|
|
||||||
is_windows_system
|
|
||||||
|
|
||||||
from obidistutils.serenity.checkpackage import install_requirements
|
|
||||||
from obidistutils.serenity.checkpackage import check_requirements
|
|
||||||
|
|
||||||
from obidistutils.serenity.util import save_argv
|
|
||||||
|
|
||||||
from obidistutils.serenity.snake import snake
|
|
||||||
|
|
||||||
|
|
||||||
def serenity_snake(envname,package,version):
|
|
||||||
old = log.set_threshold(log.INFO)
|
|
||||||
|
|
||||||
log.info("Installing %s (%s) in serenity mode" % (package,version))
|
|
||||||
|
|
||||||
enforce_good_python()
|
|
||||||
|
|
||||||
virtualpython=serenity_virtualenv(envname,package,version)
|
|
||||||
|
|
||||||
if virtualpython!=os.path.realpath(sys.executable):
|
|
||||||
log.info("Restarting installation within the %s virtualenv" % (envname))
|
|
||||||
rerun_with_anothe_python(virtualpython)
|
|
||||||
|
|
||||||
log.info("%s will be installed with python : %s" % (package,virtualpython))
|
|
||||||
|
|
||||||
if install_requirements():
|
|
||||||
log.info("Restarting installation with all dependencies ok")
|
|
||||||
rerun_with_anothe_python(virtualpython)
|
|
||||||
|
|
||||||
log.set_threshold(old)
|
|
||||||
|
|
||||||
def serenity_assert(version):
|
|
||||||
check_requirements()
|
|
||||||
|
|
||||||
|
|
||||||
def is_serenity():
|
|
||||||
from obidistutils.serenity.globals import local_serenity
|
|
||||||
return local_serenity and local_serenity[0]
|
|
||||||
|
|
||||||
def serenity_mode(package,version):
|
|
||||||
|
|
||||||
save_argv()
|
|
||||||
|
|
||||||
|
|
||||||
from obidistutils.serenity.globals import saved_args
|
|
||||||
from obidistutils.serenity.globals import local_serenity
|
|
||||||
|
|
||||||
|
|
||||||
old = log.set_threshold(log.INFO)
|
|
||||||
|
|
||||||
argparser = argparse.ArgumentParser(add_help=False)
|
|
||||||
argparser.add_argument('--serenity',
|
|
||||||
dest='serenity',
|
|
||||||
action='store_true',
|
|
||||||
default=True,
|
|
||||||
help='Switch the installer in serenity mode. Everythings are installed in a virtualenv')
|
|
||||||
|
|
||||||
argparser.add_argument('--no-serenity',
|
|
||||||
dest='serenity',
|
|
||||||
action='store_false',
|
|
||||||
default=True,
|
|
||||||
help='Switch the installer in the no serenity mode.')
|
|
||||||
|
|
||||||
argparser.add_argument('--virtualenv',
|
|
||||||
dest='virtual',
|
|
||||||
type=str,
|
|
||||||
action='store',
|
|
||||||
default="%s-%s" % (package,version),
|
|
||||||
help='Specify the name of the virtualenv used by the serenity mode [default: %s-%s]' % (package,version))
|
|
||||||
|
|
||||||
args, unknown = argparser.parse_known_args()
|
|
||||||
sys.argv = [sys.argv[0]] + unknown
|
|
||||||
|
|
||||||
if args.serenity:
|
|
||||||
local_serenity.append(True)
|
|
||||||
serenity_snake(args.virtual,package,version)
|
|
||||||
else:
|
|
||||||
local_serenity.append(False)
|
|
||||||
|
|
||||||
log.set_threshold(old)
|
|
||||||
|
|
||||||
return args.serenity
|
|
||||||
|
|
||||||
|
|
||||||
def getVersion(source,main,version):
|
|
||||||
path = os.path.join(source,main,'%s.py' % version)
|
|
||||||
spec = spec_from_file_location('version',path)
|
|
||||||
return spec.loader.load_module().version.strip()
|
|
||||||
|
|
||||||
@ -1,36 +0,0 @@
|
|||||||
'''
|
|
||||||
Created on 22 janv. 2016
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
import sys
|
|
||||||
from urllib import request
|
|
||||||
import os.path
|
|
||||||
|
|
||||||
from obidistutils.serenity.util import get_serenity_dir
|
|
||||||
from obidistutils.serenity.rerun import rerun_with_anothe_python
|
|
||||||
from obidistutils.serenity.checkpython import is_a_virtualenv_python
|
|
||||||
|
|
||||||
getpipurl="https://bootstrap.pypa.io/get-pip.py"
|
|
||||||
|
|
||||||
def bootstrap():
|
|
||||||
|
|
||||||
getpipfile=os.path.join(get_serenity_dir(),"get-pip.py")
|
|
||||||
|
|
||||||
with request.urlopen(getpipurl) as getpip:
|
|
||||||
with open(getpipfile,"wb") as out:
|
|
||||||
for l in getpip:
|
|
||||||
out.write(l)
|
|
||||||
|
|
||||||
python = sys.executable
|
|
||||||
|
|
||||||
if is_a_virtualenv_python():
|
|
||||||
command= "%s %s" % (python,getpipfile)
|
|
||||||
else:
|
|
||||||
command= "%s %s --user" % (python,getpipfile)
|
|
||||||
|
|
||||||
os.system(command)
|
|
||||||
|
|
||||||
rerun_with_anothe_python(python)
|
|
||||||
|
|
||||||
@ -1,175 +0,0 @@
|
|||||||
'''
|
|
||||||
Created on 2 oct. 2014
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
import re
|
|
||||||
|
|
||||||
from distutils.version import StrictVersion # @UnusedImport
|
|
||||||
from distutils.errors import DistutilsError
|
|
||||||
from distutils import log
|
|
||||||
|
|
||||||
import os.path
|
|
||||||
import sys
|
|
||||||
import subprocess
|
|
||||||
|
|
||||||
|
|
||||||
class RequirementError(Exception):
|
|
||||||
pass
|
|
||||||
|
|
||||||
def is_installed(requirement):
|
|
||||||
pipcommand = os.path.join(os.path.dirname(sys.executable),'pip')
|
|
||||||
pipjson = subprocess.run([pipcommand,"list","--format=json"],
|
|
||||||
capture_output=True).stdout
|
|
||||||
packages = eval(pipjson)
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
requirement_project,requirement_relation,requirement_version = parse_package_requirement(requirement)
|
|
||||||
|
|
||||||
package = [x for x in packages if x["name"]==requirement_project]
|
|
||||||
|
|
||||||
if len(package)==1:
|
|
||||||
if ( requirement_version is not None
|
|
||||||
and requirement_relation is not None):
|
|
||||||
rep = (len(package)==1) and eval("StrictVersion('%s') %s StrictVersion('%s')" % (package[0]["version"],
|
|
||||||
requirement_relation,
|
|
||||||
requirement_version)
|
|
||||||
)
|
|
||||||
else:
|
|
||||||
rep=True
|
|
||||||
else:
|
|
||||||
rep=False
|
|
||||||
|
|
||||||
if rep:
|
|
||||||
if requirement_version is not None and requirement_relation is not None:
|
|
||||||
log.info("Look for package %s (%s%s) : ok version %s installed" % (requirement_project,
|
|
||||||
requirement_relation,
|
|
||||||
requirement_version,
|
|
||||||
package[0]["version"]))
|
|
||||||
else:
|
|
||||||
log.info("Look for package %s : ok version %s installed" % (requirement_project,
|
|
||||||
package[0]["version"]))
|
|
||||||
else:
|
|
||||||
if len(package)!=1:
|
|
||||||
if requirement_version is not None and requirement_relation is not None:
|
|
||||||
log.info("Look for package %s (%s%s) : not installed" % (requirement_project,
|
|
||||||
requirement_relation,
|
|
||||||
requirement_version))
|
|
||||||
else:
|
|
||||||
log.info("Look for package %s : not installed" % requirement_project)
|
|
||||||
else:
|
|
||||||
log.info("Look for package %s (%s%s) : failed only version %s installed" % (requirement_project,
|
|
||||||
requirement_relation,
|
|
||||||
requirement_version,
|
|
||||||
package[0]["version"]))
|
|
||||||
|
|
||||||
return rep
|
|
||||||
|
|
||||||
|
|
||||||
def get_requirements(requirementfile='requirements.txt'):
|
|
||||||
|
|
||||||
try:
|
|
||||||
requirements = open(requirementfile).readlines()
|
|
||||||
requirements = [x.strip() for x in requirements]
|
|
||||||
requirements = [x for x in requirements if x[0]!='-']
|
|
||||||
|
|
||||||
except IOError:
|
|
||||||
requirements = []
|
|
||||||
|
|
||||||
return requirements
|
|
||||||
|
|
||||||
|
|
||||||
def install_requirements(requirementfile='requirements.txt'):
|
|
||||||
|
|
||||||
install_something=False
|
|
||||||
|
|
||||||
requirements = get_requirements(requirementfile)
|
|
||||||
|
|
||||||
log.info("Required packages for the installation :")
|
|
||||||
for x in requirements:
|
|
||||||
ok = is_installed(x)
|
|
||||||
if not ok:
|
|
||||||
log.info(" Installing requirement : %s" % x)
|
|
||||||
pip_install_package(x,requirement=requirementfile)
|
|
||||||
install_something=True
|
|
||||||
if x[0:3]=='pip':
|
|
||||||
return True
|
|
||||||
|
|
||||||
return install_something
|
|
||||||
|
|
||||||
|
|
||||||
def check_requirements(requirementfile='requirements.txt'):
|
|
||||||
|
|
||||||
requirements = get_requirements(requirementfile)
|
|
||||||
|
|
||||||
log.info("Required packages for the installation :")
|
|
||||||
for x in requirements:
|
|
||||||
ok = is_installed(x)
|
|
||||||
if not ok:
|
|
||||||
raise RequirementError(" Missing requirement : %s -- Package installation stopped" % x)
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
def parse_package_requirement(requirement):
|
|
||||||
|
|
||||||
version_pattern = re.compile('[=><]+(.*)$')
|
|
||||||
project_pattern = re.compile('[^=><]+')
|
|
||||||
relationship_pattern = re.compile('[=><]+')
|
|
||||||
|
|
||||||
try:
|
|
||||||
requirement_project = project_pattern.search(requirement).group(0)
|
|
||||||
requirement_version = version_pattern.search(requirement)
|
|
||||||
if requirement_version is not None:
|
|
||||||
requirement_version=requirement_version.group(1)
|
|
||||||
requirement_relation= relationship_pattern.search(requirement)
|
|
||||||
if requirement_relation is not None:
|
|
||||||
requirement_relation=requirement_relation.group(0)
|
|
||||||
except:
|
|
||||||
raise DistutilsError("Requirement : %s not correctly formated" % requirement)
|
|
||||||
|
|
||||||
return requirement_project,requirement_relation,requirement_version
|
|
||||||
|
|
||||||
|
|
||||||
def get_package_requirement(package,requirementfile='requirements.txt'):
|
|
||||||
requirements = get_requirements(requirementfile)
|
|
||||||
req = [x for x in requirements
|
|
||||||
if x[0:len(package)]==package
|
|
||||||
]
|
|
||||||
|
|
||||||
if len(req)==1:
|
|
||||||
return req[0]
|
|
||||||
else:
|
|
||||||
return None
|
|
||||||
|
|
||||||
|
|
||||||
def pip_install_package(package,directory=None,requirement=None):
|
|
||||||
|
|
||||||
pipcommand = os.path.join(os.path.dirname(sys.executable),'pip')
|
|
||||||
if directory is not None:
|
|
||||||
log.info(' installing %s in directory %s' % (package,str(directory)))
|
|
||||||
|
|
||||||
|
|
||||||
if 'http_proxy' in os.environ and 'https_proxy' not in os.environ:
|
|
||||||
os.environ['https_proxy']=os.environ['http_proxy']
|
|
||||||
|
|
||||||
args = ['install']
|
|
||||||
|
|
||||||
if requirement:
|
|
||||||
args.append('--requirement')
|
|
||||||
args.append(requirement)
|
|
||||||
|
|
||||||
if 'https_proxy' in os.environ:
|
|
||||||
args.append('--proxy=%s' % os.environ['https_proxy'])
|
|
||||||
|
|
||||||
if directory is not None:
|
|
||||||
args.append('--target=%s' % directory)
|
|
||||||
|
|
||||||
args.append(package)
|
|
||||||
|
|
||||||
pip = subprocess.run([pipcommand] + args)
|
|
||||||
|
|
||||||
return pip
|
|
||||||
|
|
||||||
@ -1,138 +0,0 @@
|
|||||||
'''
|
|
||||||
Created on 24 mai 2015
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
from distutils.version import StrictVersion
|
|
||||||
from distutils import sysconfig
|
|
||||||
import subprocess
|
|
||||||
import os
|
|
||||||
import glob
|
|
||||||
import re
|
|
||||||
|
|
||||||
from obidistutils.serenity.checksystem import is_windows_system
|
|
||||||
import sys
|
|
||||||
|
|
||||||
|
|
||||||
def is_python_version(path=None,minversion='3.4',maxversion=None):
|
|
||||||
'''
|
|
||||||
Checks that the python version is in the range {minversion,maxversion[
|
|
||||||
|
|
||||||
@param path: if None consider the running python
|
|
||||||
otherwise the python pointed by the path
|
|
||||||
@param minversion: the minimum version to consider
|
|
||||||
@param maxversion: the maximum version to consider (strictly inferior to)
|
|
||||||
|
|
||||||
@return: True if the python version match
|
|
||||||
@rtype: bool
|
|
||||||
'''
|
|
||||||
if path is None:
|
|
||||||
pythonversion = StrictVersion(sysconfig.get_python_version())
|
|
||||||
else:
|
|
||||||
command = """'%s' -c 'from distutils import sysconfig; """ \
|
|
||||||
"""print(sysconfig.get_python_version())'""" % path
|
|
||||||
|
|
||||||
p = subprocess.Popen(command,
|
|
||||||
shell=True,
|
|
||||||
stdout=subprocess.PIPE)
|
|
||||||
pythonversion=str(p.communicate()[0],'utf8').strip()
|
|
||||||
pythonversion = StrictVersion(pythonversion)
|
|
||||||
|
|
||||||
return ( pythonversion >=StrictVersion(minversion)
|
|
||||||
and ( maxversion is None
|
|
||||||
or pythonversion < StrictVersion(maxversion))
|
|
||||||
)
|
|
||||||
|
|
||||||
|
|
||||||
def lookfor_good_python(minversion='3.4',maxversion=None,followLink=False):
|
|
||||||
'''
|
|
||||||
Look for all python interpreters present in the system path that
|
|
||||||
match the version constraints.
|
|
||||||
|
|
||||||
@param minversion: the minimum version to consider
|
|
||||||
@param maxversion: the maximum version to consider (strictly inferior to)
|
|
||||||
@param followLink: a boolean value indicating if link must be substituted
|
|
||||||
by their real path.
|
|
||||||
|
|
||||||
@return: a list of path to interpreters
|
|
||||||
'''
|
|
||||||
exe = []
|
|
||||||
if not is_windows_system():
|
|
||||||
paths = os.environ['PATH'].split(os.pathsep)
|
|
||||||
for p in paths:
|
|
||||||
candidates = glob.glob(os.path.join(p,'python*'))
|
|
||||||
pexe = []
|
|
||||||
pythonpat=re.compile('python([0-9]|[0-9]\.[0-9])?$')
|
|
||||||
for e in candidates:
|
|
||||||
print(e)
|
|
||||||
if pythonpat.search(e) is not None:
|
|
||||||
if followLink and os.path.islink(e):
|
|
||||||
e = os.path.realpath(e)
|
|
||||||
if (os.path.isfile(e) and
|
|
||||||
os.access(e, os.X_OK) and
|
|
||||||
is_python_version(e,minversion,maxversion)):
|
|
||||||
pexe.append(e)
|
|
||||||
exe.extend(set(pexe))
|
|
||||||
|
|
||||||
return exe
|
|
||||||
|
|
||||||
def is_a_virtualenv_python(path=None):
|
|
||||||
'''
|
|
||||||
Check if the python is belonging a virtualenv
|
|
||||||
|
|
||||||
@param path: the path pointing to the python executable.
|
|
||||||
if path is None then the running python is
|
|
||||||
considered.
|
|
||||||
@param path: str or None
|
|
||||||
|
|
||||||
@return: True if the python belongs a virtualenv
|
|
||||||
False otherwise
|
|
||||||
@rtype: bool
|
|
||||||
|
|
||||||
'''
|
|
||||||
if path is None:
|
|
||||||
rep = sys.base_exec_prefix != sys.exec_prefix
|
|
||||||
else:
|
|
||||||
command = """'%s' -c 'import sys; print(sys.base_exec_prefix != sys.exec_prefix)'""" % path
|
|
||||||
p = subprocess.Popen(command,
|
|
||||||
shell=True,
|
|
||||||
stdout=subprocess.PIPE)
|
|
||||||
rep = eval(str(p.communicate()[0],'utf8'))
|
|
||||||
|
|
||||||
return rep
|
|
||||||
|
|
||||||
|
|
||||||
def which_virtualenv(path=None,full=False):
|
|
||||||
'''
|
|
||||||
Returns the name of the virtualenv.
|
|
||||||
@param path: the path to a python binary or None
|
|
||||||
if you want to consider the running python
|
|
||||||
@type path: str or None
|
|
||||||
|
|
||||||
@param full: if set to True, returns the absolute path,
|
|
||||||
otherwise only return a simple directory name
|
|
||||||
@type full: bool
|
|
||||||
|
|
||||||
@return: the virtual environment name or None if the
|
|
||||||
path does not belong a virtualenv
|
|
||||||
@rtype: str or None
|
|
||||||
'''
|
|
||||||
if path is None:
|
|
||||||
path = sys.executable
|
|
||||||
|
|
||||||
if is_a_virtualenv_python(path):
|
|
||||||
parts = path.split(os.sep)
|
|
||||||
try:
|
|
||||||
if full:
|
|
||||||
rep = os.sep.join(parts[0:parts.index('bin')])
|
|
||||||
rep = os.path.realpath(rep)
|
|
||||||
else:
|
|
||||||
rep = parts[parts.index('bin')-1]
|
|
||||||
except ValueError:
|
|
||||||
rep = None
|
|
||||||
else:
|
|
||||||
rep=None
|
|
||||||
|
|
||||||
return rep
|
|
||||||
|
|
||||||
|
|
||||||
@ -1,18 +0,0 @@
|
|||||||
'''
|
|
||||||
Created on 24 mai 2015
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
from distutils import util
|
|
||||||
|
|
||||||
def is_mac_system():
|
|
||||||
platform = util.get_platform().split('-')[0]
|
|
||||||
|
|
||||||
return platform=='macosx'
|
|
||||||
|
|
||||||
def is_windows_system():
|
|
||||||
platform = util.get_platform().split('-')[0]
|
|
||||||
|
|
||||||
return platform=='Windows'
|
|
||||||
|
|
||||||
@ -1,14 +0,0 @@
|
|||||||
'''
|
|
||||||
Created on 24 mai 2015
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
|
|
||||||
saved_args=[]
|
|
||||||
tmpdir=[]
|
|
||||||
local_pip=[]
|
|
||||||
local_virtualenv=[]
|
|
||||||
local_cython=[]
|
|
||||||
local_serenity=[]
|
|
||||||
|
|
||||||
@ -1,61 +0,0 @@
|
|||||||
'''
|
|
||||||
Created on 24 mai 2015
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
import sys
|
|
||||||
import os
|
|
||||||
from distutils import log
|
|
||||||
from distutils.errors import DistutilsError
|
|
||||||
|
|
||||||
|
|
||||||
from obidistutils.serenity.globals import saved_args
|
|
||||||
from obidistutils.serenity.checkpython import is_python_version,\
|
|
||||||
lookfor_good_python
|
|
||||||
|
|
||||||
|
|
||||||
def rerun_with_anothe_python(path, minversion='3.4',maxversion=None, fork=False):
|
|
||||||
|
|
||||||
if saved_args:
|
|
||||||
args = saved_args
|
|
||||||
else:
|
|
||||||
args = list(sys.argv)
|
|
||||||
|
|
||||||
|
|
||||||
assert is_python_version(path,minversion,maxversion), \
|
|
||||||
'the selected python is not adapted to the installation of this package'
|
|
||||||
|
|
||||||
args.insert(0, path)
|
|
||||||
|
|
||||||
sys.stderr.flush()
|
|
||||||
sys.stdout.flush()
|
|
||||||
|
|
||||||
if fork:
|
|
||||||
log.info('Forking a new install process')
|
|
||||||
os.system(' '.join(list(args)))
|
|
||||||
log.info('External process ended')
|
|
||||||
sys.exit(0)
|
|
||||||
else:
|
|
||||||
log.info('Install script restarting...')
|
|
||||||
os.execv(path,list(args))
|
|
||||||
|
|
||||||
def enforce_good_python(minversion='3.4',maxversion=None, fork=False):
|
|
||||||
if is_python_version(minversion=minversion,maxversion=maxversion):
|
|
||||||
log.info('You are running the good python')
|
|
||||||
return True
|
|
||||||
|
|
||||||
goodpython = lookfor_good_python(minversion,maxversion)
|
|
||||||
|
|
||||||
if not goodpython:
|
|
||||||
raise DistutilsError('No good python identified on your system')
|
|
||||||
|
|
||||||
goodpython=goodpython[0]
|
|
||||||
|
|
||||||
log.warn("========================================")
|
|
||||||
log.warn("")
|
|
||||||
log.warn(" Switching to python : %s" % goodpython)
|
|
||||||
log.warn("")
|
|
||||||
log.warn("========================================")
|
|
||||||
|
|
||||||
rerun_with_anothe_python(goodpython)
|
|
||||||
@ -1,35 +0,0 @@
|
|||||||
'''
|
|
||||||
Created on 2 oct. 2014
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
snake ="""
|
|
||||||
|
|
||||||
___
|
|
||||||
,'._,`.
|
|
||||||
(-.___.-)
|
|
||||||
(-.___.-)
|
|
||||||
`-.___.-'
|
|
||||||
(( @ @| . __
|
|
||||||
\ ` | ,\ |`. @| | | _.-._
|
|
||||||
__`.`=-=mm===mm:: | | |`. | | | ,'=` '=`.
|
|
||||||
( `-'|:/ /:/ `/ @| | | |, @| @| /---)W(---\
|
|
||||||
\ \ / / / / @| | ' (----| |----) ,~
|
|
||||||
|\ \ / /| / / @| \---| |---/ |
|
|
||||||
| \ V /||/ / `.-| |-,' |
|
|
||||||
| `-' |V / \| |/ @'
|
|
||||||
| , |-' __| |__
|
|
||||||
| .;: _,-. ,--""..| |..""--.
|
|
||||||
;;:::' " ) (`--::__|_|__::--')
|
|
||||||
,-" _, / \`--...___...--'/
|
|
||||||
( -:--'/ / /`--...___...--'\
|
|
||||||
"-._ `"'._/ /`---...___...---'\
|
|
||||||
"-._ "---. (`---....___....---')
|
|
||||||
.' ",._ ,' ) |`---....___....---'|
|
|
||||||
/`._| `| | (`---....___....---')
|
|
||||||
( \ | / \`---...___...---'/
|
|
||||||
`. `, ^"" `:--...___...--;'
|
|
||||||
`.,' hh `-._______.-'
|
|
||||||
|
|
||||||
"""
|
|
||||||
@ -1,27 +0,0 @@
|
|||||||
'''
|
|
||||||
Created on 2 oct. 2014
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
import sys
|
|
||||||
import tempfile
|
|
||||||
|
|
||||||
|
|
||||||
from obidistutils.serenity.globals import tmpdir # @UnusedImport
|
|
||||||
from obidistutils.serenity.globals import saved_args # @UnusedImport
|
|
||||||
|
|
||||||
def get_serenity_dir():
|
|
||||||
global tmpdir
|
|
||||||
|
|
||||||
if not tmpdir:
|
|
||||||
tmpdir.append(tempfile.mkdtemp())
|
|
||||||
return tmpdir[0]
|
|
||||||
|
|
||||||
def save_argv():
|
|
||||||
global saved_args
|
|
||||||
|
|
||||||
del saved_args[:]
|
|
||||||
saved_args.extend(list(sys.argv))
|
|
||||||
|
|
||||||
|
|
||||||
@ -1,69 +0,0 @@
|
|||||||
'''
|
|
||||||
Created on 2 oct. 2014
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
import os
|
|
||||||
import sys
|
|
||||||
import venv
|
|
||||||
|
|
||||||
from distutils.errors import DistutilsError
|
|
||||||
from .globals import local_virtualenv # @UnusedImport
|
|
||||||
from .checkpython import which_virtualenv,\
|
|
||||||
is_python_version, \
|
|
||||||
is_a_virtualenv_python
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
def serenity_virtualenv(envname,package,version,minversion='3.4',maxversion=None):
|
|
||||||
|
|
||||||
#
|
|
||||||
# Checks if we are already running under the good virtualenv
|
|
||||||
#
|
|
||||||
ve = which_virtualenv(full=True)
|
|
||||||
if ve == os.path.realpath(envname) and is_python_version(minversion=minversion,maxversion=maxversion):
|
|
||||||
return sys.executable
|
|
||||||
|
|
||||||
#
|
|
||||||
# Check if the virtualenv exist
|
|
||||||
#
|
|
||||||
|
|
||||||
python = None
|
|
||||||
|
|
||||||
if os.path.isdir(envname):
|
|
||||||
python = os.path.join(envname,'bin','python')
|
|
||||||
ok = (is_python_version(python,
|
|
||||||
minversion=minversion,
|
|
||||||
maxversion=maxversion) and
|
|
||||||
is_a_virtualenv_python(python))
|
|
||||||
|
|
||||||
|
|
||||||
#
|
|
||||||
# The virtualenv already exist but it is not ok
|
|
||||||
#
|
|
||||||
if not ok:
|
|
||||||
raise DistutilsError("A virtualenv %s already exists but not with the required python")
|
|
||||||
|
|
||||||
else:
|
|
||||||
ok = False
|
|
||||||
|
|
||||||
|
|
||||||
#
|
|
||||||
# Creates a new virtualenv
|
|
||||||
#
|
|
||||||
if not ok:
|
|
||||||
venv.create(envname,
|
|
||||||
system_site_packages=False,
|
|
||||||
clear=True,
|
|
||||||
symlinks=False,
|
|
||||||
with_pip=True)
|
|
||||||
|
|
||||||
# check the newly created virtualenv
|
|
||||||
return serenity_virtualenv(envname,package,version)
|
|
||||||
|
|
||||||
return os.path.realpath(python)
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
@ -1,24 +0,0 @@
|
|||||||
/*
|
|
||||||
* littlebigman.c
|
|
||||||
*
|
|
||||||
* Created on: 11 juil. 2012
|
|
||||||
* Author: coissac
|
|
||||||
*/
|
|
||||||
|
|
||||||
#include <stdio.h>
|
|
||||||
|
|
||||||
int main(int argc, char *argv[])
|
|
||||||
{
|
|
||||||
union { int entier;
|
|
||||||
char caractere[4] ;
|
|
||||||
} test;
|
|
||||||
|
|
||||||
test.entier=0x01020304;
|
|
||||||
|
|
||||||
if (test.caractere[3] == 1)
|
|
||||||
printf("-DLITTLE_END");
|
|
||||||
else
|
|
||||||
printf("-DBIG_END");
|
|
||||||
|
|
||||||
return 0;
|
|
||||||
}
|
|
||||||
@ -1,24 +0,0 @@
|
|||||||
#include <stdio.h>
|
|
||||||
#include <stdlib.h>
|
|
||||||
#include <string.h>
|
|
||||||
#include <errno.h>
|
|
||||||
#include <libproc.h>
|
|
||||||
|
|
||||||
int main (int argc, char* argv[])
|
|
||||||
{
|
|
||||||
pid_t pid; int ret;
|
|
||||||
char pathbuf[PROC_PIDPATHINFO_MAXSIZE];
|
|
||||||
|
|
||||||
if ( argc > 1 ) {
|
|
||||||
pid = (pid_t) atoi(argv[1]);
|
|
||||||
ret = proc_pidpath (pid, pathbuf, sizeof(pathbuf));
|
|
||||||
if ( ret <= 0 ) {
|
|
||||||
fprintf(stderr, "PID %d: proc_pidpath ();\n", pid);
|
|
||||||
fprintf(stderr, " %s\n", strerror(errno));
|
|
||||||
} else {
|
|
||||||
printf("proc %d: %s\n", pid, pathbuf);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
return 0;
|
|
||||||
}
|
|
||||||
2
doc/sphinx/.gitignore
vendored
Normal file
2
doc/sphinx/.gitignore
vendored
Normal file
@ -0,0 +1,2 @@
|
|||||||
|
.DS_Store
|
||||||
|
/build_dir.txt
|
||||||
1
python/.gitignore
vendored
Normal file
1
python/.gitignore
vendored
Normal file
@ -0,0 +1 @@
|
|||||||
|
/OBITools3.egg-info/
|
||||||
168
setup.py
168
setup.py
@ -1,87 +1,125 @@
|
|||||||
#!/usr/bin/env python
|
import glob
|
||||||
|
import os
|
||||||
import sys
|
import sys
|
||||||
|
import re
|
||||||
|
import subprocess
|
||||||
|
|
||||||
|
from distutils.core import setup,Extension
|
||||||
|
from distutils.sysconfig import get_python_lib
|
||||||
|
from Cython.Build import cythonize
|
||||||
|
|
||||||
|
import os.path
|
||||||
|
from distutils import log
|
||||||
|
from distutils.extension import Extension
|
||||||
|
|
||||||
|
sys.path.append(os.path.abspath("python"))
|
||||||
|
|
||||||
|
dependencies = ['sphinx',"Cython"]
|
||||||
|
|
||||||
|
|
||||||
|
def findPackage(root,base=None):
|
||||||
|
modules=[]
|
||||||
|
if base is None:
|
||||||
|
base=[]
|
||||||
|
for module in (os.path.basename(os.path.dirname(x))
|
||||||
|
for x in glob.glob(os.path.join(root,'*','__init__.py'))):
|
||||||
|
modules.append('.'.join(base+[module]))
|
||||||
|
modules.extend(findPackage(os.path.join(root,module),base+[module]))
|
||||||
|
return modules
|
||||||
|
|
||||||
|
|
||||||
PACKAGE = "OBITools3"
|
PACKAGE = "OBITools3"
|
||||||
VERSION = "0.0.0"
|
VERSION = "0.0.0"
|
||||||
AUTHOR = 'Eric Coissac'
|
AUTHOR = 'Eric Coissac'
|
||||||
EMAIL = 'eric@coissac.eu'
|
EMAIL = 'eric@metabarcoding.org'
|
||||||
URL = 'metabarcoding.org/obitools3'
|
URL = "metabarcoding.org/obitools3"
|
||||||
LICENSE = 'CeCILL-V2'
|
LICENSE = "CeCILL-V2"
|
||||||
DESCRIPTION ="Scripts and library for DNA metabarcoding",
|
DESCRIPTION = "Tools and library for DNA metabarcoding",
|
||||||
|
PYTHONMIN = '3.6'
|
||||||
|
|
||||||
SRC = 'python'
|
SRC = 'python'
|
||||||
CSRC = 'src'
|
CSRC = 'src'
|
||||||
|
|
||||||
|
REQUIRES = ['Cython>=0.24',
|
||||||
|
'Sphinx>=1.2.0',
|
||||||
|
'ipython>=3.0.0',
|
||||||
|
'breathe>=4.0.0'
|
||||||
|
]
|
||||||
|
|
||||||
|
os.environ['CFLAGS'] = '-O3 -Wall -I "src" -I "src/libecoPCR" -I "src/libjson"'
|
||||||
|
|
||||||
|
#sys.path.append("/Users/coissac/git/obitools3/python")
|
||||||
|
|
||||||
|
cython_src = [x for x in glob.iglob('python/obitools3/**/*.pyx',
|
||||||
|
recursive=True
|
||||||
|
)
|
||||||
|
]
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
#with open(os.path.join(os.path.dirname(__file__), 'README.rst')) as f:
|
||||||
|
# readme = f.read()
|
||||||
|
|
||||||
|
install_clibdir_option="-DPYTHONLIB:STRING='%s'" % get_python_lib()
|
||||||
|
|
||||||
|
subprocess.call(['cmake', install_clibdir_option, 'src'])
|
||||||
|
subprocess.call(['make', '-C', 'src','install'])
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
cython_ext = [Extension('.'.join([os.path.dirname(x).replace("python/",""),
|
||||||
|
os.path.splitext(os.path.basename(x))[0]]).replace('/','.'),
|
||||||
|
[x],
|
||||||
|
library_dirs=[get_python_lib()],
|
||||||
|
include_dirs=["src","src/libecoPCR","src/libjson"],
|
||||||
|
libraries=["cobitools3"],
|
||||||
|
runtime_library_dirs=[get_python_lib()],
|
||||||
|
extra_compile_args=['-msse2',
|
||||||
|
'-Wno-unused-function',
|
||||||
|
'-Wmissing-braces',
|
||||||
|
'-Wchar-subscripts',
|
||||||
|
'-fPIC'
|
||||||
|
],
|
||||||
|
extra_link_args=["-Wl,-rpath,"+get_python_lib(),
|
||||||
|
"-L"+get_python_lib()
|
||||||
|
]
|
||||||
|
)
|
||||||
|
for x in cython_src
|
||||||
|
]
|
||||||
|
|
||||||
|
|
||||||
|
xx = cythonize(cython_ext,
|
||||||
|
language_level=3,
|
||||||
|
annotate=True,
|
||||||
|
build_dir="build")
|
||||||
|
|
||||||
|
#, include_path=["src","src/libecoPCR","src/libjson"]
|
||||||
|
|
||||||
classifiers=['Development Status :: 1 - Planning',
|
classifiers=['Development Status :: 1 - Planning',
|
||||||
'Environment :: Console',
|
'Environment :: Console',
|
||||||
'Intended Audience :: Science/Research',
|
'Intended Audience :: Science/Research',
|
||||||
'License :: Other/Proprietary License',
|
'License :: Other/Proprietary License',
|
||||||
'Operating System :: Unix',
|
'Operating System :: Unix',
|
||||||
'Programming Language :: Python',
|
|
||||||
'Programming Language :: Python :: 3',
|
'Programming Language :: Python :: 3',
|
||||||
|
'Programming Language :: C',
|
||||||
'Topic :: Scientific/Engineering :: Bio-Informatics',
|
'Topic :: Scientific/Engineering :: Bio-Informatics',
|
||||||
'Topic :: Utilities',
|
'Topic :: Utilities',
|
||||||
]
|
]
|
||||||
|
|
||||||
|
|
||||||
PYTHONMIN='3.4'
|
|
||||||
|
|
||||||
|
setup(name=PACKAGE,
|
||||||
sys.path.append('distutils.ext')
|
description=DESCRIPTION,
|
||||||
sys.path.append(SRC)
|
classifiers=classifiers,
|
||||||
|
version=VERSION,
|
||||||
if __name__=="__main__":
|
author=AUTHOR,
|
||||||
|
author_email=EMAIL,
|
||||||
import sys
|
license=LICENSE,
|
||||||
|
url=URL,
|
||||||
print("----------------")
|
ext_modules=xx,
|
||||||
print(" ".join(sys.argv))
|
packages = findPackage('python'),
|
||||||
print("----------------")
|
package_dir = {"" : "python"},
|
||||||
|
scripts = ['scripts/obi']
|
||||||
#
|
)
|
||||||
# Horrible hack
|
|
||||||
#
|
|
||||||
|
|
||||||
if sys.argv[0]=="-c":
|
|
||||||
sys.argv[0]="setup.py"
|
|
||||||
|
|
||||||
#
|
|
||||||
# End of the horrible hack
|
|
||||||
#
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
try:
|
|
||||||
from obitools3 import version
|
|
||||||
VERSION = version.version
|
|
||||||
except ImportError:
|
|
||||||
pass
|
|
||||||
|
|
||||||
from obidistutils.serenity import serenity_mode
|
|
||||||
|
|
||||||
serenity=serenity_mode(PACKAGE,VERSION)
|
|
||||||
|
|
||||||
from obidistutils.core import setup
|
|
||||||
from obidistutils.core import CTOOLS
|
|
||||||
from obidistutils.core import CEXES
|
|
||||||
from obidistutils.core import FILES
|
|
||||||
|
|
||||||
# Produce annotated html files
|
|
||||||
import Cython.Compiler.Options
|
|
||||||
Cython.Compiler.Options.annotate = True
|
|
||||||
|
|
||||||
|
|
||||||
setup(name=PACKAGE,
|
|
||||||
description=DESCRIPTION,
|
|
||||||
classifiers=classifiers,
|
|
||||||
version=VERSION,
|
|
||||||
author=AUTHOR,
|
|
||||||
author_email=EMAIL,
|
|
||||||
license=LICENSE,
|
|
||||||
url=URL,
|
|
||||||
python_src=SRC,
|
|
||||||
sse='sse2',
|
|
||||||
serenity=serenity,
|
|
||||||
pythonmin=PYTHONMIN)
|
|
||||||
|
|
||||||
|
|||||||
5
src/.gitignore
vendored
Normal file
5
src/.gitignore
vendored
Normal file
@ -0,0 +1,5 @@
|
|||||||
|
/CMakeFiles/
|
||||||
|
/CMakeCache.txt
|
||||||
|
/cmake_install.cmake
|
||||||
|
/libcobitools3.dylib
|
||||||
|
/Makefile
|
||||||
66
src/CMakeLists.txt
Normal file
66
src/CMakeLists.txt
Normal file
@ -0,0 +1,66 @@
|
|||||||
|
cmake_minimum_required(VERSION 3.12)
|
||||||
|
set(CMAKE_POSITION_INDEPENDENT_CODE ON)
|
||||||
|
|
||||||
|
SET(PYTHONLIB "po" CACHE STRING "Location of the python site-package directory")
|
||||||
|
|
||||||
|
project (cobitools3)
|
||||||
|
set(CMAKE_BUILD_TYPE Release)
|
||||||
|
|
||||||
|
SET(CMAKE_C_COMPILER gcc)
|
||||||
|
|
||||||
|
include_directories(${CMAKE_CURRENT_SOURCE_DIR})
|
||||||
|
file(GLOB_RECURSE CSRC "*.c")
|
||||||
|
|
||||||
|
add_library(cobitools3 SHARED obierrno.c
|
||||||
|
obidms_taxonomy.c
|
||||||
|
obiblob_indexer.c
|
||||||
|
obi_lcs.c
|
||||||
|
obidmscolumn_str.c
|
||||||
|
bloom.c
|
||||||
|
build_reference_db.c
|
||||||
|
obidmscolumn_array.c
|
||||||
|
obidmscolumn_idx.c
|
||||||
|
obidmscolumn_bool.c
|
||||||
|
libjson/json_utils.c
|
||||||
|
libjson/cJSON.c
|
||||||
|
obidmscolumn_blob.c
|
||||||
|
dna_seq_indexer.c
|
||||||
|
obi_ecotag.c
|
||||||
|
encode.c
|
||||||
|
obiavl.c
|
||||||
|
sse_banded_LCS_alignment.c
|
||||||
|
kmer_similarity.c
|
||||||
|
obidmscolumn_qual.c
|
||||||
|
obi_clean.c
|
||||||
|
utils.c
|
||||||
|
uint8_indexer.c
|
||||||
|
murmurhash2.c
|
||||||
|
obidmscolumn_char.c
|
||||||
|
obiview.c
|
||||||
|
obidmscolumn_int.c
|
||||||
|
linked_list.c
|
||||||
|
obiblob.c
|
||||||
|
hashtable.c
|
||||||
|
obidmscolumn.c
|
||||||
|
char_str_indexer.c
|
||||||
|
obidmscolumn_float.c
|
||||||
|
upperband.c
|
||||||
|
crc64.c
|
||||||
|
obidmscolumn_seq.c
|
||||||
|
obilittlebigman.c
|
||||||
|
obidmscolumndir.c
|
||||||
|
obidms.c
|
||||||
|
obi_ecopcr.c
|
||||||
|
libecoPCR/libthermo/nnparams.c
|
||||||
|
libecoPCR/ecoapat.c
|
||||||
|
libecoPCR/libapat/libstki.c
|
||||||
|
libecoPCR/libapat/apat_search.c
|
||||||
|
libecoPCR/libapat/apat_parse.c
|
||||||
|
libecoPCR/ecodna.c
|
||||||
|
libecoPCR/ecoMalloc.c
|
||||||
|
libecoPCR/ecoError.c
|
||||||
|
obitypes.c
|
||||||
|
array_indexer.c)
|
||||||
|
|
||||||
|
install(TARGETS cobitools3 DESTINATION ${PYTHONLIB})
|
||||||
|
|
||||||
Reference in New Issue
Block a user