Merge release_v0.12.0 into workflows #1381
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on how to check the number of queued/running jobs in the scheduler, following up from a discussion on the Mailing List.
…_check_scheduler Adding guide to the cookbook
The correct attribute key for the source code of the inline calculation is `source_code` and not `source_file`
…inline_script Fix bug in inline_script generator of TcodExporter
The user is free to populate the context with Node instances, which means that if the WorkChain needs to be persisted that the nodes need to be serialized. Since the nodes are not necessarily stored upon calling save_instance_state, we also store them if they were not yet stored. We also use this opportunity to replace the ad hoc serialization in the pickle persister and use the new more complete serializer and deserializer.
This release of plumpy fixes an issue where the inputs of a process are recreated each time when loaded from a persisted state, meaning that inputs that were not explicitly specified but taken from the spec's default will be recreated. For default nodes in aiida-core this means that the nodes are duplicated multiple times
…kchain_context Serialize the context of a WorkChain before persisting
…pancies The kind name used to be passed directly to append_atom when there was no spin species, but this would give the same name to all sites with the same symbol but potentially different occupancies, causing append_atom to rightfully throw a ValueError
…cture_partial_occupancies Ensure kind name uniqueness for pymatgen structures with partial occupancies
This was merged into develop with PR aiidateam#1073 but needs to be back ported into release v0.11.4
The user is free to populate the context with Node instances, which means that if the WorkChain needs to be persisted that the nodes need to be serialized. Since the nodes are not necessarily stored upon calling save_instance_state, we also store them if they were not yet stored. We also use this opportunity to replace the ad hoc serialization in the pickle persister and use the new more complete serializer and deserializer.
This release of plumpy fixes an issue where the inputs of a process are recreated each time when loaded from a persisted state, meaning that inputs that were not explicitly specified but taken from the spec's default will be recreated. For default nodes in aiida-core this means that the nodes are duplicated multiple times
The verdi work list test that compared the output with and without the -a flag was failing sometimes, simply because the order was wrong but the exact string was compared. Sorting by code id will fix the order and this breaking test
This is an issue in plumpy that was also fixed there. The parsed inputs of a Process, which is returned by calling self.inputs, were being rebuilt from the raw inputs everytime the process was loaded from a persisted state. This meant that inputs that were not explicitly passed by the user and were populated with the defaults specified by the port, were being recreated upon reloading the instance. However, they should have been the ones that were created when the process was created the first time around. Therefore we persist the parsed inputs to the saved state and reload them instead of recreating them with `create_input_args`
Release v0.11.4
* add chainmap dependency to rtd
* remove duplicates in rtd requirements
* make run_apidoc less OS dependent
* fix pathlib dependency
* fix aiida.settings warning (unable to write config file)
WARNING: autodoc: failed to import module u'aiida.settings'; the following exception was raised:
Traceback (most recent call last):
File "/home/docs/checkouts/readthedocs.org/user_builds/aiida-core/envs/rtd_fix/local/lib/python2.7/site-packages/sphinx/ext/autodoc/importer.py", line 140, in import_module
__import__(modname)
File "/home/docs/checkouts/readthedocs.org/user_builds/aiida-core/checkouts/rtd_fix/docs/source/../../aiida/settings.py", line 22, in <module>
confs = get_config()
File "/home/docs/checkouts/readthedocs.org/user_builds/aiida-core/checkouts/rtd_fix/docs/source/../../aiida/common/setup.py", line 96, in get_config
return check_and_migrate_config(_load_config())
File "/home/docs/checkouts/readthedocs.org/user_builds/aiida-core/checkouts/rtd_fix/docs/source/../../aiida/common/additions/config_migrations/_utils.py", line 39, in check_and_migrate_config
store_config(config)
File "/home/docs/checkouts/readthedocs.org/user_builds/aiida-core/checkouts/rtd_fix/docs/source/../../aiida/common/setup.py", line 141, in store_config
with open(conf_file, "w") as json_file:
IOError: [Errno 2] No such file or directory: '/home/docs/.aiida/config.json'
run sphinx-apidoc on rtd
…ments_for_docs [WIP] Removing requirement of sqlalchemy-diff from docs
Also removed the duplicate entries from v0.12.0 change log that have now been backported and released in v0.11.4
…lease_v0.12.0 Merge master after release of v0.11.4 into release_v0.12.0
There was an issue where because a node was in a Session, if any of the attributes of a Node were changed by an external process the getters would not see the change. I've put in an session.expire from SQLA to handle these cases. Also refactored AbstractNode a little.
* Removing references to node.dbnode() as much as possible as this should not be part of the public api * Fixed SQLA test for loading node type that is closest to missing plugin type * Added type attribute to concrete node classes
HOWEVER: This is only fixed on Nodes and not any other AiiDA type. This will have to be done later.
…s_not_current_when_read__minimal Fix 1372 sqla attributes not current when read minimal
ltalirz
previously approved these changes
Apr 5, 2018
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muhrin
approved these changes
Apr 6, 2018
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After the fix of #1372 by PR #1379 into
release_v0.12.0, we also need to merge these changes inworkflows