praevius 0.1.0__py3-none-any.whl

praevius/__init__.py

@@ -0,0 +1,56 @@
+"""
+praevius — Hospitalisation-risk predictor for elderly patients
+==============================================================
+
+Installable Python package for the Praevius project. It exposes, at the
+package level, the scoring engine's core functions so programmatic use is
+simple:
+
+    import praevius
+    models = praevius.load_pipelines()            # load the bundled pipelines
+    df     = praevius.patient_to_dataframe({...}) # one patient's raw data
+    scores = praevius.score_patient(models, df)   # scores per horizon/model
+
+Submodules:
+  - praevius.preprocessing     ClinicalPreprocessor (preprocessing)
+  - praevius.scoring           scoring engine (single source)
+  - praevius.predict           single-patient prediction CLI
+  - praevius.report            PDF report (in memory)
+  - praevius.app               Streamlit clinical interface
+  - praevius.predictive_model  training pipeline
+"""
+
+# Package version — first installable distribution (Phase 4). Semantic
+# versioning; pre-1.0 because it's a research prototype.
+__version__ = "0.1.0"
+
+# Re-export the scoring engine's public API at the package level. Importing
+# scoring pulls numpy/pandas/sklearn; that is the project's core, so the cost
+# is acceptable and the ergonomics pay off.
+from praevius.scoring import (   # noqa: E402
+    SHAP_AVAILABLE,
+    build_example_patient,
+    load_model_card,
+    load_pipelines,
+    model_agreement,
+    patient_to_dataframe,
+    probability_display,
+    risk_band,
+    score_patient,
+    shap_explanation,
+)
+
+# Explicit list of what `from praevius import *` exports.
+__all__ = [
+    "__version__",
+    "SHAP_AVAILABLE",
+    "build_example_patient",
+    "load_model_card",
+    "load_pipelines",
+    "model_agreement",
+    "patient_to_dataframe",
+    "probability_display",
+    "risk_band",
+    "score_patient",
+    "shap_explanation",
+]

praevius/_launch.py

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+"""
+praevius._launch — Clinical-interface launcher (the `praevius-app` command)
+===========================================================================
+
+A Streamlit app runs via `streamlit run app.py`, but an installed command
+(console script) is just a Python function — not a `streamlit run`. This
+module bridges that: it locates the app.py BUNDLED in the package and invokes
+`streamlit run` programmatically.
+
+Two details it handles:
+  1. PATH — app.py is found via importlib.resources, so the command works
+     from ANY directory.
+  2. THEME — the NodNex visual theme lives in `.streamlit/config.toml`, which
+     Streamlit only reads from the working directory. Since the command runs
+     from anywhere, we apply the theme via ENVIRONMENT VARIABLES
+     (STREAMLIT_THEME_*), mirroring config.toml.
+
+Streamlit is an OPTIONAL dependency (the [app] extra); hence it is imported
+lazily, with a clear message if missing.
+
+Author: Rafael Zanarino
+"""
+
+import os
+import sys
+from importlib import resources
+
+
+# NodNex theme as Streamlit environment variables. The keys mirror `[theme]`
+# in .streamlit/config.toml (primaryColor → STREAMLIT_THEME_PRIMARY_COLOR,
+# etc.). It is the ONLY way to load the theme when the app runs outside the
+# project directory.
+_THEME_ENV = {
+    "STREAMLIT_THEME_PRIMARY_COLOR": "#7C3AED",            # brand violet
+    "STREAMLIT_THEME_BACKGROUND_COLOR": "#F5F5F4",         # stone-100
+    "STREAMLIT_THEME_SECONDARY_BACKGROUND_COLOR": "#FFFFFF",
+    "STREAMLIT_THEME_TEXT_COLOR": "#1C1917",               # stone-900
+}
+
+
+def _app_path():
+    """
+    Absolute path to the app.py bundled in the package.
+
+    Resolved via importlib.resources — works in editable installs and from
+    the wheel.
+    """
+    return str(resources.files("praevius") / "app.py")
+
+
+def _theme_env():
+    """
+    Returns the NodNex theme dict (Streamlit environment variables).
+
+    Separate function so it is testable without booting the server.
+    """
+    return dict(_THEME_ENV)
+
+
+def run(argv=None):
+    """
+    Starts the clinical interface: `streamlit run <bundled app.py>`.
+
+    Extra command-line arguments are forwarded to Streamlit, so
+    `praevius-app --server.port 8600` works.
+
+    Args:
+        argv (list[str] | None): Arguments to forward to Streamlit. None =
+                                 use the command-line arguments.
+    """
+    # User arguments (e.g. --server.port) forwarded to Streamlit.
+    extra = list(sys.argv[1:] if argv is None else argv)
+
+    # Apply the brand theme WITHOUT overriding what the user may have already
+    # set in the environment (setdefault).
+    for key, value in _THEME_ENV.items():
+        os.environ.setdefault(key, value)
+
+    # Lazy import of Streamlit (optional dependency).
+    try:
+        from streamlit.web import cli as stcli
+    except ModuleNotFoundError:
+        sys.exit(
+            "Streamlit não está instalado. Instale com:  pip install 'praevius[app]'\n"
+            "Streamlit is not installed. Install with:    pip install 'praevius[app]'"
+        )
+
+    # Build the `streamlit run <app.py> [args...]` command and run it.
+    sys.argv = ["streamlit", "run", _app_path(), *extra]
+    sys.exit(stcli.main())