feat: modernize codebase for Python 3.9+ with pydantic validation

.github/workflows/build-release.yml

@@ -8,23 +8,21 @@ jobs:
 
     steps:
       - name: Checkout code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
-      - name: Set up Python
-        uses: actions/setup-python@v2
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
         with:
-          python-version: "3.10"
+          enable-cache: true
 
-      - name: Install dependencies
-        run: |
-          pip install --upgrade pip
-          pip install build==0.7.0 pep517 setuptools wheel twine
+      - name: Set up Python
+        run: uv python install 3.10
 
       - name: Build PyPI release
-        run: python -m build
+        run: uv build
 
       - name: Check PyPI release
-        run: python -m twine check dist/*
+        run: uvx twine check dist/*
 
       - name: Upload artifact
         uses: actions/upload-artifact@v4

.github/workflows/codeqc.yml

@@ -8,58 +8,36 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: ["ubuntu-latest"]
         python-version: ["3.10"]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
-    - name: Setup Miniconda
-      uses: conda-incubator/setup-miniconda@v3
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
       with:
-        auto-update-conda: true
-        miniconda-version: "latest"
-        python-version: ${{ matrix.python-version }}
-        activate-environment: torchsurv
+        enable-cache: true
 
-    - name: Get Date
-      id: get-date
-      run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
-      shell: bash
+    - name: Set up Python ${{ matrix.python-version }}
+      run: uv python install ${{ matrix.python-version }}
 
-    - name: Cache Conda env
-      uses: actions/cache@v3
-      with:
-        path: ${{ env.CONDA }}/envs
-        key:
-          conda-${{ runner.os }}--${{ runner.arch }}--${{ steps.get-date.outputs.today }}-${{ hashFiles('dev/environment.yml') }}-${{ env.CACHE_NUMBER }}
-      env:
-        # Increase this value to reset cache if environment.yml has not changed
-        CACHE_NUMBER: 1
+    - name: Install system dependencies
+      run: sudo apt-get update && sudo apt-get install -y pandoc
 
-    - name: Update conda environment
-      run:
-        conda env update -n torchsurv -f dev/environment.yml
-      if: steps.cache.outputs.cache-hit != 'true'
+    - name: Install dependencies
+      run: uv sync --group dev --extra docs
 
     - name: Code QC
-      shell: bash -l {0}
-      run: |
-        conda activate torchsurv
-        ./dev/codeqc.sh check
+      run: uv run ./dev/codeqc.sh check
 
     - name: Tests
-      shell: bash -l {0}
       run: |
-        conda activate torchsurv
-        ./dev/run-doctests.sh
-        ./dev/run-unittests.sh
+        uv run ./dev/run-doctests.sh
+        uv run pytest
 
     - name: Test-build docs
-      shell: bash -l {0}
       run: |
-        conda activate torchsurv
-        ./dev/build-docs.sh
+        uv run ./dev/build-docs.sh
         tar czvf docs.tar.gz -C docs/_build/html .
 
     - name: 'Upload Docs Tarball'

.github/workflows/docs.yml

@@ -9,41 +9,24 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
-    - name: Setup Miniconda
-      uses: conda-incubator/setup-miniconda@v3
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
       with:
-        auto-update-conda: true
-        miniconda-version: "latest"
-        python-version: 3.11
-        activate-environment: torchsurv
-
-    - name: Get Date
-      id: get-date
-      run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
-      shell: bash
-
-    - name: Cache Conda env
-      uses: actions/cache@v3
-      with:
-        path: ${{ env.CONDA }}/envs
-        key:
-          conda-${{ runner.os }}--${{ runner.arch }}--${{ steps.get-date.outputs.today }}-${{ hashFiles('dev/environment.yml') }}-${{ env.CACHE_NUMBER }}
-      env:
-        # Increase this value to reset cache if environment.yml has not changed
-        CACHE_NUMBER: 0
-
-    - name: Update conda environment
-      run:
-        conda env update -n torchsurv -f dev/environment.yml
-      if: steps.cache.outputs.cache-hit != 'true'
+        enable-cache: true
+
+    - name: Set up Python
+      run: uv python install 3.11
+
+    - name: Install system dependencies
+      run: sudo apt-get update && sudo apt-get install -y pandoc
+
+    - name: Install dependencies
+      run: uv sync --group dev --extra docs
 
     - name: Build docs
-      shell: bash -l {0}
-      run: |
-        conda activate torchsurv
-        ./dev/build-docs.sh
+      run: uv run ./dev/build-docs.sh
 
     - name: Deploy to GitHub Pages
       run: |

.gitignore

@@ -72,10 +72,12 @@ melodie/
 # anything with -copy
 *-copy.*
 
-# LLMs
-.claude/
-.github/
-.hypothesis/
+# copilot
+.github/**
+.specify/**
+.claude/**
+specs/**
 CLAUDE.md
-specs/
-.specify/
+
+# hypothesis generated test artifacts
+.hypothesis/

.pre-commit-config.yaml

@@ -37,7 +37,7 @@ repos:
       - id: ruff-format
 
   - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.3.9009
+    rev: v0.4.3  # NOTE: was pinned to dev version v0.4.3.9009; update if a newer stable tag exists
     hooks:
     -   id: style-files
         args: [--style_pkg=styler, --style_fun=tidyverse_style]
@@ -48,7 +48,16 @@ repos:
     hooks:
       - id: sphinx-lint
 
-
+  - repo: local
+    hooks:
+      - id: mypy
+        name: mypy
+        entry: uv run --no-sync mypy
+        language: system
+        types: [python]
+        args: ["--config-file", "pyproject.toml", "src/"]
+        files: ^src/torchsurv/
+        pass_filenames: false
 
 ci:
   autofix_prs: true

CODEOWNERS.md

@@ -14,3 +14,8 @@
 * David Ohlssen (**Novartis**)
 * Berkman Sahiner (**FDA**)
 * Nicholas Petrick (**FDA**)
+
+
+### Contributors
+
+* Yao Chen (**Novartis**)

CONTRIBUTING.md

@@ -6,6 +6,18 @@ We welcome contributions from the community! Whether you're fixing bugs, adding
 
 Before contributing, please ensure you can set up the development environment by following the instructions in our [developer notes](/docs/devnotes.md).
 
+The quickest way to get started is with [uv](https://docs.astral.sh/uv/):
+
+```bash
+git clone https://github.com/Novartis/torchsurv.git
+cd torchsurv
+uv sync --group dev       # creates .venv and installs everything
+uv run pre-commit install # set up pre-commit hooks
+uv run pytest             # run the test suite
+```
+
+See the [developer notes](/docs/devnotes.md) for more details.
+
 ## How to Contribute
 
 ### Reporting Issues

README.md

@@ -8,24 +8,29 @@ Deep survival analysis made easy
 </h1>
 
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+[![uv](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json)](https://github.com/astral-sh/uv)
 [![Python](https://img.shields.io/pypi/pyversions/torchsurv?label=Python)](https://pypi.org/project/torchsurv/)
 [![PyPI - Version](https://img.shields.io/pypi/v/torchsurv?color=green&label=PyPI)](https://pypi.org/project/torchsurv/)
 [![Conda](https://img.shields.io/conda/v/conda-forge/torchsurv?label=Conda&color=green)](https://anaconda.org/conda-forge/torchsurv)
 [![PyPI Downloads](https://static.pepy.tech/personalized-badge/torchsurv?period=total&units=INTERNATIONAL_SYSTEM&left_color=GRAY&right_color=brightgreen&left_text=PyPI%20downloads)](https://pepy.tech/projects/torchsurv)
 [![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/torchsurv.svg?label=Conda%20downloads)](
 https://anaconda.org/conda-forge/torchsurv)
 
+
 ![CodeQC](https://github.com/Novartis/torchsurv/actions/workflows/codeqc.yml/badge.svg?branch=main)
 ![Docs](https://github.com/Novartis/torchsurv/actions/workflows/docs.yml/badge.svg?branch=main)
 [![CodeFactor](https://www.codefactor.io/repository/github/novartis/torchsurv/badge/main)](https://www.codefactor.io/repository/github/novartis/torchsurv/overview/main)
 [![JOSS](https://joss.theoj.org/papers/02d7496da2b9cc34f9a6e04cabf2298d/status.svg)](https://joss.theoj.org/papers/02d7496da2b9cc34f9a6e04cabf2298d)
 [![License](https://img.shields.io/badge/License-MIT-black)](https://opensource.org/licenses/MIT)
 [![Documentation](https://img.shields.io/badge/GithubPage-Sphinx-blue)](https://opensource.nibr.com/torchsurv/)
 
+
 `TorchSurv` is a Python package that serves as a companion tool to perform deep survival modeling within the `PyTorch` environment. Unlike existing libraries that impose specific parametric forms on users, `TorchSurv` enables the use of custom `PyTorch`-based deep survival models.  With its lightweight design, minimal input requirements, full `PyTorch` backend, and freedom from restrictive survival model parameterizations, `TorchSurv` facilitates efficient survival model implementation, particularly beneficial for high-dimensional input data scenarios.
 
 If you find this repository useful, please give us a star!   🌟 ⭐ 🌟
 
+[![GitHub Stars](https://img.shields.io/github/stars/Novartis/torchsurv?label=GitHub%20stars&color=yellow)](https://github.com/Novartis/torchsurv/stargazers)
+
 ---
 
 ## TL;DR
@@ -99,17 +104,17 @@ pip install torchsurv
 <details>
 <summary><em>Other installation details </em></summary>
 <br>
--  Using for local installation (latest version for example)
+-  Using for local development (latest version)
 
 ```bash
-git clone <repo>
-cd <repo>
-pip install -e .
+git clone https://github.com/Novartis/torchsurv.git
+cd torchsurv
+uv sync --group dev   # creates .venv with all dependencies
+uv run pytest          # run the test suite
 ```
 
-
-Additionally, to build the documentation (`notebooks`, `sphinx`) and for package development (`tests`), please see [the development notes](https://opensource.nibr.com/torchsurv/devnotes.html) and
-[dev/environment.yml](dev/environment.yml). This step is **not required** to use `TorchSurv` in your projects but only for optional features.
+> [uv](https://docs.astral.sh/uv/) is the recommended tool for development.
+> See the [development notes](https://opensource.nibr.com/torchsurv/devnotes.html) for full setup instructions.
 
 </details>