aiidateam · waychal · Oct 25, 2017 · Oct 24, 2017 · Oct 24, 2017 · Oct 24, 2017
diff --git a/.travis-data/test_setup.py b/.travis-data/test_setup.py
@@ -1,3 +1,12 @@
+# -*- 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               #
+###########################################################################
 """
 Integration tests for setup and quicksetup
 

diff --git a/AUTHORS.txt b/AUTHORS.txt
@@ -3,28 +3,28 @@ as well as the known contributors to the code.
 
 The current members of the AiiDA team are, in alphabetical order:
 #################################################################
-* Andrea Cepellotti
-* Fernando Gargiulo
-* Leonid Kahle
-* Boris Kozinsky
 * Rico Häuselmann
 * Sebastiaan P. Huber
+* Leonid Kahle
+* Boris Kozinsky
 * Nicola Marzari
 * Andrius Merkys
 * Nicolas Mounet
+* Elsa Passaro
 * Giovanni Pizzi
+* Leopold Talirz
 * Martin Uhrin
 * Snehal Waychal
 * Spyros Zoupanos
 
 
-
 Former members of the AiiDA team
 ################################
+* Andrea Cepellotti (2012-2016)
+* Fernando Gargiulo (2016-2017)
 * Riccardo Sabatini (2013-2015)
 
 
-
 Contributors
 ############
 We would like to thank the following people for their contibution 
@@ -34,6 +34,7 @@ We would like to thank the following people for their contibution
   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
@@ -45,11 +46,11 @@ We would like to thank the following people for their contibution
   the new plugin system (developed in 2017)
 * Phillippe Schwaller (EPFL, Switzerland): for the ICSD importer
 
-And the following people for corrections, improving the documentation, 
-spotting typos or useful suggestions:
+And the following people for general improvements to the code, fixing bugs,
+corrections and improvements to the documentation and useful suggestions:
 
-Jens Broeder, Ivano E. Castelli, Ian Lee, Gianluca Prandini, 
-Jianxing Huang, Antimo Marrazzo, Nicola Varini, Mario Zic
+Ivano E. Castelli, Ian Lee, Gianluca Prandini, Jianxing Huang, Antimo Marrazzo,
+Nicola Varini, Mario Zic, Vladimir Dikan, Michael Atambo
 
 ---
 

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,38 @@
+## v0.10.0rc1:
+
+### Major changes
+- The `DbPath` table has been removed and replaced with a dynamic transitive closure, because, among others, nested workchains could lead to the `DbPath` table exploding in size
+- Code plugins have been removed from `aiida_core` and have been migrated to their own respective plugin repositories and can be found here:
+    * [Quantum ESPRESSO](https://github.com/aiidateam/aiida-quantumespresso)
+    * [ASE](https://github.com/aiidateam/aiida-ase)
+    * [COD tools](https://github.com/aiidateam/aiida-codtools)
+    * [NWChem](https://github.com/aiidateam/aiida-nwchem)
+
+    Each can be installed from `pip` using e.g. `pip install aiida-quantumespresso`.
+    Existing installations will require a migration (see [update instructions in the documentation](https://aiida-core.readthedocs.io/en/v0.10.0/installation/updating.html#plugin-migration)).
+    For a complete overview of available plugins you can visit [the registry](https://aiidateam.github.io/aiida-registry/).
+
+### Improvements
+- New verdi command: `verdi work kill` to kill running workchains [[#821]](https://github.com/aiidateam/aiida_core/pull/821)
+- New verdi command: `verdi data remote [ls,cat,show]` to inspect the contents of `RemoteData` objects [[#743]](https://github.com/aiidateam/aiida_core/pull/743)
+- New verdi command: `verdi export migrate` allows the migration of existing export archives to new formats [[#781]](https://github.com/aiidateam/aiida_core/pull/781)
+- Implemented faster query to obtain database statistics [[#738]](https://github.com/aiidateam/aiida_core/pull/738)
+- Added testing for automatic SqlAlchemy database migrations through alembic [[#834]](https://github.com/aiidateam/aiida_core/pull/834)
+
+### Critical bug fixes
+- Export will now write the link types to the archive and import will properly recreate the link [[#760]](https://github.com/aiidateam/aiida_core/pull/760)
+- Fix bug in workchain persistence that would lead to crashed workchains under certain conditions being resubmitted [[#728]](https://github.com/aiidateam/aiida_core/pull/728)
+
+### Minor bug fixes
+- Fixed bug in `TCODexporter` [[#761]](https://github.com/aiidateam/aiida_core/pull/761)
+- `verdi profile delete` now respects the configured `dbport` setting [[#713]](https://github.com/aiidateam/aiida_core/pull/713)
+- Restore correct help text for `verdi --help` [[#704]](https://github.com/aiidateam/aiida_core/pull/704)
+- Fixed query in the ICSD importer element that caused certain structures to be erroneously skipped [[#690]](https://github.com/aiidateam/aiida_core/pull/690)
+
+### Miscellaneous
+- Improved and restructured the documentation
+
+
 ## v0.9.1:
 
 ### Critical bug fixes

diff --git a/aiida/__init__.py b/aiida/__init__.py
@@ -14,7 +14,7 @@
 
 __copyright__ = u"Copyright (c), This file is part of the AiiDA platform. For further information please visit http://www.aiida.net/. All rights reserved."
 __license__ = "MIT license, see LICENSE.txt file."
-__version__ = "0.9.1"
+__version__ = "0.10.0rc1"
 __authors__ = "The AiiDA team."
 __paper__ = """G. Pizzi, A. Cepellotti, R. Sabatini, N. Marzari, and B. Kozinsky, "AiiDA: automated interactive infrastructure and database for computational science", Comp. Mat. Sci 111, 218-230 (2016); http://dx.doi.org/10.1016/j.commatsci.2015.09.013 - http://www.aiida.net."""
 __paper_short__ = """G. Pizzi et al., Comp. Mat. Sci 111, 218 (2016)."""

diff --git a/aiida/backends/djsite/db/migrations/0005_add_cmtime_indices.py b/aiida/backends/djsite/db/migrations/0005_add_cmtime_indices.py
@@ -1,4 +1,12 @@
 # -*- 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               #
+###########################################################################
 from __future__ import unicode_literals
 
 from django.db import models, migrations

diff --git a/aiida/backends/djsite/db/migrations/0006_delete_dbpath.py b/aiida/backends/djsite/db/migrations/0006_delete_dbpath.py
@@ -1,4 +1,12 @@
 # -*- 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               #
+###########################################################################
 from __future__ import unicode_literals
 
 from django.db import models, migrations

diff --git a/aiida/backends/djsite/db/migrations/0007_update_linktypes.py b/aiida/backends/djsite/db/migrations/0007_update_linktypes.py
@@ -1,4 +1,12 @@
 # -*- 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               #
+###########################################################################
 from __future__ import unicode_literals
 
 from django.db import models, migrations

diff --git a/aiida/backends/sqlalchemy/migrations/env.py b/aiida/backends/sqlalchemy/migrations/env.py
@@ -1,3 +1,12 @@
+# -*- 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               #
+###########################################################################
 from __future__ import with_statement
 from alembic import context
 

diff --git a/aiida/backends/sqlalchemy/migrations/versions/70c7d732f1b2_delete_dbpath.py b/aiida/backends/sqlalchemy/migrations/versions/70c7d732f1b2_delete_dbpath.py
@@ -1,3 +1,12 @@
+# -*- 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               #
+###########################################################################
 """Deleting dbpath table and triggers
 
 Revision ID: 70c7d732f1b2

diff --git a/aiida/backends/sqlalchemy/migrations/versions/a6048f0ffca8_update_linktypes.py b/aiida/backends/sqlalchemy/migrations/versions/a6048f0ffca8_update_linktypes.py
@@ -1,3 +1,12 @@
+# -*- 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               #
+###########################################################################
 """Updating link types - This is a copy of the Django migration script
 
 Revision ID: a6048f0ffca8

diff --git a/aiida/backends/sqlalchemy/migrations/versions/e15ef2630a1b_initial_schema.py b/aiida/backends/sqlalchemy/migrations/versions/e15ef2630a1b_initial_schema.py
@@ -1,3 +1,12 @@
+# -*- 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               #
+###########################################################################
 """Initial schema
 
 Revision ID: e15ef2630a1b

diff --git a/aiida/backends/sqlalchemy/tests/migration_test/versions/470e57bc0936_create_account_table.py b/aiida/backends/sqlalchemy/tests/migration_test/versions/470e57bc0936_create_account_table.py
@@ -1,3 +1,12 @@
+# -*- 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               #
+###########################################################################
 """create account table
 
 Revision ID: 470e57bc0936

diff --git a/aiida/backends/sqlalchemy/tests/migration_test/versions/b947a8821295_add_a_column.py b/aiida/backends/sqlalchemy/tests/migration_test/versions/b947a8821295_add_a_column.py
@@ -1,3 +1,12 @@
+# -*- 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               #
+###########################################################################
 """Add a column
 
 Revision ID: b947a8821295

diff --git a/aiida/cmdline/tests/__init__.py b/aiida/cmdline/tests/__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               #
+###########################################################################
diff --git a/aiida/cmdline/tests/common.py b/aiida/cmdline/tests/common.py
@@ -1,3 +1,12 @@
+# -*- 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               #
+###########################################################################
 """Common code to be used in cli testing"""
 import sys
 from contextlib import contextmanager

diff --git a/aiida/cmdline/tests/test_verdi_help.py b/aiida/cmdline/tests/test_verdi_help.py
@@ -1,3 +1,12 @@
+# -*- 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               #
+###########################################################################
 """Bug regression tests for ``verdi help``"""
 import unittest
 

diff --git a/aiida/common/graph.py b/aiida/common/graph.py
@@ -1,3 +1,12 @@
+# -*- 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               #
+###########################################################################
 import os, tempfile
 
 def draw_graph(origin_node, ancestor_depth=None, descendant_depth=None, format='dot',

diff --git a/aiida/control/__init__.py b/aiida/control/__init__.py
@@ -1 +1,10 @@
+# -*- 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               #
+###########################################################################
 """User facing APIs to control AiiDA from the verdi cli, scripts or plugins"""
diff --git a/aiida/control/postgres.py b/aiida/control/postgres.py
@@ -1,3 +1,12 @@
+# -*- 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               #
+###########################################################################
 """Provides an API for postgres database maintenance tasks"""
 try:
     import subprocess32 as subprocess

diff --git a/aiida/control/tests/__init__.py b/aiida/control/tests/__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               #
+###########################################################################
diff --git a/aiida/control/tests/test_postgres.py b/aiida/control/tests/test_postgres.py
@@ -1,4 +1,12 @@
 # -*- 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               #
+###########################################################################
 """Unit tests for postgres database maintenance functionality"""
 import unittest
 

diff --git a/aiida/control/user.py b/aiida/control/user.py
@@ -1,3 +1,12 @@
+# -*- 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               #
+###########################################################################
 """Create, configure, manage users"""
 
 

diff --git a/aiida/orm/implementation/general/utils.py b/aiida/orm/implementation/general/utils.py
@@ -1,3 +1,12 @@
+# -*- 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               #
+###########################################################################
 def get_db_columns(db_class):
     """
     This function returns a dictionary where the keys are the columns of