simuci 0.1.5__tar.gz

simuci-0.1.5/.github/workflows/python-publish.yml

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+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  # ── 1. Build ────────────────────────────────────────────────
+  release-build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.13"
+
+      - name: Build release distributions
+        run: |
+          python -m pip install build
+          python -m build
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+  # ── 2. Publish to TestPyPI ──────────────────────────────────
+  testpypi-publish:
+    runs-on: ubuntu-latest
+    needs:
+      - release-build
+    permissions:
+      # mandatory for trusted publishing
+      id-token: write
+      contents: read
+
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/simuci
+
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish release distributions to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          packages-dir: dist/
+          verbose: true
+
+  # ── 3. Publish to PyPI (production) ────────────────────────
+  pypi-publish:
+    runs-on: ubuntu-latest
+    needs:
+      - testpypi-publish
+    permissions:
+      # mandatory for trusted publishing
+      id-token: write
+      contents: read
+
+    environment:
+      name: pypi
+      url: https://pypi.org/p/simuci
+
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/
+          verbose: true

simuci-0.1.5/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/

simuci-0.1.5/LICENSE

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+MIT License
+
+Copyright (c) 2026 SimUCI Team
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

simuci-0.1.5/PKG-INFO

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+Metadata-Version: 2.4
+Name: simuci
+Version: 0.1.5
+Summary: ICU discrete-event simulation engine — distribution sampling, patient clustering, and statistical validation.
+Project-URL: Repository, https://github.com/coslatte/simuci
+Author: SimUCI Team
+License: MIT License
+        
+        Copyright (c) 2026 SimUCI Team
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+License-File: LICENSE
+Keywords: discrete-event,healthcare,icu,simpy,simulation
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Typing :: Typed
+Requires-Python: <=3.14,>=3.9
+Requires-Dist: numpy>=1.26
+Requires-Dist: pandas>=2.0
+Requires-Dist: scikit-learn>=1.3
+Requires-Dist: scipy>=1.11
+Requires-Dist: simpy>=4.0
+Provides-Extra: dev
+Requires-Dist: mypy>=1.10; extra == 'dev'
+Requires-Dist: pytest-cov>=5.0; extra == 'dev'
+Requires-Dist: pytest>=8.0; extra == 'dev'
+Requires-Dist: ruff>=0.4; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# simuci
+
+ICU discrete-event simulation engine — distribution sampling, patient clustering, and statistical validation.
+
+## Installation
+
+```bash
+pip install simuci
+```
+
+For development:
+
+```bash
+git clone https://github.com/coslatte/simuci.git
+cd simuci
+pip install -e ".[dev]"
+```
+
+## Quick Start
+
+```python
+from simuci import Experiment, single_run, multiple_replication
+
+# Create an experiment with patient parameters
+exp = Experiment(
+    age=55,
+    diagnosis_admission1=11,
+    diagnosis_admission2=0,
+    diagnosis_admission3=0,
+    diagnosis_admission4=0,
+    apache=20,
+    respiratory_insufficiency=5,
+    artificial_ventilation=1,
+    uti_stay=100,
+    vam_time=50,
+    preuti_stay_time=10,
+    percent=3,
+)
+
+# Single replication (requires centroids CSV)
+result = single_run(exp, centroids_path="path/to/centroids.csv")
+print(result)
+# {'Tiempo Pre VAM': 5, 'Tiempo VAM': 89, 'Tiempo Post VAM': 168, 'Estadia UCI': 262, 'Estadia Post UCI': 45}
+
+# Multiple replications → DataFrame
+df = multiple_replication(exp, n_reps=200, centroids_path="path/to/centroids.csv")
+print(df.describe())
+```
+
+## Using Your Own Centroid Data
+
+You must pass the path to your centroid CSV explicitly:
+
+```python
+from simuci import single_run, Experiment
+
+exp = Experiment(age=55, ..., validate=False)
+
+# Point to your centroids CSV
+result = single_run(exp, centroids_path="path/to/real_centroids.csv")
+```
+
+The centroids CSV must have:
+
+- An index column (cluster IDs: 0, 1, 2)
+- At least 11 numeric columns (features used for nearest-centroid classification)
+
+You can also use the loader directly:
+
+```python
+from simuci.loaders import CentroidLoader
+
+loader = CentroidLoader()
+centroids = loader.load("path/to/centroids.csv")  # returns numpy array
+```
+
+## Statistical Validation
+
+```python
+import numpy as np
+from simuci import SimulationMetrics, Wilcoxon, Friedman
+
+# Compare simulation output to real data
+metrics = SimulationMetrics(
+    true_data=np.array(...),       # (n_patients, n_variables)
+    simulation_data=np.array(...), # (n_patients, n_replicates, n_variables)
+)
+metrics.evaluate(confidence_level=0.95, result_as_dict=True)
+
+print(metrics.coverage_percentage)
+print(metrics.error_margin)
+print(metrics.kolmogorov_smirnov_result)
+print(metrics.anderson_darling_result)
+```
+
+## Input Validation
+
+All `Experiment` inputs are validated on construction by default:
+
+```python
+from simuci import Experiment
+
+# This raises ValueError: age must be between 14 and 100
+Experiment(age=200, ...)
+```
+
+Skip validation with `validate=False` if you've already validated externally.
+
+## API Reference
+
+| Symbol | Description |
+|--------|-------------|
+| `Experiment` | Patient parameters + result container |
+| `single_run(exp)` | One simulation replication |
+| `multiple_replication(exp, n_reps)` | N replications → DataFrame |
+| `clustering(edad, ...)` | Nearest-centroid patient classifier |
+| `Wilcoxon` | Paired Wilcoxon signed-rank test |
+| `Friedman` | Friedman chi-square test |
+| `SimulationMetrics` | Full evaluation suite (coverage, RMSE, KS, AD) |
+| `StatsUtils` | Static CI helper |
+| `CentroidLoader` | CSV loader with schema validation |
+| `validate_experiment_inputs()` | Parameter range checking |
+
+## License
+
+MIT

simuci-0.1.5/README.md

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+# simuci
+
+ICU discrete-event simulation engine — distribution sampling, patient clustering, and statistical validation.
+
+## Installation
+
+```bash
+pip install simuci
+```
+
+For development:
+
+```bash
+git clone https://github.com/coslatte/simuci.git
+cd simuci
+pip install -e ".[dev]"
+```
+
+## Quick Start
+
+```python
+from simuci import Experiment, single_run, multiple_replication
+
+# Create an experiment with patient parameters
+exp = Experiment(
+    age=55,
+    diagnosis_admission1=11,
+    diagnosis_admission2=0,
+    diagnosis_admission3=0,
+    diagnosis_admission4=0,
+    apache=20,
+    respiratory_insufficiency=5,
+    artificial_ventilation=1,
+    uti_stay=100,
+    vam_time=50,
+    preuti_stay_time=10,
+    percent=3,
+)
+
+# Single replication (requires centroids CSV)
+result = single_run(exp, centroids_path="path/to/centroids.csv")
+print(result)
+# {'Tiempo Pre VAM': 5, 'Tiempo VAM': 89, 'Tiempo Post VAM': 168, 'Estadia UCI': 262, 'Estadia Post UCI': 45}
+
+# Multiple replications → DataFrame
+df = multiple_replication(exp, n_reps=200, centroids_path="path/to/centroids.csv")
+print(df.describe())
+```
+
+## Using Your Own Centroid Data
+
+You must pass the path to your centroid CSV explicitly:
+
+```python
+from simuci import single_run, Experiment
+
+exp = Experiment(age=55, ..., validate=False)
+
+# Point to your centroids CSV
+result = single_run(exp, centroids_path="path/to/real_centroids.csv")
+```
+
+The centroids CSV must have:
+
+- An index column (cluster IDs: 0, 1, 2)
+- At least 11 numeric columns (features used for nearest-centroid classification)
+
+You can also use the loader directly:
+
+```python
+from simuci.loaders import CentroidLoader
+
+loader = CentroidLoader()
+centroids = loader.load("path/to/centroids.csv")  # returns numpy array
+```
+
+## Statistical Validation
+
+```python
+import numpy as np
+from simuci import SimulationMetrics, Wilcoxon, Friedman
+
+# Compare simulation output to real data
+metrics = SimulationMetrics(
+    true_data=np.array(...),       # (n_patients, n_variables)
+    simulation_data=np.array(...), # (n_patients, n_replicates, n_variables)
+)
+metrics.evaluate(confidence_level=0.95, result_as_dict=True)
+
+print(metrics.coverage_percentage)
+print(metrics.error_margin)
+print(metrics.kolmogorov_smirnov_result)
+print(metrics.anderson_darling_result)
+```
+
+## Input Validation
+
+All `Experiment` inputs are validated on construction by default:
+
+```python
+from simuci import Experiment
+
+# This raises ValueError: age must be between 14 and 100
+Experiment(age=200, ...)
+```
+
+Skip validation with `validate=False` if you've already validated externally.
+
+## API Reference
+
+| Symbol | Description |
+|--------|-------------|
+| `Experiment` | Patient parameters + result container |
+| `single_run(exp)` | One simulation replication |
+| `multiple_replication(exp, n_reps)` | N replications → DataFrame |
+| `clustering(edad, ...)` | Nearest-centroid patient classifier |
+| `Wilcoxon` | Paired Wilcoxon signed-rank test |
+| `Friedman` | Friedman chi-square test |
+| `SimulationMetrics` | Full evaluation suite (coverage, RMSE, KS, AD) |
+| `StatsUtils` | Static CI helper |
+| `CentroidLoader` | CSV loader with schema validation |
+| `validate_experiment_inputs()` | Parameter range checking |
+
+## License
+
+MIT

simuci-0.1.5/pyproject.toml

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+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "simuci"
+version = "0.1.5"
+description = "ICU discrete-event simulation engine — distribution sampling, patient clustering, and statistical validation."
+readme = "README.md"
+license = { file = "LICENSE" }
+requires-python = ">=3.9, <=3.14"
+authors = [{ name = "SimUCI Team" }]
+keywords = ["icu", "simulation", "discrete-event", "simpy", "healthcare"]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Topic :: Scientific/Engineering :: Medical Science Apps.",
+    "Typing :: Typed",
+]
+
+dependencies = [
+    "numpy>=1.26",
+    "pandas>=2.0",
+    "scipy>=1.11",
+    "simpy>=4.0",
+    "scikit-learn>=1.3",
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest>=8.0",
+    "pytest-cov>=5.0",
+    "mypy>=1.10",
+    "ruff>=0.4",
+]
+
+[project.urls]
+Repository = "https://github.com/coslatte/simuci"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/simuci"]
+
+[tool.ruff]
+target-version = "py311"
+line-length = 120
+
+[tool.ruff.lint]
+select = ["E", "F", "W", "I", "UP", "B", "SIM"]
+
+[tool.mypy]
+python_version = "3.11"
+strict = true
+warn_return_any = true
+warn_unused_configs = true
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+

simuci-0.1.5/src/simuci/__init__.py

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+"""simuci — ICU discrete-event simulation engine.
+
+Public API
+----------
+Core simulation:
+    Experiment, single_run, multiple_replication, Simulation
+
+Clustering & distributions:
+    clustering, clear_centroid_cache
+
+Statistical validation:
+    Wilcoxon, Friedman, SimulationMetrics, StatsUtils
+
+Input validation:
+    validate_experiment_inputs, validate_simulation_runs
+
+Data loading:
+    CentroidLoader
+
+CSV utilities:
+    process_data  (sub-module)
+"""
+
+from __future__ import annotations
+
+from simuci.distributions import clear_centroid_cache, clustering
+from simuci.experiment import Experiment, multiple_replication, single_run
+from simuci.loaders import CentroidLoader
+from simuci.simulation import Simulation
+from simuci.stats import Friedman, SimulationMetrics, StatsUtils, Wilcoxon
+from simuci.validators import validate_experiment_inputs, validate_simulation_runs
+
+__version__ = "0.1.0"
+
+__all__ = [
+    # Core
+    "Experiment",
+    "Simulation",
+    "single_run",
+    "multiple_replication",
+
+    # Clustering
+    "clustering",
+    "clear_centroid_cache",
+
+    # Statistics
+    "Wilcoxon",
+    "Friedman",
+    "SimulationMetrics",
+    "StatsUtils",
+
+    # Validation
+    "validate_experiment_inputs",
+    "validate_simulation_runs",
+
+    # Loaders
+    "CentroidLoader",
+]