create env.sh and cmd.sh helper scripts in run_shell_cmd

easybuild/tools/run.py

@@ -41,6 +41,7 @@
 import locale
 import os
 import re
+import shlex
 import shutil
 import string
 import subprocess
@@ -196,6 +197,34 @@ def fileprefix_from_cmd(cmd, allowed_chars=False):
     return ''.join([c for c in cmd if c in allowed_chars])
 
 
+def save_cmd(cmd_str, work_dir, env, tmpdir):
+    # Save environment variables in it's own environment file
+    full_env = os.environ.copy()
+    if env is not None:
+        full_env.update(env)
+    env_fp = os.path.join(tmpdir, 'env.sh')
+    with open(env_fp, 'w') as fid:
+        # excludes bash functions (environment variables ending with %)
+        fid.write('\n'.join(f'export {key}={shlex.quote(value)}' for key, value in full_env.items()
+                            if not key.endswith('%')))
+        fid.write('\n\nPS1="eb-shell> "')
+        fid.write(f'\nhistory -s {shlex.quote(cmd_str)}')
+
+    # Make script that sets up bash shell with given environments set.
+    cmd_fp = os.path.join(tmpdir, 'cmd.sh')
+    with open(cmd_fp, 'w') as fid:
+        fid.write('#!/usr/bin/env bash\n')
+        fid.write('# Run this script to replicate the environment that EB used to run the shell command\n')
+        fid.write('\n'.join([
+            f'\ncd "{work_dir}"',
+            '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',
+            'bash --rcfile $EB_SCRIPT_DIR/env.sh',
+            ]))
+    os.chmod(cmd_fp, 0o775)
+
+
 def _answer_question(stdout, proc, qa_patterns, qa_wait_patterns):
     """
     Private helper function to try and answer questions raised in interactive shell commands.
@@ -335,6 +364,8 @@ def to_cmd_str(cmd):
         os.makedirs(toptmpdir, exist_ok=True)
         cmd_name = fileprefix_from_cmd(os.path.basename(cmd_str.split(' ')[0]))
         tmpdir = tempfile.mkdtemp(dir=toptmpdir, prefix=f'{cmd_name}-')
+        _log.info(f'run_shell_cmd: command environment of "{cmd_str}" will be saved to {tmpdir}')
+        save_cmd(cmd_str, work_dir, env, tmpdir)
         cmd_out_fp = os.path.join(tmpdir, 'out.txt')
         _log.info(f'run_shell_cmd: Output of "{cmd_str}" will be logged to {cmd_out_fp}')
         if split_stderr:
@@ -343,7 +374,7 @@ def to_cmd_str(cmd):
         else:
             cmd_err_fp = None
     else:
-        cmd_out_fp, cmd_err_fp = None, None
+        tmpdir, cmd_out_fp, cmd_err_fp = None, None, None
 
     interactive = bool(qa_patterns)
     interactive_msg = 'interactive ' if interactive else ''
@@ -361,7 +392,7 @@ def to_cmd_str(cmd):
 
     start_time = datetime.now()
     if not hidden:
-        _cmd_trace_msg(cmd_str, start_time, work_dir, stdin, cmd_out_fp, cmd_err_fp, thread_id, interactive=interactive)
+        _cmd_trace_msg(cmd_str, start_time, work_dir, stdin, tmpdir, thread_id, interactive=interactive)
 
     if stream_output:
         print_msg(f"(streaming) output for command '{cmd_str}':")
@@ -522,16 +553,15 @@ def to_cmd_str(cmd):
     return res
 
 
-def _cmd_trace_msg(cmd, start_time, work_dir, stdin, cmd_out_fp, cmd_err_fp, thread_id, interactive=False):
+def _cmd_trace_msg(cmd, start_time, work_dir, stdin, tmpdir, thread_id, interactive=False):
     """
     Helper function to construct and print trace message for command being run
 
     :param cmd: command being run
     :param start_time: datetime object indicating when command was started
     :param work_dir: path of working directory in which command is run
     :param stdin: stdin input value for command
-    :param cmd_out_fp: path to output file for command
-    :param cmd_err_fp: path to errors/warnings output file for command
+    :param tmpdir: path to temporary output directory for command
     :param thread_id: thread ID (None when not running shell command asynchronously)
     :param interactive: boolean indicating whether it is an interactive command, or not
     """
@@ -551,10 +581,8 @@ def _cmd_trace_msg(cmd, start_time, work_dir, stdin, cmd_out_fp, cmd_err_fp, thr
     ]
     if stdin:
         lines.append(f"\t[input: {stdin}]")
-    if cmd_out_fp:
-        lines.append(f"\t[output saved to {cmd_out_fp}]")
-    if cmd_err_fp:
-        lines.append(f"\t[errors/warnings saved to {cmd_err_fp}]")
+    if tmpdir:
+        lines.append(f"\t[output and state saved to {tmpdir}]")
 
     trace_msg('\n'.join(lines))
 

test/framework/run.py

@@ -676,7 +676,7 @@ def test_run_shell_cmd_trace(self):
             r"\techo hello",
             r"\t\[started at: .*\]",
             r"\t\[working dir: .*\]",
-            r"\t\[output saved to .*\]",
+            r"\t\[output and state saved to .*\]",
             r"  >> command completed: exit 0, ran in .*",
         ]
 
@@ -736,7 +736,7 @@ def test_run_shell_cmd_trace_stdin(self):
             r"\techo hello",
             r"\t\[started at: [0-9][0-9][0-9][0-9]-[0-9][0-9]-[0-9][0-9] [0-9][0-9]:[0-9][0-9]:[0-9][0-9]\]",
             r"\t\[working dir: .*\]",
-            r"\t\[output saved to .*\]",
+            r"\t\[output and state saved to .*\]",
             r"  >> command completed: exit 0, ran in .*",
         ]
 
@@ -1092,7 +1092,7 @@ def test_run_shell_cmd_qa_trace(self):
         pattern += r"\techo \'n: \'; read n; seq 1 \$n\n"
         pattern += r"\t\[started at: .*\]\n"
         pattern += r"\t\[working dir: .*\]\n"
-        pattern += r"\t\[output saved to .*\]\n"
+        pattern += r"\t\[output and state saved to .*\]\n"
         pattern += r'  >> command completed: exit 0, ran in .*'
         self.assertTrue(re.search(pattern, stdout), "Pattern '%s' found in: %s" % (pattern, stdout))
 

test/framework/toy_build.py

@@ -2985,7 +2985,7 @@ def test_toy_build_trace(self):
                 r"\tgcc toy.c -o toy\n"
                 r"\t\[started at: .*\]",
                 r"\t\[working dir: .*\]",
-                r"\t\[output saved to .*\]",
+                r"\t\[output and state saved to .*\]",
                 r'',
             ]),
             r"  >> command completed: exit 0, ran in .*",