fictomed 0.1.0__tar.gz

fictomed-0.1.0/LICENCE.md

@@ -0,0 +1,353 @@
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fictomed-0.1.0/PKG-INFO

@@ -0,0 +1,152 @@
+Metadata-Version: 2.4
+Name: fictomed
+Version: 0.1.0
+Summary: Add your description here
+Requires-Python: >=3.13
+Description-Content-Type: text/markdown
+License-File: LICENCE.md
+Requires-Dist: numpy>=2.4.4
+Requires-Dist: polars>=1.40.1
+Requires-Dist: pyyaml>=6.0.3
+Requires-Dist: tqdm>=4.67.3
+Dynamic: license-file
+
+# fictomed
+
+Librairie Python pour la génération de séjours médicaux fictifs et de scénarios textuels à partir de plusieurs stratégies spécifiques aux centres.
+
+![Python](https://img.shields.io/badge/python-3.13+-blue)
+[![CC BY-NC-SA 4.0](https://img.shields.io/badge/License-CC%20BY--NC--SA%204.0-green.svg)](https://creativecommons.org/licenses/by-nc-sa/4.0/)
+---
+
+## Table des matières
+
+- [Vue d'ensemble](#vue-densemble)
+- [Installation](#installation)
+- [Utilisation](#utilisation)
+- [Pipelines disponibles](#pipelines-disponibles)
+- [Architecture](#architecture)
+- [Contribuer](#contribuer)
+- [Licence](#licence)
+
+---
+
+## Vue d'ensemble
+
+L'idée est de pouvoir crée des scénarios hospitaliers fictifs à partir de séjours choisi selon la stratégie mis en place par le centre développeur de la pipeline. Ces séjours fictifs peuvent ensuite être utilisés en entrée d'un LLM pour en générer des CRH par exemple.
+
+---
+
+## Installation
+
+```bash
+uv pip install fictomed
+```
+
+Ou depuis les sources :
+
+```bash
+git clone https://github.com/CHU-brest/fictomed.git
+cd fictomed
+pip install -e .
+```
+
+### Prérequis
+
+- Python 3.13+
+- polars
+- pyyaml
+- tqdm
+
+---
+
+## Utilisation
+
+### En tant que librairie
+
+```python
+from fictomed import generate
+
+df = generate(
+    pipeline_name="brest",
+    n_sejours=500,
+    n_ccam=1,
+    n_das=5,
+    ghm5_pattern=None,
+)
+```
+
+### En ligne de commande
+
+```bash
+python main.py brest --n-sejours 100
+```
+
+---
+
+## Pipelines disponibles
+
+| Nom | Site | Description |
+|-----|------|-------------|
+| `brest` | CHU de Brest | Choix des codes CIM10 par pondération selon les extractions SNDS |
+
+---
+
+## Architecture
+
+```
+fictomed/
+├── __init__.py        # API publique
+├── core.py            # Fonction principale generate()
+├── registry.py        # Registre des pipelines (PIPELINES) ainsi que du chemin vers le fichier de config (CONFIG_DIR)
+├── config.py          # Chargement de la configuration
+├── base.py            # Définition de la pipeline de base BasePipeline
+├── ficitve.py         # Fonction général qui permet la génération des séjours fictifs
+├── scenario.py        # Fonction général qui permet la génération des scenarios fictifs
+└── sites/
+    └── brest/
+        ├── __init__.py
+        └── pipeline.py
+```
+
+---
+
+## Contribuer
+
+### Ajouter un nouveau pipeline
+
+1. Créer un dossier `fictomed/sites/<nom_site>/`
+2. Implémenter `MedPipelineBase` dans `pipeline.py`
+3. Enregistrer le pipeline dans `registry.py`
+
+```python
+# registry.py
+from fictomed.sites.nouveau_site.pipeline import NouveauSitePipeline
+
+PIPELINES = {
+    "brest": BrestPipeline,
+    "nouveau_site": NouveauSitePipeline,  # ← ajouter ici
+}
+```
+
+## Contributeurs
+ 
+| Nom | Rôle |
+|-----|------|
+| Arthur LAMARD | Data Engineer CHU Brest |
+| Dr. Basile FUCHS | Médecin DIM CHU Brest |
+| Claire Dechaux | Data Scientist INRIA |
+| Dr. Remi Flicoteaux | Médecin DIM APHP |
+
+## Licence
+ 
+Ce projet est sous licence [Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International](LICENSE.md).
+ 
+ 
+Vous êtes libre de :
+- **Partager** — copier et redistribuer le projet
+- **Adapter** — remixer et transformer le projet
+Sous les conditions suivantes :
+- **Attribution** — Vous devez citer le projet original
+- **Non Commercial** — Usage commercial interdit sans accord explicite
+- **Partage dans les mêmes conditions** — Toute modification doit être publiée sous la même licence

fictomed-0.1.0/README.md

@@ -0,0 +1,139 @@
+# fictomed
+
+Librairie Python pour la génération de séjours médicaux fictifs et de scénarios textuels à partir de plusieurs stratégies spécifiques aux centres.
+
+![Python](https://img.shields.io/badge/python-3.13+-blue)
+[![CC BY-NC-SA 4.0](https://img.shields.io/badge/License-CC%20BY--NC--SA%204.0-green.svg)](https://creativecommons.org/licenses/by-nc-sa/4.0/)
+---
+
+## Table des matières
+
+- [Vue d'ensemble](#vue-densemble)
+- [Installation](#installation)
+- [Utilisation](#utilisation)
+- [Pipelines disponibles](#pipelines-disponibles)
+- [Architecture](#architecture)
+- [Contribuer](#contribuer)
+- [Licence](#licence)
+
+---
+
+## Vue d'ensemble
+
+L'idée est de pouvoir crée des scénarios hospitaliers fictifs à partir de séjours choisi selon la stratégie mis en place par le centre développeur de la pipeline. Ces séjours fictifs peuvent ensuite être utilisés en entrée d'un LLM pour en générer des CRH par exemple.
+
+---
+
+## Installation
+
+```bash
+uv pip install fictomed
+```
+
+Ou depuis les sources :
+
+```bash
+git clone https://github.com/CHU-brest/fictomed.git
+cd fictomed
+pip install -e .
+```
+
+### Prérequis
+
+- Python 3.13+
+- polars
+- pyyaml
+- tqdm
+
+---
+
+## Utilisation
+
+### En tant que librairie
+
+```python
+from fictomed import generate
+
+df = generate(
+    pipeline_name="brest",
+    n_sejours=500,
+    n_ccam=1,
+    n_das=5,
+    ghm5_pattern=None,
+)
+```
+
+### En ligne de commande
+
+```bash
+python main.py brest --n-sejours 100
+```
+
+---
+
+## Pipelines disponibles
+
+| Nom | Site | Description |
+|-----|------|-------------|
+| `brest` | CHU de Brest | Choix des codes CIM10 par pondération selon les extractions SNDS |
+
+---
+
+## Architecture
+
+```
+fictomed/
+├── __init__.py        # API publique
+├── core.py            # Fonction principale generate()
+├── registry.py        # Registre des pipelines (PIPELINES) ainsi que du chemin vers le fichier de config (CONFIG_DIR)
+├── config.py          # Chargement de la configuration
+├── base.py            # Définition de la pipeline de base BasePipeline
+├── ficitve.py         # Fonction général qui permet la génération des séjours fictifs
+├── scenario.py        # Fonction général qui permet la génération des scenarios fictifs
+└── sites/
+    └── brest/
+        ├── __init__.py
+        └── pipeline.py
+```
+
+---
+
+## Contribuer
+
+### Ajouter un nouveau pipeline
+
+1. Créer un dossier `fictomed/sites/<nom_site>/`
+2. Implémenter `MedPipelineBase` dans `pipeline.py`
+3. Enregistrer le pipeline dans `registry.py`
+
+```python
+# registry.py
+from fictomed.sites.nouveau_site.pipeline import NouveauSitePipeline
+
+PIPELINES = {
+    "brest": BrestPipeline,
+    "nouveau_site": NouveauSitePipeline,  # ← ajouter ici
+}
+```
+
+## Contributeurs
+ 
+| Nom | Rôle |
+|-----|------|
+| Arthur LAMARD | Data Engineer CHU Brest |
+| Dr. Basile FUCHS | Médecin DIM CHU Brest |
+| Claire Dechaux | Data Scientist INRIA |
+| Dr. Remi Flicoteaux | Médecin DIM APHP |
+
+## Licence
+ 
+Ce projet est sous licence [Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International](LICENSE.md).
+ 
+ 
+Vous êtes libre de :
+- **Partager** — copier et redistribuer le projet
+- **Adapter** — remixer et transformer le projet
+Sous les conditions suivantes :
+- **Attribution** — Vous devez citer le projet original
+- **Non Commercial** — Usage commercial interdit sans accord explicite
+- **Partage dans les mêmes conditions** — Toute modification doit être publiée sous la même licence

fictomed-0.1.0/fictomed/__init__.py

@@ -0,0 +1,4 @@
+from fictomed.core import generate
+from fictomed.registry import PIPELINES, CONFIG_DIR
+
+__all__ = ["generate", "PIPELINES", "CONFIG_DIR"]

fictomed-0.1.0/fictomed/base.py

@@ -0,0 +1,43 @@
+from __future__ import annotations
+
+from abc import ABC, abstractmethod
+
+import polars as pl
+
+REPORT_SCHEMA = {
+    "generation_id": pl.Utf8,
+    "scenario": pl.Utf8,
+    "report": pl.Utf8,
+    "model": pl.Utf8,
+    "timestamp": pl.Datetime,
+}
+
+
+class BasePipeline(ABC):
+    """Base class for synthetic medical-report generation pipelines.
+
+    Provides shared building blocks (LLM wrappers, generation loop, Parquet
+    persistence) and defines the interface that each concrete pipeline must
+    implement.
+    """
+
+    name: str = "base"
+
+    def __init__(self, config: dict) -> None:
+        self.config = config
+
+    @abstractmethod
+    def check_data(self) -> None:
+        """Verify that source data is present and prepare it if needed."""
+
+    @abstractmethod
+    def load_data(self) -> dict[str, pl.LazyFrame]:
+        """Load prepared data as LazyFrames."""
+
+    @abstractmethod
+    def get_fictive(self, data: dict[str, pl.LazyFrame], **kwargs) -> pl.DataFrame:
+        """Generate fictitious hospital stays from loaded data."""
+
+    @abstractmethod
+    def get_scenario(self, df: pl.DataFrame) -> pl.DataFrame:
+        """Transform fictitious stays into text scenarios for the LLM."""