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Fix non-interactive cmd.sh #5187

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Fix non-interactive cmd.sh #5187

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3c13372
Fix non-interactive cmd.sh
Flamefire May 5, 2026
2cfc0dd
Add quotes to `echo` of `$BASH_ENV`
Flamefire May 5, 2026
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14 changes: 10 additions & 4 deletions easybuild/tools/run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -273,22 +273,28 @@ def create_cmd_scripts(cmd_str, work_dir, env, tmpdir, out_file, err_file):
# Make script that sets up bash shell with specified environment and working directory
cmd_fp = os.path.join(tmpdir, 'cmd.sh')

# using -i to force interactive shell, so env.sh is also sourced when -c is used to run commands
launch_cmd = 'bash --rcfile $EB_SCRIPT_DIR/env.sh -i "$@"'

launch_cmd = 'bash'
# prefix launch command with bwrap (if used)
bwrap_cmd = os.getenv('EB_BWRAP_CMD')
if bwrap_cmd:
launch_cmd = bwrap_cmd + ' ' + launch_cmd

# using -i for interactive shell, so env.sh is sourced
launch_cmd_interactive = f'{launch_cmd} --rcfile $EB_SCRIPT_DIR/env.sh -i'
launch_cmd_with_args = f'BASH_ENV=$EB_SCRIPT_DIR/env.sh {launch_cmd} "$@"'

with open(cmd_fp, 'w') as fid:
fid.write('#!/usr/bin/env bash\n')
fid.write('# Run this script to set up a shell environment that EasyBuild used to run the shell command\n')
fid.write('\n'.join([
'EB_SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )',
f'echo "# Shell for the command: \'"{shlex.quote(cmd_str)}"\'"',
'echo "# Use command history, exit to stop"',
launch_cmd,
'if [ "$#" -eq 0 ]; then',
' ' + launch_cmd_interactive,
'else',
' ' + launch_cmd_with_args,
'fi',
]))
os.chmod(cmd_fp, 0o775)

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15 changes: 9 additions & 6 deletions test/framework/run.py
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Expand Up @@ -266,20 +266,23 @@ def test_run_shell_cmd_basic(self):
cmd_script = os.path.join(cmd_tmpdir, 'cmd.sh')
self.assertExists(cmd_script)

cmd = f"{cmd_script} -c 'echo pwd: $PWD; echo $FOOBAR; echo $EB_CMD_OUT_FILE; cat $EB_CMD_OUT_FILE'"
cmd = f"{cmd_script} -c '"
cmd += 'echo pwd: $PWD; echo "bash_env: $BASH_ENV"; echo $FOOBAR; echo $EB_CMD_OUT_FILE; cat $EB_CMD_OUT_FILE'
cmd += "'"
with self.mocked_stdout_stderr():
res = run_shell_cmd(cmd, fail_on_error=False)
self.assertEqual(res.exit_code, 0)
regex = re.compile("pwd: .*\nfoobar\n.*/echo-.*/out.txt\nhello$")
regex = re.compile("pwd: .*\nbash_env: .*\nfoobar\n.*/echo-.*/out.txt\nhello$")
self.assertTrue(regex.search(res.output), f"Pattern '{regex.pattern}' should be found in {res.output}")

# check whether working directory is what's expected
regex = re.compile('^pwd: .*', re.M)
res = regex.findall(res.output)
self.assertEqual(len(res), 1)
pwd = res[0].strip()[5:]
matches = re.findall('^pwd: (.*)', res.output, re.M)
self.assertEqual(len(matches), 1)
pwd = matches[0]
self.assertTrue(os.path.samefile(pwd, self.test_prefix))

# BASH_ENV is that of the current shell, not the one set in the cmd.sh
self.assertEqual(re.search('^bash_env: (.*)', res.output, re.M)[1], os.environ.get('BASH_ENV', ''))
cmd = f"{cmd_script} -c 'module --version'"
with self.mocked_stdout_stderr():
res = run_shell_cmd(cmd, fail_on_error=False)
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