Merge pull request #3501 from aiidateam/merge_master

Merge master after release `v1.0.0`

.ci/pytest/test_unittest_example.py

@@ -1,4 +1,15 @@
+# -*- coding: utf-8 -*-
+###########################################################################
+# Copyright (c), The AiiDA team. All rights reserved.                     #
+# This file is part of the AiiDA code.                                    #
+#                                                                         #
+# The code is hosted on GitHub at https://github.com/aiidateam/aiida-core #
+# For further information on the license, see the LICENSE.txt file        #
+# For further information please visit http://www.aiida.net               #
+###########################################################################
 """Test running unittest test cases through pytest."""
+from __future__ import division
+from __future__ import print_function
 from __future__ import absolute_import
 import unittest
 import pytest

AUTHORS.txt

@@ -1,65 +1,79 @@
-This file lists the authors of the AiiDA code (i.e., the members of the AiiDA team)
+This file lists the authors of the AiiDA code (i.e. the members of the AiiDA team)
 as well as the known contributors to the code.
 
 The current members of the AiiDA team are, in alphabetical order:
 #################################################################
-* Casper Andersen
-* Oscar Arbelaez
-* Marco Borelli
+* Carl S. Adorf
+* Casper W. Andersen
 * Sebastiaan P. Huber
 * Leonid Kahle
-* Boris Kozinsky
 * Snehal Kumbhar
 * Nicola Marzari
-* Andrius Merkys
 * Elsa Passaro
 * Giovanni Pizzi
+* Francisco F. Ramirez
 * Leopold Talirz
 * Aliaksandr Yakutovich
-* Spyros Zoupanos
 
 
 Former members of the AiiDA team
 ################################
+* Spyros Zoupanos (2015-2019)
 * Conrad Johnston (2018-2019)
 * Martin Uhrin (2015-2019)
 * Rico Häuselmann (2016-2018)
 * Nicolas Mounet (2015-2018)
-* Andrea Cepellotti (2012-2016)
 * Fernando Gargiulo (2016-2017)
+* Andrius Merkys (2015-2017)
+* Andrea Cepellotti (2012-2016)
+* Boris Kozinsky (2012-2016)
 * Riccardo Sabatini (2013-2015)
-* Rico Häuselmann (2016-2018)
 
 
 Contributors
 ############
-We would like to thank the following people for their contibution
-(beside generic comments and bugfixes):
+We would like to thank the following people for their major contibutions:
 
-* Valentin Bersier (EPFL, Switzerland): for the early version of the
-  AiiDA web interface
-* Jocelyn Boullier (EPFL, Switzerland): for the first version of the
-  SQLAlchemy implementation
-* Jens Bröder: (FZ Jülich, Germany) contributions to the workflow engine
-* Marco Dorigo (ICAMS, Germany): for the SGE scheduler plugin
-* Marco Gibertini: for the Quantum ESPRESSO plugin for the NEB code and
-  the extension of the PW plugin to the ENVIRON code
 * Dominik Gresch (ETHZ): for the caching mechanism and contributions to the workflow engine
-* Eric Hontz (MIT, USA): for the Quantum Espresso pwimmigrant plugin
-* Daniel Marchand (EPFL, Switzerland): for the Quantum ESPRESSO plugins
-  for PP, PROJWFC, and the first version of the Wannier90 plugin
 * Tiziano Müller (ETHZ, Switzerland): for the first implementation of
-  the new plugin system (developed in 2017) and making the code python 3 compatible
-* Philippe Schwaller (EPFL, Switzerland): for the ICSD importer
+  the new plugin system (developed in 2017) and making the code python 3 compatibl
 
 And the following people for general improvements to the code, fixing bugs,
 corrections and improvements to the documentation and useful suggestions:
 
-Ivano E. Castelli, Ian Lee, Gianluca Prandini, Jianxing Huang, Antimo Marrazzo, Nicola Varini, Mario Zic,
-Vladimir Dikan, Michael Atambo, Ole Schütt, Y.-W. Fang, Philipp Rüßmann, Bonan Zhu, Andreas Stamminger, Keija Cui,
-Daniel Hollas, Espen Flage-Larsen, Chris Sewell, Jason Yu, Daniele Tomerini
+* Oscar Arbelaez
+* Michael Atambo
+* Valentin Bersier
+* Marco Borelli
+* Jocelyn Boullier
+* Jens Bröder
+* Ivano E. Castelli
+* Keija Cui
+* Vladimir Dikan
+* Marco Dorigo
+* Y.-W. Fang
+* Marco Gibertini
+* Daniel Hollas
+* Eric Hontz
+* Jianxing Huang
+* Espen Flage Larsen
+* Ian Lee
+* Daniel Marchand
+* Antimo Marrazzo
+* Simon Pintarelli
+* Gianluca Prandini
+* Philipp Rüßmann
+* Philippe Schwaller
+* Ole Schütt
+* Chris Sewell
+* Andreas Stamminger
+* Atsushi Togo
+* Daniele Tomerini
+* Nicola Varini
+* Jason Yu
+* Bonan Zhu
+* Mario Zic
 
 ---
 
-Please, don't hesitate to contact the AiiDA team if you see that
-information is wrong or missing in this file.
+Please, don't hesitate to contact the AiiDA team if you see that information is wrong or missing in this file.

aiida/__init__.py

@@ -36,7 +36,7 @@
     u'For further information please visit http://www.aiida.net/. All rights reserved.'
 )
 __license__ = 'MIT license, see LICENSE.txt file.'
-__version__ = '1.0.0b6'
+__version__ = '1.0.0'
 __authors__ = 'The AiiDA team.'
 __paper__ = (
     u'G. Pizzi, A. Cepellotti, R. Sabatini, N. Marzari, and B. Kozinsky,'

aiida/backends/djsite/utils.py

@@ -16,7 +16,7 @@
 import os
 import django
 
-from aiida.backends.utils import validate_attribute_key, SettingsManager, Setting
+from aiida.backends.utils import validate_attribute_key, SettingsManager, Setting, validate_schema_generation
 from aiida.common import NotExistent
 
 SCHEMA_VERSION_DB_KEY = 'db|schemaversion'
@@ -121,6 +121,7 @@ def unload_dbenv():
 
 def migrate_database():
     """Migrate the database to the latest schema version."""
+    validate_schema_generation()
     from django.core.management import call_command
     call_command('migrate')
 
@@ -151,6 +152,8 @@ def check_schema_version(profile_name):
     if 'db_dbsetting' not in connection.introspection.table_names():
         return
 
+    validate_schema_generation()
+
     code_schema_version = aiida.backends.djsite.db.models.SCHEMA_VERSION
     db_schema_version = get_db_schema_version()
 

aiida/backends/sqlalchemy/migrations/versions/91b573400be5_prepare_schema_reset.py

@@ -15,6 +15,8 @@
 Create Date: 2019-07-25 14:58:39.866822
 
 """
+from __future__ import division
+from __future__ import print_function
 from __future__ import absolute_import
 
 # Remove when https://github.com/PyCQA/pylint/issues/1931 is fixed

aiida/backends/sqlalchemy/utils.py

@@ -20,7 +20,7 @@
 
 from aiida.backends import sqlalchemy as sa
 from aiida.backends.sqlalchemy import get_scoped_session
-from aiida.backends.utils import validate_attribute_key, SettingsManager, Setting
+from aiida.backends.utils import validate_attribute_key, SettingsManager, Setting, validate_schema_generation
 from aiida.common import NotExistent
 
 
@@ -347,6 +347,7 @@ def migrate_database(alembic_cfg=None):
 
     :param config: alembic configuration to use, will use default if not provided
     """
+    validate_schema_generation()
     from aiida.backends import sqlalchemy as sa
 
     if alembic_cfg is None:
@@ -368,6 +369,8 @@ def check_schema_version(profile_name):
 
     alembic_cfg = get_alembic_conf()
 
+    validate_schema_generation()
+
     # Getting the version of the code and the database, reusing the existing engine (initialized by AiiDA)
     with sa.ENGINE.begin() as connection:
         alembic_cfg.attributes['connection'] = connection

aiida/backends/tests/cmdline/commands/test_node.py

@@ -74,6 +74,34 @@ def test_node_tree_printer(self):
         with Capturing():
             NodeTreePrinter.print_node_tree(self.node, max_depth=1, follow_links=())
 
+    def test_node_show(self):
+        """Test `verdi node show`"""
+        node = orm.Data().store()
+        node.label = 'SOMELABEL'
+        options = [str(node.pk)]
+        result = self.cli_runner.invoke(cmd_node.node_show, options)
+        self.assertClickResultNoException(result)
+
+        # Let's check some content in the output. At least the UUID and the label should be in there
+        self.assertIn(node.label, result.output)
+        self.assertIn(node.uuid, result.output)
+
+        ## Let's now test the '--print-groups' option
+        options.append('--print-groups')
+        result = self.cli_runner.invoke(cmd_node.node_show, options)
+        self.assertClickResultNoException(result)
+        # I don't check the list of groups - it might be in an autogroup
+
+        # Let's create a group and put the node in there
+        group_name = 'SOMEGROUPNAME'
+        group = orm.Group(group_name).store()
+        group.add_nodes(node)
+
+        result = self.cli_runner.invoke(cmd_node.node_show, options)
+        self.assertClickResultNoException(result)
+        # Now the group should be in there
+        self.assertIn(group_name, result.output)
+
     def test_node_attributes(self):
         """Test verdi node attributes"""
         options = [str(self.node.uuid)]

aiida/backends/tests/plugins/test_entry_point.py

@@ -1,5 +1,15 @@
 # -*- coding: utf-8 -*-
+###########################################################################
+# Copyright (c), The AiiDA team. All rights reserved.                     #
+# This file is part of the AiiDA code.                                    #
+#                                                                         #
+# The code is hosted on GitHub at https://github.com/aiidateam/aiida-core #
+# For further information on the license, see the LICENSE.txt file        #
+# For further information please visit http://www.aiida.net               #
+###########################################################################
 """Tests for the :py:mod:`~aiida.plugins.entry_point` module."""
+from __future__ import division
+from __future__ import print_function
 from __future__ import absolute_import
 
 from aiida.backends.testbase import AiidaTestCase

aiida/backends/tests/plugins/test_factories.py

@@ -1,5 +1,15 @@
 # -*- coding: utf-8 -*-
+###########################################################################
+# Copyright (c), The AiiDA team. All rights reserved.                     #
+# This file is part of the AiiDA code.                                    #
+#                                                                         #
+# The code is hosted on GitHub at https://github.com/aiidateam/aiida-core #
+# For further information on the license, see the LICENSE.txt file        #
+# For further information please visit http://www.aiida.net               #
+###########################################################################
 """Tests for the :py:mod:`~aiida.plugins.factories` module."""
+from __future__ import division
+from __future__ import print_function
 from __future__ import absolute_import
 
 try:

aiida/backends/tests/restapi/__init__.py

@@ -0,0 +1,9 @@
+# -*- coding: utf-8 -*-
+###########################################################################
+# Copyright (c), The AiiDA team. All rights reserved.                     #
+# This file is part of the AiiDA code.                                    #
+#                                                                         #
+# The code is hosted on GitHub at https://github.com/aiidateam/aiida-core #
+# For further information on the license, see the LICENSE.txt file        #
+# For further information please visit http://www.aiida.net               #
+###########################################################################

aiida/backends/tests/restapi/test_identifiers.py

@@ -8,6 +8,8 @@
 # For further information please visit http://www.aiida.net               #
 ###########################################################################
 """Tests for the `aiida.restapi.common.identifiers` module."""
+from __future__ import division
+from __future__ import print_function
 from __future__ import absolute_import
 from aiida.backends.testbase import AiidaTestCase
 from aiida.restapi.common.identifiers import get_full_type_filters, FULL_TYPE_CONCATENATOR, LIKE_OPERATOR_CHARACTER

aiida/backends/utils.py

@@ -21,6 +21,9 @@
 
 AIIDA_ATTRIBUTE_SEP = '.'
 
+SCHEMA_GENERATION_KEY = 'schema_generation'
+SCHEMA_GENERATION_VALUE = '1'
+
 
 Setting = collections.namedtuple('Setting', ['key', 'value', 'description', 'time'])
 
@@ -68,6 +71,32 @@ def get_settings_manager():
     return manager
 
 
+def validate_schema_generation():
+    """Verify that the database schema generation is compatible with the current code schema generation."""
+    from aiida.common.exceptions import ConfigurationError, NotExistent
+    try:
+        schema_generation_database = get_db_schema_generation().value
+    except NotExistent:
+        schema_generation_database = '1'
+
+    if schema_generation_database is None:
+        schema_generation_database = '1'
+
+    if schema_generation_database != SCHEMA_GENERATION_VALUE:
+        raise ConfigurationError(
+            'The schema generation of your database {} is newer than that of the code `{}` and is incompatible.'.format(
+                schema_generation_database, SCHEMA_GENERATION_VALUE
+            )
+        )
+
+
+def get_db_schema_generation():
+    """Get the schema generation of the current database."""
+    from aiida.backends.utils import get_settings_manager
+    manager = get_settings_manager()
+    return manager.get(SCHEMA_GENERATION_KEY)
+
+
 def validate_attribute_key(key):
     """
     Validate the key string to check if it is valid (e.g., if it does not

aiida/cmdline/commands/cmd_node.py

@@ -154,17 +154,19 @@ def node_show(nodes, print_groups):
             # pylint: disable=invalid-name
             qb = QueryBuilder()
             qb.append(Node, tag='node', filters={'id': {'==': node.pk}})
-            qb.append(Group, tag='groups', with_node='node', project=['id', 'name'])
+            qb.append(Group, tag='groups', with_node='node', project=['id', 'label', 'type_string'])
 
             echo.echo('#### GROUPS:')
 
             if qb.count() == 0:
-                echo.echo('No groups found containing node {}'.format(node.pk))
+                echo.echo('Node {} does not belong to any group'.format(node.pk))
             else:
+                echo.echo('Node {} belongs to the following groups:'.format(node.pk))
                 res = qb.iterdict()
-                for gr in res:
-                    gr_specs = '{} {}'.format(gr['groups']['name'], gr['groups']['id'])
-                    echo.echo(gr_specs)
+                table = [(gr['groups']['id'], gr['groups']['label'], gr['groups']['type_string']) for gr in res]
+                table.sort()
+
+                echo.echo(tabulate.tabulate(table, headers=['PK', 'Label', 'Group type']))
 
 
 def echo_node_dict(nodes, keys, fmt, identifier, raw, use_attrs=True):