Octue

Summary
When finalising analyses that produce output datasets, automatically upload the datasets to the `output_location` if it's specified in the app configuration. Additionally, the datasets are put in unique subdirectories within the `output_location` to avoid unintended overwriting or combining of sets of datasets.

These changes remove the need to explicitly call `Analysis.finalise` or construct a unique path to upload datasets to within an app when an `output_location` is provided in the app configuration.

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Contents ([519](https://github.com/octue/octue-sdk-python/pull/519))

Enhancements
- Automatically upload output datasets to output location specified in app configuration in `Analysis.finalise`
- Automatically use a unique subdirectory within the output location in `Analysis.finalise` to avoid data loss/pollution

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Summary
Remove confusing warnings about instantiation metadata vs. stored metadata when instantiating datafiles and datasets. Clarify the resolution order when both instantiation metadata and stored metadata are present.

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Contents ([518](https://github.com/octue/octue-sdk-python/pull/518))

**IMPORTANT:** There are 2 breaking changes.

Fixes
- Remove misleading metadata override warnings from `Datafile` and `Dataset`

Operations
- Use newer poetry syntax for installing extras

Refactoring
- 💥 **BREAKING CHANGE:** Rename Datafile `hypothetical` parameter to `ignore_stored_metadata`
- 💥 **BREAKING CHANGE:** Rename Dataset `hypothetical` parameter to `ignore_stored_metadata`

Operations
- Use latest commit message checker

---
Upgrade instructions
<details>
<summary>💥 <b>Rename Datafile `hypothetical` parameter</b></summary>

Replace `hypothetical` with `ignore_stored_metadata`.
</details>

<details>
<summary>💥 <b>Rename Dataset `hypothetical` parameter</b></summary>

Replace `hypothetical` with `ignore_stored_metadata`.
</details>

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Summary

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Contents ([517](https://github.com/octue/octue-sdk-python/pull/517))

Fixes
- Combine duplicate installations in Docker container

Operations
- Use new poetry installation script in Docker containers

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Summary
This release upgrades children to send heartbeats to parents. This allows the parent to know that a child it's asked a question to is still alive and hasn't crashed. In the event of a crash, heartbeats stop being received and the parent aborts the questions, avoiding large waits for nothing.

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Contents ([514](https://github.com/octue/octue-sdk-python/pull/514))
**IMPORTANT:** There are 2 breaking changes.

New features
- Send heartbeat messages to parents from children
- Raise error in parent if child heartbeats aren't received for too long an interval

Enhancements
- Tell user how to question a service after using `octue start` CLI command

Refactoring
- 💥 **BREAKING CHANGE:** Rename `run_subprocess_and_log_stdout_and_stderr` to `run_logged_subprocess`
- Split thread and process utilities into separate modules
- Remove redundant extra `while` loop in `OrderedMessageHandler`
- Remove redundant `unwrap` function and `AppFrom.run` method from `runner` module

Operations
- Use non-deprecated/latest Codecov action in workflows

Testing
- Increase `ChildEmulator` test coverage


---
Upgrade instructions
<details>
<summary>💥 <b>Rename run_subprocess_and_log_stdout_and_stderr to run_logged_subprocess</b></summary>

Use `octue.utils.threads.run_logged_subprocess` instead.
</details>

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Summary
Add the ability to ask a child any number of questions in parallel instead of in serial.

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Contents ([513](https://github.com/octue/octue-sdk-python/pull/513))

New features
- Add ability to ask children questions in parallel

Other
- Document parallelised question asking

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Summary
Allow recording of:
- **Sent messages by children** if they crash (if allowed by the parent on a per-question basis). This will aid child debugging and allow crashes to be replayed from the parent's perspective during testing.
- **Received messages by the parent** for the purpose of creating test fixtures of different child operation modes.

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Contents ([511](https://github.com/octue/octue-sdk-python/pull/511))

New features
- Allow child services to record messages sent to their parent
- Allow parents to record messages received from their children

Enhancements
- Save all messages sent by a child to its parent on crash instead of just its log messages

Fixes
- Only try saving crash diagnostics if a crash diagnostics cloud path has been set
- Unify `ChildEmulator` message format with `Service` message format
- Remove ability to pass `Exception` instances into `ChildEmulator`

Refactoring
- Factor out message sending in `Service`
- Factor out patching of classes used by `Service` to enable `MockService` operation
- Make `pub_sub` emulators module private

Testing
- Test the child services template app using emulated children
- Clean up `Service` tests

Documentation
- Add documentation on how to test services with `ChildEmulator`
- Add documentation on how to get crash diagnostics for a service

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