Merge develop into provenance_redesign and update pre-commit depe…

…ndencies

.pylintrc

@@ -50,7 +50,7 @@ confidence=
 # --enable=similarities". If you want to run only the classes checker, but have
 # no Warning level messages displayed, use"--disable=all --enable=classes
 # --disable=W"
-disable=bad-continuation,locally-disabled,useless-suppression,django-not-available
+disable=bad-continuation,locally-disabled,useless-suppression,django-not-available,bad-option-value
 
 # Enable the message, report, category or checker with the given id(s). You can
 # either give multiple identifier separated by comma (,) or put this option

.travis.yml

@@ -50,7 +50,7 @@ install:
     - pip install -U pip wheel setuptools
     - pip install coveralls
     # Install AiiDA with some optional dependencies
-    - if [ "$TEST_TYPE" == "docs" ]; then pip install . && pip install -r docs/requirements_for_rtd.txt; else pip install .[all]; fi
+    - if [ "$TEST_TYPE" == "docs" ]; then pip install . && pip install -r docs/requirements_for_rtd.txt; else pip install --no-cache-dir .[all]; fi
 
 env:
     ## Build matrix to test both backends, and the docs

aiida/backends/djsite/db/migrations/0020_provenance_redesign.py

@@ -75,7 +75,6 @@ def detect_unexpected_links(apps, schema_editor):
 
 def reverse_code(apps, schema_editor):
     """Reversing the inference of the process type is not possible and not necessary."""
-    pass
 
 
 class Migration(migrations.Migration):

aiida/backends/djsite/utils.py

@@ -75,6 +75,7 @@ def check_schema_version(profile_name=None):
     :raise ConfigurationError: if the two schema versions do not match.
       Otherwise, just return.
     """
+    # pylint: disable=duplicate-string-formatting-argument
     from django.db import connection
 
     import aiida.backends.djsite.db.models

aiida/backends/tests/__init__.py

@@ -63,7 +63,9 @@
         'cmdline.commands.profile': ['aiida.backends.tests.cmdline.commands.test_profile'],
         'cmdline.commands.rehash': ['aiida.backends.tests.cmdline.commands.test_rehash'],
         'cmdline.commands.run': ['aiida.backends.tests.cmdline.commands.test_run'],
+        'cmdline.commands.setup': ['aiida.backends.tests.cmdline.commands.test_setup'],
         'cmdline.commands.user': ['aiida.backends.tests.cmdline.commands.test_user'],
+        'cmdline.commands.verdi': ['aiida.backends.tests.cmdline.commands.test_verdi'],
         'cmdline.commands.work': ['aiida.backends.tests.cmdline.commands.test_work'],
         'cmdline.commands.workflow': ['aiida.backends.tests.cmdline.commands.test_workflow'],
         'cmdline.params.types.calculation': ['aiida.backends.tests.cmdline.params.types.test_calculation'],

aiida/backends/tests/calculation_node.py

@@ -50,6 +50,7 @@ class TestProcessNode(AiidaTestCase):
     @classmethod
     def setUpClass(cls, *args, **kwargs):
         super(TestProcessNode, cls).setUpClass(*args, **kwargs)
+        cls.computer.configure()  # pylint: disable=no-member
         cls.construction_options = {'resources': {'num_machines': 1, 'num_mpiprocs_per_machine': 1}}
 
         cls.calcjob = CalcJobNode()
@@ -147,3 +148,15 @@ def test_calcjob_get_options_defaults(self):
 
     def test_get_description(self):
         self.assertEqual(self.calcjob.get_desc(), self.calcjob.get_state())
+
+    def test_get_authinfo(self):
+        """Test that we can get the AuthInfo object from the calculation instance."""
+        from aiida.orm import AuthInfo
+        authinfo = self.calcjob._get_authinfo()  # pylint: disable=protected-access
+        self.assertIsInstance(authinfo, AuthInfo)
+
+    def test_get_transport(self):
+        """Test that we can get the Transport object from the calculation instance."""
+        from aiida.transport import Transport
+        transport = self.calcjob._get_transport()  # pylint: disable=protected-access
+        self.assertIsInstance(transport, Transport)

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

@@ -21,6 +21,7 @@ class TestVerdiRun(AiidaTestCase):
     """Tests for `verdi run`."""
 
     def setUp(self):
+        super(TestVerdiRun, self).setUp()
         self.cli_runner = CliRunner()
 
     def test_run_workfunction(self):

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

@@ -0,0 +1,74 @@
+# -*- 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 `verdi setup`."""
+from __future__ import division
+from __future__ import print_function
+from __future__ import absolute_import
+
+from click.testing import CliRunner
+
+from aiida.backends import settings
+from aiida.backends.testbase import AiidaTestCase
+from aiida.backends.tests.utils.configuration import with_temporary_config_instance
+from aiida.cmdline.commands import cmd_setup
+from aiida.manage import get_config
+
+
+class TestVerdiSetup(AiidaTestCase):
+    """Tests for `verdi setup`."""
+
+    def setUp(self):
+        """Create runner object to run tests."""
+        self.cli_runner = CliRunner()
+
+    @with_temporary_config_instance
+    def test_non_interactive_override(self):
+        """Tests that existing profile can be overridden in non-interactive mode with the `--force` option."""
+        config = get_config()
+        profile = config.current_profile
+
+        option_string = '--backend={backend} --email={email} --repository={repo} --db-host={db_host} ' \
+                        '--db-port={db_port} --db-name={db_name} --db-username={db_user} --db-password={db_pass} ' \
+                        '--first-name={first} --last-name={last} --institution={institution}'
+
+        profile_settings = {
+            'email': profile.dictionary['default_user_email'],
+            'backend': profile.dictionary['AIIDADB_BACKEND'],
+            'db_host': profile.dictionary['AIIDADB_HOST'],
+            'db_port': profile.dictionary['AIIDADB_PORT'],
+            'db_name': profile.dictionary['AIIDADB_NAME'],
+            'db_user': profile.dictionary['AIIDADB_USER'],
+            'db_pass': profile.dictionary['AIIDADB_PASS'],
+            'repo': '/tmp',
+            'first': 'nim',
+            'last': 'porte',
+            'institution': 'quoi',
+        }
+
+        options = ['--non-interactive'] + option_string.format(**profile_settings).split()
+
+        # Without profile name should raise exception
+        result = self.cli_runner.invoke(cmd_setup.setup, options)
+        self.assertIsNotNone(result.exception)
+        self.assertIn('Missing argument', result.output)
+        self.assertIn('profile_name', result.output)
+
+        # With existing profile name should raise exception
+        options.append(profile.name)
+        result = self.cli_runner.invoke(cmd_setup.setup, options)
+        self.assertIsNotNone(result.exception, result.output)
+
+        # Need to set the current profile to None again, otherwise it will complain that `verdi` is using `-p` flag
+        settings.AIIDADB_PROFILE = None
+
+        # Adding the `--force` option should allow it
+        options.append('--force')
+        result = self.cli_runner.invoke(cmd_setup.setup, options)
+        self.assertIsNone(result.exception, result.output)

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

@@ -0,0 +1,32 @@
+# -*- 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 `verdi`."""
+from __future__ import division
+from __future__ import print_function
+from __future__ import absolute_import
+from click.testing import CliRunner
+
+from aiida import get_version
+from aiida.backends.testbase import AiidaTestCase
+from aiida.cmdline.commands import cmd_verdi
+
+
+class TestVerdi(AiidaTestCase):
+    """Tests for `verdi run`."""
+
+    def setUp(self):
+        super(TestVerdi, self).setUp()
+        self.cli_runner = CliRunner()
+
+    def test_verdi_version(self):
+        """Regression test for #2238: verify that `verdi --version` prints the current version"""
+        result = self.cli_runner.invoke(cmd_verdi.verdi, ['--version'])
+        self.assertIsNone(result.exception, result.output)
+        self.assertIn(get_version(), result.output)

aiida/backends/tests/common/test_hashing.py

@@ -193,7 +193,7 @@ def test_numpy_arrays(self):
 
     def test_unhashable_type(self):
 
-        class MadeupClass(object):
+        class MadeupClass(object):  # pylint: disable=useless-object-inheritance
             pass
 
         with self.assertRaises(ValueError):

aiida/backends/tests/orm/node/test_node.py

@@ -213,7 +213,7 @@ def test_node_indegree_unique_pair(self):
         called.add_incoming(data, link_type=LinkType.INPUT_CALC, link_label='call')
         called.store()
 
-        uuids_incoming = set([node.uuid for node in called.get_incoming().all_nodes()])
+        uuids_incoming = set(node.uuid for node in called.get_incoming().all_nodes())
         uuids_expected = set([caller.uuid, data.uuid])
         self.assertEqual(uuids_incoming, uuids_expected)
 
@@ -232,7 +232,7 @@ def test_node_indegree_unique_triple(self):
         data.add_incoming(return_two, link_type=LinkType.RETURN, link_label='return')
         data.store()
 
-        uuids_incoming = set([node.uuid for node in data.get_incoming().all_nodes()])
+        uuids_incoming = set(node.uuid for node in data.get_incoming().all_nodes())
         uuids_expected = set([return_one.uuid, return_two.uuid])
         self.assertEqual(uuids_incoming, uuids_expected)
 
@@ -253,6 +253,6 @@ def test_node_outdegree_unique_triple(self):
         data_one.store()
         data_two.store()
 
-        uuids_outgoing = set([node.uuid for node in creator.get_outgoing().all_nodes()])
+        uuids_outgoing = set(node.uuid for node in creator.get_outgoing().all_nodes())
         uuids_expected = set([data_one.uuid, data_two.uuid])
         self.assertEqual(uuids_outgoing, uuids_expected)

aiida/backends/tests/restapi.py

@@ -612,7 +612,6 @@ def test_computers_orderby_mixed3(self):
                                   -hostname",
                                   expected_list_ids=[1,0,4,3,2])
         """
-        pass
 
     ############### list filter combinations #######################
     def test_computers_filter_mixed1(self):
@@ -675,7 +674,6 @@ def test_computers_unknown_param(self):
         from aiida.common.exceptions import InputValidationError
         RESTApiTestCase.node_exception(self, "/computers?aa=bb&id=2", InputValidationError)
         """
-        pass
 
     ############### single calculation ########################
     def test_calculations_details(self):

aiida/calculations/plugins/arithmetic/add.py

@@ -66,7 +66,7 @@ def _use_methods(cls):
 
     def _get_input_valid_types(self, key):
         """Return the valid input types for the given key."""
-        return self._use_methods[key]['valid_types']
+        return self._use_methods[key]['valid_types']  # pylint: disable=unsubscriptable-object
 
     def _get_input_valid_type(self, key):
         """Return the valid input type for the given key."""

aiida/calculations/plugins/templatereplacer.py

@@ -94,7 +94,7 @@ def _prepare_for_submission(self, tempfolder, inputdict):
         :param inputdict: a dictionary with the input nodes e.g. {label1: node1, ...} (with the Code!)
         """
         # pylint: disable=too-many-locals,too-many-statements,too-many-branches
-        from six.moves import StringIO as StringIO
+        from six.moves import StringIO
 
         from aiida.orm.data.singlefile import SinglefileData
         from aiida.orm.data.remote import RemoteData

aiida/cmdline/commands/cmd_calcjob.py

@@ -25,7 +25,6 @@
 @verdi.group('calcjob')
 def verdi_calcjob():
     """Inspect and manage calcjobs."""
-    pass
 
 
 @verdi_calcjob.command('gotocomputer')

aiida/cmdline/commands/cmd_calculation.py

@@ -31,7 +31,6 @@
 @verdi.group('calculation')
 def verdi_calculation():
     """Inspect and manage calculations."""
-    pass
 
 
 @verdi_calculation.command('gotocomputer')

aiida/cmdline/commands/cmd_code.py

@@ -27,7 +27,6 @@
 @verdi.group('code')
 def verdi_code():
     """Setup and manage codes."""
-    pass
 
 
 def get_default(key, ctx):
@@ -215,7 +214,6 @@ def reveal(codes):
 # pylint: disable=unused-argument
 def update(code):
     """Update an existing code."""
-    pass
 
 
 @verdi_code.command()

aiida/cmdline/commands/cmd_comment.py

@@ -23,7 +23,6 @@
 @verdi.group('comment')
 def verdi_comment():
     """Inspect, create and manage node comments."""
-    pass
 
 
 @verdi_comment.command()
@@ -76,7 +75,7 @@ def show(user, nodes):
             comments = [comment for comment in all_comments if comment.user.email == user.email]
 
             if not comments:
-                valid_users = ', '.join(set([comment.user.email for comment in all_comments]))
+                valid_users = ', '.join(set(comment.user.email for comment in all_comments))
                 echo.echo_warning('no comments found for user {}'.format(user))
                 echo.echo_info('valid users found for Node<{}>: {}'.format(node.pk, valid_users))
 

aiida/cmdline/commands/cmd_computer.py

@@ -33,7 +33,6 @@
 @verdi.group('computer')
 def verdi_computer():
     """Setup and manage computers."""
-    pass
 
 
 def get_computer_names():
@@ -161,8 +160,8 @@ def _computer_create_temp_file(transport, scheduler, authinfo):  # pylint: disab
     if not transport.path_exists(remote_file_path):
         echo.echo_error("* ERROR! The file was not found!")
         return False
-    else:
-        echo.echo("      [OK]")
+
+    echo.echo("      [OK]")
     echo.echo("  `-> Retrieving the file and checking its content...")
 
     handle, destfile = tempfile.mkstemp()
@@ -179,8 +178,8 @@ def _computer_create_temp_file(transport, scheduler, authinfo):  # pylint: disab
             echo.echo("** Found:")
             echo.echo(read_string)
             return False
-        else:
-            echo.echo("      [Content OK]")
+
+        echo.echo("      [Content OK]")
     finally:
         os.remove(destfile)
 
@@ -621,7 +620,6 @@ def computer_delete(computer):
 @verdi_computer.group('configure')
 def computer_configure():
     """Configure a computer with one of the available transport types."""
-    pass
 
 
 @computer_configure.command('show')

aiida/cmdline/commands/cmd_daemon.py

@@ -29,7 +29,6 @@
 @verdi.group('daemon')
 def verdi_daemon():
     """Inspect and manage the daemon."""
-    pass
 
 
 @verdi_daemon.command()

aiida/cmdline/commands/cmd_data/__init__.py

@@ -15,14 +15,13 @@
 
 from aiida.cmdline.commands.cmd_verdi import verdi
 from aiida.cmdline.commands.cmd_plugin import verdi_plugin
-from aiida.cmdline.utils import decorators, echo
+from aiida.cmdline.utils import decorators
 from aiida.cmdline.utils.pluginable import Pluginable
 
 
 @verdi.group('data', entry_point_group='aiida.cmdline.data', cls=Pluginable)
 def verdi_data():
     """Inspect, create and manage data nodes."""
-    pass
 
 
 @verdi_data.command('plugins')

aiida/cmdline/commands/cmd_data/cmd_array.py

@@ -19,7 +19,6 @@
 @verdi_data.group('array')
 def array():
     """Manipulate ArrayData objects."""
-    pass
 
 
 @array.command('show')

aiida/cmdline/commands/cmd_data/cmd_bands.py

@@ -34,7 +34,6 @@
 @verdi_data.group('bands')
 def bands():
     """Manipulate BandsData objects."""
-    pass
 
 
 # pylint: disable=too-many-arguments

aiida/cmdline/commands/cmd_data/cmd_cif.py

@@ -31,7 +31,6 @@
 @verdi_data.group('cif')
 def cif():
     """Manipulation of CIF data objects."""
-    pass
 
 
 @cif.command('list')

aiida/cmdline/commands/cmd_data/cmd_parameter.py

@@ -19,7 +19,6 @@
 @verdi_data.group('parameter')
 def parameter():
     """View and manipulate ParameterData objects."""
-    pass
 
 
 @parameter.command('show')