# **************************************************************************
# *
# * Authors: J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se) [1]
# * David Maluenda Niubo (dmaluenda@cnb.csic.es) [2]
# *
# * [1] SciLifeLab, Stockholm University
# * [2] Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# *
# * This program is free software; you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation; either version 2 of the License, or
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307 USA
# *
# * All comments concerning this program package may be sent to the
# * e-mail address 'scipion@cnb.csic.es'
# *
# **************************************************************************
import json
import subprocess
from datetime import datetime
from pyworkflow import Config
import pwem
import pyworkflow.utils as pwutils
from .base import *
from .constants import XMIPP_HOME, XMIPP_URL, XMIPP_DLTK_NAME
_logo = "xmipp_logo.png"
_references = ['delaRosaTrevin2013', 'Sorzano2013']
_currentBinVersion = '3.23.03.0'
# This will allow scipion to detect the plugin version and print it in the log.
__version__ = _currentBinVersion[2:] + ".0" # Set this to ".0" on each xmipp binary release, otherwise increase it --> ".1", ".2", ...
[docs]class Plugin(pwem.Plugin):
_homeVar = XMIPP_HOME
_pathVars = [XMIPP_HOME]
_supportedVersions = []
_url = XMIPP_URL
_condaRootPath = None
@classmethod
def _defineVariables(cls):
cls._addVar(XMIPP_HOME, pwem.Config.XMIPP_HOME)
[docs] @classmethod
def getEnviron(cls, xmippFirst=True):
""" Create the needed environment for Xmipp programs. """
environ = pwutils.Environ(os.environ)
pos = pwutils.Environ.BEGIN if xmippFirst else pwutils.Environ.END
environ.update({
'PATH': pwem.Config.CUDA_BIN,
'LD_LIBRARY_PATH': pwem.Config.CUDA_LIB
}, position=pwutils.Environ.END)
if os.path.isfile(getXmippPath('xmippEnv.json')):
with open(getXmippPath('xmippEnv.json'), 'r') as f:
compilationEnv = json.load(f)
environ.update(compilationEnv, position=pos)
environ.update({
'PATH': getXmippPath('bin'),
'LD_LIBRARY_PATH': getXmippPath('lib'),
'PYTHONPATH': getXmippPath('pylib')
}, position=pos)
environ['XMIPP_HOME'] = getXmippPath()
# Add path to python lib folder
environ.addLibrary(Config.getPythonLibFolder())
return environ
#TODO: Standardize to just: runProgram
[docs] @classmethod
def runXmippProgram(cls, program, args=""):
""" Internal shortcut function to launch a Xmipp program. """
pwutils.runJob(None, program, args, env=cls.getEnviron())
[docs] @classmethod
def getMatlabEnviron(cls, *toolPaths):
""" Return an Environment prepared for launching Matlab
scripts using the Xmipp binding.
"""
env = pwutils.Environ(os.environ)
env.set('PATH', os.environ.get('MATLAB_BINDIR', ''), pwutils.Environ.BEGIN)
env.set('LD_LIBRARY_PATH', os.environ.get('MATLAB_LIBDIR', ''),
pwutils.Environ.BEGIN)
for toolpath in toolPaths:
env.set('MATLABPATH', toolpath, pwutils.Environ.BEGIN)
env.set('MATLABPATH', os.path.join(os.environ[XMIPP_HOME],
'libraries', 'bindings', 'matlab'),
pwutils.Environ.BEGIN)
return env
[docs] @classmethod
def defineBinaries(cls, env):
""" Define the Xmipp binaries/source available tgz.
In addition, define extra software needed by some Xmipp methods
such as deepLearningToolkit.
Scipion-defined software can be used as dependencies
by using its name as string.
"""
## XMIPP SOFTWARE ##
xmippDeps = [] # Deps should be at requirements.txt (old: scons, joblib, scikit_learn)
# Installation vars for commands formating
verToken = getXmippPath('v%s' % _currentBinVersion)
confToken = getXmippPath("xmipp.conf")
installVars = {'installedToken': "installation_finished",
'bindingsToken': "bindings_linked",
'verToken': verToken,
'nProcessors': env.getProcessors(),
'xmippHome': getXmippPath(),
'bindingsSrc': getXmippPath('bindings', 'python'),
'bindingsDst': Config.getBindingsFolder(),
'xmippLib': getXmippPath('lib', 'libXmipp.so'),
'coreLib': getXmippPath('lib', 'libXmippCore.so'),
'libsDst': Config.getLibFolder(),
'confToken': confToken,
'strPlaceHolder': '%s', # to be replaced in the future
'currVersion': _currentBinVersion
}
## Installation commands (removing bindingsToken)
installCmd = ("cd {cwd} && {configCmd} && {compileCmd} N={nProcessors:d} && "
"ln -srfn build {xmippHome} && cd - && "
"touch {installedToken} && rm {bindingsToken} 2> /dev/null")
installTgt = [getXmippPath('bin', 'xmipp_reconstruct_significant'),
getXmippPath("lib/libXmippJNI.so"),
installVars['installedToken']]
## Linking bindings (removing installationToken)
bindingsAndLibsCmd = ("find {bindingsSrc} -maxdepth 1 -mindepth 1 "
r"! -name __pycache__ -exec ln -srfn {{}} {bindingsDst} \; && "
"ln -srfn {coreLib} {libsDst} && "
"touch {bindingsToken} && "
"rm {installedToken} 2> /dev/null")
bindingsAndLibsTgt = [os.path.join(Config.getBindingsFolder(), 'xmipp_base.py'),
os.path.join(Config.getBindingsFolder(), 'xmippLib.so'),
os.path.join(Config.getLibFolder(), 'libXmipp.so'),
installVars['bindingsToken']]
sourceTgt = [getXmippPath('xmipp.bashrc')] # Target for xmippSrc and xmippDev
## Allowing xmippDev if devel mode detected
# plugin = scipion-em-xmipp <-- xmipp3 <-- __init__.py
pluginDir = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
# bundle = xmipp-bundle <- src <- scipion-em-xmipp
bundleDir = os.path.dirname(os.path.dirname(pluginDir))
isPypiDev = os.path.isfile(os.path.join(pluginDir, 'setup.py'))
isXmippBu = (os.path.isdir(os.path.join(bundleDir, 'src')) and
os.path.isfile(os.path.join(bundleDir, 'xmipp')))
develMode = isPypiDev and isXmippBu
if develMode:
env.addPackage('xmippDev', tar='void.tgz',
commands=[(installCmd.format(**installVars,
cwd=bundleDir,
configCmd='pwd',
compileCmd='./xmipp all'),
installTgt+sourceTgt),
(bindingsAndLibsCmd.format(**installVars),
bindingsAndLibsTgt)],
deps=xmippDeps, default=False)
avoidConfig = os.environ.get('XMIPP_NOCONFIG', 'False') == 'True'
alreadyCompiled = os.path.isfile(getXmippPath('v' + _currentBinVersion)) # compilation token (see the xmipp script)
configSrc = ('./xmipp check_config' if avoidConfig
else './xmipp config noAsk && ./xmipp check_config')
env.addPackage('xmippSrc', version=_currentBinVersion,
# adding 'v' before version to fix a package target (post-link)
tar='xmippSrc-v' + _currentBinVersion + '.tgz',
commands=[(installCmd.format(**installVars, cwd='.',
configCmd=configSrc,
compileCmd='./xmipp compileAndInstall'),
installTgt + sourceTgt),
(bindingsAndLibsCmd.format(**installVars),
bindingsAndLibsTgt)],
deps=xmippDeps, default=not (develMode or alreadyCompiled))
## EXTRA PACKAGES ##
installDeepLearningToolkit(cls, env)