Merge pull request #3 from mtdhuynh/docs

UNIQUE Documentation Deployment to GitHub Pages

.github/workflows/docs.yml

@@ -0,0 +1,84 @@
+# Simple workflow for deploying static content to GitHub Pages
+name: UNIQUE Documentation
+
+on:
+  # Runs on pushes targeting the default branches
+  push:
+    branches: ["main", "master", "docs"]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  # Single deploy job since we're just deploying
+  deploy-documentation:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    # Sets default bash to track changes to .bashrc or .profilerc
+    # See: https://github.com/conda-incubator/setup-miniconda?tab=readme-ov-file#important
+    defaults:
+      run:
+        shell: bash -el {0}
+    # Steps to run to correctly deploy documentation
+    steps:
+      - name: Checkout repository contents
+        uses: actions/checkout@v4
+
+      # Install dependencies
+      - name: Install UNIQUE dependencies
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: .conda/unique
+          environment-file: unique-environment.yml
+          auto-activate-base: false
+
+      - name: Create UNIQUE Jupyter kernel
+        run: make jupyter-kernel
+
+      # # Cache or restore executed notebooks
+      # - name: Cache/Restore Jupyter notebooks
+      #   id: jupyter-nb-cache
+      #   uses: actions/cache@v4
+      #   env:
+      #     cache-name: unique-example-notebooks
+      #   with:
+      #     path: ./docs/.jupyter_cache/
+      #     key: ${{ env.cache-name }}-cache-${{ hashFiles('./notebooks/**/*.ipynb') }}
+      #     restore-keys: |
+      #       ${{ env.cache-name }}-cache-
+      #       ${{ env.cache-name }}-
+
+      # Install UNIQUE with dev dependencies
+      - name: Install UNIQUE
+        run: pip install -e .[dev]
+
+      # Build documentation
+      - name: Build UNIQUE documentation
+        run: make docs
+
+      # Setup GitHub pages and deploy documentation
+      - name: Setup GitHub Pages
+        uses: actions/configure-pages@v5
+
+      - name: Upload HTML artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: './docs/build/html'
+
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

Makefile

@@ -29,16 +29,16 @@ print-info:
 
 # Install environment
 env:
-	mamba env create -f unique-environment.yml -p ${CONDA_ENV}
+	conda env create -f unique-environment.yml -p ${CONDA_ENV}
 	conda config --append envs_dirs ${CONDA_ENV}
 
 jupyter-kernel:
 	${PYTHON} -m ipykernel install --sys-prefix --name unique --display-name unique
 
 # Delete environment
 clean-env:
-	mamba env remove -p ${CONDA_ENV}
-	mamba clean --all --yes
+	conda env remove -p ${CONDA_ENV}
+	conda clean --all --yes
 	rm -rf ${CONDA_ENV}
 
 # Setup pre-commit

README.md

@@ -6,6 +6,7 @@
 ![Python](https://img.shields.io/badge/Python-3.8%20%7C%203.9%20%7C%203.10%20%7C%203.11%20%7C%203.12.1-blue)
 ![version](https://img.shields.io/badge/Version-v0.1.1-green)
 [![License](https://img.shields.io/badge/License-BSD_3--Clause-red.svg)](https://opensource.org/licenses/BSD-3-Clause)
+[![chemRxiv](https://img.shields.io/badge/chemRxiv-10.26434%2Fchemrxiv--2024--fmbgk-yellow)](https://doi.org/10.26434/chemrxiv-2024-fmbgk)
 
 
 ## Introduction
@@ -83,6 +84,20 @@ Please note that we have a [Code of Conduct](./CODE_OF_CONDUCT.md) in place to e
 `UNIQUE` is licensed under the BSD 3-Clause License. See the [LICENSE](./LICENSE.md) file.
 
 
+## Cite Us
+
+If you find `UNIQUE` helpful for your work and/or research, please consider citing our work:
+
+```bibtex
+@misc{lanini2024unique,
+  title={UNIQUE: A Framework for Uncertainty Quantification Benchmarking},
+  author={Lanini, Jessica and Huynh, Minh Tam Davide and Scebba, Gaetano and Schneider, Nadine and Rodr{\'\i}guez-P{\'e}rez, Raquel},
+  year={2024},
+  doi={https://doi.org/10.26434/chemrxiv-2024-fmbgk},
+}
+```
+
+
 ## Contacts & Acknowledgements
 
 For any questions or further details about the project, please get in touch with any of the following contacts:

docs/source/development/contacts.md

@@ -8,6 +8,19 @@ For any questions or further details about the project, please get in touch with
 * **Nadine Schneider**, *nadine-1*[dot]*schneider*[at]*novartis*[dot]*com*
 * **Raquel Rodríguez-Pérez**, *raquel*[dot]*rodriguez_perez*[at]*novartis.com*
 
+## Cite Us
+
+If you find `UNIQUE` helpful for your work and/or research, please consider citing our work:
+
+```bibtex
+@misc{lanini2024unique,
+  title={UNIQUE: A Framework for Uncertainty Quantification Benchmarking},
+  author={Lanini, Jessica and Huynh, Minh Tam Davide and Scebba, Gaetano and Schneider, Nadine and Rodr{\'\i}guez-P{\'e}rez, Raquel},
+  year={2024},
+  doi={https://doi.org/10.26434/chemrxiv-2024-fmbgk},
+}
+```
+
 :::{image} ../_static/novartis_logo.png
 :alt: Novartis logo
 :align: center

docs/source/getting_started/prepare_pipeline.md

@@ -158,7 +158,7 @@ Currently supported error types (`error_type_list` argument) for {py:class}`~uni
 where {math}`y = label` and {math}`\hat{y} = prediction`.
 :::
 
-:::{deprecated} 0.2.1
+:::{deprecated} 0.1.0
 For {py:class}`~unique.input_type.base.ModelInputType` inputs, it is not necessary to specify the `metrics` argument to compute anymore.
 
 `UNIQUE` automatically detects whether to treat the model-based inputs as regression-based predictions/ensemble variance or classification-based probabilities depending on the specified `problem_type`.

docs/source/indepth/error_models.md

@@ -27,9 +27,9 @@ where {math}`y = label` and {math}`\hat{y} = prediction`.
 {{error_model_schema}}
 
 Given the original input features, along with computed UQ values, `UNIQUE` generates three different sets of input features to train the error predictors:
-1. original model’s prediction, UQ methods, and original input features provided by the user;
-2. original model’s prediction and UQ methods only;
-3. original model’s prediction and non-_transformed_ UQ methods only.
+1. Original model’s prediction, UQ methods, and original input features provided by the user;
+2. Original model’s prediction and UQ methods only;
+3. Original model’s prediction and non-_transformed_ UQ methods only.
 
 The samples are taken from the `"TRAIN"` and `"CALIBRATION"` subsets only; the `"TEST"` subset is left aside to ensure proper validation.
 

docs/source/index.md

@@ -21,10 +21,15 @@ myst:
       version_badge: "![Version badge](https://img.shields.io/badge/Version-vUNIQUE-green)"
       # See: https://github.com/executablebooks/MyST-Parser/issues/279#issuecomment-752948379
       license_badge: |
-         :::{image} https://img.shields.io/badge/License-BSD_3--Clause-red.svg
+         :::{image} https://img.shields.io/badge/License-BSD_3--Clause-red
          :alt: License
          :target: https://opensource.org/licenses/BSD-3-Clause
          :::
+      article_badge: |
+         :::{image} https://img.shields.io/badge/chemRxiv-10.26434%2Fchemrxiv--2024--fmbgk-yellow
+         :alt: Paper's DOI
+         :target: https://doi.org/10.26434/chemrxiv-2024-fmbgk
+         :::
       high_level_schema: |
          :::{figure} _static/schema_high_level.png
          :alt: UNIQUE High-Level Schema
@@ -37,10 +42,12 @@ myst:
 
 # Welcome to `UNIQUE`'s documentation!
 
-{{python_versions}} {{version_badge | replace("UNIQUE", version)}} {{license_badge}}
+{{python_versions}} {{version_badge | replace("UNIQUE", version)}} {{license_badge}} {{article_badge}}
 
 {{logo_light}} {{logo_dark}}
 
+## Introduction
+
 `UNIQUE` provides methods for quantifying and evaluating the uncertainty of Machine Learning (ML) models predictions. The library allows to:
 * combine and benchmark multiple uncertainty quantification (UQ) methods simultaneously;
 * evaluate the goodness of UQ methods against established metrics;
@@ -51,6 +58,22 @@ myst:
 
 {{high_level_schema}}
 
+## Cite Us
+
+If you find `UNIQUE` helpful for your work and/or research, please consider citing our work:
+
+```bibtex
+@misc{lanini2024unique,
+  title={UNIQUE: A Framework for Uncertainty Quantification Benchmarking},
+  author={Lanini, Jessica and Huynh, Minh Tam Davide and Scebba, Gaetano and Schneider, Nadine and Rodr{\'\i}guez-P{\'e}rez, Raquel},
+  year={2024},
+  doi={https://doi.org/10.26434/chemrxiv-2024-fmbgk},
+}
+```
+
+To request more information, check out [Contacts & Acknowledgements](development/contacts.md#contacts--acknowledgements).
+
+
 ---
 
 # Table of Contents

docs/source/installation.md

@@ -41,11 +41,7 @@ git clone https://github.com/Novartis/UNIQUE.git ./unique
 cd unique
 ```
 
-The project uses [`mamba`](https://mamba.readthedocs.io/en/latest/index.html) for dependencies management, which is a faster drop-in replacement for [`conda`](https://conda.io/projects/conda/en/latest/user-guide/install/index.html).
-
-:::{tip}
-If you still wish to use `conda`, you can change the backend solver by adding `--solver=libmamba` to your `conda install` standard command ([check out the docs](https://conda.github.io/conda-libmamba-solver/user-guide/#try-it-once)).
-:::
+The project uses [`conda`](https://conda.io/projects/conda/en/latest/user-guide/install/index.html) and/or [`mamba`](https://mamba.readthedocs.io/en/latest/index.html) for dependencies management.
 
 To set the project up, run: