add back easyblock for fastStructure, ported to run_shell_cmd and module_load_environment

easybuild/easyblocks/f/faststructure.py

@@ -0,0 +1,83 @@
+# -*- coding: utf-8 -*-
+##
+# Copyright 2009-2025 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/>.
+##
+"""
+EasyBuild support for building and installing fastStructure, implemented as an easyblock
+
+@author: Bob Dröge (University of Groningen)
+"""
+import os
+import stat
+
+from easybuild.easyblocks.generic.cmdcp import CmdCp
+from easybuild.framework.easyconfig import CUSTOM
+from easybuild.tools.filetools import adjust_permissions, change_dir, read_file, write_file
+from easybuild.tools.run import run_shell_cmd
+
+
+class EB_fastStructure(CmdCp):
+    """Support for building and installing fastStructure."""
+
+    @staticmethod
+    def extra_options(extra_vars=None):
+        """Change default values of options"""
+        extra = CmdCp.extra_options()
+        # files_to_copy is not mandatory here
+        extra['files_to_copy'][2] = CUSTOM
+        return extra
+
+    def __init__(self, *args, **kwargs):
+        """Initialisation of custom class variables for fastStructure."""
+        super(EB_fastStructure, self).__init__(*args, **kwargs)
+
+        self.cfg['files_to_copy'] = ['*']
+        self.pyfiles = ['distruct.py', 'chooseK.py', 'structure.py']
+        # custom path-like environment variables for RepeatMaskerConfig
+        self.module_load_environment.PATH = ['']
+
+    def build_step(self):
+        """Build fastStructure using setup.py."""
+        cwd = change_dir('vars')
+        run_shell_cmd("python setup.py build_ext --inplace")
+        change_dir(cwd)
+        run_shell_cmd("python setup.py build_ext --inplace")
+
+    def post_install_step(self):
+        """Add a shebang to the .py files and make them executable."""
+        for pyfile in self.pyfiles:
+            pf_path = os.path.join(self.installdir, pyfile)
+            pf_contents = read_file(pf_path)
+            write_file(pf_path, "#!/usr/bin/env python\n" + pf_contents)
+            adjust_permissions(pf_path, stat.S_IXUSR | stat.S_IXGRP | stat.S_IXOTH)
+
+        super(EB_fastStructure, self).post_install_step()
+
+    def sanity_check_step(self):
+        """Custom sanity check for fastStructure."""
+        custom_paths = {
+            'files': self.pyfiles,
+            'dirs': ['vars'],
+        }
+        super(EB_fastStructure, self).sanity_check_step(custom_paths=custom_paths)