From d12073327f0a0d64daa631ae7598882a774497f2 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 31 Jan 2024 18:52:00 +0000 Subject: [PATCH] remove unused custom easyblock for IMOD (`imod.py`) --- easybuild/easyblocks/i/imod.py | 95 ---------------------------------- 1 file changed, 95 deletions(-) delete mode 100644 easybuild/easyblocks/i/imod.py diff --git a/easybuild/easyblocks/i/imod.py b/easybuild/easyblocks/i/imod.py deleted file mode 100644 index 75d0760041..0000000000 --- a/easybuild/easyblocks/i/imod.py +++ /dev/null @@ -1,95 +0,0 @@ -## -# Copyright 2013-2023 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://vscentrum.be/nl/en), -# 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 . -## -""" -EasyBuild support for building and installing IMOD, implemented as an easyblock - -@author: Benjamin Roberts (Landcare Research NZ Ltd) -""" -import os -import shutil - -from easybuild.easyblocks.generic.binary import Binary -from easybuild.tools.build_log import EasyBuildError -from easybuild.tools.filetools import remove_dir -from easybuild.tools.run import run_cmd - - -class EB_IMOD(Binary): - """Support for building/installing IMOD.""" - - def install_step(self): - """Install IMOD using install script.""" - - # -dir: Choose location of installation directory - # -skip: do not attempt to deploy resource files in /etc - # -yes: do not prompt for confirmation - script = '{0}_{1}{2}.csh'.format(self.name.lower(), self.version, self.cfg['versionsuffix']) - cmd = "tcsh {0} -dir {1} -script {1} -skip -yes".format(script, self.installdir) - run_cmd(cmd, log_all=True, simple=True) - - # The assumption by the install script is that installdir will be something - # like /usr/local. So it creates, within the specified install location, a - # number of additional directories within which to install IMOD. We will, - # therefore, move the contents of these directories up and throw away the - # directories themselves. Doing so apparently is not a problem so long as - # IMOD_DIR is correctly set in the module. - link_to_remove = os.path.join(self.installdir, self.name) - dir_to_remove = os.path.join(self.installdir, "{0}_{1}".format(self.name.lower(), self.version)) - try: - for entry in os.listdir(dir_to_remove): - shutil.move(os.path.join(dir_to_remove, entry), self.installdir) - if os.path.realpath(link_to_remove) != os.path.realpath(dir_to_remove): - raise EasyBuildError("Something went wrong: %s doesn't point to %s", link_to_remove, dir_to_remove) - remove_dir(dir_to_remove) - os.remove(link_to_remove) - except OSError as err: - raise EasyBuildError("Failed to clean up install dir: %s", err) - - def sanity_check_step(self): - """Custom sanity check for IMOD.""" - custom_paths = { - 'files': ['bin/imod', 'IMOD-linux.sh', 'IMOD-linux.csh', 'installIMOD'], - 'dirs': ['lib'], - } - super(EB_IMOD, self).sanity_check_step(custom_paths=custom_paths) - - def make_module_extra(self): - """Define IMOD specific variables in generated module file.""" - txt = super(EB_IMOD, self).make_module_extra() - txt += self.module_generator.set_environment('IMOD_DIR', self.installdir) - txt += self.module_generator.set_environment('IMOD_PLUGIN_DIR', - os.path.join(self.installdir, 'lib', 'imodplug')) - txt += self.module_generator.set_environment('IMOD_QTLIBDIR', os.path.join(self.installdir, 'qtlib')) - if os.getenv('JAVA_HOME') is None: - raise EasyBuildError("$JAVA_HOME is not defined for some reason -- check environment") - else: - txt += self.module_generator.set_environment('IMOD_JAVADIR', os.getenv('JAVA_HOME')) - txt += self.module_generator.set_environment('FOR_DISABLE_STACK_TRACE', '1') - txt += self.module_generator.set_alias('subm', "submfg $* &") - txt += self.module_generator.msg_on_load("Please set the environment variable $IMOD_CALIB_DIR if appropriate.") - - txt += self.module_generator.msg_on_load("bash users run: 'source $EBROOTIMOD/IMOD-linux.sh") - txt += self.module_generator.msg_on_load("csh users run: 'source $EBROOTIMOD/IMOD-linux.csh'") - return txt