def build_and_install_software(ecs, init_session_state, exit_on_failure=True, hooks=None):
"""
Build and install software for all provided parsed easyconfig files.
:param ecs: easyconfig files to install software with
:param init_session_state: initial session state, to use in test reports
:param exit_on_failure: whether or not to exit on installation failure
:param hooks: list of defined pre- and post-step hooks
"""
# obtain a copy of the starting environment so each build can start afresh
# we shouldn't use the environment from init_session_state, since relevant env vars might have been set since
# e.g. via easyconfig.handle_allowed_system_deps
init_env = copy.deepcopy(os.environ)
run_hook(START, hooks)
res = []
for ec in ecs:
ec_res = {}
try:
(ec_res['success'], app_log, err) = build_and_install_one(ec, init_env, hooks=hooks)
ec_res['log_file'] = app_log
if not ec_res['success']:
ec_res['err'] = EasyBuildError(err)
except Exception, err:
# purposely catch all exceptions
ec_res['success'] = False
ec_res['err'] = err
ec_res['traceback'] = traceback.format_exc()
# keep track of success/total count
if ec_res['success']:
test_msg = "Successfully built %s" % ec['spec']
else:
test_msg = "Build of %s failed" % ec['spec']
if 'err' in ec_res:
test_msg += " (err: %s)" % ec_res['err']
# dump test report next to log file
test_report_txt = create_test_report(test_msg, [(ec, ec_res)], init_session_state)
if 'log_file' in ec_res and ec_res['log_file']:
test_report_fp = "%s_test_report.md" % '.'.join(ec_res['log_file'].split('.')[:-1])
parent_dir = os.path.dirname(test_report_fp)
# parent dir for test report may not be writable at this time, e.g. when --read-only-installdir is used
if os.stat(parent_dir).st_mode & 0200:
write_file(test_report_fp, test_report_txt)
else:
adjust_permissions(parent_dir, stat.S_IWUSR, add=True, recursive=False)
write_file(test_report_fp, test_report_txt)
adjust_permissions(parent_dir, stat.S_IWUSR, add=False, recursive=False)
if not ec_res['success'] and exit_on_failure:
if 'traceback' in ec_res:
raise EasyBuildError(ec_res['traceback'])
else:
raise EasyBuildError(test_msg)
res.append((ec, ec_res))
def build_and_install_software(ecs, init_session_state, exit_on_failure=True, hooks=None):
"""
Build and install software for all provided parsed easyconfig files.
:param ecs: easyconfig files to install software with
:param init_session_state: initial session state, to use in test reports
:param exit_on_failure: whether or not to exit on installation failure
:param hooks: list of defined pre- and post-step hooks
"""
# obtain a copy of the starting environment so each build can start afresh
# we shouldn't use the environment from init_session_state, since relevant env vars might have been set since
# e.g. via easyconfig.handle_allowed_system_deps
init_env = copy.deepcopy(os.environ)
run_hook(START, hooks)
res = []
for ec in ecs:
ec_res = {}
try:
(ec_res['success'], app_log, err) = build_and_install_one(ec, init_env, hooks=hooks)
ec_res['log_file'] = app_log
if not ec_res['success']:
ec_res['err'] = EasyBuildError(err)
except Exception, err:
# purposely catch all exceptions
ec_res['success'] = False
ec_res['err'] = err
ec_res['traceback'] = traceback.format_exc()
# keep track of success/total count
if ec_res['success']:
test_msg = "Successfully built %s" % ec['spec']
else:
test_msg = "Build of %s failed" % ec['spec']
if 'err' in ec_res:
test_msg += " (err: %s)" % ec_res['err']
# dump test report next to log file
test_report_txt = create_test_report(test_msg, [(ec, ec_res)], init_session_state)
if 'log_file' in ec_res and ec_res['log_file']:
test_report_fp = "%s_test_report.md" % '.'.join(ec_res['log_file'].split('.')[:-1])
parent_dir = os.path.dirname(test_report_fp)
# parent dir for test report may not be writable at this time, e.g. when --read-only-installdir is used
if os.stat(parent_dir).st_mode & 0200:
write_file(test_report_fp, test_report_txt)
else:
adjust_permissions(parent_dir, stat.S_IWUSR, add=True, recursive=False)
write_file(test_report_fp, test_report_txt)
adjust_permissions(parent_dir, stat.S_IWUSR, add=False, recursive=False)
if not ec_res['success'] and exit_on_failure:
if 'traceback' in ec_res:
raise EasyBuildError(ec_res['traceback'])
else:
raise EasyBuildError(test_msg)
res.append((ec, ec_res))
def test_run_hook(self):
"""Test for run_hook function."""
hooks = load_hooks(self.test_hooks_pymod)
self.mock_stdout(True)
self.mock_stderr(True)
run_hook('start', hooks)
run_hook('configure', hooks, pre_step_hook=True, args=[None])
run_hook('configure', hooks, post_step_hook=True, args=[None])
run_hook('build', hooks, pre_step_hook=True, args=[None])
run_hook('build', hooks, post_step_hook=True, args=[None])
run_hook('install', hooks, pre_step_hook=True, args=[None])
run_hook('install', hooks, post_step_hook=True, args=[None])
stdout = self.get_stdout()
stderr = self.get_stderr()
self.mock_stdout(False)
self.mock_stderr(False)
expected_stdout = '\n'.join([
"running start hook",
"running post-configure hook",
"running foo helper method",
"running pre-install hook",
])
self.assertEqual(stdout.strip(), expected_stdout)
self.assertEqual(stderr, '')
def main(args=None, logfile=None, do_build=None, testing=False, modtool=None):
"""
Main function: parse command line options, and act accordingly.
:param args: command line arguments to use
:param logfile: log file to use
:param do_build: whether or not to actually perform the build
:param testing: enable testing mode
"""
register_lock_cleanup_signal_handlers()
# if $CDPATH is set, unset it, it'll only cause trouble...
# see https://github.com/easybuilders/easybuild-framework/issues/2944
if 'CDPATH' in os.environ:
del os.environ['CDPATH']
# purposely session state very early, to avoid modules loaded by EasyBuild meddling in
init_session_state = session_state()
eb_go, cfg_settings = set_up_configuration(args=args, logfile=logfile, testing=testing)
options, orig_paths = eb_go.options, eb_go.args
global _log
(build_specs, _log, logfile, robot_path, search_query, eb_tmpdir, try_to_generate, tweaked_ecs_paths) = cfg_settings
# load hook implementations (if any)
hooks = load_hooks(options.hooks)
run_hook(START, hooks)
if modtool is None:
modtool = modules_tool(testing=testing)
# check whether any (EasyBuild-generated) modules are loaded already in the current session
modtool.check_loaded_modules()
if options.last_log:
# print location to last log file, and exit
last_log = find_last_log(logfile) or '(none)'
print_msg(last_log, log=_log, prefix=False)
# check whether packaging is supported when it's being used
if options.package:
check_pkg_support()
else:
_log.debug("Packaging not enabled, so not checking for packaging support.")
# search for easyconfigs, if a query is specified
if search_query:
search_easyconfigs(search_query, short=options.search_short, filename_only=options.search_filename,
terse=options.terse)
# GitHub options that warrant a silent cleanup & exit
if options.check_github:
check_github()
elif options.install_github_token:
install_github_token(options.github_user, silent=build_option('silent'))
elif options.close_pr:
close_pr(options.close_pr, motivation_msg=options.close_pr_msg)
elif options.list_prs:
print(list_prs(options.list_prs))
elif options.merge_pr:
merge_pr(options.merge_pr)
elif options.review_pr:
print(review_pr(pr=options.review_pr, colored=use_color(options.color)))
elif options.list_installed_software:
detailed = options.list_installed_software == 'detailed'
print(list_software(output_format=options.output_format, detailed=detailed, only_installed=True))
elif options.list_software:
print(list_software(output_format=options.output_format, detailed=options.list_software == 'detailed'))
elif options.create_index:
print_msg("Creating index for %s..." % options.create_index, prefix=False)
index_fp = dump_index(options.create_index, max_age_sec=options.index_max_age)
index = load_index(options.create_index)
print_msg("Index created at %s (%d files)" % (index_fp, len(index)), prefix=False)
# non-verbose cleanup after handling GitHub integration stuff or printing terse info
early_stop_options = [
options.check_github,
options.create_index,
options.install_github_token,
options.list_installed_software,
options.list_software,
options.close_pr,
options.list_prs,
options.merge_pr,
options.review_pr,
options.terse,
search_query,
]
if any(early_stop_options):
clean_exit(logfile, eb_tmpdir, testing, silent=True)
# update session state
eb_config = eb_go.generate_cmd_line(add_default=True)
modlist = modtool.list() # build options must be initialized first before 'module list' works
init_session_state.update({'easybuild_configuration': eb_config})
init_session_state.update({'module_list': modlist})
_log.debug("Initial session state: %s" % init_session_state)
# determine easybuild-easyconfigs package install path
easyconfigs_pkg_paths = get_paths_for(subdir=EASYCONFIGS_PKG_SUBDIR)
if not easyconfigs_pkg_paths:
_log.warning("Failed to determine install path for easybuild-easyconfigs package.")
if options.install_latest_eb_release:
if orig_paths:
raise EasyBuildError("Installing the latest EasyBuild release can not be combined with installing "
"other easyconfigs")
else:
eb_file = find_easybuild_easyconfig()
orig_paths.append(eb_file)
if len(orig_paths) == 1:
# if only one easyconfig file is specified, use current directory as target directory
target_path = os.getcwd()
elif orig_paths:
# last path is target when --copy-ec is used, so remove that from the list
target_path = orig_paths.pop() if options.copy_ec else None
categorized_paths = categorize_files_by_type(orig_paths)
# command line options that do not require any easyconfigs to be specified
pr_options = options.new_branch_github or options.new_pr or options.new_pr_from_branch or options.preview_pr
pr_options = pr_options or options.sync_branch_with_develop or options.sync_pr_with_develop
pr_options = pr_options or options.update_branch_github or options.update_pr
no_ec_opts = [options.aggregate_regtest, options.regtest, pr_options, search_query]
# determine paths to easyconfigs
determined_paths = det_easyconfig_paths(categorized_paths['easyconfigs'])
if (options.copy_ec and not tweaked_ecs_paths) or options.fix_deprecated_easyconfigs or options.show_ec:
if options.copy_ec:
if len(determined_paths) == 1:
copy_file(determined_paths[0], target_path)
print_msg("%s copied to %s" % (os.path.basename(determined_paths[0]), target_path), prefix=False)
elif len(determined_paths) > 1:
copy_files(determined_paths, target_path)
print_msg("%d file(s) copied to %s" % (len(determined_paths), target_path), prefix=False)
else:
raise EasyBuildError("One of more files to copy should be specified!")
elif options.fix_deprecated_easyconfigs:
fix_deprecated_easyconfigs(determined_paths)
elif options.show_ec:
for path in determined_paths:
print_msg("Contents of %s:" % path)
print_msg(read_file(path), prefix=False)
clean_exit(logfile, eb_tmpdir, testing)
if determined_paths:
# transform paths into tuples, use 'False' to indicate the corresponding easyconfig files were not generated
paths = [(p, False) for p in determined_paths]
elif 'name' in build_specs:
# try to obtain or generate an easyconfig file via build specifications if a software name is provided
paths = find_easyconfigs_by_specs(build_specs, robot_path, try_to_generate, testing=testing)
elif any(no_ec_opts):
paths = determined_paths
else:
print_error("Please provide one or multiple easyconfig files, or use software build " +
"options to make EasyBuild search for easyconfigs",
log=_log, opt_parser=eb_go.parser, exit_on_error=not testing)
_log.debug("Paths: %s", paths)
# run regtest
if options.regtest or options.aggregate_regtest:
_log.info("Running regression test")
# fallback: easybuild-easyconfigs install path
regtest_ok = regtest([path[0] for path in paths] or easyconfigs_pkg_paths, modtool)
if not regtest_ok:
_log.info("Regression test failed (partially)!")
sys.exit(31) # exit -> 3x1t -> 31
# read easyconfig files
easyconfigs, generated_ecs = parse_easyconfigs(paths, validate=not options.inject_checksums)
# handle --check-contrib & --check-style options
if run_contrib_style_checks([ec['ec'] for ec in easyconfigs], options.check_contrib, options.check_style):
clean_exit(logfile, eb_tmpdir, testing)
# verify easyconfig filenames, if desired
if options.verify_easyconfig_filenames:
_log.info("Verifying easyconfig filenames...")
for easyconfig in easyconfigs:
verify_easyconfig_filename(easyconfig['spec'], easyconfig['ec'], parsed_ec=easyconfig['ec'])
# tweak obtained easyconfig files, if requested
# don't try and tweak anything if easyconfigs were generated, since building a full dep graph will fail
# if easyconfig files for the dependencies are not available
if try_to_generate and build_specs and not generated_ecs:
easyconfigs = tweak(easyconfigs, build_specs, modtool, targetdirs=tweaked_ecs_paths)
if options.containerize:
# if --containerize/-C create a container recipe (and optionally container image), and stop
containerize(easyconfigs)
clean_exit(logfile, eb_tmpdir, testing)
forced = options.force or options.rebuild
dry_run_mode = options.dry_run or options.dry_run_short or options.missing_modules
# skip modules that are already installed unless forced, or unless an option is used that warrants not skipping
if not (forced or dry_run_mode or options.extended_dry_run or pr_options or options.inject_checksums):
retained_ecs = skip_available(easyconfigs, modtool)
if not testing:
for skipped_ec in [ec for ec in easyconfigs if ec not in retained_ecs]:
print_msg("%s is already installed (module found), skipping" % skipped_ec['full_mod_name'])
easyconfigs = retained_ecs
# keep track for which easyconfigs we should set the corresponding module as default
if options.set_default_module:
for easyconfig in easyconfigs:
easyconfig['ec'].set_default_module = True
# determine an order that will allow all specs in the set to build
if len(easyconfigs) > 0:
# resolve dependencies if robot is enabled, except in dry run mode
# one exception: deps *are* resolved with --new-pr or --update-pr when dry run mode is enabled
if options.robot and (not dry_run_mode or pr_options):
print_msg("resolving dependencies ...", log=_log, silent=testing)
ordered_ecs = resolve_dependencies(easyconfigs, modtool)
else:
ordered_ecs = easyconfigs
elif pr_options:
ordered_ecs = None
else:
print_msg("No easyconfigs left to be built.", log=_log, silent=testing)
ordered_ecs = []
if options.copy_ec and tweaked_ecs_paths:
all_specs = [spec['spec'] for spec in
resolve_dependencies(easyconfigs, modtool, retain_all_deps=True, raise_error_missing_ecs=False)]
tweaked_ecs_in_all_ecs = [path for path in all_specs if
any(tweaked_ecs_path in path for tweaked_ecs_path in tweaked_ecs_paths)]
if tweaked_ecs_in_all_ecs:
# Clean them, then copy them
clean_up_easyconfigs(tweaked_ecs_in_all_ecs)
copy_files(tweaked_ecs_in_all_ecs, target_path)
print_msg("%d file(s) copied to %s" % (len(tweaked_ecs_in_all_ecs), target_path), prefix=False)
# creating/updating PRs
if pr_options:
if options.new_pr:
new_pr(categorized_paths, ordered_ecs)
elif options.new_branch_github:
new_branch_github(categorized_paths, ordered_ecs)
elif options.new_pr_from_branch:
new_pr_from_branch(options.new_pr_from_branch)
elif options.preview_pr:
print(review_pr(paths=determined_paths, colored=use_color(options.color)))
elif options.sync_branch_with_develop:
sync_branch_with_develop(options.sync_branch_with_develop)
elif options.sync_pr_with_develop:
sync_pr_with_develop(options.sync_pr_with_develop)
elif options.update_branch_github:
update_branch(options.update_branch_github, categorized_paths, ordered_ecs)
elif options.update_pr:
update_pr(options.update_pr, categorized_paths, ordered_ecs)
else:
raise EasyBuildError("Unknown PR option!")
# dry_run: print all easyconfigs and dependencies, and whether they are already built
elif dry_run_mode:
if options.missing_modules:
txt = missing_deps(easyconfigs, modtool)
else:
txt = dry_run(easyconfigs, modtool, short=not options.dry_run)
print_msg(txt, log=_log, silent=testing, prefix=False)
elif options.check_conflicts:
if check_conflicts(easyconfigs, modtool):
print_error("One or more conflicts detected!")
sys.exit(1)
else:
print_msg("\nNo conflicts detected!\n", prefix=False)
# dump source script to set up build environment
elif options.dump_env_script:
dump_env_script(easyconfigs)
elif options.inject_checksums:
inject_checksums(ordered_ecs, options.inject_checksums)
# cleanup and exit after dry run, searching easyconfigs or submitting regression test
stop_options = [options.check_conflicts, dry_run_mode, options.dump_env_script, options.inject_checksums]
if any(no_ec_opts) or any(stop_options):
clean_exit(logfile, eb_tmpdir, testing)
# create dependency graph and exit
if options.dep_graph:
_log.info("Creating dependency graph %s" % options.dep_graph)
dep_graph(options.dep_graph, ordered_ecs)
clean_exit(logfile, eb_tmpdir, testing, silent=True)
# submit build as job(s), clean up and exit
if options.job:
submit_jobs(ordered_ecs, eb_go.generate_cmd_line(), testing=testing)
if not testing:
print_msg("Submitted parallel build jobs, exiting now")
clean_exit(logfile, eb_tmpdir, testing)
# build software, will exit when errors occurs (except when testing)
if not testing or (testing and do_build):
exit_on_failure = not (options.dump_test_report or options.upload_test_report)
ecs_with_res = build_and_install_software(ordered_ecs, init_session_state, exit_on_failure=exit_on_failure)
else:
ecs_with_res = [(ec, {}) for ec in ordered_ecs]
correct_builds_cnt = len([ec_res for (_, ec_res) in ecs_with_res if ec_res.get('success', False)])
overall_success = correct_builds_cnt == len(ordered_ecs)
success_msg = "Build succeeded for %s out of %s" % (correct_builds_cnt, len(ordered_ecs))
repo = init_repository(get_repository(), get_repositorypath())
repo.cleanup()
# dump/upload overall test report
test_report_msg = overall_test_report(ecs_with_res, len(paths), overall_success, success_msg, init_session_state)
if test_report_msg is not None:
print_msg(test_report_msg)
print_msg(success_msg, log=_log, silent=testing)
# cleanup and spec files
for ec in easyconfigs:
if 'original_spec' in ec and os.path.isfile(ec['spec']):
os.remove(ec['spec'])
run_hook(END, hooks)
# stop logging and cleanup tmp log file, unless one build failed (individual logs are located in eb_tmpdir)
stop_logging(logfile, logtostdout=options.logtostdout)
if overall_success:
cleanup(logfile, eb_tmpdir, testing)
def test_run_hook(self):
"""Test for run_hook function."""
hooks = load_hooks(self.test_hooks_pymod)
self.mock_stdout(True)
self.mock_stderr(True)
run_hook('start', hooks)
run_hook('parse',
hooks,
args=['<EasyConfig instance>'],
msg="Running parse hook for example.eb...")
run_hook('configure', hooks, pre_step_hook=True, args=[None])
run_hook('configure', hooks, post_step_hook=True, args=[None])
run_hook('build', hooks, pre_step_hook=True, args=[None])
run_hook('build', hooks, post_step_hook=True, args=[None])
run_hook('install', hooks, pre_step_hook=True, args=[None])
run_hook('install', hooks, post_step_hook=True, args=[None])
stdout = self.get_stdout()
stderr = self.get_stderr()
self.mock_stdout(False)
self.mock_stderr(False)
expected_stdout = '\n'.join([
"== Running start hook...",
"this is triggered at the very beginning",
"== Running parse hook for example.eb...",
"Parse hook with argument <EasyConfig instance>",
"== Running post-configure hook...",
"this is run after configure step",
"running foo helper method",
"== Running pre-install hook...",
"this is run before install step",
])
self.assertEqual(stdout.strip(), expected_stdout)
self.assertEqual(stderr, '')
recursive=False)
write_file(test_report_fp, test_report_txt)
adjust_permissions(parent_dir,
stat.S_IWUSR,
add=False,
recursive=False)
if not ec_res['success'] and exit_on_failure:
if 'traceback' in ec_res:
raise EasyBuildError(ec_res['traceback'])
else:
raise EasyBuildError(test_msg)
res.append((ec, ec_res))
run_hook(END, hooks)
return res
def check_root_usage(allow_use_as_root=False):
"""
Check whether we are running as root, and act accordingly
:param allow_use_as_root: allow use of EasyBuild as root (but do print a warning when doing so)
"""
if os.getuid() == 0:
if allow_use_as_root:
msg = "Using EasyBuild as root is NOT recommended, please proceed with care!\n"
msg += "(this is only allowed because EasyBuild was configured with "
msg += "--allow-use-as-root-and-accept-consequences)"
if os.stat(parent_dir).st_mode & 0200:
write_file(test_report_fp, test_report_txt)
else:
adjust_permissions(parent_dir, stat.S_IWUSR, add=True, recursive=False)
write_file(test_report_fp, test_report_txt)
adjust_permissions(parent_dir, stat.S_IWUSR, add=False, recursive=False)
if not ec_res['success'] and exit_on_failure:
if 'traceback' in ec_res:
raise EasyBuildError(ec_res['traceback'])
else:
raise EasyBuildError(test_msg)
res.append((ec, ec_res))
run_hook(END, hooks)
return res
def check_root_usage(allow_use_as_root=False):
"""
Check whether we are running as root, and act accordingly
:param allow_use_as_root: allow use of EasyBuild as root (but do print a warning when doing so)
"""
if os.getuid() == 0:
if allow_use_as_root:
msg = "Using EasyBuild as root is NOT recommended, please proceed with care!\n"
msg += "(this is only allowed because EasyBuild was configured with "
msg += "--allow-use-as-root-and-accept-consequences)"
def main(args=None, logfile=None, do_build=None, testing=False, modtool=None):
"""
Main function: parse command line options, and act accordingly.
:param args: command line arguments to use
:param logfile: log file to use
:param do_build: whether or not to actually perform the build
:param testing: enable testing mode
"""
# purposely session state very early, to avoid modules loaded by EasyBuild meddling in
init_session_state = session_state()
eb_go, cfg_settings = set_up_configuration(args=args, logfile=logfile, testing=testing)
options, orig_paths = eb_go.options, eb_go.args
global _log
(build_specs, _log, logfile, robot_path, search_query, eb_tmpdir, try_to_generate, tweaked_ecs_paths) = cfg_settings
# load hook implementations (if any)
hooks = load_hooks(options.hooks)
run_hook(START, hooks)
if modtool is None:
modtool = modules_tool(testing=testing)
# check whether any (EasyBuild-generated) modules are loaded already in the current session
modtool.check_loaded_modules()
if options.last_log:
# print location to last log file, and exit
last_log = find_last_log(logfile) or '(none)'
print_msg(last_log, log=_log, prefix=False)
# check whether packaging is supported when it's being used
if options.package:
check_pkg_support()
else:
_log.debug("Packaging not enabled, so not checking for packaging support.")
# search for easyconfigs, if a query is specified
if search_query:
search_easyconfigs(search_query, short=options.search_short, filename_only=options.search_filename,
terse=options.terse)
# GitHub options that warrant a silent cleanup & exit
if options.check_github:
check_github()
elif options.install_github_token:
install_github_token(options.github_user, silent=build_option('silent'))
elif options.close_pr:
close_pr(options.close_pr, motivation_msg=options.close_pr_msg)
elif options.list_prs:
print(list_prs(options.list_prs))
elif options.merge_pr:
merge_pr(options.merge_pr)
elif options.review_pr:
print(review_pr(pr=options.review_pr, colored=use_color(options.color)))
elif options.list_installed_software:
detailed = options.list_installed_software == 'detailed'
print(list_software(output_format=options.output_format, detailed=detailed, only_installed=True))
elif options.list_software:
print(list_software(output_format=options.output_format, detailed=options.list_software == 'detailed'))
# non-verbose cleanup after handling GitHub integration stuff or printing terse info
early_stop_options = [
options.check_github,
options.install_github_token,
options.list_installed_software,
options.list_software,
options.close_pr,
options.list_prs,
options.merge_pr,
options.review_pr,
options.terse,
search_query,
]
if any(early_stop_options):
clean_exit(logfile, eb_tmpdir, testing, silent=True)
# update session state
eb_config = eb_go.generate_cmd_line(add_default=True)
modlist = modtool.list() # build options must be initialized first before 'module list' works
init_session_state.update({'easybuild_configuration': eb_config})
init_session_state.update({'module_list': modlist})
_log.debug("Initial session state: %s" % init_session_state)
# determine easybuild-easyconfigs package install path
easyconfigs_pkg_paths = get_paths_for(subdir=EASYCONFIGS_PKG_SUBDIR)
if not easyconfigs_pkg_paths:
_log.warning("Failed to determine install path for easybuild-easyconfigs package.")
if options.install_latest_eb_release:
if orig_paths:
raise EasyBuildError("Installing the latest EasyBuild release can not be combined with installing "
"other easyconfigs")
else:
eb_file = find_easybuild_easyconfig()
orig_paths.append(eb_file)
categorized_paths = categorize_files_by_type(orig_paths)
# command line options that do not require any easyconfigs to be specified
new_update_preview_pr = options.new_pr or options.update_pr or options.preview_pr
no_ec_opts = [options.aggregate_regtest, options.regtest, search_query, new_update_preview_pr]
# determine paths to easyconfigs
determined_paths = det_easyconfig_paths(categorized_paths['easyconfigs'])
if determined_paths:
# transform paths into tuples, use 'False' to indicate the corresponding easyconfig files were not generated
paths = [(p, False) for p in determined_paths]
else:
if 'name' in build_specs:
# try to obtain or generate an easyconfig file via build specifications if a software name is provided
paths = find_easyconfigs_by_specs(build_specs, robot_path, try_to_generate, testing=testing)
elif any(no_ec_opts):
paths = determined_paths
else:
print_error(("Please provide one or multiple easyconfig files, or use software build "
"options to make EasyBuild search for easyconfigs"),
log=_log, opt_parser=eb_go.parser, exit_on_error=not testing)
_log.debug("Paths: %s" % paths)
# run regtest
if options.regtest or options.aggregate_regtest:
_log.info("Running regression test")
# fallback: easybuild-easyconfigs install path
regtest_ok = regtest([path[0] for path in paths] or easyconfigs_pkg_paths, modtool)
if not regtest_ok:
_log.info("Regression test failed (partially)!")
sys.exit(31) # exit -> 3x1t -> 31
# read easyconfig files
easyconfigs, generated_ecs = parse_easyconfigs(paths, validate=not options.inject_checksums)
# handle --check-contrib & --check-style options
if run_contrib_style_checks([ec['ec'] for ec in easyconfigs], options.check_contrib, options.check_style):
clean_exit(logfile, eb_tmpdir, testing)
# verify easyconfig filenames, if desired
if options.verify_easyconfig_filenames:
_log.info("Verifying easyconfig filenames...")
for easyconfig in easyconfigs:
verify_easyconfig_filename(easyconfig['spec'], easyconfig['ec'], parsed_ec=easyconfig['ec'])
# tweak obtained easyconfig files, if requested
# don't try and tweak anything if easyconfigs were generated, since building a full dep graph will fail
# if easyconfig files for the dependencies are not available
if try_to_generate and build_specs and not generated_ecs:
easyconfigs = tweak(easyconfigs, build_specs, modtool, targetdirs=tweaked_ecs_paths)
if options.containerize:
# if --containerize/-C create a container recipe (and optionally container image), and stop
containerize(easyconfigs)
clean_exit(logfile, eb_tmpdir, testing)
forced = options.force or options.rebuild
dry_run_mode = options.dry_run or options.dry_run_short
# skip modules that are already installed unless forced, or unless an option is used that warrants not skipping
if not (forced or dry_run_mode or options.extended_dry_run or new_update_preview_pr or options.inject_checksums):
retained_ecs = skip_available(easyconfigs, modtool)
if not testing:
for skipped_ec in [ec for ec in easyconfigs if ec not in retained_ecs]:
print_msg("%s is already installed (module found), skipping" % skipped_ec['full_mod_name'])
easyconfigs = retained_ecs
# determine an order that will allow all specs in the set to build
if len(easyconfigs) > 0:
# resolve dependencies if robot is enabled, except in dry run mode
# one exception: deps *are* resolved with --new-pr or --update-pr when dry run mode is enabled
if options.robot and (not dry_run_mode or new_update_preview_pr):
print_msg("resolving dependencies ...", log=_log, silent=testing)
ordered_ecs = resolve_dependencies(easyconfigs, modtool)
else:
ordered_ecs = easyconfigs
elif new_update_preview_pr:
ordered_ecs = None
else:
print_msg("No easyconfigs left to be built.", log=_log, silent=testing)
ordered_ecs = []
# creating/updating PRs
if new_update_preview_pr:
if options.new_pr:
new_pr(categorized_paths, ordered_ecs, title=options.pr_title, descr=options.pr_descr,
commit_msg=options.pr_commit_msg)
elif options.preview_pr:
print(review_pr(paths=determined_paths, colored=use_color(options.color)))
else:
update_pr(options.update_pr, categorized_paths, ordered_ecs, commit_msg=options.pr_commit_msg)
# dry_run: print all easyconfigs and dependencies, and whether they are already built
elif dry_run_mode:
txt = dry_run(easyconfigs, modtool, short=not options.dry_run)
print_msg(txt, log=_log, silent=testing, prefix=False)
elif options.check_conflicts:
if check_conflicts(easyconfigs, modtool):
print_error("One or more conflicts detected!")
sys.exit(1)
else:
print_msg("\nNo conflicts detected!\n", prefix=False)
# dump source script to set up build environment
elif options.dump_env_script:
dump_env_script(easyconfigs)
elif options.inject_checksums:
inject_checksums(ordered_ecs, options.inject_checksums)
# cleanup and exit after dry run, searching easyconfigs or submitting regression test
stop_options = [options.check_conflicts, dry_run_mode, options.dump_env_script, options.inject_checksums]
if any(no_ec_opts) or any(stop_options):
clean_exit(logfile, eb_tmpdir, testing)
# create dependency graph and exit
if options.dep_graph:
_log.info("Creating dependency graph %s" % options.dep_graph)
dep_graph(options.dep_graph, ordered_ecs)
clean_exit(logfile, eb_tmpdir, testing, silent=True)
# submit build as job(s), clean up and exit
if options.job:
submit_jobs(ordered_ecs, eb_go.generate_cmd_line(), testing=testing)
if not testing:
print_msg("Submitted parallel build jobs, exiting now")
clean_exit(logfile, eb_tmpdir, testing)
# build software, will exit when errors occurs (except when testing)
if not testing or (testing and do_build):
exit_on_failure = not (options.dump_test_report or options.upload_test_report)
ecs_with_res = build_and_install_software(ordered_ecs, init_session_state, exit_on_failure=exit_on_failure)
else:
ecs_with_res = [(ec, {}) for ec in ordered_ecs]
correct_builds_cnt = len([ec_res for (_, ec_res) in ecs_with_res if ec_res.get('success', False)])
overall_success = correct_builds_cnt == len(ordered_ecs)
success_msg = "Build succeeded for %s out of %s" % (correct_builds_cnt, len(ordered_ecs))
repo = init_repository(get_repository(), get_repositorypath())
repo.cleanup()
# dump/upload overall test report
test_report_msg = overall_test_report(ecs_with_res, len(paths), overall_success, success_msg, init_session_state)
if test_report_msg is not None:
print_msg(test_report_msg)
print_msg(success_msg, log=_log, silent=testing)
# cleanup and spec files
for ec in easyconfigs:
if 'original_spec' in ec and os.path.isfile(ec['spec']):
os.remove(ec['spec'])
run_hook(END, hooks)
# stop logging and cleanup tmp log file, unless one build failed (individual logs are located in eb_tmpdir)
stop_logging(logfile, logtostdout=options.logtostdout)
if overall_success:
cleanup(logfile, eb_tmpdir, testing)
def main(args=None, logfile=None, do_build=None, testing=False, modtool=None):
"""
Main function: parse command line options, and act accordingly.
:param args: command line arguments to use
:param logfile: log file to use
:param do_build: whether or not to actually perform the build
:param testing: enable testing mode
"""
# purposely session state very early, to avoid modules loaded by EasyBuild meddling in
init_session_state = session_state()
# initialise options
eb_go = eboptions.parse_options(args=args)
options = eb_go.options
orig_paths = eb_go.args
# set umask (as early as possible)
if options.umask is not None:
new_umask = int(options.umask, 8)
old_umask = os.umask(new_umask)
# set by option parsers via set_tmpdir
eb_tmpdir = tempfile.gettempdir()
search_query = options.search or options.search_filename or options.search_short
# initialise logging for main
global _log
_log, logfile = init_logging(logfile, logtostdout=options.logtostdout,
silent=(testing or options.terse or search_query), colorize=options.color)
# disallow running EasyBuild as root (by default)
check_root_usage(allow_use_as_root=options.allow_use_as_root_and_accept_consequences)
# log startup info
eb_cmd_line = eb_go.generate_cmd_line() + eb_go.args
log_start(eb_cmd_line, eb_tmpdir)
if options.umask is not None:
_log.info("umask set to '%s' (used to be '%s')" % (oct(new_umask), oct(old_umask)))
# process software build specifications (if any), i.e.
# software name/version, toolchain name/version, extra patches, ...
(try_to_generate, build_specs) = process_software_build_specs(options)
# determine robot path
# --try-X, --dep-graph, --search use robot path for searching, so enable it with path of installed easyconfigs
tweaked_ecs = try_to_generate and build_specs
tweaked_ecs_paths, pr_path = alt_easyconfig_paths(eb_tmpdir, tweaked_ecs=tweaked_ecs, from_pr=options.from_pr)
auto_robot = try_to_generate or options.check_conflicts or options.dep_graph or search_query
robot_path = det_robot_path(options.robot_paths, tweaked_ecs_paths, pr_path, auto_robot=auto_robot)
_log.debug("Full robot path: %s" % robot_path)
# configure & initialize build options
config_options_dict = eb_go.get_options_by_section('config')
build_options = {
'build_specs': build_specs,
'command_line': eb_cmd_line,
'external_modules_metadata': parse_external_modules_metadata(options.external_modules_metadata),
'pr_path': pr_path,
'robot_path': robot_path,
'silent': testing,
'try_to_generate': try_to_generate,
'valid_stops': [x[0] for x in EasyBlock.get_steps()],
}
# initialise the EasyBuild configuration & build options
config.init(options, config_options_dict)
config.init_build_options(build_options=build_options, cmdline_options=options)
# load hook implementations (if any)
hooks = load_hooks(options.hooks)
run_hook(START, hooks)
if modtool is None:
modtool = modules_tool(testing=testing)
# check whether any (EasyBuild-generated) modules are loaded already in the current session
modtool.check_loaded_modules()
if options.last_log:
# print location to last log file, and exit
last_log = find_last_log(logfile) or '(none)'
print_msg(last_log, log=_log, prefix=False)
# check whether packaging is supported when it's being used
if options.package:
check_pkg_support()
else:
_log.debug("Packaging not enabled, so not checking for packaging support.")
# search for easyconfigs, if a query is specified
if search_query:
search_easyconfigs(search_query, short=options.search_short, filename_only=options.search_filename,
terse=options.terse)
# GitHub options that warrant a silent cleanup & exit
if options.check_github:
check_github()
elif options.install_github_token:
install_github_token(options.github_user, silent=build_option('silent'))
elif options.merge_pr:
merge_pr(options.merge_pr)
elif options.review_pr:
print review_pr(pr=options.review_pr, colored=use_color(options.color))
elif options.list_installed_software:
detailed = options.list_installed_software == 'detailed'
print list_software(output_format=options.output_format, detailed=detailed, only_installed=True)
elif options.list_software:
print list_software(output_format=options.output_format, detailed=options.list_software == 'detailed')
# non-verbose cleanup after handling GitHub integration stuff or printing terse info
early_stop_options = [
options.check_github,
options.install_github_token,
options.list_installed_software,
options.list_software,
options.merge_pr,
options.review_pr,
options.terse,
search_query,
]
if any(early_stop_options):
clean_exit(logfile, eb_tmpdir, testing, silent=True)
# update session state
eb_config = eb_go.generate_cmd_line(add_default=True)
modlist = modtool.list() # build options must be initialized first before 'module list' works
init_session_state.update({'easybuild_configuration': eb_config})
init_session_state.update({'module_list': modlist})
_log.debug("Initial session state: %s" % init_session_state)
# determine easybuild-easyconfigs package install path
easyconfigs_pkg_paths = get_paths_for(subdir=EASYCONFIGS_PKG_SUBDIR)
if not easyconfigs_pkg_paths:
_log.warning("Failed to determine install path for easybuild-easyconfigs package.")
if options.install_latest_eb_release:
if orig_paths:
raise EasyBuildError("Installing the latest EasyBuild release can not be combined with installing "
"other easyconfigs")
else:
eb_file = find_easybuild_easyconfig()
orig_paths.append(eb_file)
categorized_paths = categorize_files_by_type(orig_paths)
# command line options that do not require any easyconfigs to be specified
new_update_preview_pr = options.new_pr or options.update_pr or options.preview_pr
no_ec_opts = [options.aggregate_regtest, options.regtest, search_query, new_update_preview_pr]
# determine paths to easyconfigs
determined_paths = det_easyconfig_paths(categorized_paths['easyconfigs'])
if determined_paths:
# transform paths into tuples, use 'False' to indicate the corresponding easyconfig files were not generated
paths = [(p, False) for p in determined_paths]
else:
if 'name' in build_specs:
# try to obtain or generate an easyconfig file via build specifications if a software name is provided
paths = find_easyconfigs_by_specs(build_specs, robot_path, try_to_generate, testing=testing)
elif any(no_ec_opts):
paths = determined_paths
else:
print_error(("Please provide one or multiple easyconfig files, or use software build "
"options to make EasyBuild search for easyconfigs"),
log=_log, opt_parser=eb_go.parser, exit_on_error=not testing)
_log.debug("Paths: %s" % paths)
# run regtest
if options.regtest or options.aggregate_regtest:
_log.info("Running regression test")
# fallback: easybuild-easyconfigs install path
regtest_ok = regtest([path[0] for path in paths] or easyconfigs_pkg_paths, modtool)
if not regtest_ok:
_log.info("Regression test failed (partially)!")
sys.exit(31) # exit -> 3x1t -> 31
# read easyconfig files
easyconfigs, generated_ecs = parse_easyconfigs(paths, validate=not options.inject_checksums)
# handle --check-contrib & --check-style options
if run_contrib_style_checks([ec['ec'] for ec in easyconfigs], options.check_contrib, options.check_style):
clean_exit(logfile, eb_tmpdir, testing)
# verify easyconfig filenames, if desired
if options.verify_easyconfig_filenames:
_log.info("Verifying easyconfig filenames...")
for easyconfig in easyconfigs:
verify_easyconfig_filename(easyconfig['spec'], easyconfig['ec'], parsed_ec=easyconfig['ec'])
# tweak obtained easyconfig files, if requested
# don't try and tweak anything if easyconfigs were generated, since building a full dep graph will fail
# if easyconfig files for the dependencies are not available
if try_to_generate and build_specs and not generated_ecs:
easyconfigs = tweak(easyconfigs, build_specs, modtool, targetdirs=tweaked_ecs_paths)
if options.containerize:
# if --containerize/-C create a container recipe (and optionally container image), and stop
containerize(easyconfigs)
clean_exit(logfile, eb_tmpdir, testing)
forced = options.force or options.rebuild
dry_run_mode = options.dry_run or options.dry_run_short
# skip modules that are already installed unless forced, or unless an option is used that warrants not skipping
if not (forced or dry_run_mode or options.extended_dry_run or new_update_preview_pr or options.inject_checksums):
retained_ecs = skip_available(easyconfigs, modtool)
if not testing:
for skipped_ec in [ec for ec in easyconfigs if ec not in retained_ecs]:
print_msg("%s is already installed (module found), skipping" % skipped_ec['full_mod_name'])
easyconfigs = retained_ecs
# determine an order that will allow all specs in the set to build
if len(easyconfigs) > 0:
# resolve dependencies if robot is enabled, except in dry run mode
# one exception: deps *are* resolved with --new-pr or --update-pr when dry run mode is enabled
if options.robot and (not dry_run_mode or new_update_preview_pr):
print_msg("resolving dependencies ...", log=_log, silent=testing)
ordered_ecs = resolve_dependencies(easyconfigs, modtool)
else:
ordered_ecs = easyconfigs
elif new_update_preview_pr:
ordered_ecs = None
else:
print_msg("No easyconfigs left to be built.", log=_log, silent=testing)
ordered_ecs = []
# creating/updating PRs
if new_update_preview_pr:
if options.new_pr:
new_pr(categorized_paths, ordered_ecs, title=options.pr_title, descr=options.pr_descr,
commit_msg=options.pr_commit_msg)
elif options.preview_pr:
print review_pr(paths=determined_paths, colored=use_color(options.color))
else:
update_pr(options.update_pr, categorized_paths, ordered_ecs, commit_msg=options.pr_commit_msg)
# dry_run: print all easyconfigs and dependencies, and whether they are already built
elif dry_run_mode:
txt = dry_run(easyconfigs, modtool, short=not options.dry_run)
print_msg(txt, log=_log, silent=testing, prefix=False)
elif options.check_conflicts:
if check_conflicts(easyconfigs, modtool):
print_error("One or more conflicts detected!")
sys.exit(1)
else:
print_msg("\nNo conflicts detected!\n", prefix=False)
# dump source script to set up build environment
elif options.dump_env_script:
dump_env_script(easyconfigs)
elif options.inject_checksums:
inject_checksums(ordered_ecs, options.inject_checksums)
# cleanup and exit after dry run, searching easyconfigs or submitting regression test
stop_options = [options.check_conflicts, dry_run_mode, options.dump_env_script, options.inject_checksums]
if any(no_ec_opts) or any(stop_options):
clean_exit(logfile, eb_tmpdir, testing)
# create dependency graph and exit
if options.dep_graph:
_log.info("Creating dependency graph %s" % options.dep_graph)
dep_graph(options.dep_graph, ordered_ecs)
clean_exit(logfile, eb_tmpdir, testing, silent=True)
# submit build as job(s), clean up and exit
if options.job:
submit_jobs(ordered_ecs, eb_go.generate_cmd_line(), testing=testing)
if not testing:
print_msg("Submitted parallel build jobs, exiting now")
clean_exit(logfile, eb_tmpdir, testing)
# build software, will exit when errors occurs (except when testing)
if not testing or (testing and do_build):
exit_on_failure = not (options.dump_test_report or options.upload_test_report)
ecs_with_res = build_and_install_software(ordered_ecs, init_session_state, exit_on_failure=exit_on_failure)
else:
ecs_with_res = [(ec, {}) for ec in ordered_ecs]
correct_builds_cnt = len([ec_res for (_, ec_res) in ecs_with_res if ec_res.get('success', False)])
overall_success = correct_builds_cnt == len(ordered_ecs)
success_msg = "Build succeeded for %s out of %s" % (correct_builds_cnt, len(ordered_ecs))
repo = init_repository(get_repository(), get_repositorypath())
repo.cleanup()
# dump/upload overall test report
test_report_msg = overall_test_report(ecs_with_res, len(paths), overall_success, success_msg, init_session_state)
if test_report_msg is not None:
print_msg(test_report_msg)
print_msg(success_msg, log=_log, silent=testing)
# cleanup and spec files
for ec in easyconfigs:
if 'original_spec' in ec and os.path.isfile(ec['spec']):
os.remove(ec['spec'])
run_hook(END, hooks)
# stop logging and cleanup tmp log file, unless one build failed (individual logs are located in eb_tmpdir)
stop_logging(logfile, logtostdout=options.logtostdout)
if overall_success:
cleanup(logfile, eb_tmpdir, testing)
def test_run_hook(self):
"""Test for run_hook function."""
hooks = load_hooks(self.test_hooks_pymod)
self.mock_stdout(True)
self.mock_stderr(True)
run_hook('start', hooks)
run_hook('parse', hooks, args=['<EasyConfig instance>'], msg="Running parse hook for example.eb...")
run_hook('configure', hooks, pre_step_hook=True, args=[None])
run_hook('configure', hooks, post_step_hook=True, args=[None])
run_hook('build', hooks, pre_step_hook=True, args=[None])
run_hook('build', hooks, post_step_hook=True, args=[None])
run_hook('install', hooks, pre_step_hook=True, args=[None])
run_hook('install', hooks, post_step_hook=True, args=[None])
stdout = self.get_stdout()
stderr = self.get_stderr()
self.mock_stdout(False)
self.mock_stderr(False)
expected_stdout = '\n'.join([
"== Running start hook...",
"this is triggered at the very beginning",
"== Running parse hook for example.eb...",
"Parse hook with argument <EasyConfig instance>",
"== Running post-configure hook...",
"this is run after configure step",
"running foo helper method",
"== Running pre-install hook...",
"this is run before install step",
])
self.assertEqual(stdout.strip(), expected_stdout)
self.assertEqual(stderr, '')
