Merge pull request duartegroup#134 from duartegroup/v1.2.2

v1.2.2

autode/__init__.py

@@ -33,7 +33,7 @@
   - Merge when tests pass
 """
 
-__version__ = '1.2.1'
+__version__ = '1.2.2'
 
 
 __all__ = [

autode/calculation.py

@@ -580,7 +580,8 @@ def file_lines(self) -> List[str]:
         if self.filename is None or not os.path.exists(self.filename):
             raise ex.NoCalculationOutput
 
-        return open(self.filename, 'r', encoding="utf-8").readlines()
+        file = open(self.filename, 'r', encoding='utf-8', errors='ignore')
+        return file.readlines()
 
     @property
     def exists(self) -> bool:

autode/utils.py

@@ -2,7 +2,7 @@
 import sys
 import shutil
 from time import time
-from typing import Any, Optional, List
+from typing import Any, Optional, Sequence
 from functools import wraps
 from subprocess import Popen, PIPE, STDOUT
 from tempfile import mkdtemp
@@ -99,8 +99,10 @@ def run_external(params, output_filename):
 
 
 @check_sufficient_memory
-def run_external_monitored(params, output_filename, break_word='MPI_ABORT',
-                           break_words=None):
+def run_external_monitored(params:          Sequence[str],
+                           output_filename: str,
+                           break_word:      str = 'MPI_ABORT',
+                           break_words:     Optional[str] = None):
     """
     Run an external process monitoring the standard output and error for a
     word that will terminate the process
@@ -111,7 +113,6 @@ def run_external_monitored(params, output_filename, break_word='MPI_ABORT',
 
         output_filename (str):
 
-    Keyword Arguments:
         break_word (str): String that if found will terminate the process
 
         break_words (list(str) | None): List of break_word-s
@@ -173,8 +174,8 @@ def wrapped_function(*args, **kwargs):
     return func_decorator
 
 
-def work_in_tmp_dir(filenames_to_copy: Optional[List[str]] = None,
-                    kept_file_exts:    Optional[List[str]] = None,
+def work_in_tmp_dir(filenames_to_copy: Optional[Sequence[str]] = None,
+                    kept_file_exts:    Optional[Sequence[str]] = None,
                     use_ll_tmp:        bool = False):
     """Execute a function in a temporary directory.
 
@@ -410,3 +411,41 @@ def hashable(_method_name: str, _object: Any):
     """Multiprocessing requires hashable top-level functions to be executed,
     so convert a method into a top-level function"""
     return getattr(_object, _method_name)
+
+
+def run_in_tmp_environment(**kwargs):
+    """
+    Apply a set of environment variables, execute a function and reset them
+    """
+
+    class EnvVar:
+        def __init__(self, name, val):
+            self.name = str(name)
+            self.val = os.getenv(str(name), None)
+            self.new_val = str(val)
+
+    env_vars = [EnvVar(k, v) for k, v in kwargs.items()]
+
+    def func_decorator(func):
+
+        @wraps(func)
+        def wrapped_function(*args, **_kwargs):
+
+            for env_var in env_vars:
+                logger.info(f'Setting the {env_var.name} to {env_var.new_val}')
+                os.environ[env_var.name] = env_var.new_val
+
+            result = func(*args, **_kwargs)
+
+            for env_var in env_vars:
+                if env_var.val is None:
+                    # Remove from the environment
+                    os.environ.pop(env_var.name)
+                else:
+                    # otherwise set it back to the old value
+                    os.environ[env_var.name] = env_var.val
+
+            return result
+
+        return wrapped_function
+    return func_decorator

autode/wrappers/XTB.py

@@ -8,7 +8,7 @@
 from autode.config import Config
 from autode.constants import Constants
 from autode.exceptions import AtomsNotFound, CouldNotGetProperty
-from autode.utils import work_in_tmp_dir
+from autode.utils import work_in_tmp_dir, run_in_tmp_environment
 from autode.log import logger
 
 
@@ -162,9 +162,9 @@ def execute(self, calc):
         @work_in_tmp_dir(filenames_to_copy=calc.input.filenames,
                          kept_file_exts=('.xyz', '.out', '.pc', '.grad'),
                          use_ll_tmp=True)
+        @run_in_tmp_environment(OMP_NUM_THREADS=calc.n_cores,
+                                GFORTRAN_UNBUFFERED_ALL=1)
         def execute_xtb():
-            logger.info(f'Setting the number of OMP threads to {calc.n_cores}')
-            os.environ['OMP_NUM_THREADS'] = str(calc.n_cores)
 
             logger.info(f'Running XTB with: {" ".join(flags)}')
             run_external(params=[calc.method.path, calc.input.filename]+flags,

doc/changelog.rst

@@ -2,6 +2,18 @@ Changelog
 =========
 
 
+1.2.2
+--------
+----------
+
+Bugfix release.
+
+
+Bug Fixes
+*********
+- Fixes output redirection from XTB calculations resulting in missed lines on Mac
+
+
 1.2.1
 --------
 ----------

setup.py

@@ -20,7 +20,7 @@
                         extra_link_args=["-std=c++11"])]
 
 setup(name='autode',
-      version='1.2.1',
+      version='1.2.2',
       packages=['autode',
                 'autode.conformers',
                 'autode.pes',

tests/test_utils.py

@@ -229,3 +229,21 @@ def f(mol):
         m.graph = None
 
         f(m)  # No graph
+
+
+def test_tmp_env():
+
+    os.environ['OMP_NUM_THREADS'] = '1'
+
+    @utils.run_in_tmp_environment(tmp_key_str='tmp_value',
+                                  tmp_key_int=1,
+                                  OMP_NUM_THREADS=9999)
+    def f():
+        assert os.environ['tmp_key_int'] == '1'
+        assert os.environ['tmp_key_str'] == 'tmp_value'
+        assert os.environ['OMP_NUM_THREADS'] == '9999'
+
+    f()
+    assert 'tmp_key_int' not in os.environ
+    assert 'tmp_key_str' not in os.environ
+    assert os.environ['OMP_NUM_THREADS'] == '1'