Hubit

Added

- Support for negative indices in query paths. The feature is illustrated in `examples/car/run.py`.
- Support for negative indices in model paths. The feature is illustrated in
- `examples/tanks/run_prices.py` and discussed in `examples/tanks/README.md`.
- `examples/wall/run_min_temperature.py` and discussed in `examples/wall/README.md`.
- Reduced computational overhead

Fixed

- Explicit indexing (e.g. 1IDX) for non-rectangular data.
- Occasional code stall when using component caching.
- Component caching in the case where an "upstream" result is queried
before a downstream. Consider a car price calculation (downstream) that consumes the prices of
all parts (upstream). The query `"cars[:].price"` would produce the car price as expected. The query `["cars[:].price", "cars[:].parts[:].price"]` would produce the car price as expected and spawning the same number of workers as `"cars[:].price"`, thus ignoring the superfluous query path `"cars[:].parts[:].price"`. The query, `["cars[:].parts[:].price", "cars[:].price"]` was, however, broken.
- Image links and model excerpt example in wall example documentation.

Fixed

- Fix broken link in README.md

Changed

- Entrypoint functions now accept only two arguments namely `_input_consumed` and `results_provided`. Previously three arguments were expected: `_input_consumed`, `_results_consumed` and `results_provided`. Now `_results_consumed` is simply included in `_input_consumed`. The changes renders entrypoint functions agnostic to the origin of their input.
- The component list in the model configuration file must now sit under a key named"components".
- The format for cache files stored in the folder `.hubit_cache` has changed. To convert old cache files see the example code below. Alternatively, clear the `Hubit` cache using the function `hubit.clear_hubit_cache()`.
- Hyphen is no longer an allowed character for index identifiers. For example this model path is no longer valid `segments[IDX_SEG].layers[IDX-LAY]`.

The example code below converts the cache file `old.yml` to `new.yml`. The file name `old.yml` will, more realistically, be named something like `a70300027991e56db5e3b91acf8b68a5.yml`.

python
import re
import yaml

with open("old.yml", "r") as stream:
old_cache_data = yaml.load(stream, Loader=yaml.FullLoader)

Replace ".DIGIT" with "[DIGIT]" in all keys (paths)
with open("new.yml", "w") as handle:
yaml.dump(
{
re.sub(r"\.(\d+)", r"[\1]", path): val
for path, val in old_cache_data.items()
},
handle,
)


All files in the Hubit cache folder `.hubit_cache` should be converted if you want them to be compatible with `Hubit` 0.4.0+.

Added

- Support for subscriptions to other domains (compartments/cells/elements). Now you can easily configure one domain to use a result from other domains as input as well as set up boundary conditions. This new feature is illustrated in the example with connected tanks in `examples/tanks/README.md`. To enable connected domains Hubit now allows
- Components to share the same entrypoint function.
- Components to be scoped using the new field `component.index_scope`.
- Components to consume specific elements in lists.
- Index offsets which enables one domain to refer to e.g. the previous domain.
- Improved performance for cases
- where only some branches in the input data tree are consumed, and
- where branches are not consumed all the way to the leaves.
- Improved model validation.
- Improved documentation for model configuration file format.

Fixed

- Fix broken example (`examples/wall/run_precompute.py`)
- The elements of lists that are leaves in the input data tree can now be referenced and queried.
- Lists of length 1 in the input were erroneously interpreted as a simple value.

Changed

- The model configuration format is defined and documented in the `HubitModelConfig` class.
- Introducing `HubitModelConfig` four configuration attributes have been renamed. Therefore, model configuration files used in Hubit 0.3- must be migrated to Hubit 0.3 format. Below is a description of the necessary migrations
- The top-level object `provides` is now named `provides_results`.
- The sub-objects `consumes.input` is now a top-level object named `consumes_input`.
- The sub-objects `consumes.results` is now a top-level object named `consumes_results`.
- The value of `module_path` should now be specified in the `path` and is interpreted as a path present in `sys.path` that can be imported as a dotted path.
The most common use case is a package in `site-packages`. If `path` is a dotted path
`is_python_path` should be set to `True`.

Added

- Improved model configuration validation
- Documentation

Added

- Model-level results caching.
- Component-level results caching.
- Introduced logging object accessed using `my_hubit_model.log()`.

Added

- First release