def _setup_env():
sysinfo = _get_ubuntu_info()
# dotfiles
run(
'[ ! -f ~/.tmux.conf ] && { '
'git clone -b minimal --single-branch --recursive '
'https://github.com/ichuan/dotfiles.git '
"&& echo 'y' | bash dotfiles/bootstrap.sh; }",
warn_only=True)
# UTC timezone
sudo('cp /usr/share/zoneinfo/UTC /etc/localtime', warn_only=True)
# limits.conf, max open files
_limits()
# rc.local after 15.04
# https://wiki.ubuntu.com/SystemdForUpstartUsers
if _V(sysinfo['release']) >= _V('15.04'):
_enable_rc_local()
# sysctl.conf
_sysctl()
# disable ubuntu upgrade check
sudo(
"sed -i 's/^Prompt.*/Prompt=never/' "
"/etc/update-manager/release-upgrades",
warn_only=True)
# douban pip config
run('mkdir -p ~/.pip', warn_only=True)
run(r'echo -e "[global]\nindex-url = https://pypi.douban.com/simple\n'
r'trusted-host = pypi.douban.com" > ~/.pip/pip.conf')
def _setup_mariadb():
'''
can be used to migrate mysql to mariadb
'''
if run('test -f /etc/mysql/conf.d/mariadb.cnf ', warn_only=True).succeeded:
print 'Already installed mariadb'
return
# user/password => root/root
sudo("debconf-set-selections <<< 'mariadb-server mysql-server/"
"root_password password root'")
sudo("debconf-set-selections <<< 'mariadb-server mysql-server/"
"root_password_again password root'")
# https://mariadb.com/kb/en/mariadb/installing-mariadb-deb-files/
sysinfo = _get_ubuntu_info()
key = '0xcbcb082a1bb943db'
if _V(sysinfo['release']) >= _V('16.04'):
key = '0xF1656F24C74CD1D8'
sudo('apt-key adv --recv-keys --keyserver hkp://keyserver.ubuntu.com:80 %s'
% key)
sudo('apt-get install -yq software-properties-common')
sudo("add-apt-repository -y 'deb http://ftp.osuosl.org/pub/mariadb/repo/"
"10.2/ubuntu %s main'" % sysinfo['codename'])
sudo('apt-get update -yq')
sudo('service mysql stop', warn_only=True)
sudo('apt-get install -yq mariadb-server libmysqld-dev', warn_only=True)
import json
import os
import sys
from distutils.version import LooseVersion as _V
from fabric.api import cd, env, get, lcd, local, prefix, run, sudo
from fabric.context_managers import shell_env
from version import VERSION
version = _V(VERSION)
env.hosts = ["systori.io"]
PROD_MEDIA_PATH = "/var/lib/systori/production"
PROD_MEDIA_FILE = "systori.media.tgz"
def prepare(service, branch):
"copy database and migrate"
settings = {
"HOST": "db",
"NAME": "systori_{}".format(service),
"USER": "******"
}
if service != "production":
local("dropdb -h {HOST} -U {USER} {NAME}".format(**settings))
local(
"createdb -T systori_production -h {HOST} -U {USER} {NAME}".format(
import sympy as sp
import re
from sympy.core.function import AppliedUndef as _AppliedUndef
from sympy.printing import StrPrinter as _StrPrinter
from sympy.printing.ccode import CCodePrinter as _CCodePrinter
from sympy.printing.latex import LatexPrinter as _LatexPrinter
from sympy.printing.latex import latex as _sympy_latex
from sympy.printing.precedence import precedence as _precedence
from modelparameters.utils import check_arg as _check_arg
from modelparameters.utils import scalars as _scalars
from distutils.version import LooseVersion as _V
_current_sympy_version = _V(sp.__version__)
# Check version for order arguments
if _current_sympy_version >= _V("0.7.2"):
_order = "none"
else:
_order = None
# A collection of language specific keywords
_cpp_keywords = ["auto", "const", "double", "float", "int", "short", "struct",
"break", "continue", "else", "for", "long", "signed", "switch",
"case", "default", "enum", "goto", "register", "sizeof", "typedef",
"char", "do", "extern", "if", "return", "static", "union", "while",
"asm", "dynamic_cast", "namespace", "reinterpret_cast", "try",
"bool", "explicit", "new", "static_cast", "typeid", "volatile",
"catch", "operator", "template", "typename",
def _default_params(exclude=None):
exclude = exclude or []
check_arg(exclude, list, itemtypes=str)
# Add not implemented parameters to excludes
exclude += ["max_terms", "parameter_contraction", "use_variables"]
# Build a dict with allowed parameters
params = {}
if "use_state_names" not in exclude:
# Use state names in code (compared to array with indices)
params["use_state_names"] = Param(
True,
description="Use state names in code "
"(compared to array with indices)",
)
if "use_parameter_names" not in exclude:
# Use parameter names in code (compared to array with indices)
params["use_parameter_names"] = Param(
True,
description="Use parameter names "
"in code (compared to array with indices)",
)
if "keep_intermediates" not in exclude:
# Keep all intermediates
params["keep_intermediates"] = Param(
True,
description="Keep intermediates in code",
)
if "use_variables" not in exclude:
# If True, code for altering variables are created
# FIXME: Not used
params["use_variables"] = Param(
False,
description="If True, code for altering variables are created",
)
if "parameter_contraction" not in exclude:
# Find sub expressions of only parameters and create a dummy parameter
# FIXME: Not used
params["parameter_contraction"] = Param(
False,
description="Find sub expressions of only parameters "
"and create a dummy parameter",
)
if "parameter_numerals" not in exclude:
# Exchange all parameters with their initial numerical values
params["parameter_numerals"] = Param(
False,
description="Exchange all parameters with their initial"
" numerical values",
)
if "max_terms" not in exclude:
# Split terms with more than max_terms into several evaluations
# FIXME: Not used
params["max_terms"] = ScalarParam(
5,
ge=2,
description="Split terms with more than max_terms "
"into several evaluations",
)
if "use_cse" not in exclude:
# Use sympy common sub expression simplifications,
# only when keep_intermediates is false
params["use_cse"] = Param(
False,
description="Use sympy common sub expression "
"simplifications, only when keep_intermediates is false",
)
if "generate_jacobian" not in exclude:
# Generate code for the computation of the jacobian
params["generate_jacobian"] = Param(
True,
description="Generate code for the computation of the jacobian",
)
if "transposed_jacobian" not in exclude:
# Generate code for the computation of the jacobian
params["transposed_jacobian"] = Param(
False,
description="The Jacobian is transposed",
)
if "generate_lu_factorization" not in exclude:
# Generate code for the factorization of the jacobian
params["generate_lu_factorization"] = Param(
True,
description="Generate code for the factorization of the jacobian",
)
if "generate_forward_backward_subst" not in exclude:
# Generate code for the forward backward substitution code
params["generate_forward_backward_subst"] = Param(
True,
description=
"Generate code for the forward backward substitution code",
)
if "generate_linearized_evaluation" not in exclude:
# Generate code for linearized evaluation
# For sympy versions lower than 0.7.2 linearized computation does not work
default_linearized_evaluation = _current_sympy_version > _V("0.7.2")
params["generate_linearized_evaluation"] = Param(
default_linearized_evaluation,
description="Generate code for linearized evaluation",
)
# Return the ParameterDict
return ParameterDict(**params)
from modelparameters.parameterdict import ScalarParam
from modelparameters.sympy import cse
from modelparameters.sympytools import iter_symbol_params_from_expr
from modelparameters.sympytools import sp
from modelparameters.utils import check_arg
from modelparameters.utils import check_kwarg
from ..model.ode import ODE
from ..model.odecomponent import Comment
from ..model.odecomponent import ODEComponent
# System imports
# Model parametrs imports
# Local gotran imports
_current_sympy_version = _V(sp.__version__)
_jacobian_pattern = re.compile("_([0-9]+)")
def _iszero(x):
"""Returns True if x is zero."""
x = sp.sympify(x)
return x.is_zero
def _default_params(exclude=None):
exclude = exclude or []
check_arg(exclude, list, itemtypes=str)
# Add not implemented parameters to excludes
exclude += ["max_terms", "parameter_contraction", "use_variables"]