Merge pull request #4 from mtdhuynh/docs

Release UNIQUE v0.2.0

.github/workflows/build.yml

@@ -0,0 +1,93 @@
+# Simple workflow for deploying static content to GitHub Pages
+name: UNIQUE Build
+
+on:
+  # Runs on pushes targeting the default branches
+  push:
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# 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: "package-build"
+  cancel-in-progress: false
+
+jobs:
+  # Single deploy job since we're just deploying
+  build-package:
+    name: Build distribution 📦
+    runs-on: ubuntu-latest
+
+    # Steps to run to correctly build pypi package
+    steps:
+      # Check out repo
+      - name: Checkout repository contents
+        uses: actions/checkout@v4
+      # Install correct Python version in VM
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ">=3.8 <=3.12.1"
+      # Install flit and build binary wheel/source tarball
+      - name: Install flit
+        run: python3 -m pip install flit --user
+      - name: Build package with flit
+        run: flit build
+      # Store distribution packages
+      - name: Store distribution packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: unique-package-distributions
+          path: dist/
+
+  # PyPI
+  publish-to-pypi:
+    name: >-
+      Publish Python 🐍 distribution 📦 to PyPI
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
+    needs:
+    - build-package
+    runs-on: ubuntu-latest
+
+    environment:
+      name: pypi
+      url: https://pypi.org/p/unique-uncertainty
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: unique-package-distributions
+          path: dist/
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  # TestPyPI
+  publish-to-testpypi:
+    name: Publish Python 🐍 distribution 📦 to TestPyPI
+    needs:
+    - build-package
+    runs-on: ubuntu-latest
+
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/unique-uncertainty
+
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: unique-package-distributions
+        path: dist/
+    - name: Publish distribution 📦 to TestPyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        repository-url: https://test.pypi.org/legacy/
+        skip-existing: true

README.md

@@ -3,10 +3,13 @@
   <figcaption align=center><u><b>UN</b></u>certa<u><b>I</b></u>nty <u><b>QU</b></u>antification b<u><b>E</b></u>nchmark: a Python library for benchmarking uncertainty estimation and quantification methods for Machine Learning models predictions.</figcaption>
 </figure>
 
-![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)
+[![Python](https://img.shields.io/pypi/pyversions/unique-uncertainty?label=Python)](https://pypi.org/project/unique-uncertainty/)
+[![version](https://img.shields.io/pypi/v/unique-uncertainty?color=green&label=PyPI)](https://pypi.org/project/unique-uncertainty/)
+[![PyPI downloads](https://img.shields.io/pypi/dm/unique-uncertainty?label=Downloads)](https://pypi.org/project/unique-uncertainty/)
+[![License](https://img.shields.io/badge/License-BSD_3--Clause-red)](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)
+[![Docs](https://github.com/Novartis/UNIQUE/actions/workflows/docs.yml/badge.svg?branch=main)](https://opensource.nibr.com/UNIQUE/)
+[![Build](https://github.com/Novartis/UNIQUE/actions/workflows/build.yml/badge.svg?branch=main)](https://pypi.org/project/unique-uncertainty/)
 
 
 ## Introduction
@@ -23,20 +26,23 @@
 
 ## Installation
 
-![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)
+[![Python](https://img.shields.io/pypi/pyversions/unique-uncertainty?label=Python)](https://pypi.org/project/unique-uncertainty/)
+[![version](https://img.shields.io/pypi/v/unique-uncertainty?color=green&label=PyPI)](https://pypi.org/project/unique-uncertainty/)
+[![PyPI downloads](https://img.shields.io/pypi/dm/unique-uncertainty?label=Downloads)](https://pypi.org/project/unique-uncertainty/)
+[![Build](https://github.com/Novartis/UNIQUE/actions/workflows/build.yml/badge.svg?branch=main)](https://pypi.org/project/unique-uncertainty/)
 
 `UNIQUE` is currently compatible with Python 3.8 through 3.12.1. To install the latest release and use the package as is, run the following in a compatible environment of choice:
 
 ```bash
-pip install git+https://github.com/Novartis/UNIQUE.git
+pip install unique-uncertainty
 ```
 
-Check out the docs for more installation instructions.
+Check out the [docs](https://opensource.nibr.com/UNIQUE/installation.html#installation) for more installation instructions.
 
 
 ## Getting Started
 
-Check out the docs for a complete set of instructions on how to prepare your data and the possible configurations offered by `UNIQUE`.
+Check out the [docs](https://opensource.nibr.com/UNIQUE/getting_started/index.html#getting-started) for a complete set of instructions on how to prepare your data and the possible configurations offered by `UNIQUE`.
 
 
 ## Usage
@@ -64,12 +70,12 @@ Additionally, `UNIQUE` also generates graphical outputs in the form of tables an
 
 ### Examples
 
-For more hands-on examples and detailed usage, check out some of the examples in the docs.
+For more hands-on examples and detailed usage, check out some of the examples in the [docs](https://opensource.nibr.com/UNIQUE/examples/index.html#examples).
 
 
 ## Deep Dive
 
-Check out the docs for an in-depth overview of `UNIQUE`'s concepts, functionalities, outputs, and references.
+Check out the [docs](https://opensource.nibr.com/UNIQUE/indepth/index.html#deep-dive) for an in-depth overview of `UNIQUE`'s concepts, functionalities, outputs, and references.
 
 
 ## Contributing

docs/source/conf.py

@@ -12,9 +12,10 @@
 copyright = "2024, Novartis Pharma AG"
 author = "Novartis Pharma AG"
 # author = 'Minh Tam Davide Huynh, Gaetano Scebba, Jessica Lanini, Raquel Rodriguez-Perez'
-version = str(unique.__version__)
 
-version_badge_url = f"https://img.shields.io/badge/Version-v{version}-green"
+version_badge_url = (
+    "https://img.shields.io/pypi/v/unique-uncertainty?label=PyPI&color=green"
+)
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
@@ -50,8 +51,10 @@
 myst_heading_anchors = 3
 
 myst_substitutions = {
-    "version": version,
-    "python_versions": r"![Python versions](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)",
+    "pypi_build_badge": "[![PyPI build](https://github.com/Novartis/UNIQUE/actions/workflows/build.yml/badge.svg?branch=main)](https://pypi.org/project/unique-uncertainty)",
+    "pypi_downloads_badge": "[![PyPI downloads](https://img.shields.io/pypi/dm/unique-uncertainty?label=Downloads)](https://pypi.org/project/unique-uncertainty)",
+    "pypi_version_badge": "[![PyPI version](https://img.shields.io/pypi/v/unique-uncertainty?label=PyPI&color=green)](https://pypi.org/project/unique-uncertainty)",
+    "python_versions_badge": "![Python versions](https://img.shields.io/pypi/pyversions/unique-uncertainty?label=Python)",
 }
 
 source_suffix = {
@@ -135,8 +138,8 @@
 html_theme_options = {
     "icon_links": [
         {
-            "name": "Version",
-            "url": "https://github.com/Novartis/UNIQUE",
+            "name": "PyPI Version",
+            "url": "https://pypi.org/project/unique-uncertainty",
             "icon": version_badge_url,
             "type": "url",
         }
@@ -146,7 +149,7 @@
         "image_dark": "_static/unique_logo_dark_blue.png",
     },
     "repository_branch": "master",
-    "repository_provider": "bitbucket",
+    "repository_provider": "github",
     "repository_url": "https://github.com/Novartis/UNIQUE",
     "path_to_docs": "./docs/source",
     "show_navbar_depth": 1,

docs/source/index.md

@@ -18,7 +18,6 @@ myst:
 
          {{description}}
          :::
-      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
@@ -30,6 +29,11 @@ myst:
          :alt: Paper's DOI
          :target: https://doi.org/10.26434/chemrxiv-2024-fmbgk
          :::
+      docs_badge: |
+         :::{image} https://github.com/Novartis/UNIQUE/actions/workflows/docs.yml/badge.svg?branch=main
+         :alt: Documentation build status
+         :target: https://opensource.nibr.com/UNIQUE/
+         :::
       high_level_schema: |
          :::{figure} _static/schema_high_level.png
          :alt: UNIQUE High-Level Schema
@@ -42,7 +46,7 @@ myst:
 
 # Welcome to `UNIQUE`'s documentation!
 
-{{python_versions}} {{version_badge | replace("UNIQUE", version)}} {{license_badge}} {{article_badge}}
+{{python_versions_badge}} {{pypi_version_badge}} {{license_badge}} {{article_badge}} {{docs_badge}} {{pypi_build_badge}} {{pypi_downloads_badge}}
 
 {{logo_light}} {{logo_dark}}
 
@@ -51,7 +55,7 @@ myst:
 `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;
-* generate intuitive visualizations to qualitatively assess how well the computed UQ methods represent the actual model uncertainty;
+* generate intuiti ve visualizations to qualitatively assess how well the computed UQ methods represent the actual model uncertainty;
 * enable the users to get a comprehensive overview of their ML model's performances from an uncertainty quantification perspective.
 
 `UNIQUE` is a model-agnostic tool, meaning that it does not depend on any specific ML model building platform nor provides any ML model training functionality. It only requires the user to input their model's inputs and predictions.

docs/source/installation.md

@@ -10,12 +10,12 @@ myst:
 ---
 # Installation
 
-{{python_versions}}
+{{python_versions_badge}} {{pypi_version_badge}} {{pypi_downloads_badge}} {{pypi_build_badge}}
 
 `UNIQUE` is currently compatible with Python 3.8 through 3.12.1. To install the latest release and use the package as is, run the following in a compatible environment of choice:
 
 ```bash
-pip install git+https://github.com/Novartis/UNIQUE.git
+pip install unique-uncertainty
 ```
 
 :::{tip}

pyproject.toml

@@ -3,7 +3,7 @@ requires = ["flit_core >=3.2,<4"]
 build-backend = "flit_core.buildapi"
 
 [project]
-name = "unique"
+name = "unique-uncertainty"
 authors = [
 	{name = "Raquel Rodriguez-Perez"},
 	{name = "Jessica Lanini"},
@@ -17,7 +17,6 @@ classifiers = [
 	"Intended Audience :: Education",
 	"Intended Audience :: Science/Research",
     "License :: OSI Approved :: BSD License",
-	"Private :: Do Not Upload",
     "Programming Language :: Python",
 	"Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
@@ -33,7 +32,7 @@ classifiers = [
 	"Topic :: Software Development :: Libraries",
 	"Topic :: Software Development :: Libraries :: Python Modules",
 ]
-version = "0.1.1"
+version = "0.2.0"
 license = {file="LICENSE.md"}
 description = "UNIQUE is a Python package for uncertainty quantification and benchmarking of ML models' predictions."
 requires-python = ">=3.8,<=3.12.1"
@@ -57,7 +56,8 @@ dependencies = [
 ]
 
 [project.urls]
-Source = "https://github.com/Novartis/UNIQUE"
+Repository = "https://github.com/Novartis/UNIQUE"
+Documentation = "https://opensource.nibr.com/UNIQUE"
 
 [project.optional-dependencies]
 dev = [
@@ -81,6 +81,9 @@ dev = [
     "tox-conda>=0.10,<=0.10.2",
 ]
 
+[tool.flit.module]
+name = "unique"
+
 [tool.black]
 line-length = 88
 target-version = ["py38", "py39", "py310", "py311", "py312"]

unique/__init__.py

@@ -31,5 +31,3 @@
 from .pipeline import Pipeline
 
 __all__ = ["Pipeline"]
-
-__version__ = "0.1.1"