Merge pull request easybuilders#4654 from boegel/5.0.x

sync with develop (20240923)

RELEASE_NOTES

@@ -4,6 +4,18 @@ For more detailed information, please see the git log.
 These release notes can also be consulted at https://easybuild.readthedocs.io/en/latest/Release_notes.html.
 
 
+v4.9.4 (22 September 2024)
+--------------------------
+
+update/bugfix release
+
+- various enhancements, including:
+  - set $LMOD_TERSE_DECORATIONS to 'no' to avoid additional info in output produced by 'ml --terse avail' (#4648)
+- various bug fixes, including:
+  - implement workaround for permission error when copying read-only files that have extended attributes set and using Python 3.6 (#4642)
+  - take into account alternate sysroot for /bin/bash used by run_cmd (#4646)
+
+
 v4.9.3 (14 September 2024)
 --------------------------
 

easybuild/_deprecated.py

@@ -131,7 +131,7 @@ def get_output_from_process(proc, read_size=None, asynchronous=False, print_depr
 @run_cmd_cache
 def run_cmd(cmd, log_ok=True, log_all=False, simple=False, inp=None, regexp=True, log_output=False, path=None,
             force_in_dry_run=False, verbose=True, shell=None, trace=True, stream_output=None, asynchronous=False,
-            with_hooks=True):
+            with_hooks=True, with_sysroot=True):
     """
     Run specified command (in a subshell)
     :param cmd: command to run
@@ -149,6 +149,7 @@ def run_cmd(cmd, log_ok=True, log_all=False, simple=False, inp=None, regexp=True
     :param stream_output: enable streaming command output to stdout
     :param asynchronous: run command asynchronously (returns subprocess.Popen instance if set to True)
     :param with_hooks: trigger pre/post run_shell_cmd hooks (if defined)
+    :param with_sysroot: prepend sysroot to exec_cmd (if defined)
     """
 
     _log.deprecated("run_cmd is deprecated, use run_shell_cmd from easybuild.tools.run instead", '6.0')
@@ -228,6 +229,16 @@ def run_cmd(cmd, log_ok=True, log_all=False, simple=False, inp=None, regexp=True
 
     exec_cmd = "/bin/bash"
 
+    # if EasyBuild is configured to use an alternate sysroot,
+    # we should also run shell commands using the bash shell provided in there,
+    # since /bin/bash may not be compatible with the alternate sysroot
+    if with_sysroot:
+        sysroot = build_option('sysroot')
+        if sysroot:
+            sysroot_bin_bash = os.path.join(sysroot, 'bin', 'bash')
+            if os.path.exists(sysroot_bin_bash):
+                exec_cmd = sysroot_bin_bash
+
     if not shell:
         if isinstance(cmd, list):
             exec_cmd = None
@@ -237,6 +248,8 @@ def run_cmd(cmd, log_ok=True, log_all=False, simple=False, inp=None, regexp=True
         else:
             raise EasyBuildError("Don't know how to prefix with /usr/bin/env for commands of type %s", type(cmd))
 
+    _log.info("Using %s as shell for running cmd: %s", exec_cmd, cmd)
+
     if with_hooks:
         hooks = load_hooks(build_option('hooks'))
         hook_res = run_hook(RUN_SHELL_CMD, hooks, pre_step_hook=True, args=[cmd], kwargs={'work_dir': os.getcwd()})

easybuild/tools/filetools.py

@@ -42,11 +42,13 @@
 """
 import datetime
 import difflib
+import filecmp
 import glob
 import hashlib
 import inspect
 import itertools
 import os
+import platform
 import re
 import shutil
 import signal
@@ -61,6 +63,7 @@
 import urllib.request as std_urllib
 
 from easybuild.base import fancylogger
+from easybuild.tools import LooseVersion
 # import build_log must stay, to use of EasyBuildLog
 from easybuild.tools.build_log import EasyBuildError, EasyBuildExit, CWD_NOTFOUND_ERROR
 from easybuild.tools.build_log import dry_run_msg, print_msg, print_warning
@@ -2427,8 +2430,42 @@ def copy_file(path, target_path, force_in_dry_run=False):
             else:
                 mkdir(os.path.dirname(target_path), parents=True)
                 if path_exists:
-                    shutil.copy2(path, target_path)
-                    _log.info("%s copied to %s", path, target_path)
+                    try:
+                        # on filesystems that support extended file attributes, copying read-only files with
+                        # shutil.copy2() will give a PermissionError, when using Python < 3.7
+                        # see https://bugs.python.org/issue24538
+                        shutil.copy2(path, target_path)
+                        _log.info("%s copied to %s", path, target_path)
+                    # catch the more general OSError instead of PermissionError,
+                    # since Python 2.7 doesn't support PermissionError
+                    except OSError as err:
+                        # if file is writable (not read-only), then we give up since it's not a simple permission error
+                        if os.path.exists(target_path) and os.stat(target_path).st_mode & stat.S_IWUSR:
+                            raise EasyBuildError("Failed to copy file %s to %s: %s", path, target_path, err)
+
+                        pyver = LooseVersion(platform.python_version())
+                        if pyver >= LooseVersion('3.7'):
+                            raise EasyBuildError("Failed to copy file %s to %s: %s", path, target_path, err)
+                        elif LooseVersion('3.7') > pyver >= LooseVersion('3'):
+                            if not isinstance(err, PermissionError):
+                                raise EasyBuildError("Failed to copy file %s to %s: %s", path, target_path, err)
+
+                        # double-check whether the copy actually succeeded
+                        if not os.path.exists(target_path) or not filecmp.cmp(path, target_path, shallow=False):
+                            raise EasyBuildError("Failed to copy file %s to %s: %s", path, target_path, err)
+
+                        try:
+                            # re-enable user write permissions in target, copy xattrs, then remove write perms again
+                            adjust_permissions(target_path, stat.S_IWUSR)
+                            shutil._copyxattr(path, target_path)
+                            adjust_permissions(target_path, stat.S_IWUSR, add=False)
+                        except OSError as err:
+                            raise EasyBuildError("Failed to copy file %s to %s: %s", path, target_path, err)
+
+                        msg = ("Failed to copy extended attributes from file %s to %s, due to a bug in shutil (see "
+                               "https://bugs.python.org/issue24538). Copy successful with workaround.")
+                        _log.info(msg, path, target_path)
+
                 elif os.path.islink(path):
                     if os.path.isdir(target_path):
                         target_path = os.path.join(target_path, os.path.basename(path))

easybuild/tools/modules.py

@@ -1477,6 +1477,9 @@ def __init__(self, *args, **kwargs):
         setvar('LMOD_REDIRECT', 'no', verbose=False)
         # disable extended defaults within Lmod (introduced and set as default in Lmod 8.0.7)
         setvar('LMOD_EXTENDED_DEFAULT', 'no', verbose=False)
+        # disabled decorations in "ml --terse avail" output
+        # (introduced in Lmod 8.8, see also https://github.com/TACC/Lmod/issues/690)
+        setvar('LMOD_TERSE_DECORATIONS', 'no', verbose=False)
 
         super(Lmod, self).__init__(*args, **kwargs)
         version = LooseVersion(self.version)

easybuild/tools/options.py

@@ -2046,7 +2046,7 @@ def set_tmpdir(tmpdir=None, raise_error=False):
             os.chmod(tmptest_file, 0o700)
             res = run_shell_cmd(tmptest_file, fail_on_error=False, in_dry_run=True, hidden=True, stream_output=False,
                                 with_hooks=False)
-            if res.exit_code:
+            if res.exit_code != EasyBuildExit.SUCCESS:
                 msg = "The temporary directory (%s) does not allow to execute files. " % tempfile.gettempdir()
                 msg += "This can cause problems in the build process, consider using --tmpdir."
                 if raise_error:

test/framework/filetools.py

@@ -32,6 +32,7 @@
 @author: Maxime Boissonneault (Compute Canada, Universite Laval)
 """
 import datetime
+import filecmp
 import glob
 import logging
 import os
@@ -52,6 +53,8 @@
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import IGNORE, ERROR, WARN, build_option, update_build_option
 from easybuild.tools.multidiff import multidiff
+from easybuild.tools.run import run_shell_cmd
+from easybuild.tools.systemtools import LINUX, get_os_type
 
 
 class FileToolsTest(EnhancedTestCase):
@@ -1976,6 +1979,49 @@ def test_copy_file(self):
         # However, if we add 'force_in_dry_run=True' it should throw an exception
         self.assertErrorRegex(EasyBuildError, "Could not copy *", ft.copy_file, src, target, force_in_dry_run=True)
 
+    def test_copy_file_xattr(self):
+        """Test copying a file with extended attributes using copy_file."""
+        # test copying a read-only files with extended attributes set
+        # first, create a special file with extended attributes
+        special_file = os.path.join(self.test_prefix, 'special.txt')
+        ft.write_file(special_file, 'special')
+        # make read-only, and set extended attributes
+        attr = ft.which('attr')
+        xattr = ft.which('xattr')
+        # try to attr (Linux) or xattr (macOS) to set extended attributes foo=bar
+        cmd = None
+        if attr:
+            cmd = "attr -s foo -V bar %s" % special_file
+        elif xattr:
+            cmd = "xattr -w foo bar %s" % special_file
+
+        if cmd:
+            with self.mocked_stdout_stderr():
+                res = run_shell_cmd(cmd, fail_on_error=False)
+
+            # need to make file read-only after setting extended attribute
+            ft.adjust_permissions(special_file, stat.S_IWUSR | stat.S_IWGRP | stat.S_IWOTH, add=False)
+
+            # only proceed if setting extended attribute worked
+            if res.exit_code == 0:
+                target = os.path.join(self.test_prefix, 'copy.txt')
+                ft.copy_file(special_file, target)
+                self.assertTrue(os.path.exists(target))
+                self.assertTrue(filecmp.cmp(special_file, target, shallow=False))
+
+                # only verify wheter extended attributes were also copied on Linux,
+                # since shutil.copy2 doesn't copy them on macOS;
+                # see warning at https://docs.python.org/3/library/shutil.html
+                if get_os_type() == LINUX:
+                    if attr:
+                        cmd = "attr -g foo %s" % target
+                    else:
+                        cmd = "xattr -l %s" % target
+                    with self.mocked_stdout_stderr():
+                        res = run_shell_cmd(cmd, fail_on_error=False)
+                    self.assertEqual(res.exit_code, 0)
+                    self.assertTrue(res.output.endswith('\nbar\n'))
+
     def test_copy_files(self):
         """Test copy_files function."""
         test_ecs = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs', 'test_ecs')

test/framework/run.py

@@ -2087,12 +2087,42 @@ def test_run_shell_cmd_delete_cwd(self):
             f"rm -rf {workdir} && echo 'Working directory removed.'"
         )
 
-        error_pattern = rf"Failed to return to {workdir} after executing command"
+        error_pattern = rf"Failed to return to .*/{os.path.basename(self.test_prefix)}/workdir after executing command"
 
         mkdir(workdir, parents=True)
         with self.mocked_stdout_stderr():
             self.assertErrorRegex(EasyBuildError, error_pattern, run_shell_cmd, cmd_workdir_rm, work_dir=workdir)
 
+    def test_run_cmd_sysroot(self):
+        """Test with_sysroot option of run_cmd function."""
+
+        # use of run_cmd/run_cmd_qa is deprecated, so we need to allow it here
+        self.allow_deprecated_behaviour()
+
+        # put fake /bin/bash in place that will be picked up when using run_cmd with with_sysroot=True
+        bin_bash = os.path.join(self.test_prefix, 'bin', 'bash')
+        bin_bash_txt = '\n'.join([
+            "#!/bin/bash",
+            "echo 'Hi there I am a fake /bin/bash in %s'" % self.test_prefix,
+            '/bin/bash "$@"',
+        ])
+        write_file(bin_bash, bin_bash_txt)
+        adjust_permissions(bin_bash, stat.S_IXUSR)
+
+        update_build_option('sysroot', self.test_prefix)
+
+        with self.mocked_stdout_stderr():
+            (out, ec) = run_cmd("echo hello")
+        self.assertEqual(ec, 0)
+        self.assertTrue(out.startswith("Hi there I am a fake /bin/bash in"))
+        self.assertTrue(out.endswith("\nhello\n"))
+
+        # picking up on alternate sysroot is enabled by default, but can be disabled via with_sysroot=False
+        with self.mocked_stdout_stderr():
+            (out, ec) = run_cmd("echo hello", with_sysroot=False)
+        self.assertEqual(ec, 0)
+        self.assertEqual(out, "hello\n")
+
 
 def suite():
     """ returns all the testcases in this module """