toxsim 0.1.0__tar.gz

toxsim-0.1.0/.gitignore

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+__pycache__/
+*.py[cod]
+*.egg-info/
+.pytest_cache/
+.coverage
+build/
+dist/
+.venv/
+venv/
+.DS_Store

toxsim-0.1.0/PKG-INFO

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+Metadata-Version: 2.5
+Name: toxsim
+Version: 0.1.0
+Summary: Context-aware synthetic poisoned-patient simulator
+Author: toxsim contributors
+License: MIT
+Requires-Python: >=3.10
+Requires-Dist: numpy>=1.23
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: scipy>=1.9
+Provides-Extra: cli
+Requires-Dist: rich>=13.0; extra == 'cli'
+Requires-Dist: tqdm>=4.64; extra == 'cli'
+Provides-Extra: test
+Requires-Dist: pytest>=7.0; extra == 'test'
+Description-Content-Type: text/markdown
+
+# toxsim
+
+`toxsim` generates context-aware synthetic poisoned-patient presentations. It
+ports the latent-severity behavior from INTOXICATE: intoxication class affects
+severity, which in turn influences GCS, respiratory failure, dysrhythmia, heart
+rate, and systolic blood pressure.
+
+## Installation
+
+```shell
+python -m pip install toxsim
+# Include optional progress and rich CLI output:
+python -m pip install "toxsim[cli]"
+```
+
+## Model data
+
+The package includes the canonical clinical model configuration as package
+data, including `predictive_variables.yml`, each variable's score file, and
+`model.schema.yml`. `load_model_data()` uses these resources by default and
+never depends on the current working directory.
+
+```text
+toxsim/data/
+  model.schema.yml
+  model/
+  predictive_variables.yml
+  <variable-name>_score.yml
+```
+
+Pass a directory to `load_model_data()` or `toxsim-generate
+--model-data-dir` to override the bundled model with a compatible
+configuration. An override directory contains `predictive_variables.yml` and
+one `<variable-name>_score.yml` file for every predictive variable.
+
+## Python API
+
+```python
+from toxsim import create_patient, create_patients
+
+patient = create_patient(seed=2026)
+patients = create_patients(count=100, seed=2026)
+```
+
+Both functions lazily load the bundled model data by default. A seed produces
+the same patient data across runs, including the generated patient ID. Each
+presentation entry has `name`, `value`, and `score`; continuous variables also
+include the model range and whether its underlying value was within that range.
+The patient-level `risk` equals the sum of presentation scores.
+
+To use a compatible external model directory, pass
+`model_data_dir="/path/to/model-data"`. Advanced callers can use
+`create_patient(predictive_variables=variables, scores=score_tables)` or load
+once with `model = load_model_data(...)` and pass that `ModelData` object as
+the first argument to `create_patient(model)` or `create_patients(model,
+count=100)`.
+
+## CLI
+
+```shell
+toxsim-generate \
+  --count 100 \
+  --output patients.jsonl \
+  --seed 2026
+```
+
+`--output` writes one file and infers the format from its `.json` or `.jsonl`
+suffix. To generate named default files in a directory instead, use
+`--destination ./generated --format both`; `--format` accepts `json`, `jsonl`,
+or `both` (the default). Add `--model-data-dir /path/to/model-data` to use a
+compatible override.

toxsim-0.1.0/README.md

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+# toxsim
+
+`toxsim` generates context-aware synthetic poisoned-patient presentations. It
+ports the latent-severity behavior from INTOXICATE: intoxication class affects
+severity, which in turn influences GCS, respiratory failure, dysrhythmia, heart
+rate, and systolic blood pressure.
+
+## Installation
+
+```shell
+python -m pip install toxsim
+# Include optional progress and rich CLI output:
+python -m pip install "toxsim[cli]"
+```
+
+## Model data
+
+The package includes the canonical clinical model configuration as package
+data, including `predictive_variables.yml`, each variable's score file, and
+`model.schema.yml`. `load_model_data()` uses these resources by default and
+never depends on the current working directory.
+
+```text
+toxsim/data/
+  model.schema.yml
+  model/
+  predictive_variables.yml
+  <variable-name>_score.yml
+```
+
+Pass a directory to `load_model_data()` or `toxsim-generate
+--model-data-dir` to override the bundled model with a compatible
+configuration. An override directory contains `predictive_variables.yml` and
+one `<variable-name>_score.yml` file for every predictive variable.
+
+## Python API
+
+```python
+from toxsim import create_patient, create_patients
+
+patient = create_patient(seed=2026)
+patients = create_patients(count=100, seed=2026)
+```
+
+Both functions lazily load the bundled model data by default. A seed produces
+the same patient data across runs, including the generated patient ID. Each
+presentation entry has `name`, `value`, and `score`; continuous variables also
+include the model range and whether its underlying value was within that range.
+The patient-level `risk` equals the sum of presentation scores.
+
+To use a compatible external model directory, pass
+`model_data_dir="/path/to/model-data"`. Advanced callers can use
+`create_patient(predictive_variables=variables, scores=score_tables)` or load
+once with `model = load_model_data(...)` and pass that `ModelData` object as
+the first argument to `create_patient(model)` or `create_patients(model,
+count=100)`.
+
+## CLI
+
+```shell
+toxsim-generate \
+  --count 100 \
+  --output patients.jsonl \
+  --seed 2026
+```
+
+`--output` writes one file and infers the format from its `.json` or `.jsonl`
+suffix. To generate named default files in a directory instead, use
+`--destination ./generated --format both`; `--format` accepts `json`, `jsonl`,
+or `both` (the default). Add `--model-data-dir /path/to/model-data` to use a
+compatible override.