Merge 6d30bab into bb9f2a9

.ci/check_travis_tag.py

@@ -7,8 +7,6 @@
 # For further information on the license, see the LICENSE.txt file.           #
 ###############################################################################
 """Check travis tag"""
-from __future__ import print_function
-from __future__ import absolute_import
 
 import os
 import sys

.coveragerc

@@ -0,0 +1,2 @@
+[run]
+parallel=True

.docker/my_init.d/add-codes.sh

@@ -4,4 +4,4 @@ set -em
 su -c /opt/add-codes.sh aiida
 
 # Make /opt/aiida-cp2k folder editable for the $SYSTEM_USER.
-chown -R aiida:aiida /opt/aiida-cp2k/
+chown -R ${SYSTEM_USER}:${SYSTEM_USER} /opt/aiida-cp2k/

.docker/opt/add-codes.sh

@@ -6,4 +6,5 @@ set -x
 # Environment
 export SHELL=/bin/bash
 
+# Install cp2k code.
 verdi code show cp2k@localhost || verdi code setup --config /opt/aiida-cp2k/.docker/cp2k-code.yml --non-interactive

.pre-commit-config.yaml

@@ -1,17 +1,6 @@
 # # Install pre-commit hooks via
 # pre-commit install
 
-# modernizer: make sure our code-base is Python 3 ready
-- repo: https://github.com/python-modernize/python-modernize.git
-  sha: a234ce4e185cf77a55632888f1811d83b4ad9ef2
-  hooks:
-  - id: python-modernize
-    exclude: ^docs/
-    args:
-      - --write
-      - --nobackups
-      - --nofix=dict_six
-
 - repo: local
   hooks:
   # yapf = yet another python formatter

.pylintrc

@@ -273,10 +273,6 @@ ignored-argument-names=_.*|^ignored_|^unused_
 # Tells whether we should check for unused import in __init__ files.
 init-import=no
 
-# List of qualified module names which can have objects that can redefine
-# builtins.
-redefining-builtins-modules=six.moves,future.builtins
-
 
 [MISCELLANEOUS]
 

.travis.yml

@@ -7,10 +7,9 @@ before_install:
   - python .ci/check_travis_tag.py
   - docker build -t aiida_cp2k_test .
   - export DOCKERID=`docker run -d aiida_cp2k_test`
-  - sleep 30 # wait until the container is launched
 
 script:
-  - "echo \"Docker ID: $DOCKERID\""
+  - docker exec --tty $DOCKERID wait-for-services
   - docker exec -it --user aiida $DOCKERID /bin/bash -l -c 'cd /opt/aiida-cp2k/ && pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )'
   - docker exec -it --user aiida $DOCKERID /bin/bash -l -c 'cd /opt/aiida-cp2k/ && py.test --cov aiida_cp2k --cov-append .'
   - docker exec -it --user aiida $DOCKERID /bin/bash -l -c 'cd /opt/aiida-cp2k/docs && make'

Dockerfile

@@ -5,11 +5,7 @@
 # For further information on the license, see the LICENSE.txt file.           #
 ###############################################################################
 
-FROM aiidateam/aiida-docker-stack
-
-# Set HOME and PATH variables.
-ENV HOME="/home/aiida"
-ENV PATH="${HOME}/.local/bin:${PATH}"
+FROM aiidateam/aiida-core:latest
 
 # To prevent the container to exit prematurely.
 ENV KILL_ALL_RPOCESSES_TIMEOUT=50
@@ -28,6 +24,4 @@ RUN pip install coveralls
 
 # Install the cp2k code.
 COPY .docker/opt/add-codes.sh /opt/
-COPY .docker/my_init.d/add-codes.sh /etc/my_init.d/40_add-codes.sh
-
-RUN chown -R aiida:aiida ${HOME}
+COPY .docker/my_init.d/add-codes.sh /etc/my_init.d/50_add-codes.sh

aiida_cp2k/__init__.py

@@ -7,6 +7,6 @@
 ###############################################################################
 """AiiDA-CP2K plugins, parsers, workflows, etc ..."""
 
-__version__ = "1.0.0"
+__version__ = "1.1.0"
 
 # EOF

aiida_cp2k/calculations/__init__.py

@@ -7,11 +7,7 @@
 ###############################################################################
 """AiiDA-CP2K input plugin."""
 
-from __future__ import absolute_import
-
 import io
-import six
-from six.moves import map
 
 from aiida.engine import CalcJob
 from aiida.orm import Computer, Dict, SinglefileData, StructureData, RemoteData, BandsData
@@ -51,16 +47,13 @@ def define(cls, spec):
                              dynamic=True)
 
         # Specify default parser.
-        spec.input('metadata.options.parser_name',
-                   valid_type=six.string_types,
-                   default=cls._DEFAULT_PARSER,
-                   non_db=True)
+        spec.input('metadata.options.parser_name', valid_type=str, default=cls._DEFAULT_PARSER, non_db=True)
 
         # Add input_filename attribute.
-        spec.input('metadata.options.input_filename', valid_type=six.string_types, default=cls._DEFAULT_INPUT_FILE)
+        spec.input('metadata.options.input_filename', valid_type=str, default=cls._DEFAULT_INPUT_FILE)
 
         # Add output_filename attribute.
-        spec.input('metadata.options.output_filename', valid_type=six.string_types, default=cls._DEFAULT_OUTPUT_FILE)
+        spec.input('metadata.options.output_filename', valid_type=str, default=cls._DEFAULT_OUTPUT_FILE)
 
         # Use mpi by default.
         spec.input('metadata.options.withmpi', valid_type=bool, default=True)
@@ -95,6 +88,8 @@ def define(cls, spec):
         spec.output('output_bands', valid_type=BandsData, required=False, help='optional band structure')
         spec.default_output_node = 'output_parameters'
 
+        spec.outputs.dynamic = True
+
     def prepare_for_submission(self, folder):
         """Create the input files from the input nodes passed to this instance of the `CalcJob`.
 
@@ -129,7 +124,7 @@ def prepare_for_submission(self, folder):
             try:
                 fobj.write(inp.render())
             except ValueError as exc:
-                six.raise_from(InputValidationError("invalid keys or values in input parameters found"), exc)
+                raise InputValidationError("Invalid keys or values in input parameters found") from exc
 
         settings = self.inputs.settings.get_dict() if 'settings' in self.inputs else {}
 

aiida_cp2k/parsers/__init__.py

@@ -6,7 +6,6 @@
 # For further information on the license, see the LICENSE.txt file.           #
 ###############################################################################
 """AiiDA-CP2K output parser."""
-from __future__ import absolute_import
 
 import io
 import os

aiida_cp2k/utils/__init__.py

@@ -6,9 +6,8 @@
 # For further information on the license, see the LICENSE.txt file.           #
 ###############################################################################
 """AiiDA-CP2K utils"""
-from __future__ import absolute_import
 
-from .input_generator import Cp2kInput
+from .input_generator import Cp2kInput, add_restart_sections
 from .parser import parse_cp2k_output
 from .parser import parse_cp2k_output_advanced
 from .parser import parse_cp2k_trajectory

aiida_cp2k/utils/input_generator.py

@@ -5,18 +5,14 @@
 # AiiDA-CP2K is hosted on GitHub at https://github.com/aiidateam/aiida-cp2k   #
 # For further information on the license, see the LICENSE.txt file.           #
 ###############################################################################
-"""AiiDA-CP2K input generator"""
-
-from __future__ import absolute_import
-from __future__ import division
+"""AiiDA-CP2K input generator."""
 
 from copy import deepcopy
+from collections.abc import Mapping, Sequence
 
-import six
-if six.PY2:
-    from collections import Mapping, Sequence  # pylint: disable=import-error, no-name-in-module
-else:
-    from collections.abc import Mapping, Sequence  # pylint: disable=import-error, no-name-in-module
+from aiida.orm import Dict
+from aiida.engine import calcfunction
+from .workchains import merge_dict
 
 
 class Cp2kInput:  # pylint: disable=old-style-class
@@ -55,7 +51,7 @@ def add_keyword(self, kwpath, value, override=True, conflicting_keys=None):
             added.
         """
 
-        if isinstance(kwpath, six.string_types):
+        if isinstance(kwpath, str):
             kwpath = kwpath.split("/")
 
         Cp2kInput._add_keyword(kwpath, value, self._params, ovrd=override, cfct=conflicting_keys)
@@ -89,7 +85,7 @@ def _add_keyword(kwpath, value, params, ovrd, cfct):
             Cp2kInput._add_keyword(kwpath[1:], value, params[kwpath[0]], ovrd, cfct)
 
         # if it is a list, loop over its elements
-        elif isinstance(params[kwpath[0]], Sequence) and not isinstance(params[kwpath[0]], six.string_types):
+        elif isinstance(params[kwpath[0]], Sequence) and not isinstance(params[kwpath[0]], str):
             for element in params[kwpath[0]]:
                 Cp2kInput._add_keyword(kwpath[1:], value, element, ovrd, cfct)
 
@@ -151,7 +147,7 @@ def _render_section(output, params, indent=0):
                 Cp2kInput._render_section(output, val, indent + 3)
                 output.append('{}&END {}'.format(' ' * indent, key))
 
-            elif isinstance(val, Sequence) and not isinstance(val, six.string_types):
+            elif isinstance(val, Sequence) and not isinstance(val, str):
                 for listitem in val:
                     Cp2kInput._render_section(output, {key: listitem}, indent)
 
@@ -161,3 +157,23 @@ def _render_section(output, params, indent=0):
 
             else:
                 output.append('{}{} {}'.format(' ' * indent, key, val))
+
+
+@calcfunction
+def add_restart_sections(input_dict):
+    """Add restart section to the input dictionary."""
+
+    params = input_dict.get_dict()
+    restart_wfn_dict = {
+        'FORCE_EVAL': {
+            'DFT': {
+                'RESTART_FILE_NAME': './parent_calc/aiida-RESTART.wfn',
+                'SCF': {
+                    'SCF_GUESS': 'RESTART',
+                },
+            },
+        },
+    }
+    merge_dict(params, restart_wfn_dict)
+    params['EXT_RESTART'] = {'RESTART_FILE_NAME': './parent_calc/aiida-1.restart'}
+    return Dict(dict=params)

aiida_cp2k/utils/parser.py

@@ -7,9 +7,6 @@
 ###############################################################################
 """AiiDA-CP2K input plugin."""
 
-from __future__ import absolute_import
-from __future__ import division
-
 import re
 import math
 

aiida_cp2k/utils/workchains.py

@@ -7,7 +7,6 @@
 ###############################################################################
 """AiiDA-CP2K utilities for workchains"""
 
-from __future__ import absolute_import
 from aiida.engine import calcfunction
 from aiida.orm import Dict, StructureData