Aiida-core

Bug fixes
- RabbitMQ: update `topika` requirement to fix SSL connections and remove validation of `broker_parameters` from profile [[4542]](https://github.com/aiidateam/aiida-core/pull/4542)
- Fix `UnboundLocalError` in `aiida.cmdline.utils.edit_multiline_template`, which affected `verdi code/computer setup` [[4436]](https://github.com/aiidateam/aiida-core/pull/4436)

Critical bug fixes
- `CalcJob`: make sure `local_copy_list` files do not end up in the node's repository folder [[4415]](https://github.com/aiidateam/aiida-core/pull/4415)

Improvements
- `verdi setup`: forward broker defaults to interactive mode [[4405]](https://github.com/aiidateam/aiida-core/pull/4405)

Bug fixes
- `verdi setup`: improve validation and help string of broker virtual host [[4408]](https://github.com/aiidateam/aiida-core/pull/4408)
- Implement `next` and `iter` for the `Node.open` deprecation wrapper [[4399]](https://github.com/aiidateam/aiida-core/pull/4399)
- Dependencies: increase minimum version requirement `plumpy~=0.15.1` to suppress noisy warning at end of interpreter that ran processes [[4398]](https://github.com/aiidateam/aiida-core/pull/4398)

Improvements
- Add defaults for configure options of the `SshTransport` plugin [[4223]](https://github.com/aiidateam/aiida-core/pull/4223)
- `verdi status`: distinguish database schema version incompatible [[4319]](https://github.com/aiidateam/aiida-core/pull/4319)
- `SlurmScheduler`: implement `parse_output` to detect OOM and OOW [[3931]](https://github.com/aiidateam/aiida-core/pull/3931)

Features
- Make the RabbitMQ connection parameters configurable [[4341]](https://github.com/aiidateam/aiida-core/pull/4341)
- Add infrastructure to parse scheduler output for `CalcJobs` [[3906]](https://github.com/aiidateam/aiida-core/pull/3906)
- Add support for "peer" authentication with PostgreSQL [[4255]](https://github.com/aiidateam/aiida-core/pull/4255)
- Add the `--paused` flag to `verdi process list` [[4213]](https://github.com/aiidateam/aiida-core/pull/4213)
- Make the loglevel of the daemonizer configurable [[4276]](https://github.com/aiidateam/aiida-core/pull/4276)
- `Transport`: add option to not use a login shell for all commands [[4271]](https://github.com/aiidateam/aiida-core/pull/4271)
- Implement `skip_orm` option for SqlAlchemy `Group.remove_nodes` [[4214]](https://github.com/aiidateam/aiida-core/pull/4214)
- `Dict`: allow setting attributes through setitem and `AttributeManager` [[4351]](https://github.com/aiidateam/aiida-core/pull/4351)
- `CalcJob`: allow nested target paths for `local_copy_list` [[4373]](https://github.com/aiidateam/aiida-core/pull/4373)
- `verdi export migrate`: add `--in-place` flag to migrate archive in place [[4220]](https://github.com/aiidateam/aiida-core/pull/4220)

Bug fixes
- `verdi`: make `--prepend-text` and `--append-text` options properly interactive [[4318]](https://github.com/aiidateam/aiida-core/pull/4318)
- `verdi computer test`: fix failing result in harmless `stderr` responses [[4316]](https://github.com/aiidateam/aiida-core/pull/4316)
- `QueryBuilder`: Accept empty string for `entity_type` in `append` method [[4299]](https://github.com/aiidateam/aiida-core/pull/4299)
- `verdi status`: do not except when no profile is configured [[4253]](https://github.com/aiidateam/aiida-core/pull/4253)
- `ArithmeticAddParser`: attach output before checking for negative value [[4267]](https://github.com/aiidateam/aiida-core/pull/4267)
- `CalcJob`: fix bug in `retrieve_list` affecting entries without wildcards [[4275]](https://github.com/aiidateam/aiida-core/pull/4275)
- `TemplateReplacerCalculation`: make `files` namespace dynamic [[4348]](https://github.com/aiidateam/aiida-core/pull/4348)

Developers
- Rename folder `test.fixtures` to `test.static` [[4219]](https://github.com/aiidateam/aiida-core/pull/4219)
- Remove all files from the pre-commit exclude list [[4196]](https://github.com/aiidateam/aiida-core/pull/4196)
- ORM: move attributes/extras methods of frontend and backend nodes to mixins [[4376]](https://github.com/aiidateam/aiida-core/pull/4376)

Dependencies
- Dependencies: update minimum requirement `paramiko~=2.7` [[4222]](https://github.com/aiidateam/aiida-core/pull/4222)
- Depedencies: remove upper limit and allow `numpy~=1.17` [[4378]](https://github.com/aiidateam/aiida-core/pull/4378)

Deprecations
- Deprecate getter and setter methods of `Computer` properties [[4252]](https://github.com/aiidateam/aiida-core/pull/4252)
- Deprecate methods that refer to a computer's label as name [[4309]](https://github.com/aiidateam/aiida-core/pull/4309)

Changes
- `BaseRestartWorkChain`: do not run `process_handler` when `exit_codes=[]` [[4380]](https://github.com/aiidateam/aiida-core/pull/4380)
- `SlurmScheduler`: always raise for non-zero exit code [[4332]](https://github.com/aiidateam/aiida-core/pull/4332)
- Remove superfluous `ERROR_NO_RETRIEVED_FOLDER` from `CalcJob` subclasses [[3906]](https://github.com/aiidateam/aiida-core/pull/3906)

Bug fixes:
- Fix a file handle leak due to the `Runner` not closing the event loop if it created it itself [[4307]](https://github.com/aiidateam/aiida-core/pull/4307)
- `ArithmeticAddParser`: attach output before checking for negative value [[4267]](https://github.com/aiidateam/aiida-core/pull/4267)

Improvements
- Comprehensive restructuring and revamp of the online documentation [[4141]](https://github.com/aiidateam/aiida-core/pull/4141)
- Improve defaults for `verdi computer configure ssh` [[4055]](https://github.com/aiidateam/aiida-core/pull/4055)
- Provenance graphs: enable highlighting specific node classes (and highlight root node by default) [[4081]](https://github.com/aiidateam/aiida-core/pull/4081)

Performance
- Enable event-based monitoring of work chain child processes (they were being polled every second) [[4154]](https://github.com/aiidateam/aiida-core/pull/4154)
- Increase the default for `runner.poll.interval` config option from 1 to 60 seconds [[4150]](https://github.com/aiidateam/aiida-core/pull/4150)
- Increase the efficiency of the `SqlaGroup.nodes` iterator [[4094]](https://github.com/aiidateam/aiida-core/pull/4094)

Features
- Add a progress bar for export and import related functionality [[3599]](https://github.com/aiidateam/aiida-core/pull/3599)
- Enable loading config.yml files from URL in `verdi` commands with `--config` option [[3977]](https://github.com/aiidateam/aiida-core/pull/3977)
- `QueryBuilder`: add the `flat` argument to the `.all()` method [[3945]](https://github.com/aiidateam/aiida-core/pull/3945)
- `verdi status`: add `--no-rmq` flag to skip the RabbitMQ check [[4181]](https://github.com/aiidateam/aiida-core/pull/4181)
- Add support for process functions in `verdi plugin list` [[4117]](https://github.com/aiidateam/aiida-core/pull/4117)
- Allow profile selection in ipython magic `%aiida` [[4071]](https://github.com/aiidateam/aiida-core/pull/4071)
- Support more complex formula formats in `aiida.orm.data.cif.parse_formula` [[3954]](https://github.com/aiidateam/aiida-core/pull/3954)

Bug fixes
- `BaseRestartWorkChain`: do not assume `metadata` exists in inputs in `run_process` [[4210]](https://github.com/aiidateam/aiida-core/pull/4210)
- `BaseRestartWorkChain`: fix bug in `inspect_process` [[4166]](https://github.com/aiidateam/aiida-core/pull/4166)
- `BaseRestartWorkChain`: fix the "unhandled failure mechanism" for dealing with failures of subprocesses [[4155]](https://github.com/aiidateam/aiida-core/pull/4155)
- Fix exception handling in commands calling `list_repository_contents` [[3968]](https://github.com/aiidateam/aiida-core/pull/3968)
- Fix bug in `Code.get_full_text_info` [[4083]](https://github.com/aiidateam/aiida-core/pull/4083)
- Fix bug in `verdi daemon restart --reset` [[3969]](https://github.com/aiidateam/aiida-core/pull/3969)
- Fix tab-completion for `LinkManager` and `AttributeManager` [[3985]](https://github.com/aiidateam/aiida-core/pull/3985)
- `CalcJobResultManager`: fix bug that broke tab completion [[4187]](https://github.com/aiidateam/aiida-core/pull/4187)
- `SshTransport.gettree`: allow non-existing nested target directories [[4175]](https://github.com/aiidateam/aiida-core/pull/4175)
- `CalcJob`: move job resource validation to the `Scheduler` class fixing a problem for the SGE and LSF scheduler plugins [[4192]](https://github.com/aiidateam/aiida-core/pull/4192)
- `WorkChain`: guarantee to maintain order of appended awaitables [[4156]](https://github.com/aiidateam/aiida-core/pull/4156)
- Add support for binary files to the various `verdi` cat commands [[4077]](https://github.com/aiidateam/aiida-core/pull/4077)
- Ensure `verdi group show --limit` respects limit even in raw mode [[4092]](https://github.com/aiidateam/aiida-core/pull/4092)
- `QueryBuilder`: fix type string filter generation for `Group` subclasses [[4144]](https://github.com/aiidateam/aiida-core/pull/4144)
- Raise when calling `Node.objects.delete` for node with incoming links [[4168]](https://github.com/aiidateam/aiida-core/pull/4168)
- Properly handle multiple requests to threaded REST API [[3974]](https://github.com/aiidateam/aiida-core/pull/3974)
- `NodeTranslator`: do not assume `get_export_formats` exists [[4188]](https://github.com/aiidateam/aiida-core/pull/4188)
- Only color directories in `verdi node repo ls --color` [[4195]](https://github.com/aiidateam/aiida-core/pull/4195)

Developers
- Add arithmetic workflows and restructure calculation plugins [[4124]](https://github.com/aiidateam/aiida-core/pull/4124)
- Add minimal `mypy` run to the pre-commit hooks. [[4176]](https://github.com/aiidateam/aiida-core/pull/4176)
- Fix timeout in `tests.cmdline.commands.test_process:test_pause_play_kill` [[4052]](https://github.com/aiidateam/aiida-core/pull/4052)
- Revise update-dependency flow to resolve issue 3930 [[3957]](https://github.com/aiidateam/aiida-core/pull/3957)
- Add GitHub action for transifex upload [[3958]](https://github.com/aiidateam/aiida-core/pull/3958)

Deprecations
- The `get_valid_schedulers` class method of the `Scheduler` class has been deprecated in favor of `aiida.plugins.entry_point.get_entry_point_names` [[4192]](https://github.com/aiidateam/aiida-core/pull/4192)