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from fabric.api import *
import tarfile
import os
import zipfile
import fabfile_settings
env.hosts = []
if hasattr(fabfile_settings, 'osx_host'):
osx_host = fabfile_settings.osx_host
env.hosts.append(osx_host)
if '@' in osx_host:
osx_host = osx_host.split('@')[1]
if ':' in osx_host:
osx_host = osx_host.split(':')[0]
else:
osx_host = ''
if hasattr(fabfile_settings, 'linux_host'):
linux_host = fabfile_settings.linux_host
env.hosts.append(linux_host)
if '@' in linux_host:
linux_host = linux_host.split('@')[1]
if ':' in linux_host:
linux_host = linux_host.split(':')[0]
else:
linux_host = ''
if hasattr(fabfile_settings, 'run_tests'):
run_tests = fabfile_settings.run_tests
else:
run_tests=False
import sys, os
sys.path.append("site_scons")
from defaults import productVersion
pv = productVersion.replace(' ', '_')
class TarWrapper():
def __init__(self, name, prefix=None):
self.prefix = prefix
self.tar = tarfile.open(name, 'w:gz')
def add(self, name, arcname=None):
if self.prefix is not None:
if arcname is not None:
arcname = os.path.join(self.prefix, arcname)
else:
arcname = os.path.join(self.prefix, name)
self.tar.add(name, arcname)
print(('Packing file: ' + name if arcname is None else arcname))
def close(self):
self.tar.close()
def pack():
tar = start_src_tar()
if env.host == linux_host:
tar.add('apbs_libs/linux/apbslib.py','pdb2pka/apbslib.py')
tar.add('apbs_libs/linux/_apbslib.so','pdb2pka/_apbslib.so')
elif env.host == osx_host:
tar.add('apbs_libs/osx/apbslib.py','pdb2pka/apbslib.py')
tar.add('apbs_libs/osx/_apbslib.so','pdb2pka/_apbslib.so')
tar.close()
@runs_once
def pack_for_nbcr():
create_dist_folder()
tar = start_src_tar('pdb2pqr-src-nbcr-'+pv+'.tar.gz', 'pdb2pqr-src-'+pv)
tar.add('apbs_libs/linux/apbslib.py','pdb2pka/apbslib.py')
tar.add('apbs_libs/linux/_apbslib.so','pdb2pka/_apbslib.so')
tar.close()
local("move pdb2pqr-src-nbcr-"+pv+'.tar.gz dist_files\\')
def start_src_tar(name='pdb2pqr.tgz', prefix=None):
file_list = local('git ls-tree -r --name-only HEAD', capture=True).split('\n')
tar = TarWrapper(name, prefix)
for f in file_list:
tar.add(f)
return tar
@runs_once
def create_dist_folder():
with settings(warn_only=True):
local('mkdir dist_files')
@runs_once
def pack_for_ditro():
create_dist_folder()
tar = start_src_tar('pdb2pqr-src-'+pv+'.tar.gz', 'pdb2pqr-src-'+pv)
tar.close()
local('copy Changelog.md "dist_files\PDB2PQR-' + pv + '-ReleaseNotes.txt"')
local("move pdb2pqr-src-"+pv+'.tar.gz dist_files\\')
def deploy():
python = 'python3'
put('pdb2pqr.tgz', '~/')
with settings(warn_only=True):
run('rm -rf tmp')
run('mkdir tmp')
with cd('~/tmp/'):
run('tar -zxvf ~/pdb2pqr.tgz')
run('scons')
if run_tests:
run('scons -j 4 pdb2pka-test')
run('scons -j 4 complete-test')
def install_on_deployed():
python = 'python3'
with settings(warn_only=True):
with cd('~/www/pdb2pqr'):
run('rm -rf *')
with cd('~/tmp/'):
configopts = ''
if hasattr(fabfile_settings, 'APBS'):
configopts += ' APBS='+fabfile_settings.APBS
if hasattr(fabfile_settings, 'URL'):
configopts += ' URL='+fabfile_settings.URL
if hasattr(fabfile_settings, 'PREFIX'):
configopts += ' PREFIX='+fabfile_settings.PREFIX
if hasattr(fabfile_settings, 'OPAL'):
configopts += ' OPAL='+fabfile_settings.OPAL
if hasattr(fabfile_settings, 'APBS_OPAL'):
configopts += ' APBS_OPAL='+fabfile_settings.APBS_OPAL
# if True:
# configopts += ' URL=http://PT24098/d3k084/pdb2pqr_opal'
# configopts += ' PREFIX=/Users/d3k084/www/pdb2pqr_opal/'
# configopts += ' APBS_OPAL=http://nbcr-222.ucsd.edu/opal2/services/apbs_1.3'
# configopts += ' OPAL=http://nbcr-222.ucsd.edu/opal2/services/pdb2pqr_2.0.0'
# else:
# configopts += ' PREFIX=/Users/d3k084/www/pdb2pqr/'
# configopts += ' URL=http://PT24098/d3k084/pdb2pqr'
run('scons ' + configopts)
run('scons install ' + configopts)
def build_binary_from_deploy():
create_dist_folder()
with cd('~/tmp/'):
os_string = 'NOT_SET_FIX_ME'
if env.host == linux_host:
os_string = 'linux'
if env.host == osx_host:
os_string = 'osx'
run('pyinstaller pdb2pqr.spec')
name = 'pdb2pqr-' + os_string + '-bin64-' + pv
run('mv dist/pdb2pqr dist/' + name)
with cd('dist/'):
run('tar -zcvf ' + name + '.tar.gz ' + name)
if run_tests:
with cd(name):
run('./pdb2pqr --ff=parse --verbose --ligand=examples/ligands/LIG_1ABF.mol2 1ABF 1ABF.pqr')
run('./pdb2pqr --with-ph=7.0 --ph-calc-method=pdb2pka --ff=parse --verbose 1a1p 1a1p.pqr')
get("~/tmp/dist/*.tar.gz","dist_files/")
def linux_bin_cross_platform_test():
'''
Push the linux bin to a host and test it.
'''
os_string = 'linux'
name = 'pdb2pqr-' + os_string + '-bin64-' + pv
put('dist_files/' + name + '.tar.gz', '~/')
run('tar -zxvf ~/' + name + '.tar.gz')
with cd(name):
run('./pdb2pqr --ff=parse --verbose --ligand=examples/ligands/LIG_1ABF.mol2 1ABF 1ABF.pqr')
run('./pdb2pqr --with-ph=7.0 --ph-calc-method=pdb2pka --ff=parse --verbose 1a1p 1a1p.pqr')
run('rm -rf '+name)
@runs_once
def build_windows():
local(r'copy apbs_libs\windows\* pdb2pka\\')
local(r'python3 scons\scons.py -c')
local(r'python3 scons\scons.py')
if run_tests:
local(r'python3 scons\scons.py -j 4 pdb2pka-test')
local(r'python3 scons\scons.py -j 7 complete-test')
build_windows_binary()
if run_tests:
test_windows_binary()
@runs_once
def test_windows_binary():
name = 'pdb2pqr-windows-bin64-' + pv
with lcd(r'dist\\' + name):
local(r'pdb2pqr --ff=parse --verbose --ligand=examples\ligands\LIG_1ABF.mol2 1ABF 1ABF.pqr')
local('pdb2pqr --with-ph=7.0 --ph-calc-method=pdb2pka --ff=parse --verbose 1a1p 1a1p.pqr')
@runs_once
def build_windows_binary():
with settings(warn_only=True):
local('del /Q /F dist')
local('pyinstaller pdb2pqr.spec')
name = 'pdb2pqr-windows-bin64-' + pv
local(r'move /Y dist\pdb2pqr dist\\' + name)
zip_file = zipfile.ZipFile(name + '.zip', 'w', zipfile.ZIP_DEFLATED)
for root, _, files in os.walk(r'dist\\'+name):
new_root = root.split('/', 1)[-1]
print(root)
for f in files:
zip_file_path = os.path.join(new_root,f)
real_file_path = os.path.join(root,f)
zip_file.write(real_file_path, zip_file_path)
print('Zipping ' + zip_file_path)
zip_file.close()
create_dist_folder()
local('move /Y ' + name + '.zip' + r' dist_files\\' + name + '.zip')
def build_all_tarballs():
pack_for_ditro()
pack_for_nbcr()
def build_all_binaries():
pack()
deploy()
build_binary_from_deploy()
build_windows()
def deploy_and_install():
pack()
deploy()
install_on_deployed()
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