update devnotes (#30)

* update devnotes * Update README.md * Update devnotes.md * updated notebooks and dependencies --------- Co-authored-by: Thibaud Coroller <[email protected]> Co-authored-by: corolth1 <[email protected]>
Novartis · Apr 19, 2024 · f69f163 · f69f163
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diff --git a/README.md b/README.md
@@ -54,23 +54,8 @@ or for local installation (from package root / clone of this git repository):
 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).
+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.
 
 ## Getting started
 

diff --git a/docs/devnotes.md b/docs/devnotes.md
@@ -2,6 +2,21 @@
 
 ## Set up a development environment via conda
 
+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 use conda to install all package dependencies locally and start development,
 run the following commands in the root directory of the repository.
 
@@ -20,7 +35,7 @@ conda activate torchsurv
 
 ## Test and develop the package
 
-To run all unit tests either use `dev/run-unittests.sh` or run the 
+To run all unit tests either use `dev/run-unittests.sh` or run the
 following command from the repository root directory:
 
 ```bash
@@ -100,3 +115,42 @@ make latexpdf LATEXMKOPTS="-silent -f"
 There are a few errors in the PDF build due to layout issues,
 but the PDF can still be used to summarize the package in a single
 file.
+
+## Steps to create a new release
+
+Follow the steps below, ensure each one is successful.
+
+1. Update the version number in `pyproject.toml`.
+2. Ensure [CHANGELOG.md](CHANGELOG.md) is up-to-date with the new version number and changes.
+3. Ensure all PRs to be included are merged with `main`, pushed to Github and that all tests & checks have run successfully.
+4. Build the release from the latest main branch: `git checkout main && git pull && rm -rf dist && python -m build`
+5. Check the built package: `python -m twine check dist/*`
+6. Upload the package to testPyPI: `python -m twine upload -r testpypi dist/*`
+7. Check if the package can be installed (also check this installs the correct version):
+
+    ```bash
+    rm -rf testenv # ensure a new test env is created
+    python -m virtualenv testenv
+    . ./testenv/bin/activate
+    # these don't simply install from testpypi
+    pip install torch torchmetrics scipy numpy
+    pip install -i https://test.pypi.org/simple/ torchsurv
+    python
+    >>> from torchsurv.loss import cox
+    >>> from torchsurv.metrics.cindex import ConcordanceIndex
+    ```
+
+8. Upload to pypi: `python -m twine upload -r pypi dist/*`
+9. Check that the package can be installed:
+
+    ```bash
+    rm -rf testenv # ensure a new test env is created
+    python -m virtualenv testenv
+    . ./testenv/bin/activate
+    pip install torchsurv
+    python
+    >>> from torchsurv.loss import cox
+    >>> from torchsurv.metrics.cindex import ConcordanceIndex
+    ```
+
+10. Create a new tag for the release, e.g. `git tag -a v0.1.2 -m "Version 0.1.2"`. Push the tag to Github: `git push origin v0.1.2`. Create a release on Github from the tag via <https://github.com/Novartis/torchsurv/releases>.
diff --git a/docs/notebooks/helpers_momentum.py b/docs/notebooks/helpers_momentum.py
@@ -1,11 +1,9 @@
-import pytorch_lightning as L
+import lightning as L
 import torch
 from torch.utils.data import DataLoader, random_split
 from torchvision.datasets import MNIST
-from torchvision.transforms import v2
 
 from torchsurv.loss.cox import neg_partial_log_likelihood
-from torchsurv.loss.momentum import Momentum
 from torchsurv.metrics.cindex import ConcordanceIndex
 
 

diff --git a/docs/notebooks/introduction.ipynb b/docs/notebooks/introduction.ipynb