def build_venv(name):
old_build_name = env.get('build_name')
env['build_name'] = name
build_dir = "/code/deploy/builds/%s" % name
with cd("%s" % build_dir):
docker_exec("[ -f bin/pip ] || virtualenv . --never-download")
with path(os.path.join(build_dir, 'bin'), behavior='prepend'):
yield
env['build_name'] = old_build_name
def build_venv(name):
old_build_name = env.get('build_name')
env['build_name'] = name
build_dir = "/code/deploy/builds/%s" % name
with cd("%s" % build_dir):
docker_exec("[ -f bin/pip ] || virtualenv . --never-download")
with path(os.path.join(build_dir, 'bin'), behavior='prepend'):
yield
env['build_name'] = old_build_name
def perl():
if not dir_exists("~/.plenv"):
run("git clone https://github.com/tokuhirom/plenv.git ~/.plenv/")
run("git clone https://github.com/tokuhirom/Perl-Build.git ~/.plenv/plugins/perl-build/")
with path("~/.plenv/bin:~/.plenv/shims"):
run("eval '$(plenv init -)'")
run("plenv install 5.18.1")
run("plenv global 5.18.1")
run("PLENV_INSTALL_CPANM='-v' plenv install-cpanm")
run("cpanm --self-upgrade")
def install_data(config_source):
"""Main entry point for installing useful biological data.
"""
_check_version()
# Append a potentially custom system install path to PATH so tools are found
with path(os.path.join(env.system_install, 'bin')):
genomes, genome_indexes, config = _get_genomes(config_source)
genome_indexes += [x for x in DEFAULT_GENOME_INDEXES if x not in genome_indexes]
_data_ngs_genomes(genomes, genome_indexes)
_install_additional_data(genomes, genome_indexes, config)
def install_data(config_source):
"""Main entry point for installing useful biological data.
"""
_check_version()
# Append a potentially custom system install path to PATH so tools are found
with path(os.path.join(env.system_install, 'bin')):
genomes, genome_indexes, config = _get_genomes(config_source)
genome_indexes += DEFAULT_GENOME_INDEXES
_data_ngs_genomes(genomes, genome_indexes)
_install_additional_data(genomes, genome_indexes, config)
def deploy_web():
version = build_web()
tarball = "stiny-%s.tar.gz" % version
fab.put("dist/" + tarball)
fab.sudo("if [ ! -e {0} ]; then virtualenv {0}; fi"
.format(CONSTANTS['venv']))
with path(CONSTANTS['venv'] + '/bin', behavior='prepend'):
fab.sudo("yes | pip uninstall stiny || true")
fab.sudo("pip install pastescript")
fab.sudo("pip install %s" % tarball)
_render_put('prod.ini.tmpl', '/etc/emperor/stiny.ini', use_sudo=True)
def install_data(config_source=CONFIG_FILE, do_setup_environment=True):
"""Main entry point for installing useful biological data.
"""
_check_version()
if do_setup_environment:
setup_environment()
# Append a potentially custom system install path to PATH so tools are found
with path(os.path.join(env.system_install, 'bin')):
genomes, genome_indexes, config = _get_genomes(config_source)
_data_ngs_genomes(genomes, genome_indexes + DEFAULT_GENOME_INDEXES)
_install_additional_data(genomes, config)
def local_makemessages():
"""第一次自己在locale下手动建立需要翻译的目录"""
with path(
'/usr/local/opt/gettext/bin'): # OS X下brew install gettext 需手动path
local_workon(
'python manage.py makemessages -l en --ignore={}/templates/registration/* --no-wrap'
.format(env.project_name))
# local_workon('python manage.py makemessages -d djangojs --no-wrap')
puts(green('完成, 请用rosetta翻译英文然后执行tx_sync'))
def build_rpi_gpio_wheel():
gpio_wheel = 'RPi.GPIO-0.6.2-cp27-cp27mu-linux_armv6l.whl'
fab.local('mkdir -p pex_wheels')
# Generate the RPI.GPIO wheel on the raspberry pi
fab.run('rm -rf /tmp/gpiobuild')
fab.run('mkdir -p /tmp/gpiobuild')
with fab.cd('/tmp/gpiobuild'):
fab.run('virtualenv venv')
with path('/tmp/gpiobuild/venv/bin', behavior='prepend'):
fab.run('pip install wheel')
fab.run('pip wheel RPi.GPIO==0.6.2 --wheel-dir=/tmp/gpiobuild')
fab.get(gpio_wheel, os.path.join('pex_wheels', gpio_wheel))
fab.run('rm -rf /tmp/gpiobuild')
def run(self, dest=None, verbose='n', **options):
self.options.update(options)
if dest is not None:
self.dest = dest
verbose = verbose.lower().strip().startswith('y')
files = self.get_files()
if verbose is True:
print(green('Minifying files:'))
for filename in files:
print(' %s' % filename)
node_path = os.path.join(os.getcwd(), 'node_modules', '.bin')
with path(node_path):
self.minify(files, self.dest)
def run(self, dest=None, verbose='n', **options):
self.options.update(options)
if dest is not None:
self.dest = dest
verbose = verbose.lower().strip().startswith('y')
files = self.get_files()
if verbose is True:
print(green('Minifying files:'))
for filename in files:
print(' %s' % filename)
node_path = os.path.join(os.getcwd(), 'node_modules', '.bin')
with path(node_path):
self.minify(files, self.dest)
def run(self):
with settings(warn_only=True):
if self.extra_path() != "":
with path(self.extra_path()):
with shell_env(**self.shell_env()):
self.pre_action()
result = self.run_command()
self.post_action(result)
else:
with shell_env(**self.env):
self.pre_action()
result = self.run_command()
self.post_action(result)
return result
def deploy():
""" Deploy the website """
version = bundle()
tarball = "stevetags-%s.tar.gz" % version
fab.put("dist/" + tarball)
with path(CONSTANTS['venv'] + '/bin', behavior='prepend'):
fab.sudo("yes | pip uninstall stevetags || true")
fab.sudo("pip install %s" % tarball)
fab.sudo('st-deploy /var/nginx/stevetags/%s' %
CONSTANTS['asset_prefix'])
_render_put('etc/stevetags.ini', '/etc/emperor/stevetags.ini',
use_sudo=True)
fab.run("rm " + tarball)
print green("Deployed stevetags %s" % version)
def install_data(config_source, approaches=None):
"""Main entry point for installing useful biological data.
"""
PREP_FNS = {"s3": _download_s3_index,
"raw": _prep_raw_index}
if approaches is None: approaches = ["raw"]
ready_approaches = []
for approach in approaches:
ready_approaches.append((approach, PREP_FNS[approach]))
_check_version()
# Append a potentially custom system install path to PATH so tools are found
with path(os.path.join(env.system_install, 'bin')):
genomes, genome_indexes, config = _get_genomes(config_source)
genome_indexes += [x for x in DEFAULT_GENOME_INDEXES if x not in genome_indexes]
_prep_genomes(env, genomes, genome_indexes, ready_approaches)
_install_additional_data(genomes, genome_indexes, config)
def deploy():
global commitMsg
commitMsg = raw_input("请输入此次commit: ")
gitCommit()
with cd(workDir):
with path(PATH):
with prefix("export GOPATH=/root/dev/gopath"):
run("git reset --hard")
run("go get github.com/smartwalle/alipay")
run("go get github.com/satori/go.uuid")
run("git pull")
run("go build")
run("cp /root/dev/gopath/src/memplus.conf %s/conf/app.conf" %
workDir)
run("supervisorctl restart memoryplus")
def install_data(config_source, approaches=None):
"""Main entry point for installing useful biological data.
"""
PREP_FNS = {"s3": _download_s3_index,
"raw": _prep_raw_index}
if approaches is None: approaches = ["raw"]
ready_approaches = []
for approach in approaches:
ready_approaches.append((approach, PREP_FNS[approach]))
_check_version()
# Append a potentially custom system install path to PATH so tools are found
with path(os.path.join(env.system_install, 'bin')):
genomes, genome_indexes, config = _get_genomes(config_source)
genome_indexes += [x for x in DEFAULT_GENOME_INDEXES if x not in genome_indexes]
_prep_genomes(env, genomes, genome_indexes, ready_approaches)
_install_additional_data(genomes, genome_indexes, config)
def source_to_binary(source_file):
"""Upload source code, build it, and return the path to the binary."""
sandbox_dir = '/home/{}'.format(CABAL_USER)
[remote_path] = list(put(source_file, '/tmp/'))
with cd(sandbox_dir):
with settings(sudo_user=CABAL_USER,
sudo_prefix="sudo -S -i -p '{}'".format(
env.sudo_prompt)):
with path(CABAL_PATH, behavior='prepend'):
deps = upload_source_deps(SOURCE_DEPENDENCIES, sandbox_dir)
sudo('tar -xf {}'.format(remote_path))
sudo('cabal sandbox init --sandbox .')
for src_dir in deps:
sudo('cabal sandbox add-source {}'.format(src_dir))
src_dir = tarball_directory(source_file)
with cd(src_dir):
sudo('cabal sandbox init --sandbox {}'.format(sandbox_dir))
sudo('cabal install --dependencies-only')
sudo('cabal build')
return '/home/{}/{}'.format(CABAL_USER, src_dir)
def manage(cmd, options=""):
with path(env.bin_dir, "prepend"):
run("%s/bin/python ~/webapps/%s/src/manage.py %s --settings=%s %s" % (env.virtualenv, env.app_name,cmd,env.settings_module, options))
def test_use_of_path_appends_by_default(self):
"""
'with path' appends by default
"""
with path('foo'):
eq_(self.via_local(), self.real + ":foo")
def test_use_of_path_appends_by_default(self):
"""
'with path' appends by default
"""
with path('foo'):
eq_(self.via_local(), self.real + ":foo")
def workon(settings_module='noripyt.settings.production'):
with cd(str(PROJECT_PATH)):
with path(str(VIRTUALENV_PATH / 'bin'), behavior='prepend'):
with shell_env(DJANGO_SETTINGS_MODULE=settings_module):
yield
def wrapped():
node_path = os.path.join(os.getcwd(), 'node_modules', '.bin')
with path(node_path):
orig()
def workon_dezede(settings_module='dezede.settings.prod'):
set_env()
with cd(f'{env.project_path}'):
with path(f"{env.virtual_env / 'bin'}", behavior='prepend'):
with shell_env(DJANGO_SETTINGS_MODULE=settings_module):
yield
def run(self, cmd):
wrapped = "junest -f {}".format(cmd)
with path(self.junest_bin):
run(wrapped)
def local_makemessages():
"""第一次自己在locale下手动建立需要翻译的目录"""
with path('/usr/local/opt/gettext/bin'): # OS X下brew install gettext 需手动path
local_workon('python manage.py makemessages -l en --ignore={}/templates/registration/* --no-wrap'.format(env.project_name))
# local_workon('python manage.py makemessages -d djangojs --no-wrap')
puts(green('完成, 请用rosetta翻译英文然后执行tx_sync'))
def wrapped():
node_path = os.path.join(os.getcwd(), 'node_modules', '.bin')
with path(node_path):
orig()
def workon_dezede(settings_module='dezede.settings.prod'):
set_env()
with cd(f'{env.project_path}'):
with path(f"{env.virtual_env / 'bin'}", behavior='prepend'):
with shell_env(DJANGO_SETTINGS_MODULE=settings_module):
yield
def local_compilemessages():
"""编译语言文件"""
with path('/usr/local/opt/gettext/bin'):
local_workon('python manage.py compilemessages')
def local_compilemessages():
"""编译语言文件"""
with path('/usr/local/opt/gettext/bin'):
local_workon('python manage.py compilemessages')
def _update_nodeenv(venv, nodeenv, source_path):
if not exists(nodeenv + "/bin/npm"):
sudo("%s/bin/nodeenv %s" % (venv, nodeenv), user="******")
with path(nodeenv + "/bin", "prepend"):
sudo("npm -C %s install --no-progress --production" % (source_path), user="******")
def _update_bundles(venv, nodeenv, source_path):
with path("%s/bin:%s/bin" % (nodeenv, venv), "prepend"):
sudo("npm -C %s run build" % (source_path), user="******")
