Update dependencies & changes (#26)

* Update dependencies & changes

* Try fix action to check changelog

* ...

* mailto links

added malto link for each maintainer with subject title

* removed banner

* Shorten README.md

* bump version

---------

Co-authored-by: Thibaud Coroller <[email protected]>

Author: kruscpe1

.github/workflows/check-changelog.yml

@@ -0,0 +1,25 @@
+name: "Check Changelog Update"
+
+on:
+  pull_request:
+    branches: [ main ]  # or the default branch of your repo
+
+jobs:
+  check-changelog:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Check for Changelog Updates
+        run: |
+          HEAD_CHANGELOG_HASH=$(git log -1 --format=format:%H -- docs/CHANGELOG.md)
+          git fetch origin ${{ github.base_ref }}
+          git checkout origin/${{ github.base_ref }}
+          BASE_CHANGELOG_HASH=$(git log -1 --format=format:%H -- docs/CHANGELOG.md)
+
+          if [ "$BASE_CHANGELOG_HASH" == "$HEAD_CHANGELOG_HASH" ]; then
+            echo "Changelog must be updated with every pull request."
+            exit 1
+          fi

README.md

@@ -1,15 +1,12 @@
 # Deep survival analysis made easy
 
-> :warning: :construction: **We are still working on the publication of this project and appreciate your patience until everything will be ready.** :construction: :warning:
-
 ![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)
 [![PyPI - Version](https://img.shields.io/pypi/v/torchsurv)](https://pypi.org/project/torchsurv/)
 [![arXiv](https://img.shields.io/badge/arXiv-2404.10761-f9f107.svg)](https://arxiv.org/abs/2404.10761)
 [![Documentation](https://img.shields.io/badge/GithubPage-Sphinx-blue)](https://opensource.nibr.com/torchsurv/)
 [![Downloads](https://static.pepy.tech/badge/torchsurv)](https://pepy.tech/project/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.
 
 ## TL;DR
@@ -43,15 +40,15 @@ cindex.p_value(method="noether", alternative="two_sided")
 cindex.compare(cindexB)
 ```
 
-## Installation
+## Installation and dependencies
 
 First, install the package:
 
 ```bash
 pip install torchsurv
 ```
 
-or for local installation (from package root)
+or for local installation (from package root / clone of this git repository):
 
 ```bash
 pip install -e .
@@ -60,6 +57,21 @@ pip install -e .
 If you use Conda, you can install requirements into a conda environment
 using the `environment.yml` file included in the `dev` subfolder of the source repository.
 
+Using the package has the following dependencies which will be installed automatically via pip:
+
+* [torch](https://pytorch.org/): Consider pre-installing if you have specific system requirements (CPU / GPU / CUDA version).
+* [scipy](https://scipy.org/): We use some statistical helper functions to calculate metrics.
+* [torchmetrics](https://lightning.ai/docs/torchmetrics/stable/): We use some statistical helper functions to calculate metrics.
+
+To run the tests and example notebooks, you need to install the following additional packages:
+
+* [lifelines](https://lifelines.readthedocs.io/en/latest/)
+* [scikit-survival](https://scikit-survival.readthedocs.io/en/stable/)
+* [pytorch_lightning](https://lightning.ai/docs/pytorch/stable/) (and [lightning](https://lightning.ai/))
+
+To build the documentation and for package development, please see [the development notes](https://opensource.nibr.com/torchsurv/devnotes.html) and
+[dev/environment.yml](dev/environment.yml).
+
 ## Getting started
 
 We recommend starting with the [introductory guide](https://opensource.nibr.com/torchsurv/notebooks/introduction.html), where you'll find an overview of the package's functionalities.
@@ -213,10 +225,10 @@ By contributing to this project, you agree to license your contributions under t
 
 ## Contacts
 
-* Thibaud Coroller [email protected] `(creator, maintainer)`
-* Mélodie Monod [email protected] `(creator, maintainer)`
-* Peter Krusche [email protected] `(author, maintainer)`
-* Qian Cao [email protected] `(author, maintainer)`
+* [Thibaud Coroller](mailto:[email protected]?subject=TorchSurv) `(creator, maintainer)`
+* [Mélodie Monod](mailto:[email protected]?subject=TorchSurv) `(creator, maintainer)`
+* [Peter Krusche](mailto:[email protected]?subject=TorchSurv) `(author, maintainer)`
+* [Qian Cao](mailto:[email protected]@novartis.com?subject=TorchSurv) `(author, maintainer)`
 
 If you have any questions, suggestions, or feedback, feel free to reach out the developement team [us](https://opensource.nibr.com/torchsurv/AUTHORS.html).
 

docs/CHANGELOG.md

@@ -1,6 +1,12 @@
 Change log
 =========
 
+Version 0.1.2
+-------------
+
+* Updated package documentation with publication links & badges (#9, #14, #16, #19, #21, #22, #24)
+* Fixed and documented package dependencies (#1)
+
 Version 0.1.1
 -------------
 

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "torchsurv"
-version = "0.1.1"
+version = "0.1.2"
 description = "Survival analysis made easy with pytorch"
 authors = [
     {name = "Thibaud Coroller", email = "[email protected]"},
@@ -30,7 +30,6 @@ classifiers = [
 
 dependencies = [
   "torch",
-  "lightning",
   "scipy",
   "numpy",
   "torchmetrics",