Merge pull request #24 from DiogoRibeiro7/codex/fix-version-mismatch-between-pyproject-and-github-tag

Add version consistency check

Author: DiogoRibeiro7

.github/workflows/version-check.yml

@@ -0,0 +1,18 @@
+name: Check Version Consistency
+
+on:
+  pull_request:
+    branches: [main]
+
+jobs:
+  version:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - name: Verify version matches tag
+        run: python scripts/check_version_match.py

CHANGELOG.md

@@ -1,6 +1,13 @@
 # CHANGELOG
 
 
+## v1.0.0 (2025-06-06)
+
+### Misc
+
+- Align pyproject version with GitHub tag
+- Add project Code of Conduct
+
 ## v0.7.1 (2025-04-13)
 
 ### Bug Fixes

CODE_OF_CONDUCT.md

@@ -0,0 +1,126 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, sex characteristics, gender identity and
+expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+- Demonstrating empathy and kindness toward other people
+- Being respectful of differing opinions, viewpoints, and experiences
+- Giving and gracefully accepting constructive feedback
+- Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+- Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+- The use of sexualized language or imagery, and sexual attention or advances
+  of any kind
+- Trolling, insulting or derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+- Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail
+address, posting via an official social media account, or acting as an
+appointed representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+[[email protected]](mailto:[email protected]).
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of
+Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+their audience, for a specified period of time. This includes avoiding
+interactions in community spaces as well as external channels like social
+media. Violating these terms may lead to a temporary or permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with their audience, is allowed during this period. Violating these terms may
+lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+https://www.contributor-covenant.org/version/2/1/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder](https://github.com/mozilla/diversity).
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.

CONTRIBUTING.md

@@ -0,0 +1,28 @@
+# Contributing to gen_surv
+
+Thank you for taking the time to contribute to **gen_surv**! This document provides a brief overview of the recommended workflow for feature requests and pull requests.
+
+## Getting Started
+
+1. Fork the repository and create your feature branch from `main`.
+2. Install dependencies with `poetry install`.
+3. Ensure the test suite passes with `poetry run pytest`.
+4. 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.
+2. Push to your branch and open a pull request.
+3. Ensure your PR description explains the motivation and summarizes your changes.
+
+We appreciate your contributions and feedback!

README.md

@@ -23,10 +23,11 @@ poetry install
 ```
 ## ✨ Features
 
-- Consistent interface across models  
-- Censoring support (`uniform` or `exponential`)  
-- Easy integration with `pandas` and `NumPy`  
-- Suitable for benchmarking survival algorithms and teaching 
+- Consistent interface across models
+- Censoring support (`uniform` or `exponential`)
+- Easy integration with `pandas` and `NumPy`
+- Suitable for benchmarking survival algorithms and teaching
+- Accelerated Failure Time (Log-Normal) model generator
 
 ## 🧪 Example
 
@@ -62,6 +63,7 @@ generate(model="thmm", n=100, qmat=[[0, 0.2, 0], [0.1, 0, 0.1], [0, 0.3, 0]],
 | `gen_cmm()`  | Continuous-Time Multi-State Markov Model   |
 | `gen_tdcm()` | Time-Dependent Covariate Model             |
 | `gen_thmm()` | Time-Homogeneous Markov Model              |
+| `gen_aft_log_normal()` | Accelerated Failure Time Log-Normal  |
 
 
 ```text
@@ -95,3 +97,21 @@ genSurvPy/
 ## 🧠 License
 
 MIT License. See [LICENSE](LICENSE) for details.
+
+
+## 🔖 Release Process
+
+This project uses Git tags to manage releases. A GitHub Actions workflow
+(`version-check.yml`) verifies that the version declared in `pyproject.toml`
+matches the latest Git tag. If they diverge, the workflow fails and prompts a
+correction before merging. Run `python scripts/check_version_match.py` locally
+before creating a tag to catch issues early.
+
+## 🌟 Code of Conduct
+
+Please read our [Code of Conduct](CODE_OF_CONDUCT.md) to learn about the
+expectations for participants in this project.
+
+## 🤝 Contributing
+
+Please read [CONTRIBUTING.md](CONTRIBUTING.md) for guidelines on setting up your environment, running tests, and submitting pull requests.

docs/source/index.md

@@ -53,3 +53,4 @@ generate(model="thmm", n=100, qmat=[[0, 0.2, 0], [0.1, 0, 0.1], [0, 0.3, 0]],
 
 - [Source Code](https://github.com/DiogoRibeiro7/genSurvPy)
 - [License](https://github.com/DiogoRibeiro7/genSurvPy/blob/main/LICENSE)
+- [Code of Conduct](https://github.com/DiogoRibeiro7/genSurvPy/blob/main/CODE_OF_CONDUCT.md)

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "gen_surv"
-version = "0.7.4"
+version = "1.0.0"
 description = "A Python package for simulating survival data, inspired by the R package genSurv"
 authors = ["Diogo Ribeiro <[email protected]>"]
 license = "MIT"

scripts/check_version_match.py

@@ -0,0 +1,48 @@
+#!/usr/bin/env python3
+"""Check that pyproject version matches the latest git tag."""
+from pathlib import Path
+import subprocess
+import sys
+import tomllib
+
+ROOT = Path(__file__).resolve().parents[1]
+
+
+def pyproject_version() -> str:
+    pyproject_path = ROOT / "pyproject.toml"
+    with pyproject_path.open("rb") as f:
+        data = tomllib.load(f)
+    return data["tool"]["poetry"]["version"]
+
+
+def latest_tag() -> str | None:
+    try:
+        tag = subprocess.check_output(
+            ["git", "describe", "--tags", "--abbrev=0"], cwd=ROOT, text=True
+        ).strip()
+        return tag.lstrip("v")
+    except subprocess.CalledProcessError:
+        return None
+
+
+def main() -> int:
+    tag = latest_tag()
+    version = pyproject_version()
+
+    if not tag:
+        print("No git tag found", file=sys.stderr)
+        return 1
+
+    if version != tag:
+        print(
+            f"Version mismatch: pyproject.toml has {version} but latest tag is {tag}",
+            file=sys.stderr,
+        )
+        return 1
+
+    print(f"Version matches latest tag: {version}")
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())