Merge branch 'links_doc' of github.com:szoupanos/aiida_core into link…

…s_doc

.travis-data/computer-setup-input.txt

@@ -4,6 +4,7 @@ localhost
 True
 ssh
 torque
+#!/bin/bash
 /scratch/{username}/aiida_run
 mpirun -np {tot_num_mpiprocs}
 1

.travis-data/set_daemon_times.py

@@ -1,4 +1,13 @@
 #!/usr/bin/env python
+# -*- 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               #
+###########################################################################
 """
 For AiiDA 0.10.0, we set the times of the daemon
 to 5 seconds.

.travis-data/test_daemon.py

@@ -26,10 +26,10 @@
 
 def print_daemon_log():
     home = os.environ['HOME']
-    print "Output of 'cat {}/.aiida/daemon/log/aiida_daemon.log':".format(home)
+    print "Output of 'cat {}/.aiida/daemon/log/celery.log':".format(home)
     try:
         print subprocess.check_output(
-            ["cat", "{}/.aiida/daemon/log/aiida_daemon.log".format(home)], 
+            ["cat", "{}/.aiida/daemon/log/celery.log".format(home)],
             stderr=subprocess.STDOUT,
         )
     except subprocess.CalledProcessError as e:
@@ -98,6 +98,65 @@ def validate_workchains(expected_results):
 
     return valid
 
+def validate_cached(cached_calcs):
+    """
+    Check that the calculations with created with caching are indeed cached.
+    """
+    return all(
+        '_aiida_cached_from' in calc.extras() and
+        calc.get_hash() == calc.get_extra('_aiida_hash')
+        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']
+            })
+    calc = code.new_calc()
+    calc.set_max_wallclock_seconds(5 * 60)  # 5 min
+    calc.set_resources({"num_machines": 1})
+    calc.set_withmpi(False)
+    calc.set_parser_name('simpleplugins.templatereplacer.test.doubler')
+
+    calc.use_parameters(parameters)
+    calc.use_template(template)
+    calc.store_all(use_cache=use_cache)
+    expected_result = {
+        'value': 2 * inputval,
+        'retrieved_temporary_files': {
+            'triple_value.tmp': str(inputval * 3)
+        }
+    }
+    print "[{}] created calculation {}, pk={}".format(
+        counter, calc.uuid, calc.dbnode.pk)
+    return calc, expected_result
+
+def submit_calculation(code, counter, inputval):
+    calc, expected_result = create_calculation(
+        code=code, counter=counter, inputval=inputval
+    )
+    calc.submit()
+    print "[{}] calculation submitted.".format(counter)
+    return calc, expected_result
+
+def create_cache_calc(code, counter, inputval):
+    calc, expected_result = create_calculation(
+        code=code, counter=counter, inputval=inputval, use_cache=True
+    )
+    print "[{}] created cached calculation.".format(counter)
+    return calc, expected_result
+
 def main():
 
     # Submitting the Calculations
@@ -106,39 +165,10 @@ def main():
     expected_results_calculations = {}
     for counter in range(1, number_calculations + 1):
         inputval = counter
-        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']
-                })
-        calc = code.new_calc()
-        calc.set_max_wallclock_seconds(5 * 60)  # 5 min
-        calc.set_resources({"num_machines": 1})
-        calc.set_withmpi(False)
-        calc.set_parser_name('simpleplugins.templatereplacer.test.doubler')
-
-        calc.use_parameters(parameters)
-        calc.use_template(template)
-        calc.store_all()
-        print "[{}] created calculation {}, pk={}".format(
-            counter, calc.uuid, calc.dbnode.pk)
-        expected_results_calculations[calc.pk] = {
-            'value': inputval * 2,
-            'retrieved_temporary_files': {
-                'triple_value.tmp': str(inputval * 3)
-            }
-        }
-        calc.submit()
-        print "[{}] calculation submitted.".format(counter)
+        calc, expected_result = submit_calculation(
+            code=code, counter=counter, inputval=inputval
+        )
+        expected_results_calculations[calc.pk] = expected_result
 
     # Submitting the Workchains
     print "Submitting {} workchains to the daemon".format(number_workchains)
@@ -158,7 +188,7 @@ def main():
     exited_with_timeout = True
     while time.time() - start_time < timeout_secs:
         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
 
@@ -168,7 +198,7 @@ def main():
         print "Output of 'verdi calculation list -a':"
         try:
             print subprocess.check_output(
-                ["verdi", "calculation", "list", "-a"], 
+                ["verdi", "calculation", "list", "-a"],
                 stderr=subprocess.STDOUT,
             )
         except subprocess.CalledProcessError as e:
@@ -177,7 +207,7 @@ def main():
         print "Output of 'verdi work list':"
         try:
             print subprocess.check_output(
-                ['verdi', 'work', 'list'], 
+                ['verdi', 'work', 'list'],
                 stderr=subprocess.STDOUT,
             )
         except subprocess.CalledProcessError as e:
@@ -186,7 +216,7 @@ def main():
         print "Output of 'verdi daemon status':"
         try:
             print subprocess.check_output(
-                ["verdi", "daemon", "status"], 
+                ["verdi", "daemon", "status"],
                 stderr=subprocess.STDOUT,
             )
         except subprocess.CalledProcessError as e:
@@ -204,8 +234,18 @@ def main():
             timeout_secs)
         sys.exit(2)
     else:
+        # create cached calculations -- these should be FINISHED immediately
+        cached_calcs = []
+        for counter in range(1, number_calculations + 1):
+            inputval = counter
+            calc, expected_result = create_cache_calc(
+                code=code, counter=counter, inputval=inputval
+            )
+            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_workchains(expected_results_workchains)
+            and validate_cached(cached_calcs)):
             print_daemon_log()
             print ""
             print "OK, all calculations have the expected parsed result"

.travis-data/test_fixtures.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               #
+###########################################################################
 """Unittests for plugin test fixture manager"""
 import os
 import unittest

.travis-data/test_plugin_testcase.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               #
+###########################################################################
 """
 Test the plugin test case
 
@@ -21,24 +30,32 @@ def determine_backend():
 
 
 class PluginTestcaseTestCase(PluginTestCase):
-    """Test the PluginTestcase from utils.fixtures"""
+    """
+    Test the PluginTestcase from utils.fixtures
+    """
     BACKEND = determine_backend()
 
     def setUp(self):
-        from aiida.orm import DataFactory
-        from aiida.orm import Computer
         self.temp_dir = tempfile.mkdtemp()
         self.data = self.get_data()
         self.data_pk = self.data.pk
         self.computer = self.get_computer(temp_dir=self.temp_dir)
 
-    def get_data(self):
+    @staticmethod
+    def get_data():
+        """
+        Return some ParameterData
+        """
         from aiida.orm import DataFactory
         data = DataFactory('parameter')(dict={'data': 'test'})
         data.store()
         return data
 
-    def get_computer(self, temp_dir):
+    @staticmethod
+    def get_computer(temp_dir):
+        """
+        Create and store a new computer, and return it
+        """
         from aiida.orm import Computer
         computer = Computer(
             name='localhost',
@@ -52,14 +69,20 @@ def get_computer(self, temp_dir):
         return computer
 
     def test_data_loaded(self):
+        """
+        Check that the data is indeed in the DB when calling load_node
+        """
         from aiida.orm import Computer
         from aiida.orm import load_node
         self.assertTrue(is_dbenv_loaded())
         self.assertEqual(load_node(self.data_pk).uuid, self.data.uuid)
         self.assertEqual(Computer.get('localhost').uuid, self.computer.uuid)
 
-
     def test_tear_down(self):
+        """
+        Check that after tearing down, the previously stored nodes
+        are not there anymore. Then remove the temporary folder.
+        """
         from aiida.orm import load_node
         super(PluginTestcaseTestCase, self).tearDown()
         with self.assertRaises(Exception):

.travis-data/test_script.sh

@@ -24,6 +24,6 @@ case "$TEST_TYPE" in
         verdi -p $TEST_AIIDA_BACKEND run ${TRAVIS_BUILD_DIR}/.travis-data/test_daemon.py
         ;;
     pre-commit)
-        pre-commit run --all-files || git status --short && git diff
+        pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
         ;;
 esac

.travis.yml

@@ -42,11 +42,11 @@ install:
     # Upgrade pip setuptools and wheel to be able to run the next command
     - pip install -U pip wheel setuptools
     # Install AiiDA with some optional dependencies
-    - pip install .[REST,docs,atomic_tools,testing,dev_precommit]
+    - if [ "$TEST_TYPE" == "docs" ]; then pip install . && pip install -r docs/requirements_for_rtd.txt; else pip install .[rest,docs,atomic_tools,testing,dev_precommit]; fi
 
 env:
 ## Build matrix to test both backends, and the docs
-## I still let it create the test backend for django 
+## I still let it create the test backend for django
 ## also when building the docs
 ## because otherwise the code would complain. Also, I need latex.
 - TEST_TYPE="pre-commit"

AUTHORS.txt

@@ -50,7 +50,7 @@ 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
+Nicola Varini, Mario Zic, Vladimir Dikan, Michael Atambo, Ole Schütt, Marco Borelli
 
 ---