openbraininstitute / neurodamus / 25495620626 / 4 – unit-mpi
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unit-mpi – 25495620626.4

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adapt to new libsonata (#517)

## Context

The new libsonata brings some new small but useful features like:
- rejects duplicate modification names
- `list_input_names` now preserves order

This allows us to:
- accept a `libsonata.SimulationConfig` object instead of the path of a
file. Useful for last minute patches and dummy simulation_configs. No
more juggling with temp files
- simplification in a couple of places of the logic. Stuff is already
handled by libsonata. Less bookkeping

## Scope

- Use `libsonata.SimulationConfig.list_input_names` directly instead of
re-reading the JSON file to get input order (`_stable_inputs_order`
removed)
- `SonataConfig`, `Node`, and `Neurodamus` now accept a
`libsonata.SimulationConfig` object in addition to a file path
- Removed double config parsing: `Node.__init__` no longer parses the
config separately — `SimConfig.init` handles everything
- Let `libsonata.SonataError` propagate naturally instead of wrapping it
in `ConfigurationError`
- Skip `.SUCCESS` file creation when config is passed as an object (no
file path available)

## Very small improvements/cosmetics:

- Let `libsonata.SonataError` propagate naturally instead of wrapping it
in `ConfigurationError`
- Renamed `config_file` → `config_path_or_obj` with type hints and
docstrings


## Testing

- Dropped `test_configure_all_sections_AugAssign_name_clash` — libsonata
now rejects duplicate modification names
- Updated `test_modification_wrong_target_multiple_types` to expect
`libsonata.SonataError` directly
- Added test: `test_sonata_config_from_simulation_config_object`
- Added test: `test_neurodamus_accepts_simulation_config_object`

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Source Files on job unit-mpi - 25495620626.4