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bis-aria
ariaec
Commits
ec11aa34
Commit
ec11aa34
authored
May 31, 2017
by
Fabrice ALLAIN
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Cleaner version of setuptools installation
parent
57f42c78
Changes
7
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7 changed files
with
109 additions
and
94 deletions
+109
-94
.svnignore
.svnignore
+0
-9
MANIFEST.in
MANIFEST.in
+2
-1
ariaec/pdbstat.py
ariaec/pdbstat.py
+3
-0
setup.cfg
setup.cfg
+1
-1
setup.py
setup.py
+24
-71
svnignore.txt
svnignore.txt
+0
-9
version.py
version.py
+79
-3
No files found.
.svnignore
deleted
100644 → 0
View file @
57f42c78
.venv
.idea
.eggs
.git
*.pyc
data
docs/_static
docs/_templates
docs/_builds
\ No newline at end of file
MANIFEST.in
View file @
ec11aa34
graft ariaec/conf
graft ariaec/templates
graft ariaec/data
graft docs
\ No newline at end of file
graft docs
prune examples*
ariaec/pdbstat.py
View file @
ec11aa34
...
...
@@ -273,6 +273,9 @@ class PDBStat(object):
# pool = ProcessingPool(nodes=ncpus)
# iteresults = pool.imap(self.subdist, [dists]*len(groups), groups)
# interdists = []
# TODO: use sql to select subdataframes in order to work with heavy
# data http://pythondata.com/working-large-csv-files-python/
tqdm_out
=
TqdmToLogger
(
LOG
,
level
=
logging
.
INFO
)
interdists
=
[
self
.
subdist
(
dists
,
group
)
for
group
in
tqdm
(
groups
,
file
=
tqdm_out
,
...
...
setup.cfg
View file @
ec11aa34
...
...
@@ -4,4 +4,4 @@
# will need to generate wheels for each Python version that you support.
universal=1
[egg_info]
tag_build = .dev
#
tag_build = .dev
setup.py
View file @
ec11aa34
...
...
@@ -6,13 +6,14 @@ from __future__ import absolute_import, division, print_function
import
os
import
sys
import
re
import
textwrap
import
subprocess
import
pkg_resources
from
version
import
get_version
from
setuptools
import
Command
,
find_packages
,
setup
DOCLINES
=
__doc__
.
split
(
"
\n
"
)
DOCLINES
=
re
.
sub
(
"
\n
"
,
" "
,
re
.
sub
(
" {2,}"
,
""
,
__doc__
)
)
CLASSIFIERS
=
"""
\
Development Status :: 3 - Alpha
...
...
@@ -35,13 +36,6 @@ Operating System :: Unix
Operating System :: MacOS
"""
MAJOR
=
0
MINOR
=
1
MICRO
=
0
ISRELEASED
=
False
# TODO: get version tag in ariabase.py ?
VERSION
=
'%d.%d.%d'
%
(
MAJOR
,
MINOR
,
MICRO
)
# Compatibility checks
# TODO: Change this line after python 3 compatibility done !
...
...
@@ -90,61 +84,16 @@ def is_installed(requirement):
pkg_resources
.
require
(
requirement
)
except
pkg_resources
.
ResolutionError
:
return
False
else
:
finally
:
return
True
def
git_version
():
"""
Return the git revision as a string
"""
def
_minimal_ext_cmd
(
cmd
):
# construct minimal environment
env
=
{}
for
k
in
[
'SYSTEMROOT'
,
'PATH'
]:
v
=
os
.
environ
.
get
(
k
)
if
v
is
not
None
:
env
[
k
]
=
v
# LANGUAGE is used on win32
env
[
'LANGUAGE'
]
=
'C'
env
[
'LANG'
]
=
'C'
env
[
'LC_ALL'
]
=
'C'
return
subprocess
.
Popen
(
cmd
,
stdout
=
subprocess
.
PIPE
,
env
=
env
).
communicate
()[
0
]
try
:
out
=
_minimal_ext_cmd
([
'git'
,
'rev-parse'
,
'HEAD'
])
git_revision
=
out
.
strip
().
decode
(
'ascii'
)
except
OSError
:
git_revision
=
"Unknown"
return
git_revision
def
get_version_info
():
"""
Return full version number with git revision string
"""
# Adding the git rev number needs to be done inside write_version_py(),
# otherwise the import of aria.version messes up the build under Python 3.
full_version
=
VERSION
if
os
.
path
.
exists
(
'.git'
):
git_revision
=
git_version
()
else
:
git_revision
=
"Unknown"
if
not
ISRELEASED
:
full_version
+=
'.dev0+'
+
git_revision
[:
7
]
return
full_version
,
git_revision
def
setup_package
():
"""Main function"""
metadata
=
dict
(
name
=
'ariaec'
,
version
=
get_version
_info
()[
0
]
,
version
=
get_version
()
,
maintainer
=
"ARIA Developers"
,
# maintainer_email="bardiaux@pasteur.fr",
author
=
"Allain Fabrice"
,
...
...
@@ -197,24 +146,28 @@ def setup_package():
# TODO: solution to enable zip_safe
zip_safe
=
False
,
package_dir
=
{
'ariaec'
:
'./ariaec'
},
# Doesn't works if we use package_dir with include_package_data
# package_dir={'ariaec': './ariaec'},
packages
=
find_packages
(),
packages
=
find_packages
(
exclude
=
(
"examples"
,)
),
# Install any data files found in the package
include_package_data
=
True
,
package_data
=
{
# If any package contains these files, include them
''
:
[
'*.txt'
,
'*.rst'
],
# And include files found in the 'ariaec' package, too:
'ariaec'
:
[
'conf/*'
,
'templates/*'
,
'data/cullpdb/160427/*'
,
'data/cullpdb/170315/*'
'data/*'
,
],
},
# Using MANIFEST file, we do not need package_data which doesn't work
# for all kind of building process ...
# package_data={
# # If any package contains these files, include them
# '': ['*.txt', '*.rst', '*.p', '*.pro'],
# # And include files found in the 'ariaec' package, too:
# 'ariaec': ['conf/*',
# 'templates/*',
# 'data/pdbdists/*'
# 'data/cullpdb/160427/*',
# 'data/cullpdb/170315/*'
# 'data/*',
# ],
# },
# If we want to include non data files (documentation, examples, ..)
# in the sys.prefix directory. The package can't access these files !
...
...
@@ -231,7 +184,7 @@ Error: numpy needs to be installed first. You can install it via:
$ pip install numpy
"""
),
file
=
sys
.
stderr
)
exit
(
1
)
sys
.
exit
(
1
)
if
not
is_installed
(
'matplotlib'
):
...
...
@@ -240,7 +193,7 @@ Error: matplotlib needs to be installed first. You can install it via:
$ pip install matplotlib
"""
),
file
=
sys
.
stderr
)
exit
(
1
)
sys
.
exit
(
1
)
if
__name__
==
'__main__'
:
...
...
svnignore.txt
deleted
100644 → 0
View file @
57f42c78
.venv
.idea
.eggs
.git
*.pyc
data
docs/_static
docs/_templates
docs/_builds
\ No newline at end of file
version.py
View file @
ec11aa34
# coding=utf-8
# This program is placed into the public domain.
"""
VERSION
Gets the current version number.
If in a git repository, it is the current git tag.
Otherwise it is the one contained in the PKG-INFO file.
To use this script, simply import it in your setup.py file
and use the results of get_version() as your package version:
from version import *
setup(
...
version=get_version(),
...
)
"""
# Do not edit this file, pipeline versioning is governed by git tags
__version__
=
'v0.1.0'
__all__
=
'get_version'
from
os.path
import
dirname
,
isdir
,
join
import
sys
import
os
import
re
import
subprocess
version_re
=
re
.
compile
(
'^Version: (.+)$'
,
re
.
M
)
def
get_version
():
"""
Returns
-------
"""
d
=
dirname
(
__file__
)
version
=
''
dirty
=
''
if
isdir
(
join
(
d
,
'.git'
)):
# Get the version using "git describe".
cmd
=
'git describe --tags'
.
split
()
try
:
version
=
subprocess
.
check_output
(
cmd
).
decode
().
strip
()
except
subprocess
.
CalledProcessError
:
print
(
'Unable to get version number from git tags'
)
sys
.
exit
(
1
)
# PEP 386 compatibility
if
'-'
in
version
:
version
=
'.post'
.
join
(
version
.
split
(
'-'
)[:
2
])
# Don't declare a version "dirty" merely because a time stamp has
# changed. If it is dirty, append a ".dev1" suffix to indicate a
# development revision after the release.
with
open
(
os
.
devnull
,
'w'
)
as
fd_devnull
:
subprocess
.
call
([
'git'
,
'status'
],
stdout
=
fd_devnull
,
stderr
=
fd_devnull
)
cmd
=
'git diff-index --name-only HEAD'
.
split
()
try
:
dirty
=
subprocess
.
check_output
(
cmd
).
decode
().
strip
()
except
subprocess
.
CalledProcessError
:
print
(
'Unable to get git index status'
)
sys
.
exit
(
1
)
if
dirty
!=
''
:
version
+=
'.dev1'
else
:
# Extract the version from the PKG-INFO file.
with
open
(
join
(
d
,
'PKG-INFO'
))
as
f
:
version
=
version_re
.
search
(
f
.
read
()).
group
(
1
)
return
version
if
__name__
==
'__main__'
:
print
(
get_version
())
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