Added structured logging, fixed file structure.

.gitignore

@@ -55,4 +55,4 @@ lib/
 env/
 
 # Egg
-parser/parser-nwchem/nwchemparser.egg-info/
+nwchemparser.egg-info/

parser/parser-nwchem/nwchemparser/parser.py → nwchemparser/parser.py

 # Copyright 2016-2018 Lauri Himanen, Fawzi Mohamed
-# 
+#
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.
 #   You may obtain a copy of the License at
-# 
+#
 #     http://www.apache.org/licenses/LICENSE-2.0
-# 
+#
 #   Unless required by applicable law or agreed to in writing, software
 #   distributed under the License is distributed on an "AS IS" BASIS,
 #   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 #   See the License for the specific language governing permissions and
 #   limitations under the License.
 
-from builtins import next
-from builtins import range
+# from builtins import next
+# from builtins import range
 import os
 import re
 import logging
@@ -30,8 +30,20 @@ class NWChemParser(ParserInterface):
     After the implementation has been setup, you can parse the files with
     parse().
     """
-    def __init__(self, metainfo_to_keep=None, backend=None, default_units=None, metainfo_units=None, debug=True, log_level=logging.ERROR, store=True):
-        super(NWChemParser, self).__init__(metainfo_to_keep, backend, default_units, metainfo_units, debug, log_level, store)
+    def __init__(
+        self, metainfo_to_keep=None, backend=None, default_units=None,
+        metainfo_units=None, debug=True, logger = None,
+        log_level=logging.ERROR, store=True
+    ):
+        super(NWChemParser, self).__init__(
+            metainfo_to_keep, backend, default_units,
+            metainfo_units, debug, log_level, store
+        )
+        if logger is not None:
+            self.logger = logger
+            self.logger.debug('received logger')
+        else:
+            self.logger = logging.getLogger(__name__)
 
     def setup_version(self):
         """Setups the version by looking at the output file and the version
@@ -50,7 +62,7 @@ class NWChemParser(ParserInterface):
 
         if version_id is None:
             msg = "Could not find a version specification from the given main file."
-            logger.exception(msg)
+            self.logger.exception(msg)
             raise RuntimeError(msg)
 
         # Setup the root folder to the fileservice that is used to access files
@@ -78,16 +90,16 @@ class NWChemParser(ParserInterface):
         try:
             parser_module = importlib.import_module(base)
         except ImportError:
-            logger.warning("Could not find a parser for version '{}'. Trying to default to the base implementation for NWChem 6.6".format(version_id))
+            self.logger.warning("Could not find a parser for version '{}'. Trying to default to the base implementation for NWChem 6.6".format(version_id))
             base = "nwchemparser.versions.nwchem66.mainparser"
             try:
                 parser_module = importlib.import_module(base)
             except ImportError:
-                logger.exception("Tried to default to the NWChem 6.6 implementation but could not find the correct module.")
+                self.logger.exception("Tried to default to the NWChem 6.6 implementation but could not find the correct module.")
                 raise
         try:
             parser_class = getattr(parser_module, "NWChemMainParser")
         except AttributeError:
-            logger.exception("A parser class 'NWChemMainParser' could not be found in the module '[]'.".format(parser_module))
+            self.logger.exception("A parser class 'NWChemMainParser' could not be found in the module '[]'.".format(parser_module))
             raise
         self.main_parser = parser_class(self.parser_context)

setup.py

 # Copyright 2016-2018 Lauri Himanen, Fawzi Mohamed
-# 
+#
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.
 #   You may obtain a copy of the License at
-# 
+#
 #     http://www.apache.org/licenses/LICENSE-2.0
-# 
+#
 #   Unless required by applicable law or agreed to in writing, software
 #   distributed under the License is distributed on an "AS IS" BASIS,
 #   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -23,7 +23,7 @@ def main():
         author="Lauri Himanen",
         author_email="lauri.himanen@aalto.fi",
         license="GPL3",
-        package_dir={'': 'parser/parser-nwchem'},
+        package_dir={'': './'},
         packages=find_packages(),
         install_requires=[
             'nomadcore',