docs: refresh readme (#90)

Author: DiogoRibeiro7

.github/workflows/version-check.yml

@@ -14,16 +14,6 @@ Thank you for taking the time to contribute to **gen_surv**! This document provi
 4. Ensure the test suite passes with `poetry run pytest`.
 5. If you add a feature or fix a bug, update `CHANGELOG.md` accordingly.
 
-## Version Consistency
-
-Releases are tagged in Git. Before creating a release, verify that the version declared in `pyproject.toml` matches the latest Git tag:
-
-```bash
-python scripts/check_version_match.py
-```
-
-The CI workflow `version-check.yml` runs this same script on pull requests to `main`.
-
 ## Submitting Changes
 
 1. Commit your changes with clear messages.

CONTRIBUTING.md

@@ -16,7 +16,7 @@
 [ci-link]: https://github.com/DiogoRibeiro7/genSurvPy/actions/workflows/ci.yml
 [py-badge]: https://img.shields.io/pypi/pyversions/gen_surv
 
-**gen_surv** is a Python library for simulating survival data under a wide range of statistical models. Inspired by the R package [genSurv](https://cran.r-project.org/package=genSurv), it offers a unified interface for generating realistic datasets for research, teaching and benchmarking.
+**gen_surv** is a Python library for simulating survival data and producing visualizations under a wide range of statistical models. Inspired by the R package [genSurv](https://cran.r-project.org/package=genSurv), it offers a unified interface for generating realistic datasets for research, teaching and benchmarking.
 
 ---
 
@@ -29,10 +29,10 @@
 - Time-homogeneous hidden Markov model (THMM)
 - Mixture cure and piecewise exponential models
 - Competing risks generators (constant and Weibull hazards)
-- Visualization utilities for simulated datasets
+- Visualization helpers built on matplotlib and lifelines
 - Scikit-learn compatible data generator
-- Conversion helpers for scikit-survival and lifelines
-- Command-line interface and export utilities
+- Conversion utilities for scikit-survival
+- Command-line interface for dataset creation and visualization
 
 ## Installation
 
@@ -44,29 +44,34 @@ Install the latest release from PyPI:
 pip install gen-surv
 ```
 
+`gen_surv` installs matplotlib and lifelines for visualization. Support for scikit-survival is optional; install it to enable integration with the scikit-survival ecosystem or to run the full test suite:
+
+```bash
+pip install gen-surv[dev]
+```
+
 To develop locally with all extras:
 
 ```bash
 git clone https://github.com/DiogoRibeiro7/genSurvPy.git
 cd genSurvPy
-# Install runtime and development dependencies
-# (scikit-survival is optional but required for integration tests).
-# On Debian/Ubuntu you may need `build-essential gfortran libopenblas-dev` to
-# build scikit-survival.
 poetry install --with dev
 ```
 
-Integration tests that rely on scikit-survival are automatically skipped if the package is not installed.
+On Debian/Ubuntu you may need `build-essential gfortran libopenblas-dev` to build scikit-survival.
 
-## Development Setup
+## Development
 
-Before committing changes, install the pre-commit hooks:
+Before committing changes, install the pre-commit hooks and run the tests:
 
 ```bash
 pre-commit install
 pre-commit run --all-files
+pytest
 ```
 
+Tests that depend on optional packages such as scikit-survival are skipped automatically when those packages are missing.
+
 ## Usage
 
 ### Python API
@@ -75,7 +80,6 @@ pre-commit run --all-files
 from gen_surv import generate, export_dataset, to_sksurv
 from gen_surv.visualization import plot_survival_curve
 
-# basic Cox proportional hazards data
 sim = generate(
     model="cphm",
     n=100,
@@ -96,12 +100,16 @@ See the [usage guide](https://gensurvpy.readthedocs.io/en/latest/getting_started
 
 ### Command Line
 
-Datasets can be generated without writing Python code:
+Generate datasets and plots without writing Python code:
 
 ```bash
 python -m gen_surv dataset cphm --n 1000 -o survival.csv
+
+python -m gen_surv visualize survival.csv --output survival_plot.png
 ```
 
+`visualize` accepts custom column names via `--time-col` and `--status-col` and can stratify by group with `--group-col`.
+
 ## Supported Models
 
 | Model | Description |
@@ -145,3 +153,4 @@ If you use **gen_surv** in your research, please cite the project using the meta
 - ORCID: <https://orcid.org/0009-0001-2022-7072>
 - Professional email: <[email protected]>
 - Personal email: <[email protected]>
+- GitHub: [@DiogoRibeiro7](https://github.com/DiogoRibeiro7)

README.md

@@ -35,4 +35,15 @@ def to_sksurv(
     except ImportError as exc:  # pragma: no cover - optional dependency
         raise ImportError("scikit-survival is required for this feature.") from exc
 
-    return Surv.from_dataframe(event_col, time_col, df)
+    # ``Surv.from_dataframe`` expects the event indicator to be boolean.
+    # Validate the column is binary before casting to avoid silently
+    # accepting unexpected values (e.g., NaNs or numbers other than 0/1).
+    df_copy = df.copy()
+    events = df_copy[event_col]
+    if events.isna().any():
+        raise ValueError("event indicator contains missing values")
+    if not events.isin([0, 1, False, True]).all():
+        raise ValueError("event indicator must be binary")
+    df_copy[event_col] = events.astype(bool)
+
+    return Surv.from_dataframe(event_col, time_col, df_copy)

gen_surv/integration.py

@@ -49,34 +49,6 @@ def test(c: Context) -> None:
             print(stderr_output)
 
 
-@task
-def checkversion(c: Context) -> None:
-    """Check that ``pyproject.toml`` matches the latest Git tag.
-
-    This task executes ``scripts/check_version_match.py`` to ensure the version
-    declared in ``pyproject.toml`` agrees with the most recent tag.
-
-    Args:
-        c: Invoke context used to run shell commands.
-
-    Raises:
-        TypeError: If ``c`` is not an Invoke :class:`Context`.
-    """
-    if not isinstance(c, Context):
-        raise TypeError(f"Expected Invoke Context, got {type(c).__name__!r}")
-
-    # Execute the version check script with Poetry.
-    cmd = "poetry run python scripts/check_version_match.py"
-    result = c.run(cmd, warn=True, pty=False)
-
-    # Report based on the exit code from the script.
-    if result.ok:
-        print("✔️  pyproject version matches the latest git tag.")
-    else:
-        print("❌  Version mismatch detected.")
-        print(result.stderr)
-
-
 @task
 def docs(c: Context) -> None:
     """Build the Sphinx documentation.