Revert "correct executable permissions addition for user and group"

This reverts commit 6a20fc3.

Author: stefdoerr

jobqueues/celeryfiles/tasks.py

@@ -1,6 +1,6 @@
 from celery.exceptions import SoftTimeLimitExceeded
 from billiard import current_process
-from jobqueues.util import _getVisibleGPUdevices, _make_executable
+from jobqueues.util import _getVisibleGPUdevices
 
 
 visibledevs = _getVisibleGPUdevices()
@@ -105,4 +105,4 @@ def _createJobScript(
             if os.path.abspath(odir) != os.path.abspath(workdir):
                 f.write("\nmv {} {}".format(" ".join(copyextensions), odir))
 
-    _make_executable(fname)
+    os.chmod(fname, 0o700)

jobqueues/localqueue.py

@@ -4,7 +4,7 @@
 # No redistribution in whole or part
 #
 from jobqueues.simqueue import SimQueue
-from jobqueues.util import _getGPUdevices, _filterVisibleGPUdevices, _make_executable
+from jobqueues.util import _getGPUdevices, _filterVisibleGPUdevices
 from protocolinterface import val
 import queue
 import os
@@ -137,7 +137,7 @@ def _createJobScript(self, fname, workdir, runsh, gpudevice=None):
                 if os.path.abspath(odir) != os.path.abspath(workdir):
                     f.write("\nmv {} {}".format(" ".join(self.copy), odir))
 
-        _make_executable(fname)
+        os.chmod(fname, 0o700)
 
     def _setRunning(self, path):
         self._states[path] = "R"
@@ -433,7 +433,7 @@ def _getmemory(self):
         from math import floor
         import psutil
 
-        memory = psutil.virtual_memory().total / 1024**2
+        memory = psutil.virtual_memory().total / 1024 ** 2
         memory *= max(0, min(1, self.ncpu / psutil.cpu_count()))  # Clamp to [0, 1]
         memory = int(floor(memory))
 

jobqueues/lsfqueue.py

@@ -10,7 +10,7 @@
 from subprocess import check_output, CalledProcessError, DEVNULL
 from protocolinterface import val
 from jobqueues.simqueue import SimQueue
-from jobqueues.util import ensurelist, _make_executable
+from jobqueues.util import ensurelist
 from jobqueues.config import loadConfig
 import unittest
 import yaml
@@ -279,7 +279,7 @@ def _createJobScript(self, fname, workdir, runsh):
                 os.makedirs(datadir, exist_ok=True)
                 f.write(f"\nmv *.{self.trajext} {datadir}")
 
-        _make_executable(fname)
+        os.chmod(fname, 0o700)
 
     def retrieve(self):
         # Nothing to do

jobqueues/pbsqueue.py

@@ -11,7 +11,6 @@
 from protocolinterface import val
 from jobqueues.simqueue import SimQueue
 from jobqueues.config import loadConfig
-from jobqueues.util import _make_executable
 import logging
 
 logger = logging.getLogger(__name__)
@@ -187,7 +186,7 @@ def _createJobScript(self, fname, workdir, runsh):
                 os.makedirs(datadir, exist_ok=True)
                 f.write(f"\nmv *.{self.trajext} {datadir}")
 
-        _make_executable(fname)
+        os.chmod(fname, 0o700)
 
     def retrieve(self):
         # Nothing to do

jobqueues/sgequeue.py

@@ -10,7 +10,7 @@
 from subprocess import check_output, CalledProcessError, DEVNULL
 from protocolinterface import val
 from jobqueues.simqueue import SimQueue
-from jobqueues.util import ensurelist, _make_executable
+from jobqueues.util import ensurelist
 from jobqueues.config import loadConfig
 from math import ceil
 import logging
@@ -223,7 +223,7 @@ def _createJobScript(self, fname, workdir, runsh):
         with open(fname, "w") as f:
             f.write(job_str)
 
-        _make_executable(fname)
+        os.chmod(fname, 0o700)
 
     def retrieve(self):
         # Nothing to do

jobqueues/slurmqueue.py

@@ -8,11 +8,13 @@
 import random
 import string
 from jobqueues.config import loadConfig
+import yaml
 from subprocess import check_output, CalledProcessError
 from protocolinterface import val
 from jobqueues.simqueue import SimQueue, QueueJobStatus, _inProgressStatus
-from jobqueues.util import ensurelist, _make_executable
+from jobqueues.util import ensurelist
 import getpass
+import unittest
 import logging
 
 logger = logging.getLogger(__name__)
@@ -400,7 +402,7 @@ def _createJobScript(self, fname, workdir, runsh, nvidia_mps=False, commands=Non
         )
         with open(fname, "w") as f:
             f.write(job_str)
-        _make_executable(fname)
+        os.chmod(fname, 0o700)
 
     def retrieve(self):
         # Nothing to do

jobqueues/util.py

@@ -62,14 +62,3 @@ def _filterVisibleGPUdevices(devices, _logger):
         # Only keep the selected visible devices. intersect of the two lists
         devices = [dd for dd in devices if dd in visible_devices]
     return devices
-
-
-def _make_executable(fname):
-    import os
-    import stat
-
-    # Get current permissions
-    st = os.stat(fname)
-
-    # Add execute permission for user and group
-    os.chmod(fname, st.st_mode | stat.S_IXUSR | stat.S_IXGRP)