Merge release_v0.12.0 into workflows

.travis-data/test_daemon.py

@@ -30,6 +30,7 @@
 number_calculations = 15 # Number of calculations to submit
 number_workchains = 8 # Number of workchains to submit
 
+
 def print_daemon_log():
     daemon_client = DaemonClient()
     daemon_log = daemon_client.daemon_log_file
@@ -42,6 +43,7 @@ def print_daemon_log():
     except subprocess.CalledProcessError as e:
         print "Note: the command failed, message: {}".format(e.message)
 
+
 def jobs_have_finished(pks):
     finished_list = [load_node(pk).is_terminated for pk in pks]
     node_list = [load_node(pk) for pk in pks]
@@ -53,16 +55,18 @@ def jobs_have_finished(pks):
     print "{}/{} finished".format(num_finished, len(finished_list))
     return not (False in finished_list)
 
+
 def print_logshow(pk):
     print "Output of 'verdi calculation logshow {}':".format(pk)
     try:
         print subprocess.check_output(
             ["verdi", "calculation", "logshow", "{}".format(pk)],
             stderr=subprocess.STDOUT,
-            )
+        )
     except subprocess.CalledProcessError as e2:
         print "Note: the command failed, message: {}".format(e2.message)
 
+
 def validate_calculations(expected_results):
     valid = True
     actual_dict = {}
@@ -93,6 +97,7 @@ def validate_calculations(expected_results):
 
     return valid
 
+
 def validate_workchains(expected_results):
     valid = True
     for pk, expected_value in expected_results.iteritems():
@@ -110,6 +115,7 @@ def validate_workchains(expected_results):
 
     return valid
 
+
 def validate_cached(cached_calcs):
     """
     Check that the calculations with created with caching are indeed cached.
@@ -120,21 +126,22 @@ def validate_cached(cached_calcs):
         for calc in cached_calcs
     )
 
+
 def create_calculation(code, counter, inputval, use_cache=False):
     parameters = ParameterData(dict={'value': inputval})
     template = ParameterData(dict={
-            ## The following line adds a significant sleep time.
-            ## I set it to 1 second to speed up tests
-            ## I keep it to a non-zero value because I want
-            ## To test the case when AiiDA finds some calcs
-            ## in a queued state
-            #'cmdline_params': ["{}".format(counter % 3)], # Sleep time
-            'cmdline_params': ["1"],
-            'input_file_template': "{value}", # File just contains the value to double
-            'input_file_name': 'value_to_double.txt',
-            'output_file_name': 'output.txt',
-            'retrieve_temporary_files': ['triple_value.tmp']
-            })
+        ## The following line adds a significant sleep time.
+        ## I set it to 1 second to speed up tests
+        ## I keep it to a non-zero value because I want
+        ## To test the case when AiiDA finds some calcs
+        ## in a queued state
+        # 'cmdline_params': ["{}".format(counter % 3)], # Sleep time
+        'cmdline_params': ["1"],
+        'input_file_template': "{value}",  # File just contains the value to double
+        'input_file_name': 'value_to_double.txt',
+        'output_file_name': 'output.txt',
+        'retrieve_temporary_files': ['triple_value.tmp']
+    })
     calc = code.new_calc()
     calc.set_max_wallclock_seconds(5 * 60)  # 5 min
     calc.set_resources({"num_machines": 1})
@@ -150,9 +157,10 @@ def create_calculation(code, counter, inputval, use_cache=False):
             'triple_value.tmp': str(inputval * 3)
         }
     }
-    print "[{}] created calculation {}, pk={}".format(counter, calc.uuid, calc.dbnode.pk)
+    print "[{}] created calculation {}, pk={}".format(counter, calc.uuid, calc.pk)
     return calc, expected_result
 
+
 def submit_calculation(code, counter, inputval):
     calc, expected_result = create_calculation(
         code=code, counter=counter, inputval=inputval
@@ -219,7 +227,6 @@ def create_cache_calc(code, counter, inputval):
 def main():
     expected_results_calculations = {}
     expected_results_workchains = {}
-
     code = Code.get_from_string(codename)
 
     # Submitting the Calculations the old way, creating and storing a JobCalc first and submitting it
@@ -291,14 +298,14 @@ def main():
     start_time = time.time()
     exited_with_timeout = True
     while time.time() - start_time < timeout_secs:
-        time.sleep(15) # Wait a few seconds
+        time.sleep(15)  # Wait a few seconds
 
         # Print some debug info, both for debugging reasons and to avoid
         # that the test machine is shut down because there is no output
 
-        print "#"*78
+        print "#" * 78
         print "####### TIME ELAPSED: {} s".format(time.time() - start_time)
-        print "#"*78
+        print "#" * 78
         print "Output of 'verdi calculation list -a':"
         try:
             print subprocess.check_output(
@@ -348,8 +355,8 @@ def main():
             cached_calcs.append(calc)
             expected_results_calculations[calc.pk] = expected_result
         if (validate_calculations(expected_results_calculations)
-            and validate_workchains(expected_results_workchains)
-            and validate_cached(cached_calcs)):
+                and validate_workchains(expected_results_workchains)
+                and validate_cached(cached_calcs)):
             print_daemon_log()
             print ""
             print "OK, all calculations have the expected parsed result"

CHANGELOG.md

@@ -1,3 +1,41 @@
+## v0.12.0
+
+### Improvements
+- Hashing, caching and fast-forwarding [[#652]](https://github.com/aiidateam/aiida_core/pull/652)
+- Calculation no longer stores full source file [[#1082]](https://github.com/aiidateam/aiida_core/pull/1082)
+- Delete nodes via `verdi node delete` [[#1083]](https://github.com/aiidateam/aiida_core/pull/1083)
+- Import structures using ASE [[#1085]](https://github.com/aiidateam/aiida_core/pull/1085)
+- `StructureData` - `pymatgen` - `StructureData` roundtrip works for arbitrary kind names [[#1285]](https://github.com/aiidateam/aiida_core/pull/1285) [[#1306]](https://github.com/aiidateam/aiida_core/pull/1306) [[#1357]](https://github.com/aiidateam/aiida_core/pull/1357)
+
+### Critical bug fixes
+- Add `parser_name` `JobProcess` options [[#1118]](https://github.com/aiidateam/aiida_core/pull/1118)
+
+### Minor bug fixes
+- Cell vectors not printed correctly [[#1087]](https://github.com/aiidateam/aiida_core/pull/1087)
+- Fix read-the-docs issues [[#1120]](https://github.com/aiidateam/aiida_core/pull/1120) [[#1143]](https://github.com/aiidateam/aiida_core/pull/1143)
+- Fix structure/band visualization in REST API [[#1167]](https://github.com/aiidateam/aiida_core/pull/1167) [[#1182]](https://github.com/aiidateam/aiida_core/pull/1182)
+- Fix `verdi work list` test [[#1286]](https://github.com/aiidateam/aiida_core/pull/1286)
+- Fix `_inline_to_standalone_script` in `TCODExporter` [[#1351]](https://github.com/aiidateam/aiida_core/pull/1351)
+
+### Miscellaneous
+- Bump `qe-tools` version [[#1090]](https://github.com/aiidateam/aiida_core/pull/1090)
+- Document link types [[#1174]](https://github.com/aiidateam/aiida_core/pull/1174)
+- Switch to trusty + postgres 9.5 on Travis [[#1180]](https://github.com/aiidateam/aiida_core/pull/1180)
+- Use raw SQL in sqlalchemy migration of `Code` [[#1291]](https://github.com/aiidateam/aiida_core/pull/1291)
+- Document querying of list attributes [[#1326]](https://github.com/aiidateam/aiida_core/pull/1326)
+- Cookbook: how to check the number of queued/running jobs in the scheduler [[#1349]](https://github.com/aiidateam/aiida_core/pull/1349)
+
+
+## v0.11.4
+
+### Improvements
+- PyCifRW upgraded to 4.2.1 [[#1073]](https://github.com/aiidateam/aiida_core/pull/1073)
+
+### Critical bug fixes
+- Persist and load parsed workchain inputs and do not recreate to avoid creating duplicates for default inputs [[#1362]](https://github.com/aiidateam/aiida_core/pull/1362)
+- Serialize `WorkChain` context before persisting [[#1354]](https://github.com/aiidateam/aiida_core/pull/1354)
+
+
 ## v0.11.3
 
 ### Improvements

aiida/__init__.py

@@ -13,7 +13,7 @@
 
 __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__ = "0.11.3"
+__version__ = "0.11.4"
 __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)."""

aiida/backends/djsite/db/subtests/djangomigrations.py

@@ -38,7 +38,7 @@ def test_unexpected_calc_states(self):
             job = JobCalculation(**calc_params)
             job.store()
             # Now save the errant state
-            DbCalcState(dbnode=job.dbnode, state=state).save()
+            DbCalcState(dbnode=job._dbnode, state=state).save()
 
             time_before_fix = timezone.now()
 

aiida/backends/djsite/db/subtests/generic.py

@@ -16,7 +16,6 @@
 from aiida.orm.node import Node
 
 
-
 class TestComputer(AiidaTestCase):
     """
     Test the Computer class.
@@ -43,8 +42,6 @@ def test_deletion(self):
 
         _ = JobCalculation(**calc_params).store()
 
-        #print "Node stored with pk:",  _.dbnode.pk
-
         # This should fail, because there is at least a calculation
         # using this computer (the one created just above)
         with self.assertRaises(InvalidOperation):
@@ -156,31 +153,32 @@ class TestDbExtrasDjango(AiidaTestCase):
     """
     Test DbAttributes.
     """
+
     def test_replacement_1(self):
         from aiida.backends.djsite.db.models import DbExtra
 
         n1 = Node().store()
         n2 = Node().store()
 
-        DbExtra.set_value_for_node(n1.dbnode, "pippo", [1, 2, 'a'])
-        DbExtra.set_value_for_node(n1.dbnode, "pippobis", [5, 6, 'c'])
-        DbExtra.set_value_for_node(n2.dbnode, "pippo2", [3, 4, 'b'])
+        DbExtra.set_value_for_node(n1._dbnode, "pippo", [1, 2, 'a'])
+        DbExtra.set_value_for_node(n1._dbnode, "pippobis", [5, 6, 'c'])
+        DbExtra.set_value_for_node(n2._dbnode, "pippo2", [3, 4, 'b'])
 
         self.assertEquals(n1.get_extras(), {'pippo': [1, 2, 'a'],
-                                             'pippobis': [5, 6, 'c'],
-                                             '_aiida_hash': n1.get_hash()
-                                             })
+                                            'pippobis': [5, 6, 'c'],
+                                            '_aiida_hash': n1.get_hash()
+                                            })
         self.assertEquals(n2.get_extras(), {'pippo2': [3, 4, 'b'],
                                             '_aiida_hash': n2.get_hash()
                                             })
 
         new_attrs = {"newval1": "v", "newval2": [1, {"c": "d", "e": 2}]}
 
-        DbExtra.reset_values_for_node(n1.dbnode, attributes=new_attrs)
+        DbExtra.reset_values_for_node(n1._dbnode, attributes=new_attrs)
         self.assertEquals(n1.get_extras(), new_attrs)
         self.assertEquals(n2.get_extras(), {'pippo2': [3, 4, 'b'], '_aiida_hash': n2.get_hash()})
 
-        DbExtra.del_value_for_node(n1.dbnode, key='newval2')
+        DbExtra.del_value_for_node(n1._dbnode, key='newval2')
         del new_attrs['newval2']
         self.assertEquals(n1.get_extras(), new_attrs)
         # Also check that other nodes were not damaged

aiida/backends/sqlalchemy/__init__.py

@@ -10,7 +10,7 @@
 
 # The next two serve as 'global' variables, set in the load_dbenv
 # call. They are properly reset upon forking.
-engine =  None
+engine = None
 scopedsessionclass = None
 
 
@@ -28,4 +28,3 @@ def get_scoped_session():
         s = scopedsessionclass()
 
     return s
-

aiida/backends/sqlalchemy/models/base.py

@@ -16,12 +16,11 @@
 import aiida.backends.sqlalchemy
 from aiida.common.exceptions import InvalidOperation
 
+
 # Taken from
 # https://github.com/mitsuhiko/flask-sqlalchemy/blob/master/flask_sqlalchemy/__init__.py#L491
 
 
-
-
 class _QueryProperty(object):
 
     def __init__(self, query_class=orm.Query):
@@ -63,8 +62,8 @@ def __iter__(self):
 
 from aiida.backends.sqlalchemy import get_scoped_session
 
-class Model(object):
 
+class Model(object):
     query = _QueryProperty()
 
     session = _SessionProperty()
@@ -92,4 +91,6 @@ def delete(self, commit=True):
         sess.delete(self)
         if commit:
             sess.commit()
+
+
 Base = declarative_base(cls=Model, name='Model')