File bootstrap_eb.py of Package easybuild
#!/usr/bin/env python
##
# Copyright 2013-2021 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (FWO) (http://www.fwo.be/en)
# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
#
# https://github.com/easybuilders/easybuild
#
# EasyBuild 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 v2.
#
# EasyBuild 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 EasyBuild. If not, see <http://www.gnu.org/licenses/>.
##
"""
Bootstrap script for EasyBuild
Installs distribute with included (patched) distribute_setup.py script to obtain easy_install,
and then performs a staged install of EasyBuild:
* stage 0: install setuptools (which provides easy_install), unless already available
* stage 1: install EasyBuild with easy_install to a temporary directory
* stage 2: install EasyBuild with EasyBuild from stage 1 to specified install directory
Authors: Kenneth Hoste (UGent), Stijn Deweirdt (UGent), Ward Poelmans (UGent)
License: GPLv2
inspired by https://bitbucket.org/pdubroy/pip/raw/tip/getpip.py
(via http://dubroy.com/blog/so-you-want-to-install-a-python-package/)
"""
import codecs
import copy
import glob
import os
import re
import shutil
import site
import sys
import tempfile
import traceback
from distutils.version import LooseVersion
from hashlib import md5
from platform import python_version
IS_PY3 = sys.version_info[0] == 3
if not IS_PY3:
import urllib2 as std_urllib
else:
import urllib.request as std_urllib
EB_BOOTSTRAP_VERSION = '20210618.01'
# argparse preferrred, optparse deprecated >=2.7
HAVE_ARGPARSE = False
try:
import argparse
HAVE_ARGPARSE = True
except ImportError:
import optparse
PYPI_SOURCE_URL = 'https://pypi.python.org/packages/source'
VSC_BASE = 'vsc-base'
VSC_INSTALL = 'vsc-install'
# Python 3 is not supported by the vsc-* packages
EASYBUILD_PACKAGES = (([] if IS_PY3 else [VSC_INSTALL, VSC_BASE]) +
['easybuild-framework', 'easybuild-easyblocks', 'easybuild-easyconfigs'])
STAGE1_SUBDIR = 'eb_stage1'
# the EasyBuild bootstrap script is deprecated, and will only run if $EASYBUILD_BOOTSTRAP_DEPRECATED is defined
EASYBUILD_BOOTSTRAP_DEPRECATED = os.environ.pop('EASYBUILD_BOOTSTRAP_DEPRECATED', None)
# set print_debug to True for detailed progress info
print_debug = os.environ.pop('EASYBUILD_BOOTSTRAP_DEBUG', False)
# install with --force in stage2?
forced_install = os.environ.pop('EASYBUILD_BOOTSTRAP_FORCED', False)
# don't add user site directory to sys.path (equivalent to python -s), see https://www.python.org/dev/peps/pep-0370/
os.environ['PYTHONNOUSERSITE'] = '1'
site.ENABLE_USER_SITE = False
# clean PYTHONPATH to avoid finding readily installed stuff
os.environ['PYTHONPATH'] = ''
EASYBUILD_BOOTSTRAP_SOURCEPATH = os.environ.pop('EASYBUILD_BOOTSTRAP_SOURCEPATH', None)
EASYBUILD_BOOTSTRAP_SKIP_STAGE0 = os.environ.pop('EASYBUILD_BOOTSTRAP_SKIP_STAGE0', False)
EASYBUILD_BOOTSTRAP_FORCE_VERSION = os.environ.pop('EASYBUILD_BOOTSTRAP_FORCE_VERSION', None)
# keep track of original environment (after clearing PYTHONPATH)
orig_os_environ = copy.deepcopy(os.environ)
# If the modules tool is specified, use it
easybuild_modules_tool = os.environ.get('EASYBUILD_MODULES_TOOL', None)
easybuild_module_syntax = os.environ.get('EASYBUILD_MODULE_SYNTAX', None)
# If modules subdir specifications are defined, use them
easybuild_installpath_modules = os.environ.get('EASYBUILD_INSTALLPATH_MODULES', None)
easybuild_subdir_modules = os.environ.get('EASYBUILD_SUBDIR_MODULES', 'modules')
easybuild_suffix_modules_path = os.environ.get('EASYBUILD_SUFFIX_MODULES_PATH', 'all')
#
# Utility functions
#
def debug(msg):
"""Print debug message."""
if print_debug:
print("[[DEBUG]] " + msg)
def info(msg):
"""Print info message."""
print("[[INFO]] " + msg)
def error(msg, exit=True):
"""Print error message and exit."""
print("[[ERROR]] " + msg)
sys.exit(1)
def mock_stdout_stderr():
"""Mock stdout/stderr channels"""
try:
from cStringIO import StringIO
except ImportError:
from io import StringIO
orig_stdout, orig_stderr = sys.stdout, sys.stderr
sys.stdout.flush()
sys.stdout = StringIO()
sys.stderr.flush()
sys.stderr = StringIO()
return orig_stdout, orig_stderr
def restore_stdout_stderr(orig_stdout, orig_stderr):
"""Restore stdout/stderr channels after mocking"""
# collect output
sys.stdout.flush()
stdout = sys.stdout.getvalue()
sys.stderr.flush()
stderr = sys.stderr.getvalue()
# restore original stdout/stderr
sys.stdout = orig_stdout
sys.stderr = orig_stderr
return stdout, stderr
def det_lib_path(libdir):
"""Determine relative path of Python library dir."""
if libdir is None:
libdir = 'lib'
pyver = '.'.join([str(x) for x in sys.version_info[:2]])
return os.path.join(libdir, 'python%s' % pyver, 'site-packages')
def det_modules_path(install_path):
"""Determine modules path."""
if easybuild_installpath_modules is not None:
modules_path = os.path.join(easybuild_installpath_modules, easybuild_suffix_modules_path)
else:
modules_path = os.path.join(install_path, easybuild_subdir_modules, easybuild_suffix_modules_path)
return modules_path
def find_egg_dir_for(path, pkg):
"""Find full path of egg dir for given package."""
res = None
for libdir in ['lib', 'lib64']:
full_libpath = os.path.join(path, det_lib_path(libdir))
eggdir_regex = re.compile('%s-[0-9a-z.]+-py[0-9.]+.egg' % pkg.replace('-', '_'))
subdirs = (os.path.exists(full_libpath) and sorted(os.listdir(full_libpath))) or []
for subdir in subdirs:
if eggdir_regex.match(subdir):
eggdir = os.path.join(full_libpath, subdir)
if res is None:
debug("Found egg dir for %s at %s" % (pkg, eggdir))
res = eggdir
else:
debug("Found another egg dir for %s at %s (ignoring it)" % (pkg, eggdir))
# no egg dir found
if res is None:
debug("Failed to determine egg dir path for %s in %s (subdirs: %s)" % (pkg, path, subdirs))
return res
def prep(path):
"""Prepare for installing a Python package in the specified path."""
debug("Preparing for path %s" % path)
# restore original environment first
os.environ = copy.deepcopy(orig_os_environ)
debug("os.environ['PYTHONPATH'] after reset: %s" % os.environ['PYTHONPATH'])
# update PATH
os.environ['PATH'] = os.pathsep.join([os.path.join(path, 'bin')] +
[x for x in os.environ.get('PATH', '').split(os.pathsep) if len(x) > 0])
debug("$PATH: %s" % os.environ['PATH'])
# update actual Python search path
sys.path.insert(0, path)
# make sure directory exists (this is required by setuptools)
# usually it's 'lib', but can be 'lib64' as well
for libdir in ['lib', 'lib64']:
full_libpath = os.path.join(path, det_lib_path(libdir))
if not os.path.exists(full_libpath):
os.makedirs(full_libpath)
# PYTHONPATH needs to be set as well, otherwise setuptools will fail
pythonpaths = [x for x in os.environ.get('PYTHONPATH', '').split(os.pathsep) if len(x) > 0]
os.environ['PYTHONPATH'] = os.pathsep.join([full_libpath] + pythonpaths)
debug("$PYTHONPATH: %s" % os.environ['PYTHONPATH'])
os.environ['EASYBUILD_MODULES_TOOL'] = easybuild_modules_tool
debug("$EASYBUILD_MODULES_TOOL set to %s" % os.environ['EASYBUILD_MODULES_TOOL'])
if easybuild_module_syntax:
# if module syntax is specified, use it
os.environ['EASYBUILD_MODULE_SYNTAX'] = easybuild_module_syntax
debug("Using specified module syntax: %s" % os.environ['EASYBUILD_MODULE_SYNTAX'])
elif easybuild_modules_tool != 'Lmod':
# Lua is the default module syntax, but that requires Lmod
# if Lmod is not being used, use Tcl module syntax
os.environ['EASYBUILD_MODULE_SYNTAX'] = 'Tcl'
debug("$EASYBUILD_MODULE_SYNTAX set to %s" % os.environ['EASYBUILD_MODULE_SYNTAX'])
def check_module_command(tmpdir):
"""Check which module command is available, and prepare for using it."""
global easybuild_modules_tool
if easybuild_modules_tool is not None:
info("Using modules tool specified by $EASYBUILD_MODULES_TOOL: %s" % easybuild_modules_tool)
return easybuild_modules_tool
def check_cmd_help(modcmd):
"""Check 'help' output for specified command."""
modcmd_re = re.compile(r'module\s.*command')
cmd = "%s python help" % modcmd
os.system("%s > %s 2>&1" % (cmd, out))
txt = open(out, 'r').read()
debug("Output from %s: %s" % (cmd, txt))
return modcmd_re.search(txt)
def is_modulecmd_tcl_modulestcl():
"""Determine if modulecmd.tcl is EnvironmentModulesTcl."""
modcmd_re = re.compile('Modules Release Tcl')
cmd = "modulecmd.tcl python --version"
os.system("%s > %s 2>&1" % (cmd, out))
txt = open(out, 'r').read()
debug("Output from %s: %s" % (cmd, txt))
return modcmd_re.search(txt)
# order matters, which is why we don't use a dict
known_module_commands = [
('lmod', 'Lmod'),
('modulecmd.tcl', 'EnvironmentModules'),
('modulecmd', 'EnvironmentModulesC'),
]
out = os.path.join(tmpdir, 'module_command.out')
modtool = None
for modcmd, modtool in known_module_commands:
if check_cmd_help(modcmd):
# distinguish between EnvironmentModulesTcl and EnvironmentModules
if modcmd == 'modulecmd.tcl' and is_modulecmd_tcl_modulestcl():
modtool = 'EnvironmentModulesTcl'
easybuild_modules_tool = modtool
info("Found module command '%s' (%s), so using it." % (modcmd, modtool))
break
elif modcmd == 'lmod':
# check value of $LMOD_CMD as fallback
modcmd = os.environ.get('LMOD_CMD')
if modcmd and check_cmd_help(modcmd):
easybuild_modules_tool = modtool
info("Found module command '%s' via $LMOD_CMD (%s), so using it." % (modcmd, modtool))
break
elif modtool == 'EnvironmentModules':
# check value of $MODULESHOME as fallback
moduleshome = os.environ.get('MODULESHOME', 'MODULESHOME_NOT_DEFINED')
modcmd = os.path.join(moduleshome, 'libexec', 'modulecmd.tcl')
if os.path.exists(modcmd) and check_cmd_help(modcmd):
easybuild_modules_tool = modtool
info("Found module command '%s' via $MODULESHOME (%s), so using it." % (modcmd, modtool))
break
if easybuild_modules_tool is None:
mod_cmds = [m for (m, _) in known_module_commands]
msg = [
"Could not find any module command, make sure one available in your $PATH.",
"Known module commands are checked in order, and include: %s" % ', '.join(mod_cmds),
"Check the output of 'type module' to determine the location of the module command you are using.",
]
error('\n'.join(msg))
return modtool
def check_setuptools():
"""Check whether a suitable setuptools installation is already available."""
debug("Checking whether suitable setuptools installation is available...")
res = None
_, outfile = tempfile.mkstemp()
# note: we need to be very careful here, because switching to a different setuptools installation (e.g. in stage0)
# after the setuptools module was imported is very tricky...
# So, we'll check things by running commands through os.system rather than importing setuptools directly.
cmd_tmpl = "%s -c '%%s' > %s 2>&1" % (sys.executable, outfile)
# check setuptools version
try:
os.system(cmd_tmpl % "import setuptools; print(setuptools.__version__)")
setuptools_ver = LooseVersion(open(outfile).read().strip())
debug("Found setuptools version %s" % setuptools_ver)
min_setuptools_ver = '0.6c11'
if setuptools_ver < LooseVersion(min_setuptools_ver):
debug("Minimal setuptools version %s not satisfied, found '%s'" % (min_setuptools_ver, setuptools_ver))
res = False
except Exception as err:
debug("Failed to check setuptools version: %s" % err)
res = False
os.system(cmd_tmpl % "from setuptools.command import easy_install; print(easy_install.__file__)")
out = open(outfile).read().strip()
debug("Location of setuptools' easy_install module: %s" % out)
if 'setuptools/command/easy_install' not in out:
debug("Module 'setuptools.command.easy_install not found")
res = False
if res is None:
os.system(cmd_tmpl % "import setuptools; print(setuptools.__file__)")
setuptools_loc = open(outfile).read().strip()
res = os.path.dirname(os.path.dirname(setuptools_loc))
debug("Location of setuptools installation: %s" % res)
try:
os.remove(outfile)
except Exception:
pass
return res
def run_easy_install(args):
"""Run easy_install with specified list of arguments"""
import setuptools
debug("Active setuptools installation: %s" % setuptools.__file__)
from setuptools.command import easy_install
orig_stdout, orig_stderr = mock_stdout_stderr()
try:
easy_install.main(args)
easy_install_stdout, easy_install_stderr = restore_stdout_stderr(orig_stdout, orig_stderr)
except (Exception, SystemExit) as err:
easy_install_stdout, easy_install_stderr = restore_stdout_stderr(orig_stdout, orig_stderr)
error("Running 'easy_install %s' failed: %s\n%s" % (' '.join(args), err, traceback.format_exc()))
debug("stdout for 'easy_install %s':\n%s" % (' '.join(args), easy_install_stdout))
debug("stderr for 'easy_install %s':\n%s" % (' '.join(args), easy_install_stderr))
def check_easy_install_cmd():
"""Try to make sure available 'easy_install' command matches active 'setuptools' installation."""
debug("Checking whether available 'easy_install' command matches active 'setuptools' installation...")
_, outfile = tempfile.mkstemp()
import setuptools
debug("Location of active setuptools installation: %s" % setuptools.__file__)
easy_install_regex = re.compile('^(setuptools|distribute) %s' % setuptools.__version__)
debug("Pattern for 'easy_install --version': %s" % easy_install_regex.pattern)
pythonpath = os.getenv('PYTHONPATH', '')
cmd = "PYTHONPATH='%s' %s -m easy_install --version" % (pythonpath, sys.executable)
os.system("%s > %s 2>&1" % (cmd, outfile))
outtxt = open(outfile).read().strip()
debug("Output of '%s':\n%s" % (cmd, outtxt))
res = bool(easy_install_regex.match(outtxt))
debug("Result: %s" % res)
if res:
debug("Found right 'easy_install' command")
return
error("Failed to find right 'easy_install' command!")
#
# Stage functions
#
def stage0(tmpdir):
"""STAGE 0: Prepare and install distribute via included (patched) distribute_setup.py script."""
print('\n')
info("+++ STAGE 0: installing distribute via included (patched) distribute_setup.py...\n")
txt = DISTRIBUTE_SETUP_PY
if not print_debug:
# silence distribute_setup.py by redirecting output to /dev/null
txt = re.sub(r'([^\n]*)(return subprocess.call\(args)(\) == 0)',
r"\1f = open(os.devnull, 'w'); \2, stdout=f, stderr=f\3",
txt)
# silence distribute_setup.py completely by setting high log level threshold
txt = re.sub(r'([^\n]*)(# extracting the tarball[^\n]*)', r'\1log.set_verbosity(1000)\n\1\2', txt)
# write distribute_setup.py to file (with correct header)
distribute_setup = os.path.join(tmpdir, 'distribute_setup.py')
f = open(distribute_setup, "w")
f.write(txt)
f.close()
# create expected directories, set Python search path
debug("preparing environment...")
prep(tmpdir)
import distribute_setup
debug("distribute_setup.__file__: %s" % distribute_setup.__file__)
# install easy_install to temporary directory
from distribute_setup import main as distribute_setup_main
orig_sys_argv = sys.argv[:] # make a copy
sys.argv.append('--prefix=%s' % tmpdir)
# We download a custom version of distribute: it uses a newer version of markerlib to avoid a bug (#1099)
# It's is the source of distribute 0.6.49 with the file _markerlib/markers.py replaced by the 0.6 version of
# markerlib which can be found at https://pypi.python.org/pypi/markerlib/0.6.0
sys.argv.append('--download-base=https://easybuilders.github.io/easybuild/files/')
distribute_setup_main(version="0.6.49-patched1")
sys.argv = orig_sys_argv
# sanity check
if os.path.exists(os.path.join(tmpdir, 'bin', 'easy_install')):
debug("easy_install sanity check OK")
else:
error("Installing distribute which should deliver easy_install failed?")
# prepend distribute egg dir to sys.path, so we know which setuptools we're using
distribute_egg_dir = find_egg_dir_for(tmpdir, 'distribute')
if distribute_egg_dir is None:
error("Failed to determine egg dir path for distribute_egg_dir in %s" % tmpdir)
else:
sys.path.insert(0, distribute_egg_dir)
# make sure we're getting the setuptools we expect
import setuptools
from setuptools.command import easy_install
for mod, path in [('setuptools', setuptools.__file__), ('easy_install', easy_install.__file__)]:
if tmpdir not in path:
error("Found another %s module than expected: %s" % (mod, path))
else:
debug("Found %s in expected path, good!" % mod)
info("Installed setuptools version %s (%s)" % (setuptools.__version__, setuptools.__file__))
return distribute_egg_dir
def stage1(tmpdir, sourcepath, distribute_egg_dir, forcedversion):
"""STAGE 1: temporary install EasyBuild using distribute's easy_install."""
print('\n')
info("+++ STAGE 1: installing EasyBuild in temporary dir with easy_install...\n")
# determine locations of source tarballs, if sources path is specified
source_tarballs = {}
if sourcepath is not None:
info("Fetching sources from %s..." % sourcepath)
for pkg in EASYBUILD_PACKAGES:
pkg_tarball_glob = os.path.join(sourcepath, '%s*.tar.gz' % pkg)
pkg_tarball_paths = glob.glob(pkg_tarball_glob)
if len(pkg_tarball_paths) > 1:
error("Multiple tarballs found for %s: %s" % (pkg, pkg_tarball_paths))
elif len(pkg_tarball_paths) == 0:
if pkg not in [VSC_BASE, VSC_INSTALL]:
# vsc-base package is not strictly required
# it's only a dependency since EasyBuild v2.0;
# with EasyBuild v2.0, it will be pulled in from PyPI when installing easybuild-framework;
# vsc-install is an optional dependency, only required to run unit tests
error("Missing source tarball: %s" % pkg_tarball_glob)
else:
info("Found %s for %s package" % (pkg_tarball_paths[0], pkg))
source_tarballs.update({pkg: pkg_tarball_paths[0]})
if print_debug:
debug("$ easy_install --help")
run_easy_install(['--help'])
# prepare install dir
targetdir_stage1 = os.path.join(tmpdir, STAGE1_SUBDIR)
prep(targetdir_stage1) # set PATH, Python search path
# install latest EasyBuild with easy_install from PyPi
cmd = [
'--upgrade', # make sure the latest version is pulled from PyPi
'--prefix=%s' % targetdir_stage1,
]
post_vsc_base = []
if source_tarballs:
# install provided source tarballs (order matters)
cmd.extend([source_tarballs[pkg] for pkg in EASYBUILD_PACKAGES if pkg in source_tarballs])
# add vsc-base again at the end, to avoid that the one available on the system is used instead
if VSC_BASE in source_tarballs:
cmd.append(source_tarballs[VSC_BASE])
else:
# install meta-package easybuild from PyPI
if forcedversion:
cmd.append('easybuild==%s' % forcedversion)
elif IS_PY3:
cmd.append('easybuild>=4.0') # Python 3 support added in EasyBuild 4
else:
cmd.append('easybuild')
if not IS_PY3:
# install vsc-base again at the end, to avoid that the one available on the system is used instead
post_vsc_base = cmd[:]
post_vsc_base[-1] = VSC_BASE + '<2.9.0'
if not print_debug:
cmd.insert(0, '--quiet')
# There is no support for Python3 in the older vsc-* packages and EasyBuild 4 includes working versions of vsc-*
if not IS_PY3:
# install vsc-install version prior to 0.11.4, where mock was introduced as a dependency
# workaround for problem reported in https://github.com/easybuilders/easybuild-framework/issues/2712
# also stick to vsc-base < 2.9.0 to avoid requiring 'future' Python package as dependency
for pkg in [VSC_INSTALL + '<0.11.4', VSC_BASE + '<2.9.0']:
precmd = cmd[:-1] + [pkg]
info("running pre-install command 'easy_install %s'" % (' '.join(precmd)))
run_easy_install(precmd)
info("installing EasyBuild with 'easy_install %s'\n" % (' '.join(cmd)))
syntax_error_note = '\n'.join([
"Note: a 'SyntaxError' may be reported for the easybuild/tools/py2vs3/py%s.py module." % ('3', '2')[IS_PY3],
"You can safely ignore this message, it will not affect the functionality of the EasyBuild installation.",
'',
])
info(syntax_error_note)
run_easy_install(cmd)
if post_vsc_base:
info("running post install command 'easy_install %s'" % (' '.join(post_vsc_base)))
run_easy_install(post_vsc_base)
pkg_egg_dir = find_egg_dir_for(targetdir_stage1, VSC_BASE)
if pkg_egg_dir is None:
# if vsc-base available on system is the same version as the one being installed,
# the .egg directory may not get installed...
# in that case, try to have it *copied* by also including --always-copy;
# using --always-copy should be used as a last resort, since it can result in all kinds of problems
info(".egg dir for vsc-base not found, trying again with --always-copy...")
post_vsc_base.insert(0, '--always-copy')
info("running post install command 'easy_install %s'" % (' '.join(post_vsc_base)))
run_easy_install(post_vsc_base)
# clear the Python search path, we only want the individual eggs dirs to be in the PYTHONPATH (see below)
# this is needed to avoid easy-install.pth controlling what Python packages are actually used
if distribute_egg_dir is not None:
os.environ['PYTHONPATH'] = distribute_egg_dir
else:
del os.environ['PYTHONPATH']
# template string to inject in template easyconfig
templates = {}
for pkg in EASYBUILD_PACKAGES:
templates.update({pkg: ''})
pkg_egg_dir = find_egg_dir_for(targetdir_stage1, pkg)
if pkg_egg_dir is None:
if pkg in [VSC_BASE, VSC_INSTALL]:
# vsc-base is optional in older EasyBuild versions
continue
# prepend EasyBuild egg dirs to Python search path, so we know which EasyBuild we're using
sys.path.insert(0, pkg_egg_dir)
pythonpaths = [x for x in os.environ.get('PYTHONPATH', '').split(os.pathsep) if len(x) > 0]
os.environ['PYTHONPATH'] = os.pathsep.join([pkg_egg_dir] + pythonpaths)
debug("$PYTHONPATH: %s" % os.environ['PYTHONPATH'])
if source_tarballs:
if pkg in source_tarballs:
templates.update({pkg: "'%s'," % os.path.basename(source_tarballs[pkg])})
else:
# determine per-package versions based on egg dirs, to use them in easyconfig template
version_regex = re.compile('%s-([0-9a-z.-]*)-py[0-9.]*.egg' % pkg.replace('-', '_'))
pkg_egg_dirname = os.path.basename(pkg_egg_dir)
res = version_regex.search(pkg_egg_dirname)
if res is not None:
pkg_version = res.group(1)
debug("Found version for easybuild-%s: %s" % (pkg, pkg_version))
templates.update({pkg: "'%s-%s.tar.gz'," % (pkg, pkg_version)})
else:
tup = (pkg, pkg_egg_dirname, version_regex.pattern)
error("Failed to determine version for easybuild-%s package from %s with %s" % tup)
# figure out EasyBuild version via eb command line
# note: EasyBuild uses some magic to determine the EasyBuild version based on the versions of the individual pkgs
ver_regex = {'ver': '[0-9.]*[a-z0-9]*'}
pattern = r"This is EasyBuild (?P<version>%(ver)s) \(framework: %(ver)s, easyblocks: %(ver)s\)" % ver_regex
version_re = re.compile(pattern)
version_out_file = os.path.join(tmpdir, 'eb_version.out')
eb_version_cmd = 'from easybuild.tools.version import this_is_easybuild; print(this_is_easybuild())'
cmd = "%s -c '%s' > %s 2>&1" % (sys.executable, eb_version_cmd, version_out_file)
debug("Determining EasyBuild version using command '%s'" % cmd)
os.system(cmd)
txt = open(version_out_file, "r").read()
res = version_re.search(txt)
if res:
eb_version = res.group(1)
debug("installing EasyBuild v%s" % eb_version)
else:
error("Stage 1 failed, could not determine EasyBuild version (txt: %s)." % txt)
templates.update({'version': eb_version})
# clear PYTHONPATH before we go to stage2
# PYTHONPATH doesn't need to (and shouldn't) include the stage1 egg dirs
os.environ['PYTHONPATH'] = ''
# make sure we're getting the expected EasyBuild packages
import easybuild.framework
import easybuild.easyblocks
pkgs_to_check = [easybuild.framework, easybuild.easyblocks]
# vsc is part of EasyBuild 4
if LooseVersion(eb_version) < LooseVersion('4'):
import vsc.utils.fancylogger
pkgs_to_check.append(vsc.utils.fancylogger)
for pkg in pkgs_to_check:
if tmpdir not in pkg.__file__:
error("Found another %s than expected: %s" % (pkg.__name__, pkg.__file__))
else:
debug("Found %s in expected path, good!" % pkg.__name__)
debug("templates: %s" % templates)
return templates
def stage2(tmpdir, templates, install_path, distribute_egg_dir, sourcepath):
"""STAGE 2: install EasyBuild to temporary dir with EasyBuild from stage 1."""
print('\n')
info("+++ STAGE 2: installing EasyBuild in %s with EasyBuild from stage 1...\n" % install_path)
preinstallopts = ''
eb_looseversion = LooseVersion(templates['version'])
# setuptools is no longer required for EasyBuild v4.0 & newer, so skip the setuptools stuff in that case
if eb_looseversion < LooseVersion('4.0') and distribute_egg_dir is not None:
# inject path to distribute installed in stage 0 into $PYTHONPATH via preinstallopts
# other approaches are not reliable, since EasyBuildMeta easyblock unsets $PYTHONPATH;
# this is required for the easy_install from stage 0 to work
preinstallopts += "export PYTHONPATH=%s:$PYTHONPATH && " % distribute_egg_dir
# ensure that (latest) setuptools is installed as well alongside EasyBuild,
# since it is a required runtime dependency for recent vsc-base and EasyBuild versions
# this is necessary since we provide our own distribute installation during the bootstrap (cfr. stage0)
preinstallopts += "%s -m easy_install -U --prefix %%(installdir)s setuptools && " % sys.executable
# vsc-install is no longer required for EasyBuild v4.0, so skip pre-installed vsc-install in that case
if eb_looseversion < LooseVersion('4.0'):
# vsc-install is a runtime dependency for the EasyBuild unit test suite,
# and is easily picked up from stage1 rather than being actually installed, so force it
vsc_install = "'%s<0.11.4'" % VSC_INSTALL
if sourcepath:
vsc_install_tarball_paths = glob.glob(os.path.join(sourcepath, 'vsc-install*.tar.gz'))
if len(vsc_install_tarball_paths) == 1:
vsc_install = vsc_install_tarball_paths[0]
preinstallopts += "%s -m easy_install -U --prefix %%(installdir)s %s && " % (sys.executable, vsc_install)
templates.update({
'preinstallopts': preinstallopts,
})
# determine PyPI URLs for individual packages
pkg_urls = []
for pkg in EASYBUILD_PACKAGES:
# vsc-base and vsc-install are not dependencies anymore for EasyBuild v4.0,
# so skip them here for recent EasyBuild versions
if eb_looseversion >= LooseVersion('4.0') and pkg in [VSC_INSTALL, VSC_BASE]:
continue
# format of pkg entries in templates: "'<pkg_filename>',"
pkg_filename = templates[pkg][1:-2]
# the lines below implement a simplified version of the 'pypi_source_urls' and 'derive_alt_pypi_url' functions,
# which we can't leverage here, partially because of transitional changes in PyPI (#md5= -> #sha256=)
# determine download URL via PyPI's 'simple' API
pkg_simple = None
try:
pkg_simple = std_urllib.urlopen('https://pypi.python.org/simple/%s' % pkg, timeout=10).read()
except (std_urllib.URLError, std_urllib.HTTPError) as err:
# failing to figure out the package download URl may be OK when source tarballs are provided
if sourcepath:
info("Ignoring failed attempt to determine '%s' download URL since source tarballs are provided" % pkg)
else:
raise err
if pkg_simple:
if IS_PY3:
pkg_simple = pkg_simple.decode('utf-8')
pkg_url_part_regex = re.compile('/(packages/[^#]+)/%s#' % pkg_filename)
res = pkg_url_part_regex.search(pkg_simple)
if res:
pkg_url = 'https://pypi.python.org/' + res.group(1)
pkg_urls.append(pkg_url)
elif sourcepath:
info("Ignoring failure to determine source URL for '%s' (source tarballs are provided)" % pkg_filename)
else:
error_msg = "Failed to determine PyPI package URL for %s using pattern '%s': %s\n"
error(error_msg % (pkg, pkg_url_part_regex.pattern, pkg_simple))
# vsc-base and vsc-install are no longer required for EasyBuild v4.0.0,
# so only include them in 'sources' for older versions
sources_tmpl = "%(easybuild-framework)s%(easybuild-easyblocks)s%(easybuild-easyconfigs)s"
if eb_looseversion < LooseVersion('4.0'):
sources_tmpl = "%(vsc-install)s%(vsc-base)s" + sources_tmpl
templates.update({
'source_urls': '\n'.join(["'%s'," % x for x in pkg_urls]),
'sources': sources_tmpl % templates,
'pythonpath': distribute_egg_dir,
})
# create easyconfig file
ebfile = os.path.join(tmpdir, 'EasyBuild-%s.eb' % templates['version'])
handle = open(ebfile, 'w')
ebfile_txt = EASYBUILD_EASYCONFIG_TEMPLATE % templates
handle.write(ebfile_txt)
handle.close()
debug("Contents of generated easyconfig file:\n%s" % ebfile_txt)
# set command line arguments for eb
eb_args = ['eb', ebfile, '--allow-modules-tool-mismatch']
if print_debug:
eb_args.extend(['--debug', '--logtostdout'])
if forced_install:
info("Performing FORCED installation, as requested...")
eb_args.append('--force')
# make sure we don't leave any stuff behind in default path $HOME/.local/easybuild
# and set build and install path explicitely
if LooseVersion(templates['version']) < LooseVersion('1.3.0'):
os.environ['EASYBUILD_PREFIX'] = tmpdir
os.environ['EASYBUILD_BUILDPATH'] = tmpdir
if install_path is not None:
os.environ['EASYBUILD_INSTALLPATH'] = install_path
else:
# only for v1.3 and up
eb_args.append('--prefix=%s' % tmpdir)
eb_args.append('--buildpath=%s' % tmpdir)
if install_path is not None:
eb_args.append('--installpath=%s' % install_path)
if sourcepath is not None:
eb_args.append('--sourcepath=%s' % sourcepath)
# make sure EasyBuild can find EasyBuild-*.eb easyconfig file when it needs to;
# (for example when HierarchicalMNS is used as module naming scheme,
# see https://github.com/easybuilders/easybuild-framework/issues/2393)
eb_args.append('--robot-paths=%s:' % tmpdir)
# make sure parent modules path already exists (Lmod trips over a non-existing entry in $MODULEPATH)
if install_path is not None:
modules_path = det_modules_path(install_path)
if not os.path.exists(modules_path):
os.makedirs(modules_path)
debug("Created path %s" % modules_path)
debug("Running EasyBuild with arguments '%s'" % ' '.join(eb_args))
sys.argv = eb_args
# location to 'eb' command (from stage 1) may be expected to be included in $PATH
# it usually is there after stage1, unless 'prep' is called again with another location
# (only when stage 0 is not skipped)
# cfr. https://github.com/easybuilders/easybuild-framework/issues/2279
curr_path = [x for x in os.environ.get('PATH', '').split(os.pathsep) if len(x) > 0]
os.environ['PATH'] = os.pathsep.join([os.path.join(tmpdir, STAGE1_SUBDIR, 'bin')] + curr_path)
debug("$PATH: %s" % os.environ['PATH'])
# install EasyBuild with EasyBuild
from easybuild.main import main as easybuild_main
easybuild_main()
if print_debug:
os.environ['EASYBUILD_DEBUG'] = '1'
# make sure the EasyBuild module was actually installed
# EasyBuild configuration options that are picked up from configuration files/environment may break the bootstrap,
# for example by having $EASYBUILD_VERSION defined or via a configuration file specifies a value for 'stop'...
from easybuild.tools.config import build_option, install_path, get_module_syntax
from easybuild.framework.easyconfig.easyconfig import ActiveMNS
eb_spec = {
'name': 'EasyBuild',
'hidden': False,
'toolchain': {'name': 'dummy', 'version': 'dummy'},
'version': templates['version'],
'versionprefix': '',
'versionsuffix': '',
'moduleclass': 'tools',
}
mod_path = os.path.join(install_path('mod'), build_option('suffix_modules_path'))
debug("EasyBuild module should have been installed to %s" % mod_path)
eb_mod_name = ActiveMNS().det_full_module_name(eb_spec)
debug("EasyBuild module name: %s" % eb_mod_name)
eb_mod_path = os.path.join(mod_path, eb_mod_name)
if get_module_syntax() == 'Lua':
eb_mod_path += '.lua'
if os.path.exists(eb_mod_path):
info("EasyBuild module installed: %s" % eb_mod_path)
else:
error("EasyBuild module not found at %s, define $EASYBUILD_BOOTSTRAP_DEBUG to debug" % eb_mod_path)
def main():
"""Main script: bootstrap EasyBuild in stages."""
self_txt = open(__file__).read()
if IS_PY3:
self_txt = self_txt.encode('utf-8')
url = 'https://docs.easybuild.io/en/latest/Installation.html'
info("Use of the EasyBuild boostrap script is DEPRECATED (since June 2021).")
info("It is strongly recommended to use one of the installation methods outlined at %s instead!\n" % url)
if not EASYBUILD_BOOTSTRAP_DEPRECATED:
error("The EasyBuild bootstrap script will only run if $EASYBUILD_BOOTSTRAP_DEPRECATED is defined.")
else:
msg = "You have opted to continue with the EasyBuild bootstrap script by defining "
msg += "$EASYBUILD_BOOTSTRAP_DEPRECATED. Good luck!\n"
info(msg)
info("EasyBuild bootstrap script (version %s, MD5: %s)" % (EB_BOOTSTRAP_VERSION, md5(self_txt).hexdigest()))
info("Found Python %s\n" % '; '.join(sys.version.split('\n')))
# disallow running as root, since stage 2 will fail
if os.getuid() == 0:
error("Don't run the EasyBuild bootstrap script as root, "
"since stage 2 (installing EasyBuild with EasyBuild) will fail.")
# general option/argument parser
if HAVE_ARGPARSE:
bs_argparser = argparse.ArgumentParser()
bs_argparser.add_argument("prefix", help="Installation prefix directory",
type=str)
bs_args = bs_argparser.parse_args()
# prefix specification
install_path = os.path.abspath(bs_args.prefix)
else:
bs_argparser = optparse.OptionParser(usage="usage: %prog [options] prefix")
(bs_opts, bs_args) = bs_argparser.parse_args()
# poor method, but should prefer argparse module for better pos arg support.
if len(bs_args) < 1:
error("Too few arguments\n" + bs_argparser.get_usage())
elif len(bs_args) > 1:
error("Too many arguments\n" + bs_argparser.get_usage())
# prefix specification
install_path = os.path.abspath(str(bs_args[0]))
info("Installation prefix %s" % install_path)
sourcepath = EASYBUILD_BOOTSTRAP_SOURCEPATH
if sourcepath is not None:
info("Fetching sources from %s..." % sourcepath)
forcedversion = EASYBUILD_BOOTSTRAP_FORCE_VERSION
if forcedversion:
info("Forcing specified version %s..." % forcedversion)
if IS_PY3 and LooseVersion(forcedversion) < LooseVersion('4'):
error('Python 3 support is only available with EasyBuild 4.x but you are trying to install EasyBuild %s'
% forcedversion)
# create temporary dir for temporary installations
tmpdir = tempfile.mkdtemp()
debug("Going to use %s as temporary directory" % tmpdir)
os.chdir(tmpdir)
# check whether a module command is available, we need that
modtool = check_module_command(tmpdir)
# clean sys.path, remove paths that may contain EasyBuild packages or stuff installed with easy_install
orig_sys_path = sys.path[:]
sys.path = []
for path in orig_sys_path:
include_path = True
# exclude path if it's potentially an EasyBuild/VSC package, providing the 'easybuild'/'vsc' namespace, resp.
if any([os.path.exists(os.path.join(path, pkg, '__init__.py')) for pkg in ['easyblocks', 'easybuild', 'vsc']]):
include_path = False
# exclude any .egg paths
if path.endswith('.egg'):
include_path = False
# exclude any path that contains an easy-install.pth file
if os.path.exists(os.path.join(path, 'easy-install.pth')):
include_path = False
if include_path:
sys.path.append(path)
else:
debug("Excluding %s from sys.path" % path)
debug("sys.path after cleaning: %s" % sys.path)
# install EasyBuild in stages
# STAGE 0: install distribute, which delivers easy_install
distribute_egg_dir = None
if EASYBUILD_BOOTSTRAP_SKIP_STAGE0:
info("Skipping stage 0, using local distribute/setuptools providing easy_install")
else:
setuptools_loc = check_setuptools()
if setuptools_loc:
info("Suitable setuptools installation already found, skipping stage 0...")
sys.path.insert(0, setuptools_loc)
else:
info("No suitable setuptools installation found, proceeding with stage 0...")
distribute_egg_dir = stage0(tmpdir)
# STAGE 1: install EasyBuild using easy_install to tmp dir
templates = stage1(tmpdir, sourcepath, distribute_egg_dir, forcedversion)
# add location to easy_install provided through stage0 to $PATH
# this must be done *after* stage1, since $PATH is reset during stage1
if distribute_egg_dir:
prep(tmpdir)
# make sure the active 'easy_install' is the right one (i.e. it matches the active setuptools installation)
check_easy_install_cmd()
# STAGE 2: install EasyBuild using EasyBuild (to final target installation dir)
stage2(tmpdir, templates, install_path, distribute_egg_dir, sourcepath)
# clean up the mess
debug("Cleaning up %s..." % tmpdir)
shutil.rmtree(tmpdir)
print('')
info('Bootstrapping EasyBuild completed!\n')
if install_path is not None:
info('EasyBuild v%s was installed to %s, so make sure your $MODULEPATH includes %s' %
(templates['version'], install_path, det_modules_path(install_path)))
else:
info('EasyBuild v%s was installed to configured install path, make sure your $MODULEPATH is set correctly.' %
templates['version'])
info('(default config => add "$HOME/.local/easybuild/modules/all" in $MODULEPATH)')
print('')
info("Run 'module load EasyBuild', and run 'eb --help' to get help on using EasyBuild.")
info("Set $EASYBUILD_MODULES_TOOL to '%s' to use the same modules tool as was used now." % modtool)
print('')
info("By default, EasyBuild will install software to $HOME/.local/easybuild.")
info("To install software with EasyBuild to %s, set $EASYBUILD_INSTALLPATH accordingly." % install_path)
info("See http://easybuild.readthedocs.org/en/latest/Configuration.html for details on configuring EasyBuild.")
# template easyconfig file for EasyBuild
EASYBUILD_EASYCONFIG_TEMPLATE = """
easyblock = 'EB_EasyBuildMeta'
name = 'EasyBuild'
version = '%(version)s'
homepage = 'http://easybuilders.github.com/easybuild/'
description = \"\"\"EasyBuild is a software build and installation framework
written in Python that allows you to install software in a structured,
repeatable and robust way.\"\"\"
toolchain = {'name': 'dummy', 'version': 'dummy'}
source_urls = [%(source_urls)s]
sources = [%(sources)s]
# EasyBuild is a (set of) Python packages, so it depends on Python
# usually, we want to use the system Python, so no actual Python dependency is listed
allow_system_deps = [('Python', SYS_PYTHON_VERSION)]
preinstallopts = "%(preinstallopts)s"
sanity_check_paths = {
'files': ['bin/eb'],
'dirs': ['lib'],
}
moduleclass = 'tools'
"""
# check Python version
loose_pyver = LooseVersion(python_version())
min_pyver2 = LooseVersion('2.6')
min_pyver3 = LooseVersion('3.5')
if loose_pyver < min_pyver2 or (loose_pyver >= LooseVersion('3') and loose_pyver < min_pyver3):
sys.stderr.write("ERROR: Incompatible Python version: %s (should be Python 2 >= %s or Python 3 >= %s)\n"
% (python_version(), min_pyver2, min_pyver3))
sys.exit(1)
# distribute_setup.py script (https://pypi.python.org/pypi/distribute)
#
# A compressed copy of a patched distribute_setup.py (version 0.6.49), generated like so:
# >>> import base64
# >>> import zlib
# >>> base64.b64encode(zlib.compress(open("distribute_setup.py").read()))
# compressed copy below is for setuptools 0.6c11, after applying patch:
#
# --- distribute_setup.py.orig 2013-07-05 03:50:13.000000000 +0200
# +++ distribute_setup.py 2015-11-27 12:20:12.040032041 +0100
# @@ -528,6 +528,8 @@
# log.warn("--user requires Python 2.6 or later")
# raise SystemExit(1)
# install_args.append('--user')
# + if options.prefix_install:
# + install_args.append('--prefix=%s' % options.prefix_install)
# return install_args
#
# def _parse_args():
# @@ -539,6 +541,8 @@
# '--user', dest='user_install', action='store_true', default=False,
# help='install in user site package (requires Python 2.6 or later)')
# parser.add_option(
# + '--prefix', dest='prefix_install', metavar="PATH", help='install in prefix')
# + parser.add_option(
# '--download-base', dest='download_base', metavar="URL",
# default=DEFAULT_URL,
# help='alternative URL from where to download the distribute package')
# @@ -549,7 +553,7 @@
# def main(version=DEFAULT_VERSION):
# """Install or upgrade setuptools and EasyInstall"""
# options = _parse_args()
# - tarball = download_setuptools(download_base=options.download_base)
# + tarball = download_setuptools(version=version, download_base=options.download_base)
# return _install(tarball, _build_install_args(options))
#
# if __name__ == '__main__':
#
DISTRIBUTE_SETUP_PY = """
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"""
if IS_PY3:
DISTRIBUTE_SETUP_PY = DISTRIBUTE_SETUP_PY.encode('ascii')
DISTRIBUTE_SETUP_PY = codecs.decode(codecs.decode(DISTRIBUTE_SETUP_PY, "base64"), "zlib")
# run main function as body of script
main()
