apply_DAMASK_modifications script needs to be independent from damask installation (except solver variables)

install/MarcMentat/apply_DAMASK_modifications.py

@@ -1,20 +1,51 @@
 #!/usr/bin/env python3
-
 import os
 import sys
 import glob
 import argparse
 import shutil
 from pathlib import Path
+import importlib.machinery
+import signal
+import subprocess
+import shlex
+from functools import partial
+
+solver = importlib.machinery.SourceFileLoader(
+                    'damask',f'{str(Path(__file__).parent.absolute().parents[1])}/python/damask/solver/_marc.py').load_module()
+
+def run(cmd, wd='./', env=None, timeout=None):
+    def pass_signal(sig,_,proc,default):
+        proc.send_signal(sig)
+        signal.signal(sig,default)
+        signal.raise_signal(sig)
+    signals = [signal.SIGINT,signal.SIGTERM]
+    print(f"running '{cmd}' in '{wd}'")
+    process = subprocess.Popen(shlex.split(cmd),
+                             stdout = subprocess.PIPE,
+                             stderr = subprocess.PIPE,
+                             env = os.environ if env is None else env,
+                             cwd = wd,
+                             encoding = 'utf-8')
+    sig_states = [signal.signal(sig,partial(pass_signal,proc=process,default=signal.getsignal(sig))) for sig in signals]
+    try:
+        stdout,stderr = process.communicate(timeout=timeout)
+    finally:
+        for sig,state in zip(signals,sig_states):
+            signal.signal(sig,state)
+    if process.returncode != 0:
+        print(stdout)
+        print(stderr)
+        raise RuntimeError(f"'{cmd}' failed with returncode {process.returncode}")
+    return stdout, stderr
 
-import damask
 
 def copy_and_patch(patch,orig,editor):
     try:
         shutil.copyfile(orig,orig.parent/patch.stem)
     except shutil.SameFileError:
         pass
-    damask.util.run(f'patch {orig.parent/patch.stem} {patch} --backup --forward')
+    run(f'patch {orig.parent/patch.stem} {patch} --backup --forward')
     with open(orig.parent/patch.stem) as f_in:
         content = f_in.read()
     with open(orig.parent/patch.stem,'w') as f_out:
@@ -28,15 +59,16 @@ parser = argparse.ArgumentParser(
 parser.add_argument('--editor', dest='editor', metavar='string', default='vi',
                     help='Name of the editor (executable) used by Marc Mentat')
 parser.add_argument('--marc-root', dest='marc_root', metavar='string',
-                    default=damask.solver._marc._marc_root,
+                    default=solver._marc_root,
                     help='Marc root directory')
 parser.add_argument('--marc-version', dest='marc_version', metavar='string',
-                    default=damask.solver._marc._marc_version,
+                    default=solver._marc_version,
                     help='Marc version')
 parser.add_argument('--damask-root', dest='damask_root', metavar = 'string',
-                    default=damask.solver._marc._damask_root,
+                    default=solver._damask_root,
                     help='DAMASK root directory')
 
+
 args = parser.parse_args()
 marc_root = Path(args.marc_root).expanduser()
 damask_root = Path(args.damask_root).expanduser()
@@ -52,7 +84,7 @@ matches = {'Marc_tools':  [['comp_user','comp_damask_*mp'],
 
 for cmd in ['patch','xvfb-run']:
     try:
-        damask.util.run(f'{cmd} --help')
+        run(f'{cmd} --help')
     except FileNotFoundError:
         print(f'"{cmd}" not found, please install')
         sys.exit()
@@ -71,7 +103,7 @@ print('compiling Mentat menu binaries...')
 
 executable = marc_root/f'mentat{marc_version}/bin/mentat'
 menu_file  = marc_root/f'mentat{marc_version}/menus/linux64/main.msb'
-damask.util.run(f'xvfb-run -a {executable} -compile {menu_file}')
+run(f'xvfb-run -a {executable} -compile {menu_file}')
 
 print('setting file access rights...')