Merge b05a943 into ca18340

.ci/install_conda.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+# See https://conda.io/docs/user-guide/tasks/use-conda-with-travis-ci.html#the-travis-yml-file
+if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
+  wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
+else
+  wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+fi
+bash miniconda.sh -b -p $HOME/miniconda
+export PATH="$HOME/miniconda/bin:$PATH"
+hash -r
+conda config --set always_yes yes --set changeps1 no
+conda update -q conda
+# Useful for debugging any issues with conda
+conda info -a

.ci/test_script.sh

@@ -48,4 +48,12 @@ case "$TEST_TYPE" in
     pre-commit)
         pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
         ;;
+    conda)
+        # Note: Not added to install in order not to slow down other tests
+        source ${CI_DIR}/install_conda.sh
+
+        # Replace dep1 dep2 ... with your dependencies
+        conda env create -f environment.yml -n test-environment python=$TRAVIS_PYTHON_VERSION
+        source activate test-environment
+        ;;
 esac

.pre-commit-config.yaml

@@ -197,7 +197,6 @@
         aiida/transports/plugins/test_local.py|
         aiida/transports/plugins/test_ssh.py|
         utils/create_requirements.py|
-        utils/validate_pyproject.py|
         .ci/test_daemon.py|
         .ci/workchains.py|
       )$
@@ -226,13 +225,24 @@
 
   - id: pyproject
     name: Validating pyproject.toml
-    entry: python ./utils/validate_pyproject.py
+    entry: python ./utils/validate_consistency.py toml
     language: system
     files: >-
       (?x)^(
         setup.json|
         setup.py|
-        utils/validate_pyproject|
+        utils/validate_consistency.py|
+      )$
+    pass_filenames: false
+  - id: conda
+    name: Validating environment.yml
+    entry: python ./utils/validate_consistency.py conda
+    language: system
+    files: >-
+      (?x)^(
+        setup_requirements.py|
+        utils/validate_consistency.py|
+        environment.yml|
       )$
     pass_filenames: false
 
@@ -245,11 +255,12 @@
 
   - id: version-number
     name: Check version numbers
-    entry: python ./utils/validate_version.py
+    entry: python ./utils/validate_consistency.py version
     language: system
     files: >-
       (?x)^(
         setup.json|
+        utils/validate_consistency.py|
         aiida/__init__.py
       )$
     pass_filenames: false

.prospector.yaml

@@ -9,7 +9,6 @@ ignore-paths:
 pylint:
   run: true
 
-
 pyflakes:
   run: false
 

.pylintrc

@@ -321,7 +321,8 @@ ignored-classes=optparse.Values,thread._local,_thread._local
 # (useful for modules/projects where namespaces are manipulated during runtime
 # and thus existing member attributes cannot be deduced by static analysis. It
 # supports qualified module names, as well as Unix pattern matching.
-ignored-modules=
+# This is a pylint issue https://github.com/PyCQA/pylint/issues/73
+ignored-modules=distutils
 
 # Show a hint with possible names when a member name was not found. The aspect
 # of finding the hint is based on edit distance.

.travis.yml

@@ -50,7 +50,7 @@ before_install:
 
 install:
     # Upgrade pip setuptools and wheel to be able to run the next command
-    - pip install -U pip==18.1 wheel setuptools
+    - pip install -U pip==18.1 wheel setuptools coveralls
     - 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 --no-cache-dir .[all]; fi
@@ -64,6 +64,7 @@ env:
     - TEST_AIIDA_BACKEND=django TEST_TYPE="docs"
     - TEST_AIIDA_BACKEND=django TEST_TYPE="tests"
     - TEST_AIIDA_BACKEND=sqlalchemy TEST_TYPE="tests"
+    # - TEST_TYPE="conda"
 
 before_script:
     - .ci/setup_profiles.sh

AUTHORS.txt

@@ -3,6 +3,9 @@ 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
 * Sebastiaan P. Huber
 * Conrad Johnston
 * Leonid Kahle
@@ -13,12 +16,15 @@ The current members of the AiiDA team are, in alphabetical order:
 * Elsa Passaro
 * Giovanni Pizzi
 * Leopold Talirz
-* Martin Uhrin
+* Aliaksandr Yakutovich
 * Spyros Zoupanos
 
 
 Former members of the AiiDA team
 ################################
+* Martin Uhrin (2015-2019)
+* Rico Häuselmann (2016-2018)
+* Nicolas Mounet (2015-2018)
 * Andrea Cepellotti (2012-2016)
 * Fernando Gargiulo (2016-2017)
 * Riccardo Sabatini (2013-2015)
@@ -50,9 +56,9 @@ We would like to thank the following people for their contibution
 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, Marco Borelli,
-Y.-W. Fang, Espen Flage-Larsen
+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, Philipp Rüßmann, Keija Cui,
+Daniel Hollas, Jianxing Huang, Espen Flage-Larsen
 
 ---
 

CHANGELOG.md

@@ -102,6 +102,29 @@
 - Enable tab-completion for `verdi devel tests` [[#1809]](https://github.com/aiidateam/aiida_core/pull/1809)
 - Add `-v/--verbose` flag to `verdi devel tests` [[#1807]](https://github.com/aiidateam/aiida_core/pull/1807)
 
+## v0.12.3
+### Improvements
+- Fast addition of nodes to groups with `skip_orm=True` [[#2471]](https://github.com/aiidateam/aiida_core/pull/2471)
+- Add `environment.yml` for installing dependencies using conda; release of `aiida-core` on conda-forge channel [[#2081]](https://github.com/aiidateam/aiida_core/pull/2081)
+- REST API: io tree response now includes link type and node label [[#2033]](https://github.com/aiidateam/aiida_core/pull/2033) [[#2511]](https://github.com/aiidateam/aiida_core/pull/2511)
+- Backport postgres improvements for quicksetup [[#2433]](https://github.com/aiidateam/aiida_core/pull/2433)
+- Backport `aiida.get_strict_version` (for plugin development) [[#2099]](https://github.com/aiidateam/aiida_core/pull/2099)
+
+### Minor bug fixes
+- Fix security vulnerability by upgrading `paramiko` to `2.4.2` [[#2043]](https://github.com/aiidateam/aiida_core/pull/2043)
+- Disable caching for inline calculations (broken since move to ``workfunction``-based implementation) [[#1872]](https://github.com/aiidateam/aiida_core/pull/1872)
+- Let `verdi help` return exit status 0 [[#2434]](https://github.com/aiidateam/aiida_core/pull/2434)
+- Decode dict keys only if strings (backport) [[#2436]](https://github.com/aiidateam/aiida_core/pull/2436)
+- Remove broken verdi-plug entry point [[#2356]](https://github.com/aiidateam/aiida_core/pull/2356)
+- `verdi node delete` (without arguments) no longer tries to delete all nodes [[#2545]](https://github.com/aiidateam/aiida_core/pull/2545)
+- Fix plotting of `BandsData` objects [[#2492]](https://github.com/aiidateam/aiida_core/pull/2492)
+
+### Miscellaneous
+- REST API: add tests for random sorting list entries of same type [[#2106]](https://github.com/aiidateam/aiida_core/pull/2106)
+- Add various badges to README [[#1969]](https://github.com/aiidateam/aiida_core/pull/1969)
+- Minor documentation improvements [[#1955]](https://github.com/aiidateam/aiida_core/pull/1955)
+- Add license file to MANIFEST [[#2339]](https://github.com/aiidateam/aiida_core/pull/2339)
+- Add instructions when `verdi import` fails [[#2420]](https://github.com/aiidateam/aiida_core/pull/2420)
 
 ## v0.12.2
 

MANIFEST.in

@@ -8,3 +8,4 @@ include setup.json
 include AUTHORS.txt
 include CHANGELOG.md
 include pyproject.toml
+include LICENSE.txt

aiida/__init__.py

@@ -90,7 +90,7 @@ def get_strict_version():
 
     :returns: StrictVersion instance with the current version
     """
-    from distutils.version import StrictVersion  # pylint: disable=import-error,no-name-in-module
+    from distutils.version import StrictVersion
     return StrictVersion(__version__)
 
 

aiida/backends/sqlalchemy/tests/test_generic.py

@@ -16,6 +16,7 @@
 
 from aiida.backends.testbase import AiidaTestCase
 from aiida.orm import Data, Node
+from six.moves import range
 
 
 class TestComputer(AiidaTestCase):
@@ -164,6 +165,25 @@ def test_group_general(self):
         group.add_nodes([node_01], skip_orm=True)
         self.assertEqual(set(_.pk for _ in nodes), set(_.pk for _ in group.nodes))
 
+    def test_group_batch_size(self):
+        """
+        Test that the group addition in batches works as expected.
+        """
+        from aiida.orm.groups import Group
+
+        # Create 100 nodes
+        nodes = []
+        for _ in range(100):
+            nodes.append(Data().store().backend_entity)
+
+        # Add nodes to groups using different batch size. Check in the end the
+        # correct addition.
+        batch_sizes = (1, 3, 10, 1000)
+        for batch_size in batch_sizes:
+            group = Group(name='test_batches_' + str(batch_size)).store()
+            group.backend_entity.add_nodes(nodes, skip_orm=True, batch_size=batch_size)
+            self.assertEqual(set(_.pk for _ in nodes), set(_.pk for _ in group.nodes))
+
 
 class TestDbExtrasSqla(AiidaTestCase):
     """

aiida/backends/tests/test_restapi.py

@@ -284,8 +284,6 @@ def process_test(self,
                     from aiida.common.exceptions import InputValidationError
                     raise InputValidationError("Pass the expected range of the dummydata")
 
-                self.assertEqual(len(response["data"][result_name]), len(expected_data))
-
                 expected_node_uuids = [node['uuid'] for node in expected_data]
                 result_node_uuids = [node['uuid'] for node in response["data"][result_name]]
                 self.assertEqual(expected_node_uuids, result_node_uuids)
@@ -304,7 +302,6 @@ def test_computers_details(self):
         Requests the details of single computer
         """
         node_uuid = self.get_dummy_data()["computers"][1]["uuid"]
-
         RESTApiTestCase.process_test(
             self, "computers", "/computers/" + str(node_uuid), expected_list_ids=[1], uuid=node_uuid)
 
@@ -709,6 +706,23 @@ def test_calculation_input_filters(self):
             result_node_type="data",
             result_name="inputs")
 
+    def test_calculation_iotree(self):
+        """
+        Get filtered inputs list for given calculations
+        """
+        node_uuid = self.get_dummy_data()["calculations"][1]["uuid"]
+        url = self.get_url_prefix() + '/calculations/' + str(node_uuid) + '/io/tree?in_limit=1&out_limit=1'
+        with self.app.test_client() as client:
+            response_value = client.get(url)
+            response = json.loads(response_value.data)
+            self.assertEqual(len(response["data"]["nodes"]), 3)
+            self.assertEqual(len(response["data"]["edges"]), 2)
+            expected_attr = ["nodelabel", "nodetype", "linklabel", "linktype", "nodeuuid", "description"]
+            received_attr = response["data"]["nodes"][1].keys()
+            for attr in expected_attr:
+                self.assertIn(attr, received_attr)
+            RESTApiTestCase.compare_extra_response_data(self, "calculations", url, response, uuid=node_uuid)
+
     ############### calculation attributes #############
     def test_calculation_attributes(self):
         """

aiida/cmdline/commands/cmd_import.py

@@ -128,7 +128,6 @@ def cmd_import(archives, webpages, group, extras_mode_existing, extras_mode_new,
                 comment_mode=comment_mode)
         except exceptions.IncompatibleArchiveVersionError as exception:
             echo.echo_warning('{} cannot be imported: {}'.format(archive, exception))
-            echo.echo_warning('run `verdi export migrate {}` to update it'.format(archive))
             continue
         except Exception:
             echo.echo_error('an exception occurred while importing the archive {}'.format(archive))

aiida/manage/external/postgres.py

@@ -18,6 +18,7 @@
 from __future__ import division
 from __future__ import print_function
 from __future__ import absolute_import
+
 try:
     import subprocess32 as subprocess
 except ImportError:

aiida/manage/fixtures.py

@@ -96,20 +96,19 @@ class FixtureManager(object):  # pylint: disable=too-many-public-methods,useless
 
         @pytest.fixture(scope='session')
         def aiida_profile():
-            with aiida.manage.fixtures.fixture_manager() as fixture_mgr:
-                fixture_mgr.create_profile()
+            # set up a test profile for the duration of the tests
+            with aiida.manage.fixtures.fixture_manager() as fixture_manager:
                 yield fixture_manager
 
         @pytest.fixture(scope='function')
-        def test_data(aiida_profile):
-            # load my test data
-            yield
-            fixture_manager.reset_db()
+        def new_database(aiida_profile):
+            # clear the database after each test
+            yield aiida_profile
+            aiida_profile.reset_db()
 
-        def test_my_stuff(test_data):
+        def test_my_stuff(new_database):
             # run a test
 
-
     """
 
     _test_case = None

aiida/orm/importexport.py

@@ -17,6 +17,7 @@
 import six
 from six.moves import zip
 from six.moves.html_parser import HTMLParser
+from distutils.version import StrictVersion
 from aiida.common import exceptions
 from aiida.common.utils import export_shard_uuid, get_class_string, grouper, get_new_uuid
 from aiida.orm import Computer, Group, GroupTypeString, Node, QueryBuilder, User, Log, Comment
@@ -621,7 +622,7 @@ def import_data_dj(in_path, user_group=None, ignore_unknown_nodes=False,
     from aiida.backends.djsite.db.models import suppress_auto_now
 
     # This is the export version expected by this function
-    expected_export_version = '0.4'
+    expected_export_version = StrictVersion('0.4')
 
     # The name of the subfolder in which the node files are stored
     nodes_export_subfolder = 'nodes'
@@ -673,9 +674,16 @@ def import_data_dj(in_path, user_group=None, ignore_unknown_nodes=False,
         ######################
         # PRELIMINARY CHECKS #
         ######################
-        if metadata['export_version'] != expected_export_version:
-            raise exceptions.IncompatibleArchiveVersionError('Archive schema version {} is incompatible with the '
-                'currently supported schema version {}'.format(metadata['export_version'], expected_export_version))
+        export_version = StrictVersion(str(metadata['export_version']))
+        if export_version != expected_export_version:
+            msg = "Export file version is {}, can import only version {}"\
+                    .format(metadata['export_version'], expected_export_version)
+            if export_version < expected_export_version:
+                msg += "\nUse 'verdi export migrate' to update this export file."
+            else:
+                msg += "\nUpdate your AiiDA version in order to import this file."
+
+            raise exceptions.IncompatibleArchiveVersionError(msg)
 
         ##########################################################################
         # CREATE UUID REVERSE TABLES AND CHECK IF I HAVE ALL NODES FOR THE LINKS #
@@ -1272,7 +1280,7 @@ def import_data_sqla(in_path, user_group=None, ignore_unknown_nodes=False,
     from aiida.common import json
 
     # This is the export version expected by this function
-    expected_export_version = '0.4'
+    expected_export_version = StrictVersion('0.4')
 
     # The name of the subfolder in which the node files are stored
     nodes_export_subfolder = 'nodes'
@@ -1319,9 +1327,16 @@ def import_data_sqla(in_path, user_group=None, ignore_unknown_nodes=False,
         ######################
         # PRELIMINARY CHECKS #
         ######################
-        if metadata['export_version'] != expected_export_version:
-            raise exceptions.IncompatibleArchiveVersionError('Archive schema version {} is incompatible with the '
-                'currently supported schema version {}'.format(metadata['export_version'], expected_export_version))
+        export_version = StrictVersion(str(metadata['export_version']))
+        if export_version != expected_export_version:
+            msg = "Export file version is {}, can import only version {}"\
+                    .format(metadata['export_version'], expected_export_version)
+            if export_version < expected_export_version:
+                msg += "\nUse 'verdi export migrate' to update this export file."
+            else:
+                msg += "\nUpdate your AiiDA version in order to import this file."
+
+            raise exceptions.IncompatibleArchiveVersionError(msg)
 
         ###################################################################
         #           CREATE UUID REVERSE TABLES AND CHECK IF               #
@@ -1919,11 +1934,9 @@ def import_data_sqla(in_path, user_group=None, ignore_unknown_nodes=False,
                         else:
                             counter += 1
 
-                # Add all the nodes to the new group
                 # Adding nodes to group avoiding the SQLA ORM to increase speed
                 nodes = [entry[0].backend_entity for entry in QueryBuilder().append(Node, filters={'id': {'in': pks_for_group}}).all()]
                 group.backend_entity.add_nodes(nodes, skip_orm=True)
-
                 if not silent:
                     print("IMPORTED NODES GROUPED IN IMPORT GROUP NAMED '{}'".format(group.label))
             else: