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ORG.Asm
ORG.Asm
Commits
da7c0a0e
Commit
da7c0a0e
authored
Aug 16, 2015
by
Eric Coissac
Browse files
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First version of get-orgasm.py working correctly
parent
d73af4c3
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18 changed files
with
222 additions
and
88 deletions
+222
-88
MANIFEST.in
MANIFEST.in
+1
-0
VERSION
VERSION
+2
-0
build.py
distutils.ext/obidistutils/command/build.py
+16
-20
build_cexe.py
distutils.ext/obidistutils/command/build_cexe.py
+16
-4
build_ctools.py
distutils.ext/obidistutils/command/build_ctools.py
+7
-3
build_exe.py
distutils.ext/obidistutils/command/build_exe.py
+1
-0
build_ext.py
distutils.ext/obidistutils/command/build_ext.py
+17
-0
build_files.py
distutils.ext/obidistutils/command/build_files.py
+10
-0
build_sphinx.py
distutils.ext/obidistutils/command/build_sphinx.py
+21
-20
install.py
distutils.ext/obidistutils/command/install.py
+6
-1
install_scripts.py
distutils.ext/obidistutils/command/install_scripts.py
+10
-6
pidname.py
distutils.ext/obidistutils/command/pidname.py
+4
-0
core.py
distutils.ext/obidistutils/core.py
+39
-13
dist.py
distutils.ext/obidistutils/dist.py
+7
-5
get-orgasm.py
get_orgasm/get-orgasm.py
+50
-5
version.py
python/orgasm/version.py
+3
-3
requirements.txt
requirements.txt
+2
-2
setup.py
setup.py
+10
-6
No files found.
MANIFEST.in
View file @
da7c0a0e
...
...
@@ -9,3 +9,4 @@ include doc/sphinx/make.bat
include doc/sphinx/Makefile
include README.txt
include requirements.txt
include VERSION
VERSION
0 → 100644
View file @
da7c0a0e
0.1.0a1
\ No newline at end of file
distutils.ext/obidistutils/command/build.py
View file @
da7c0a0e
...
...
@@ -10,33 +10,29 @@ from obidistutils.serenity.checksystem import is_mac_system
class
build
(
ori_build
):
def
has_ctools
(
self
):
return
self
.
distribution
.
has_ctools
()
def
has_files
(
self
):
return
self
.
distribution
.
has_files
()
def
has_executables
(
self
):
return
self
.
distribution
.
has_executables
()
def
has_ext_modules
(
self
):
return
self
.
distribution
.
has_ext_modules
()
def
has_littlebigman
(
self
):
return
True
def
has_pidname
(
self
):
return
is_mac_system
()
def
has_doc
(
self
):
return
True
def
has_littlebigman
(
self
):
return
True
sub_commands
=
[(
'littlebigman'
,
has_littlebigman
),
(
'pidname'
,
has_pidname
),
(
'build_ctools'
,
has_ctools
),
(
'build_files'
,
has_files
),
(
'build_cexe'
,
has_executables
)]
\
+
ori_build
.
sub_commands
+
\
[(
'build_sphinx'
,
has_doc
)]
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
distutils.ext/obidistutils/command/build_cexe.py
View file @
da7c0a0e
...
...
@@ -4,10 +4,11 @@ Created on 20 oct. 2012
@author: coissac
'''
from
obidistutils.command.build_ctools
import
build_ctools
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
):
...
...
@@ -38,7 +39,9 @@ class build_cexe(build_ctools):
self
.
set_undefined_options
(
'build_files'
,
(
'files'
,
'built_files'
))
self
.
executables
=
self
.
distribution
.
executables
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
)
...
...
@@ -70,4 +73,13 @@ class build_cexe(build_ctools):
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
)
distutils.ext/obidistutils/command/build_ctools.py
View file @
da7c0a0e
...
...
@@ -5,7 +5,7 @@ Created on 20 oct. 2012
'''
from
obidistutils.command
.build_exe
import
build_exe
from
.build_exe
import
build_exe
from
distutils
import
log
class
build_ctools
(
build_exe
):
...
...
@@ -38,7 +38,7 @@ class build_ctools(build_exe):
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
)]
...
...
@@ -50,10 +50,14 @@ class build_ctools(build_exe):
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
)
distutils.ext/obidistutils/command/build_exe.py
View file @
da7c0a0e
...
...
@@ -208,3 +208,4 @@ class build_exe(Command):
output_dir
=
self
.
build_cexe
,
debug
=
self
.
debug
)
distutils.ext/obidistutils/command/build_ext.py
View file @
da7c0a0e
...
...
@@ -14,6 +14,8 @@ from Cython.Compiler import Options as cython_options # @UnresolvedImport
from
distutils.errors
import
DistutilsSetupError
class
build_ext
(
ori_build_ext
):
def
modifyDocScripts
(
self
):
build_dir_file
=
open
(
"doc/sphinx/build_dir.txt"
,
"w"
)
print
(
self
.
build_lib
,
file
=
build_dir_file
)
...
...
@@ -86,10 +88,25 @@ class build_ext(ori_build_ext):
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
distutils.ext/obidistutils/command/build_files.py
View file @
da7c0a0e
...
...
@@ -28,6 +28,10 @@ class build_files(Command):
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
)
...
...
@@ -48,6 +52,12 @@ class build_files(Command):
log
.
info
(
"Done.
\n
"
)
def
has_ctools
(
self
):
return
self
.
distribution
.
has_ctools
()
sub_commands
=
[(
'build_ctools'
,
has_ctools
)]
+
\
Command
.
sub_commands
distutils.ext/obidistutils/command/build_sphinx.py
View file @
da7c0a0e
...
...
@@ -4,23 +4,24 @@ Created on 10 mars 2015
@author: coissac
'''
from
sphinx.setup_command
import
BuildDoc
as
ori_build_sphinx
# @UnresolvedImport
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
'''
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
)
\ No newline at end of file
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
\ No newline at end of file
distutils.ext/obidistutils/command/install.py
View file @
da7c0a0e
...
...
@@ -3,8 +3,13 @@ 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
#from setuptools.command.install import install as install_ori
class
install
(
install_ori
):
...
...
distutils.ext/obidistutils/command/install_scripts.py
View file @
da7c0a0e
...
...
@@ -3,6 +3,12 @@ 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
...
...
@@ -18,12 +24,10 @@ class install_scripts(ori_install_scripts):
def
install_public_link
(
self
):
self
.
mkpath
(
self
.
public_dir
)
for
file
in
self
.
get_outputs
():
if
self
.
dry_run
:
log
.
info
(
"changing mode of
%
s"
,
file
)
else
:
log
.
info
(
"exporting file
%
s ->
%
s"
,
file
,
os
.
path
.
join
(
self
.
public_dir
,
os
.
path
.
split
(
file
)[
1
]
))
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
]
)
...
...
distutils.ext/obidistutils/command/pidname.py
View file @
da7c0a0e
...
...
@@ -41,6 +41,10 @@ class pidname(build_exe):
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
():
...
...
distutils.ext/obidistutils/core.py
View file @
da7c0a0e
...
...
@@ -9,8 +9,11 @@ import os.path
import
glob
import
sys
# try:
# from setuptools.extension import Extension
# except ImportError:
# from distutils.extension import Extension
from
distutils.core
import
setup
as
ori_setup
from
distutils.extension
import
Extension
from
obidistutils.serenity.checkpackage
import
install_requirements
,
\
...
...
@@ -22,6 +25,7 @@ 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
):
...
...
@@ -81,8 +85,8 @@ def rootname(x):
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_sphinx
import
build_sphinx
from
obidistutils.command.build_ext
import
build_ext
from
obidistutils.command.build_ctools
import
build_ctools
from
obidistutils.command.build_files
import
build_files
...
...
@@ -92,8 +96,11 @@ def prepare_commands():
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
,
...
...
@@ -101,12 +108,22 @@ def prepare_commands():
'build_cexe'
:
build_cexe
,
'build_ext'
:
build_ext
,
'build_scripts'
:
build_scripts
,
'build_sphinx'
:
build_sphinx
,
'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
...
...
@@ -142,19 +159,21 @@ def setup(**attrs):
del
attrs
[
'requirements'
]
except
KeyError
:
pass
enforce_good_python
(
minversion
,
maxversion
,
fork
)
if
is_serenity
():
if
(
install_requirements
(
requirementfile
)):
rerun_with_anothe_python
(
sys
.
executable
,
minversion
,
maxversion
,
fork
)
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
)
try
:
check_requirements
(
requirementfile
)
except
RequirementError
as
e
:
log
.
error
(
e
)
sys
.
exit
(
1
)
if
'distclass'
not
in
attrs
:
attrs
[
'distclass'
]
=
Distribution
...
...
@@ -196,5 +215,12 @@ def setup(**attrs):
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
ori_setup
(
**
attrs
)
distutils.ext/obidistutils/dist.py
View file @
da7c0a0e
...
...
@@ -4,10 +4,12 @@ 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
# 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
):
...
...
@@ -37,7 +39,7 @@ class Distribution(ori_Distribution):
Uses the list of commands found and cache of command objects
created by 'get_command_obj()'.
"""
self
.
run_command
(
'littlebigman'
)
#
self.run_command('littlebigman')
ori_Distribution
.
run_commands
(
self
)
...
...
get_orgasm/get-orgasm.py
View file @
da7c0a0e
#!/usr/bin/env python2
from
fileinput
import
filename
from
platform
import
system
SOFT
=
"O
rg.A
sm"
SOFT
=
"O
RG.a
sm"
LIB
=
"orgasm"
PIP_MINVERSION
=
'1.5'
MODE
=
"pypi"
# or "svn"
...
...
@@ -37331,7 +37332,7 @@ def cleanModules():
def
pip_download_package
(
package
):
tmpdir
=
getTmpDir
()
args
=
[
'install'
]
args
=
[
'
pip
install'
]
if
'http_proxy'
in
os
.
environ
and
'https_proxy'
not
in
os
.
environ
:
os
.
environ
[
'https_proxy'
]
=
os
.
environ
[
'http_proxy'
]
...
...
@@ -37340,13 +37341,21 @@ def pip_download_package(package):
args
.
append
(
'--proxy=
%
s'
%
os
.
environ
[
'http_proxy'
])
args
.
append
(
'--download=
%
s'
%
tmpdir
)
args
.
append
(
'--index-url=https://pypi.python.org/simple/'
)
#
args.append('--index-url=https://pypi.python.org/simple/')
args
.
append
(
'--no-deps'
)
args
.
append
(
'-I'
)
args
.
append
(
'--pre'
)
args
.
append
(
'--no-cache-dir'
)
args
.
append
(
package
)
#print(args)
os
.
system
(
" "
.
join
(
args
))
pip
.
main
(
args
)
#pip.main(args)
#print("####>>>>>> DONE")
filename
=
glob
.
glob
(
os
.
path
.
join
(
tmpdir
,
"
%
s*"
%
package
))[
0
]
tar
=
tarfile
.
open
(
filename
)
...
...
@@ -37389,6 +37398,7 @@ def main():
elif
MODE
==
'pypi'
:
filename
=
pypidownload
()
sys
.
path
.
insert
(
0
,
filename
)
import
setup
# @UnresolvedImport
...
...
@@ -37396,6 +37406,7 @@ def main():
current
=
os
.
getcwd
()
virtualenvname
=
"
%
s/
%
s-
%
s"
%
(
current
,
setup
.
PACKAGE
,
setup
.
VERSION
)
# virtualenvname = "%s/%s-%s" % (current,setup.PACKAGE,'0.0.0a9')
os
.
chdir
(
filename
)
command
=
"
%
s setup.py --serenity --virtualenv='
%
s' install"
%
(
sys
.
executable
,
...
...
@@ -37412,6 +37423,40 @@ def main():
st
=
os
.
stat
(
activate
)
os
.
chmod
(
activate
,
st
.
st_mode
|
stat
.
S_IEXEC
)
st
=
os
.
stat
(
activate
)
os
.
chmod
(
activate
,
st
.
st_mode
|
stat
.
S_IEXEC
)
envactivate
=
open
(
os
.
path
.
join
(
virtualenvname
,
'bin'
,
'activate'
))
.
readlines
()
print
(
envactivate
)
line
=
0
try
:
while
True
:
if
envactivate
[
line
]
==
'PATH="$VIRTUAL_ENV/bin:$PATH"
\n
'
:
envactivate
[
line
]
=
'PATH="$VIRTUAL_ENV/export/bin:$PATH"
\n
'
envactivate
.
insert
(
line
+
2
,
'export MANPATH="$VIRTUAL_ENV/export/share/man:$MANPATH"
\n
'
)
line
+=
1
except
IndexError
:
pass
print
(
""
.
join
(
envactivate
),
file
=
open
(
os
.
path
.
join
(
virtualenvname
,
'bin'
,
'activate'
),
"w"
))
envactivate
=
open
(
os
.
path
.
join
(
virtualenvname
,
'bin'
,
'activate.csh'
))
.
readlines
()
line
=
0
try
:
while
True
:
if
envactivate
[
line
]
==
'setenv PATH "$VIRTUAL_ENV/bin:$PATH"
\n
'
:
envactivate
[
line
]
=
'setenv PATH "$VIRTUAL_ENV/export/bin:$PATH"
\n
'
envactivate
.
insert
(
line
+
1
,
'setenv MANPATH "$VIRTUAL_ENV/export/share/man:$MANPATH"
\n
'
)
line
+=
1
except
IndexError
:
pass
print
(
""
.
join
(
envactivate
),
file
=
open
(
os
.
path
.
join
(
virtualenvname
,
'bin'
,
'activate.csh'
),
"w"
))
shutil
.
rmtree
(
os
.
path
.
join
(
virtualenvname
,
'src'
),
ignore_errors
=
True
)
shutil
.
copytree
(
filename
,
os
.
path
.
join
(
virtualenvname
,
'src'
),
symlinks
=
True
)
python/orgasm/version.py
View file @
da7c0a0e
major
=
0
minor
=
'
0a7
'
serial
=
'
alpha
'
minor
=
'
1
'
serial
=
'
0a0
'
version
=
"
%2
d.
%
s
"
%
(
major
,
minor
)
version
=
"
%2
d.
%
s
.
%
s"
%
(
major
,
minor
,
serial
)
requirements.txt
View file @
da7c0a0e
--extra-index-url https://pypi.python.org/simple/
pip
>=7.1
Cython
>=0.2
2
Sphinx
>=1.3
.1
Cython
>=0.2
3
Sphinx
>=1.3
setup.py
View file @
da7c0a0e
#!/usr/bin/env python
import
sys
import
os
PACKAGE
=
"ORG.asm"
AUTHOR
=
'Eric Coissac'
...
...
@@ -12,7 +13,7 @@ DESCRIPTION ="A de novo assembler dedicated to organelle genome assembling",
SRC
=
'python'
CSRC
=
'src'
classifiers
=
[
'Development Status ::
1 - Planning
'
,
classifiers
=
[
'Development Status ::
3 - Alpha
'
,
'Environment :: Console'
,
'Intended Audience :: Science/Research'
,
'License :: Other/Proprietary License'
,
...
...
@@ -26,16 +27,19 @@ classifiers=['Development Status :: 1 - Planning',
PYTHONMIN
=
'3.4'
directory
=
os
.
path
.
dirname
(
os
.
path
.
realpath
(
__file__
))
sys
.
path
.
append
(
os
.
path
.
join
(
directory
,
'distutils.ext'
))
sys
.
path
.
append
(
os
.
path
.
join
(
directory
,
SRC
))
print
(
sys
.
path
)
VERSION
=
open
(
os
.
path
.
join
(
directory
,
'VERSION'
))
.
read
()
.
strip
()
sys
.
path
.
append
(
'distutils.ext'
)
sys
.
path
.
append
(
SRC
)
if
__name__
==
"__main__"
:
from
obidistutils.serenity
import
serenity_mode
from
obidistutils.serenity
import
getVersion
VERSION
=
getVersion
(
SRC
,
'orgasm'
,
'version'
)
serenity
=
serenity_mode
(
PACKAGE
,
VERSION
)
...
...
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