From 30cbbae5baf71f673499372792c85217681878e0 Mon Sep 17 00:00:00 2001
From: Lauri Himanen <lauri.himanen@aalto.fi>
Date: Tue, 17 Apr 2018 16:16:23 +0200
Subject: [PATCH] Made the code to use the new module structure in
python-common.
---
parser/parser-cp2k/cp2kparser/parser.py | 2 +-
.../versions/cp2k262/commonparser.py | 8 +++----
.../versions/cp2k262/geooptparser.py | 14 ++++++-------
.../versions/cp2k262/inputparser.py | 9 +++++---
.../cp2kparser/versions/cp2k262/mdparser.py | 21 +++++++++----------
.../cp2k262/singlepointforceparser.py | 2 +-
.../versions/cp2k262/singlepointparser.py | 6 +++---
regtests/regtests.py | 2 +-
8 files changed, 33 insertions(+), 31 deletions(-)
diff --git a/parser/parser-cp2k/cp2kparser/parser.py b/parser/parser-cp2k/cp2kparser/parser.py
index ab55422..e9e6d9a 100644
--- a/parser/parser-cp2k/cp2kparser/parser.py
+++ b/parser/parser-cp2k/cp2kparser/parser.py
@@ -4,7 +4,7 @@ import os
import re
import logging
import importlib
-from nomadcore.baseclasses import ParserInterface
+from nomadcore.parsing.baseclasses import ParserInterface
# Needs to be imported in order for the importlib calls to work in python 2.7
import cp2kparser.versions.cp2k262.singlepointparser
diff --git a/parser/parser-cp2k/cp2kparser/versions/cp2k262/commonparser.py b/parser/parser-cp2k/cp2kparser/versions/cp2k262/commonparser.py
index 6f822fb..d6dd036 100644
--- a/parser/parser-cp2k/cp2kparser/versions/cp2k262/commonparser.py
+++ b/parser/parser-cp2k/cp2kparser/versions/cp2k262/commonparser.py
@@ -3,10 +3,10 @@ from builtins import str
import re
import numpy as np
import logging
-from nomadcore.simple_parser import SimpleMatcher as SM
-from nomadcore.caching_backend import CachingLevel
-from nomadcore.unit_conversion.unit_conversion import convert_unit
-from nomadcore.baseclasses import CommonParser
+from nomadcore.parsing.simple_parser import SimpleMatcher as SM
+from nomadcore.parsing.caching_backend import CachingLevel
+from nomadcore.parsing.unit_conversion import convert_unit
+from nomadcore.parsing.baseclasses import CommonParser
from .inputparser import CP2KInputParser
from collections import defaultdict
logger = logging.getLogger("nomad")
diff --git a/parser/parser-cp2k/cp2kparser/versions/cp2k262/geooptparser.py b/parser/parser-cp2k/cp2kparser/versions/cp2k262/geooptparser.py
index ac7d739..4ecc51f 100644
--- a/parser/parser-cp2k/cp2kparser/versions/cp2k262/geooptparser.py
+++ b/parser/parser-cp2k/cp2kparser/versions/cp2k262/geooptparser.py
@@ -2,12 +2,12 @@ from __future__ import print_function
from __future__ import absolute_import
from builtins import next
from builtins import range
-from nomadcore.simple_parser import SimpleMatcher as SM
-from nomadcore.baseclasses import MainHierarchicalParser
-import nomadcore.configurationreading
-import nomadcore.csvparsing
+from nomadcore.parsing.simple_parser import SimpleMatcher as SM
+from nomadcore.parsing.baseclasses import MainHierarchicalParser
+import nomadcore.parsing.configurationreading
+import nomadcore.parsing.csvparsing
from .commonparser import CP2KCommonParser
-from nomadcore.caching_backend import CachingLevel
+from nomadcore.parsing.caching_backend import CachingLevel
import logging
logger = logging.getLogger("nomad")
@@ -267,10 +267,10 @@ class CP2KGeoOptParser(MainHierarchicalParser):
# Use special parsing for CP2K pdb files because they don't follow the proper syntax
if traj_format == "PDB":
- self.traj_iterator = nomadcore.csvparsing.iread(traj_file, columns=[3, 4, 5], start="CRYST", end="END")
+ self.traj_iterator = nomadcore.parsing.csvparsing.iread(traj_file, columns=[3, 4, 5], start="CRYST", end="END")
else:
try:
- self.traj_iterator = nomadcore.configurationreading.iread(traj_file)
+ self.traj_iterator = nomadcore.parsing.configurationreading.iread(traj_file)
except ValueError:
pass
diff --git a/parser/parser-cp2k/cp2kparser/versions/cp2k262/inputparser.py b/parser/parser-cp2k/cp2kparser/versions/cp2k262/inputparser.py
index 23157f6..35249c4 100644
--- a/parser/parser-cp2k/cp2kparser/versions/cp2k262/inputparser.py
+++ b/parser/parser-cp2k/cp2kparser/versions/cp2k262/inputparser.py
@@ -3,12 +3,15 @@ standard_library.install_aliases()
from builtins import object
import os
import re
-from io import StringIO
+try:
+ from StringIO import StringIO
+except ImportError:
+ from io import StringIO
import logging
import pickle
import numpy as np
-from nomadcore.baseclasses import AbstractBaseParser
-import nomadcore.configurationreading
+from nomadcore.parsing.baseclasses import AbstractBaseParser
+import nomadcore.parsing.configurationreading
from cp2kparser.generic.inputparsing import metainfo_data_prefix, metainfo_section_prefix
from pint import UnitRegistry
import ase
diff --git a/parser/parser-cp2k/cp2kparser/versions/cp2k262/mdparser.py b/parser/parser-cp2k/cp2kparser/versions/cp2k262/mdparser.py
index 2b7dac3..7aaffce 100644
--- a/parser/parser-cp2k/cp2kparser/versions/cp2k262/mdparser.py
+++ b/parser/parser-cp2k/cp2kparser/versions/cp2k262/mdparser.py
@@ -2,13 +2,12 @@ from __future__ import absolute_import
from builtins import next
from builtins import range
import numpy as np
-from nomadcore.simple_parser import SimpleMatcher as SM
-from nomadcore.baseclasses import MainHierarchicalParser
-import nomadcore.configurationreading
-import nomadcore.csvparsing
+from nomadcore.parsing.simple_parser import SimpleMatcher as SM
+from nomadcore.parsing.baseclasses import MainHierarchicalParser
from .commonparser import CP2KCommonParser
-from nomadcore.caching_backend import CachingLevel
-from nomadcore.unit_conversion.unit_conversion import convert_unit
+from nomadcore.parsing.caching_backend import CachingLevel
+from nomadcore.parsing.unit_conversion import convert_unit
+from nomadcore.parsing import configurationreading, csvparsing
import logging
logger = logging.getLogger("nomad")
@@ -196,10 +195,10 @@ class CP2KMDParser(MainHierarchicalParser):
# Use special parsing for CP2K pdb files because they don't follow the proper syntax
if traj_format == "PDB":
- self.traj_iterator = nomadcore.csvparsing.iread(coord_filepath, columns=[3, 4, 5], start="CRYST", end="END")
+ self.traj_iterator = csvparsing.iread(coord_filepath, columns=[3, 4, 5], start="CRYST", end="END")
else:
try:
- self.traj_iterator = nomadcore.configurationreading.iread(coord_filepath)
+ self.traj_iterator = configurationreading.iread(coord_filepath)
except ValueError:
pass
@@ -207,17 +206,17 @@ class CP2KMDParser(MainHierarchicalParser):
vel_format = self.cache_service["velocity_format"]
if vel_format is not None and vel_filepath is not None:
try:
- self.vel_iterator = nomadcore.configurationreading.iread(vel_filepath)
+ self.vel_iterator = configurationreading.iread(vel_filepath)
except ValueError:
pass
# Setup energy file iterator
if energies_filepath is not None:
- self.energy_iterator = nomadcore.csvparsing.iread(energies_filepath, columns=[0, 1, 2, 3, 4, 5, 6], comments="#")
+ self.energy_iterator = csvparsing.iread(energies_filepath, columns=[0, 1, 2, 3, 4, 5, 6], comments="#")
# Setup cell file iterator
if cell_filepath is not None:
- self.cell_iterator = nomadcore.csvparsing.iread(cell_filepath, columns=[2, 3, 4, 5, 6, 7, 8, 9, 10], comments="#")
+ self.cell_iterator = csvparsing.iread(cell_filepath, columns=[2, 3, 4, 5, 6, 7, 8, 9, 10], comments="#")
def onClose_x_cp2k_section_md(self, backend, gIndex, section):
diff --git a/parser/parser-cp2k/cp2kparser/versions/cp2k262/singlepointforceparser.py b/parser/parser-cp2k/cp2kparser/versions/cp2k262/singlepointforceparser.py
index 403f5d2..574cde7 100644
--- a/parser/parser-cp2k/cp2kparser/versions/cp2k262/singlepointforceparser.py
+++ b/parser/parser-cp2k/cp2kparser/versions/cp2k262/singlepointforceparser.py
@@ -1,6 +1,6 @@
import logging
import numpy as np
-from nomadcore.baseclasses import AbstractBaseParser
+from nomadcore.parsing.baseclasses import AbstractBaseParser
logger = logging.getLogger("nomad")
diff --git a/parser/parser-cp2k/cp2kparser/versions/cp2k262/singlepointparser.py b/parser/parser-cp2k/cp2kparser/versions/cp2k262/singlepointparser.py
index 9582b40..1f4ce2f 100644
--- a/parser/parser-cp2k/cp2kparser/versions/cp2k262/singlepointparser.py
+++ b/parser/parser-cp2k/cp2kparser/versions/cp2k262/singlepointparser.py
@@ -1,8 +1,8 @@
from __future__ import absolute_import
-from nomadcore.simple_parser import SimpleMatcher as SM
-from nomadcore.baseclasses import MainHierarchicalParser
+from nomadcore.parsing.simple_parser import SimpleMatcher as SM
+from nomadcore.parsing.baseclasses import MainHierarchicalParser
+from nomadcore.parsing.caching_backend import CachingLevel
from cp2kparser.versions.cp2k262.singlepointforceparser import CP2KSinglePointForceParser
-from nomadcore.caching_backend import CachingLevel
from cp2kparser.versions.cp2k262.commonparser import CP2KCommonParser
import logging
logger = logging.getLogger("nomad")
diff --git a/regtests/regtests.py b/regtests/regtests.py
index a2adc1b..01e0018 100644
--- a/regtests/regtests.py
+++ b/regtests/regtests.py
@@ -4,7 +4,7 @@ import unittest
import logging
import numpy as np
from cp2kparser import CP2KParser
-from nomadcore.unit_conversion.unit_conversion import convert_unit
+from nomadcore.parsing.unit_conversion import convert_unit
def get_result(folder, metaname=None):
--
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