clean installation directory instead of hard removing it in various easyblocks

easybuild/easyblocks/a/amber.py

@@ -42,7 +42,7 @@
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.modules import get_software_root
 from easybuild.tools.run import run_shell_cmd
-from easybuild.tools.filetools import remove_dir, which
+from easybuild.tools.filetools import clean_dir, which
 
 
 class EB_Amber(CMakeMake):
@@ -130,8 +130,8 @@ def configure_step(self):
             return
 
         # CMake will search a previous install directory for Amber-compiled libs. We will therefore
-        # manually remove the install directory prior to configuration.
-        remove_dir(self.installdir)
+        # manually clean the install directory prior to configuration.
+        clean_dir(self.installdir)
 
         external_libs_list = []
 

easybuild/easyblocks/a/anaconda.py

@@ -33,7 +33,7 @@
 import stat
 
 from easybuild.easyblocks.generic.binary import Binary
-from easybuild.tools.filetools import adjust_permissions, remove_dir
+from easybuild.tools.filetools import adjust_permissions, clean_dir
 from easybuild.tools.modules import MODULE_LOAD_ENV_HEADERS
 from easybuild.tools.run import run_shell_cmd
 
@@ -59,7 +59,7 @@ def __init__(self, *args, **kwargs):
     def install_step(self):
         """Copy all files in build directory to the install directory"""
 
-        remove_dir(self.installdir)
+        clean_dir(self.installdir)
         install_script = self.src[0]['name']
 
         adjust_permissions(os.path.join(self.builddir, install_script), stat.S_IRUSR | stat.S_IXUSR)

easybuild/easyblocks/f/fdtd_solutions.py

@@ -64,7 +64,7 @@ def build_step(self):
     def install_step(self):
         """Install FDTD Solutions using copy tree."""
         fdtd_dir = os.path.join(self.cfg['start_dir'], 'opt', 'lumerical', 'fdtd')
-        copy_dir(fdtd_dir, self.installdir, symlinks=self.cfg['keepsymlinks'])
+        copy_dir(fdtd_dir, self.installdir, symlinks=self.cfg['keepsymlinks'], dirs_exist_ok=True)
 
     def sanity_check_step(self):
         """Custom sanity check for FDTD Solutions."""

easybuild/easyblocks/g/gate.py

@@ -40,6 +40,7 @@
 from easybuild.easyblocks.generic.cmakemake import CMakeMake
 from easybuild.framework.easyconfig import CUSTOM
 from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.filetools import clean_dir, copy_dir
 from easybuild.tools.run import run_shell_cmd
 from easybuild.tools.systemtools import get_shared_lib_ext
 
@@ -138,8 +139,8 @@ def install_step(self):
 
             # copy all the things
             try:
-                shutil.rmtree(self.installdir)
-                shutil.copytree(self.cfg['start_dir'], self.installdir)
+                clean_dir(self.installdir)
+                copy_dir(self.cfg['start_dir'], self.installdir, dirs_exist_ok=True)
             except OSError as err:
                 raise EasyBuildError("Failed to copy %s to %s: %s", self.cfg['start_dir'], self.installdir, err)
 

easybuild/easyblocks/g/go.py

@@ -29,13 +29,12 @@
 @author: Kenneth Hoste (HPC-UGent)
 """
 import os
-import shutil
 
 from easybuild.tools import LooseVersion
 
 from easybuild.easyblocks.generic.configuremake import ConfigureMake
 from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.filetools import remove_dir
+from easybuild.tools.filetools import clean_dir, copy_dir
 from easybuild.tools.run import run_shell_cmd
 from easybuild.tools.modules import get_software_root
 
@@ -76,7 +75,7 @@ def install_step(self):
         run_shell_cmd(cmd, work_dir=srcdir)
 
         try:
-            remove_dir(self.installdir)
-            shutil.copytree(self.cfg['start_dir'], self.installdir, symlinks=self.cfg['keepsymlinks'])
+            clean_dir(self.installdir)
+            copy_dir(self.cfg['start_dir'], self.installdir, symlinks=self.cfg['keepsymlinks'], dirs_exist_ok=True)
         except OSError as err:
             raise EasyBuildError("Failed to copy installation to %s: %s", self.installdir, err)

easybuild/easyblocks/generic/binary.py

@@ -32,14 +32,13 @@
 @author: Jens Timmerman (Ghent University)
 """
 
-import shutil
 import os
 import stat
 
 from easybuild.framework.easyblock import EasyBlock
 from easybuild.framework.easyconfig import CUSTOM
 from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.filetools import adjust_permissions, copy_file, mkdir, remove_dir
+from easybuild.tools.filetools import adjust_permissions, clean_dir, copy_dir, copy_file, mkdir
 from easybuild.tools.run import run_shell_cmd
 
 
@@ -116,8 +115,8 @@ def install_step(self):
         if install_cmd is None and install_cmds is None:
             try:
                 # shutil.copytree doesn't allow the target directory to exist already
-                remove_dir(self.installdir)
-                shutil.copytree(self.cfg['start_dir'], self.installdir, symlinks=self.cfg['keepsymlinks'])
+                clean_dir(self.installdir)
+                copy_dir(self.cfg['start_dir'], self.installdir, symlinks=self.cfg['keepsymlinks'], dirs_exist_ok=True)
             except OSError as err:
                 raise EasyBuildError("Failed to copy %s to %s: %s", self.cfg['start_dir'], self.installdir, err)
         else:
@@ -142,14 +141,8 @@ def post_processing_step(self):
         if self.cfg.get('staged_install', False):
             staged_installdir = self.installdir
             self.installdir = self.actual_installdir
-            try:
-                # copytree expects target directory to not exist yet
-                if os.path.exists(self.installdir):
-                    remove_dir(self.installdir)
-                shutil.copytree(staged_installdir, self.installdir)
-            except OSError as err:
-                raise EasyBuildError("Failed to move staged install from %s to %s: %s",
-                                     staged_installdir, self.installdir, err)
+            clean_dir(self.installdir)
+            copy_dir(staged_installdir, self.installdir, dirs_exist_ok=True)
 
         super().post_processing_step()
 

easybuild/easyblocks/generic/tarball.py

@@ -40,7 +40,7 @@
 from easybuild.framework.extensioneasyblock import ExtensionEasyBlock
 from easybuild.framework.easyconfig import CUSTOM
 from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.filetools import copy_dir, extract_file, remove_dir
+from easybuild.tools.filetools import clean_dir, copy_dir, extract_file, remove_dir
 from easybuild.tools.run import run_shell_cmd
 
 
@@ -102,27 +102,23 @@ def install_step(self, src=None):
         if self.cfg['install_type'] == 'subdir':
             # Wipe and install in a sub-directory with the name of the package
             install_path = os.path.join(self.installdir, self.name.lower())
-            dirs_exist_ok = False
             install_logmsg = "Copying tarball contents of %s to sub-directory %s..."
+            remove_dir(install_path)
         elif self.cfg['install_type'] == 'merge':
             # Enable merging with root of existing installdir
             install_path = self.installdir
-            dirs_exist_ok = True
             install_logmsg = "Merging tarball contents of %s into %s..."
         elif self.cfg['install_type'] is None:
-            # Wipe and copy root of installation directory (default)
+            # Clean and copy root of installation directory (default)
             install_path = self.installdir
-            dirs_exist_ok = False
-            install_logmsg = "Copying tarball contents of %s into %s after wiping it..."
+            install_logmsg = "Copying tarball contents of %s into %s after cleaning it..."
+            clean_dir(install_path)
         else:
             raise EasyBuildError("Unknown option '%s' for index_type.", self.cfg['install_type'])
 
         self.log.info(install_logmsg, self.name, install_path)
 
-        if not dirs_exist_ok:
-            remove_dir(install_path)
-
-        copy_dir(source_path, install_path, symlinks=self.cfg['keepsymlinks'], dirs_exist_ok=dirs_exist_ok)
+        copy_dir(source_path, install_path, symlinks=self.cfg['keepsymlinks'], dirs_exist_ok=True)
 
     def sanity_check_rpath(self):
         """Skip the rpath sanity check, this is binary software"""

easybuild/easyblocks/j/java.py

@@ -36,7 +36,7 @@
 from easybuild.easyblocks.generic.packedbinary import PackedBinary
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option
-from easybuild.tools.filetools import adjust_permissions, change_dir, copy_dir, copy_file, remove_dir, which
+from easybuild.tools.filetools import adjust_permissions, change_dir, clean_dir, copy_dir, copy_file, which
 from easybuild.tools.run import run_shell_cmd
 from easybuild.tools.systemtools import AARCH64, POWER, RISCV64, X86_64, get_cpu_architecture, get_shared_lib_ext
 from easybuild.tools.utilities import nub
@@ -82,8 +82,8 @@ def extract_step(self):
     def install_step(self):
         """Custom install step: just copy unpacked installation files."""
         if LooseVersion(self.version) < LooseVersion('1.7'):
-            remove_dir(self.installdir)
-            copy_dir(os.path.join(self.builddir, 'jdk%s' % self.version), self.installdir)
+            clean_dir(self.installdir)
+            copy_dir(os.path.join(self.builddir, 'jdk%s' % self.version), self.installdir, dirs_exist_ok=True)
         else:
             PackedBinary.install_step(self)
 

easybuild/easyblocks/m/molpro.py

@@ -29,7 +29,6 @@
 """
 import glob
 import os
-import shutil
 import re
 
 from easybuild.easyblocks.generic.binary import Binary
@@ -39,7 +38,7 @@
 from easybuild.tools import LooseVersion
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option
-from easybuild.tools.filetools import apply_regex_substitutions, change_dir, mkdir, read_file, symlink
+from easybuild.tools.filetools import apply_regex_substitutions, change_dir, clean_dir, mkdir, read_file, symlink
 from easybuild.tools.run import run_shell_cmd
 
 
@@ -208,8 +207,8 @@ def install_step(self):
 
             for src in self.src:
                 if LooseVersion(self.version) >= LooseVersion('2015'):
-                    # install dir must be non-existent
-                    shutil.rmtree(self.installdir)
+                    # install dir must be non-existent or empty
+                    clean_dir(self.installdir)
                     cmd = "./{0} -batch -prefix {1}".format(src['name'], self.installdir)
                 else:
                     cmd = "./{0} -batch -instbin {1}/bin -instlib {1}/lib".format(src['name'], self.installdir)

easybuild/easyblocks/t/tkinter.py

@@ -39,7 +39,7 @@
 from easybuild.easyblocks.generic.pythonpackage import det_pylibdir
 from easybuild.easyblocks.python import EB_Python
 from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.filetools import move_file, remove_dir
+from easybuild.tools.filetools import clean_dir, move_file
 from easybuild.tools.modules import get_software_root
 from easybuild.tools.systemtools import get_shared_lib_ext
 
@@ -95,7 +95,7 @@ def install_step(self):
         # Reset the install directory and remove it if it already exists. It will not have been removed automatically
         # at the start of the install step, as self.installdir pointed at the temporary install directory.
         self.installdir = self.orig_installdir
-        remove_dir(self.installdir)
+        clean_dir(self.installdir)
 
         dest_pylibdir = os.path.join(self.installdir, det_pylibdir())