From d45e5f71af1275d1e0214c48e96a7cbd45d2386c Mon Sep 17 00:00:00 2001 From: Tam Huynh Date: Wed, 25 Sep 2024 16:37:36 +0200 Subject: [PATCH 1/9] Update dependencies --- pyproject.toml | 3 ++- unique-environment.yml | 1 + 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index ffd8e71..d1ef35c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -34,7 +34,7 @@ classifiers = [ ] version = "0.2.1" license = {file="LICENSE.md"} -description = "UNIQUE is a Python package for uncertainty quantification and benchmarking of ML models' predictions." +description = "UNIQUE is a Python package for benchmarking uncertainty estimation and quantification methods for Machine Learning models predictions." requires-python = ">=3.8,<=3.12.1" dependencies = [ "colorcet>=3.0,<=3.0.1", @@ -77,6 +77,7 @@ dev = [ "sphinx-autodoc2>=0.5.0", "sphinx-book-theme>=1.1.2", "sphinx-copybutton==0.5.2", + "sphinx-design>=0.5,<0.7", "tox>=3.27,<=4.12.1", "tox-conda>=0.10,<=0.10.2", ] diff --git a/unique-environment.yml b/unique-environment.yml index 928146a..3851dff 100644 --- a/unique-environment.yml +++ b/unique-environment.yml @@ -26,6 +26,7 @@ dependencies: - sphinx-autodoc2 >=0.5.0 - sphinx-book-theme >=1.1.2 - sphinx-copybutton ==0.5.2 + - sphinx-design >=0.5,<0.7 - pre-commit >=3.6.2, <=3.7 - pyarrow <=16.1.0 - python >=3.8,<=3.12.1 From aa75a50679118f9e245ef8421617e63e89db1313 Mon Sep 17 00:00:00 2001 From: Tam Huynh Date: Wed, 25 Sep 2024 16:44:58 +0200 Subject: [PATCH 2/9] Update docs --- README.md | 18 ++++++++++++++---- docs/source/conf.py | 25 ++++++++++++++++++------- docs/source/index.md | 2 +- docs/source/installation.md | 27 ++++++++++++++++++++++++--- 4 files changed, 57 insertions(+), 15 deletions(-) diff --git a/README.md b/README.md index 6c9f6bb..2986fcc 100644 --- a/README.md +++ b/README.md @@ -4,8 +4,10 @@ [![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/) +[![PyPI version](https://img.shields.io/pypi/v/unique-uncertainty?color=yellowgreen&label=PyPI)](https://pypi.org/project/unique-uncertainty/) +[![Conda version](https://img.shields.io/conda/vn/conda-forge/unique-uncertainty?color=yellowgreen&label=conda-forge)](https://anaconda.org/conda-forge/unique-uncertainty) +[![PyPI downloads](https://img.shields.io/pypi/dm/unique-uncertainty?color=brightgreen&label=PyPI%20downloads)](https://pypi.org/project/unique-uncertainty/) +[![Conda downloads](https://img.shields.io/conda/dn/conda-forge/unique-uncertainty?color=brightgreen&label=conda%20downloads)](https://anaconda.org/conda-forge/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/) @@ -27,8 +29,10 @@ ## Installation [![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/) +[![PyPI version](https://img.shields.io/pypi/v/unique-uncertainty?color=yellowgreen&label=PyPI)](https://pypi.org/project/unique-uncertainty/) +[![Conda version](https://img.shields.io/conda/vn/conda-forge/unique-uncertainty?color=yellowgreen&label=conda-forge)](https://anaconda.org/conda-forge/unique-uncertainty) +[![PyPI downloads](https://img.shields.io/pypi/dm/unique-uncertainty?color=brightgreen&label=PyPI%20downloads)](https://pypi.org/project/unique-uncertainty/) +[![Conda downloads](https://img.shields.io/conda/dn/conda-forge/unique-uncertainty?color=brightgreen&label=conda%20downloads)](https://anaconda.org/conda-forge/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: @@ -37,6 +41,12 @@ pip install unique-uncertainty ``` +or: + +```bash +conda install -c conda-forge unique-uncertainty +``` + Check out the [docs](https://opensource.nibr.com/UNIQUE/installation.html#installation) for more installation instructions. diff --git a/docs/source/conf.py b/docs/source/conf.py index 10d62a0..8cb83d9 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -13,10 +13,12 @@ author = "Novartis Pharma AG" # author = 'Minh Tam Davide Huynh, Gaetano Scebba, Jessica Lanini, Raquel Rodriguez-Perez' -version_badge_url = ( - "https://img.shields.io/pypi/v/unique-uncertainty?label=PyPI&color=green" +pypi_version_badge_url = ( + "https://img.shields.io/pypi/v/unique-uncertainty?color=yellowgreen&label=PyPI" ) +conda_version_badge_url = "https://img.shields.io/conda/vn/conda-forge/unique-uncertainty?color=yellowgreen&label=conda-forge" + # -- General configuration --------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration @@ -25,6 +27,7 @@ # "autodoc2", # Instead of 'sphinx.ext.autodoc', "myst_nb", "sphinx_copybutton", + "sphinx_design", # "sphinx.ext.autodoc", # "sphinx.ext.autosummary", "sphinx.ext.napoleon", @@ -51,9 +54,11 @@ myst_heading_anchors = 3 myst_substitutions = { + "conda_downloads_badge": "[![Conda downloads](https://img.shields.io/conda/dn/conda-forge/unique-uncertainty?color=brightgreen&label=conda%20downloads)](https://anaconda.org/conda-forge/unique-uncertainty)", + "conda_version_badge": "[![Conda version](https://img.shields.io/conda/vn/conda-forge/unique-uncertainty?color=yellowgreen&label=conda-forge)](https://anaconda.org/conda-forge/unique-uncertainty)", "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)", + "pypi_downloads_badge": "[![PyPI downloads](https://img.shields.io/pypi/dm/unique-uncertainty?color=brightgreen&label=PyPI%20downloads)](https://pypi.org/project/unique-uncertainty)", + "pypi_version_badge": "[![PyPI version](https://img.shields.io/pypi/v/unique-uncertainty?color=yellowgreen&label=PyPI)](https://pypi.org/project/unique-uncertainty)", "python_versions_badge": "![Python versions](https://img.shields.io/pypi/pyversions/unique-uncertainty?label=Python)", } @@ -140,15 +145,21 @@ { "name": "PyPI Version", "url": "https://pypi.org/project/unique-uncertainty", - "icon": version_badge_url, + "icon": pypi_version_badge_url, + "type": "url", + }, + { + "name": "Conda Version", + "url": "https://anaconda.org/conda-forge/unique-uncertainty", + "icon": conda_version_badge_url, "type": "url", - } + }, ], "logo": { "alt_text": "UNIQUE's Documentation - Home", "image_dark": "_static/unique_logo_dark_blue.png", }, - "repository_branch": "master", + "repository_branch": "main", "repository_provider": "github", "repository_url": "https://github.com/Novartis/UNIQUE", "path_to_docs": "./docs/source", diff --git a/docs/source/index.md b/docs/source/index.md index 1440400..c453da7 100644 --- a/docs/source/index.md +++ b/docs/source/index.md @@ -46,7 +46,7 @@ myst: # Welcome to `UNIQUE`'s documentation! -{{python_versions_badge}} {{pypi_version_badge}} {{license_badge}} {{article_badge}} {{docs_badge}} {{pypi_build_badge}} {{pypi_downloads_badge}} +{{python_versions_badge}} {{pypi_version_badge}} {{conda_version_badge}} {{license_badge}} {{article_badge}} {{docs_badge}} {{pypi_build_badge}} {{pypi_downloads_badge}} {{conda_downloads_badge}} {{logo_light}} {{logo_dark}} diff --git a/docs/source/installation.md b/docs/source/installation.md index 17f69a2..7266373 100644 --- a/docs/source/installation.md +++ b/docs/source/installation.md @@ -10,13 +10,27 @@ myst: --- # Installation -{{python_versions_badge}} {{pypi_version_badge}} {{pypi_downloads_badge}} {{pypi_build_badge}} +{{python_versions_badge}} {{pypi_version_badge}} {{conda_version_badge}} {{pypi_downloads_badge}} {{conda_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: +::::{tab-set} + +:::{tab-item} `pip` + ```bash pip install unique-uncertainty ``` +::: + +:::{tab-item} `conda` + +```bash +conda install -c conda-forge unique-uncertainty +``` +::: + +:::: :::{tip} To create a dedicated virtual environment for `UNIQUE` using `conda`/`mamba` with all the required and compatible dependencies, check out: [For Developers](#for-developers). @@ -43,17 +57,24 @@ cd unique 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: +Install first the `conda` dependencies and the Jupyter kernel needed to run the examples: ```bash # Install conda environment and jupyter kernel locally make env && make jupyter-kernel conda activate .conda/unique +``` +Next, enable the pre-commit hooks for automatic code formatting/linting: + +```bash # Setup precommit hooks make pre-commit +``` + +Lastly, install `UNIQUE` from source: -# Install UNIQUE +```bash pip install -e . # Use `pip install -e .[dev]` to also install optional dependencies ``` From 5c75cd7f3ad207dc51277b1b537983d395426196 Mon Sep 17 00:00:00 2001 From: Tam Huynh Date: Wed, 25 Sep 2024 16:45:15 +0200 Subject: [PATCH 3/9] Beta release --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index d1ef35c..e423aaf 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,7 @@ authors = [ ] readme = "README.md" classifiers = [ - "Development Status :: 3 - Alpha", + "Development Status :: 4 - Beta", "Intended Audience :: Developers", "Intended Audience :: Education", "Intended Audience :: Science/Research", From 861d11b263ac0bd39ff9d8dc2602cc88d7b9318c Mon Sep 17 00:00:00 2001 From: Tam Huynh Date: Thu, 26 Sep 2024 17:06:14 +0200 Subject: [PATCH 4/9] Update README.md --- README.md | 27 ++++++++++++++++----------- 1 file changed, 16 insertions(+), 11 deletions(-) diff --git a/README.md b/README.md index 2986fcc..47db4b8 100644 --- a/README.md +++ b/README.md @@ -1,15 +1,15 @@
- UNIQUE Logo + UNIQUE Logo
UNcertaInty QUantification bEnchmark: a Python library for benchmarking uncertainty estimation and quantification methods for Machine Learning models predictions.
[![Python](https://img.shields.io/pypi/pyversions/unique-uncertainty?label=Python)](https://pypi.org/project/unique-uncertainty/) -[![PyPI version](https://img.shields.io/pypi/v/unique-uncertainty?color=yellowgreen&label=PyPI)](https://pypi.org/project/unique-uncertainty/) -[![Conda version](https://img.shields.io/conda/vn/conda-forge/unique-uncertainty?color=yellowgreen&label=conda-forge)](https://anaconda.org/conda-forge/unique-uncertainty) -[![PyPI downloads](https://img.shields.io/pypi/dm/unique-uncertainty?color=brightgreen&label=PyPI%20downloads)](https://pypi.org/project/unique-uncertainty/) -[![Conda downloads](https://img.shields.io/conda/dn/conda-forge/unique-uncertainty?color=brightgreen&label=conda%20downloads)](https://anaconda.org/conda-forge/unique-uncertainty) +[![PyPI version](https://img.shields.io/pypi/v/unique-uncertainty?color=green&label=PyPI)](https://pypi.org/project/unique-uncertainty/) +[![Conda version](https://img.shields.io/conda/vn/conda-forge/unique-uncertainty?color=green&label=conda-forge)](https://anaconda.org/conda-forge/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) +[![PyPI downloads](https://img.shields.io/pypi/dm/unique-uncertainty?color=yellowgreen&label=PyPI%20downloads)](https://pypi.org/project/unique-uncertainty/) +[![Conda downloads](https://img.shields.io/conda/dn/conda-forge/unique-uncertainty?color=yellowgreen&label=conda%20downloads)](https://anaconda.org/conda-forge/unique-uncertainty) [![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/) @@ -21,7 +21,7 @@ `UNIQUE` is a model-agnostic tool, meaning that it does not depend on any specific ML model building platform or provides any ML model training functionality. It is lightweight, because it only requires the user to input their model's inputs and predictions.
- UNIQUE High Level Schema + UNIQUE High Level Schema
High-level schema of UNIQUE's components.
@@ -29,10 +29,10 @@ ## Installation [![Python](https://img.shields.io/pypi/pyversions/unique-uncertainty?label=Python)](https://pypi.org/project/unique-uncertainty/) -[![PyPI version](https://img.shields.io/pypi/v/unique-uncertainty?color=yellowgreen&label=PyPI)](https://pypi.org/project/unique-uncertainty/) -[![Conda version](https://img.shields.io/conda/vn/conda-forge/unique-uncertainty?color=yellowgreen&label=conda-forge)](https://anaconda.org/conda-forge/unique-uncertainty) -[![PyPI downloads](https://img.shields.io/pypi/dm/unique-uncertainty?color=brightgreen&label=PyPI%20downloads)](https://pypi.org/project/unique-uncertainty/) -[![Conda downloads](https://img.shields.io/conda/dn/conda-forge/unique-uncertainty?color=brightgreen&label=conda%20downloads)](https://anaconda.org/conda-forge/unique-uncertainty) +[![PyPI version](https://img.shields.io/pypi/v/unique-uncertainty?color=green&label=PyPI)](https://pypi.org/project/unique-uncertainty/) +[![Conda version](https://img.shields.io/conda/vn/conda-forge/unique-uncertainty?color=green&label=conda-forge)](https://anaconda.org/conda-forge/unique-uncertainty) +[![PyPI downloads](https://img.shields.io/pypi/dm/unique-uncertainty?color=yellowgreen&label=PyPI%20downloads)](https://pypi.org/project/unique-uncertainty/) +[![Conda downloads](https://img.shields.io/conda/dn/conda-forge/unique-uncertainty?color=yellowgreen&label=conda%20downloads)](https://anaconda.org/conda-forge/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: @@ -45,6 +45,7 @@ or: ```bash conda install -c conda-forge unique-uncertainty +# mamba install -c conda-forge unique-uncertainty ``` Check out the [docs](https://opensource.nibr.com/UNIQUE/installation.html#installation) for more installation instructions. @@ -97,11 +98,15 @@ Please note that we have a [Code of Conduct](./CODE_OF_CONDUCT.md) in place to e ## License +[![License](https://img.shields.io/badge/License-BSD_3--Clause-red)](https://opensource.org/licenses/BSD-3-Clause) + `UNIQUE` is licensed under the BSD 3-Clause License. See the [LICENSE](./LICENSE.md) file. ## Cite Us +[![chemRxiv](https://img.shields.io/badge/chemRxiv-10.26434%2Fchemrxiv--2024--fmbgk-yellow)](https://doi.org/10.26434/chemrxiv-2024-fmbgk) + If you find `UNIQUE` helpful for your work and/or research, please consider citing our work: ```bibtex @@ -125,4 +130,4 @@ For any questions or further details about the project, please get in touch with * **[Raquel Rodríguez-Pérez](mailto:raquel.rodriguez_perez@novartis.com?subject=UNIQUE)** -![Novartis Logo](./docs/source/_static/novartis_logo.png) +![Novartis Logo](https://github.com/Novartis/UNIQUE/raw/main/docs/source/_static/novartis_logo.png) From 9b87ae4e5ad99ad37ab1d940278500743fea6793 Mon Sep 17 00:00:00 2001 From: Tam Huynh Date: Thu, 26 Sep 2024 17:12:44 +0200 Subject: [PATCH 5/9] Update docs --- docs/source/conf.py | 49 +++++++++++++++++++++++------ docs/source/development/contacts.md | 2 ++ docs/source/indepth/error_models.md | 1 + docs/source/indepth/overview.md | 1 + docs/source/index.md | 24 +++++--------- docs/source/installation.md | 13 ++++++-- 6 files changed, 60 insertions(+), 30 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index 8cb83d9..b3a6f68 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -13,11 +13,31 @@ author = "Novartis Pharma AG" # author = 'Minh Tam Davide Huynh, Gaetano Scebba, Jessica Lanini, Raquel Rodriguez-Perez' + +## URLs +chemrxiv_doi = "https://doi.org/10.26434/chemrxiv-2024-fmbgk" +conda_url = "https://anaconda.org/conda-forge/unique-uncertainty" +docs_url = "https://opensource.nibr.com/UNIQUE/" +license_url = "https://opensource.org/licenses/BSD-3-Clause" +pypi_url = "https://pypi.org/project/unique-uncertainty" + +## Badges +chemrxiv_doi_badge_url = ( + "https://img.shields.io/badge/chemRxiv-10.26434%2Fchemrxiv--2024--fmbgk-yellow" +) +conda_version_badge_url = "https://img.shields.io/conda/vn/conda-forge/unique-uncertainty?color=green&label=conda-forge" +conda_downloads_badge_url = "https://img.shields.io/conda/dn/conda-forge/unique-uncertainty?color=yellowgreen&label=conda%20downloads" +github_build_badge_url = "https://github.com/Novartis/UNIQUE/actions/workflows/build.yml/badge.svg?branch=main" +github_docs_badge_url = "https://github.com/Novartis/UNIQUE/actions/workflows/docs.yml/badge.svg?branch=main" +license_badge_url = "https://img.shields.io/badge/License-BSD_3--Clause-red" pypi_version_badge_url = ( - "https://img.shields.io/pypi/v/unique-uncertainty?color=yellowgreen&label=PyPI" + "https://img.shields.io/pypi/v/unique-uncertainty?color=green&label=PyPI" +) +pypi_downloads_badge_url = "https://img.shields.io/pypi/dm/unique-uncertainty?color=yellowgreen&label=PyPI%20downloads" +python_versions_badge_url = ( + "https://img.shields.io/pypi/pyversions/unique-uncertainty?label=Python" ) -conda_version_badge_url = "https://img.shields.io/conda/vn/conda-forge/unique-uncertainty?color=yellowgreen&label=conda-forge" # -- General configuration --------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration @@ -54,12 +74,15 @@ myst_heading_anchors = 3 myst_substitutions = { - "conda_downloads_badge": "[![Conda downloads](https://img.shields.io/conda/dn/conda-forge/unique-uncertainty?color=brightgreen&label=conda%20downloads)](https://anaconda.org/conda-forge/unique-uncertainty)", - "conda_version_badge": "[![Conda version](https://img.shields.io/conda/vn/conda-forge/unique-uncertainty?color=yellowgreen&label=conda-forge)](https://anaconda.org/conda-forge/unique-uncertainty)", - "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?color=brightgreen&label=PyPI%20downloads)](https://pypi.org/project/unique-uncertainty)", - "pypi_version_badge": "[![PyPI version](https://img.shields.io/pypi/v/unique-uncertainty?color=yellowgreen&label=PyPI)](https://pypi.org/project/unique-uncertainty)", - "python_versions_badge": "![Python versions](https://img.shields.io/pypi/pyversions/unique-uncertainty?label=Python)", + "chemrxiv_badge": f"[![ChemRxiv DOI]({chemrxiv_doi_badge_url})]({chemrxiv_doi})", + "conda_downloads_badge": f"[![Conda downloads]({conda_downloads_badge_url})]({conda_url})", + "conda_version_badge": f"[![Conda version]({conda_version_badge_url})]({conda_url})", + "docs_badge": f"[![Documentation build]({github_docs_badge_url})]({docs_url})", + "license_badge": f"[![License]({license_badge_url})]({license_url})", + "pypi_build_badge": f"[![PyPI build]({github_build_badge_url})]({pypi_url})", + "pypi_downloads_badge": f"[![PyPI downloads]({pypi_downloads_badge_url})]({pypi_url})", + "pypi_version_badge": f"[![PyPI version]({pypi_version_badge_url})]({pypi_url})", + "python_versions_badge": f"![Python versions]({python_versions_badge_url})", } source_suffix = { @@ -144,16 +167,22 @@ "icon_links": [ { "name": "PyPI Version", - "url": "https://pypi.org/project/unique-uncertainty", + "url": pypi_url, "icon": pypi_version_badge_url, "type": "url", }, { "name": "Conda Version", - "url": "https://anaconda.org/conda-forge/unique-uncertainty", + "url": conda_url, "icon": conda_version_badge_url, "type": "url", }, + { + "name": "chemRxiv DOI", + "url": chemrxiv_doi, + "icon": chemrxiv_doi_badge_url, + "type": "url", + }, ], "logo": { "alt_text": "UNIQUE's Documentation - Home", diff --git a/docs/source/development/contacts.md b/docs/source/development/contacts.md index 06b1020..91caf54 100644 --- a/docs/source/development/contacts.md +++ b/docs/source/development/contacts.md @@ -10,6 +10,8 @@ For any questions or further details about the project, please get in touch with ## Cite Us +{{chemrxiv_badge}} + If you find `UNIQUE` helpful for your work and/or research, please consider citing our work: ```bibtex diff --git a/docs/source/indepth/error_models.md b/docs/source/indepth/error_models.md index bf68b8b..04005a6 100644 --- a/docs/source/indepth/error_models.md +++ b/docs/source/indepth/error_models.md @@ -3,6 +3,7 @@ myst: substitutions: error_model_schema: | :::{figure} ../_static/error_model_schema.png + :target: _images/error_model_schema.png :alt: UNIQUE Error Model Schema :align: center :class: dark-light diff --git a/docs/source/indepth/overview.md b/docs/source/indepth/overview.md index e85683d..dcacc6a 100644 --- a/docs/source/indepth/overview.md +++ b/docs/source/indepth/overview.md @@ -3,6 +3,7 @@ myst: substitutions: low_level_schema: | ```{figure} ../_static/schema_low_level.png + :target: _images/schema_low_level.png :alt: UNIQUE Low Level Schema :class: dark-light diff --git a/docs/source/index.md b/docs/source/index.md index c453da7..576dc83 100644 --- a/docs/source/index.md +++ b/docs/source/index.md @@ -18,24 +18,9 @@ myst: {{description}} ::: - # See: https://github.com/executablebooks/MyST-Parser/issues/279#issuecomment-752948379 - license_badge: | - :::{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 - ::: - 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 + :target: _images/schema_high_level.png :alt: UNIQUE High-Level Schema :align: center :class: dark-light @@ -46,7 +31,7 @@ myst: # Welcome to `UNIQUE`'s documentation! -{{python_versions_badge}} {{pypi_version_badge}} {{conda_version_badge}} {{license_badge}} {{article_badge}} {{docs_badge}} {{pypi_build_badge}} {{pypi_downloads_badge}} {{conda_downloads_badge}} +{{python_versions_badge}} {{pypi_version_badge}} {{conda_version_badge}} {{license_badge}} {{chemrxiv_badge}} {{pypi_downloads_badge}} {{conda_downloads_badge}} {{docs_badge}} {{pypi_build_badge}} {{logo_light}} {{logo_dark}} @@ -62,8 +47,13 @@ myst: {{high_level_schema}} + +Check out [Installation](./installation.md) to get started! + ## Cite Us +{{chemrxiv_badge}} + If you find `UNIQUE` helpful for your work and/or research, please consider citing our work: ```bibtex diff --git a/docs/source/installation.md b/docs/source/installation.md index 7266373..01aa661 100644 --- a/docs/source/installation.md +++ b/docs/source/installation.md @@ -12,7 +12,7 @@ myst: {{python_versions_badge}} {{pypi_version_badge}} {{conda_version_badge}} {{pypi_downloads_badge}} {{conda_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: +`UNIQUE` is currently compatible with Python 3.8 through 3.12.1. To install the latest release, run the following in a compatible environment of choice: ::::{tab-set} @@ -30,6 +30,13 @@ conda install -c conda-forge unique-uncertainty ``` ::: +:::{tab-item} `mamba` + +```bash +mamba install -c conda-forge unique-uncertainty +``` +::: + :::: :::{tip} @@ -38,7 +45,7 @@ To create a dedicated virtual environment for `UNIQUE` using `conda`/`mamba` wit ## For Developers - {{precommit}} {{codestyle}} + {{license_badge}} {{precommit}} {{codestyle}} :::{seealso} If you wish to work on the codebase itself, check first [how to best contribute to `UNIQUE`](./development/contributing.md). @@ -79,7 +86,7 @@ pip install -e . # Use `pip install -e .[dev]` to also install optional dependencies ``` -In this way, you will have access to the `UNIQUE` codebase and be able to make local modifications to the source code, within the `.conda/unique` environment that contains all the required dependencies. +In this way, you will have access to the `UNIQUE` codebase and be able to make local modifications to the source code, within the `./.conda/unique` local environment that contains all the required dependencies. Additionally, if you use Jupyter Notebooks, the `unique` kernel will be available in the "Select kernel" menu of the JupyterLab/JupyterNotebook UI. From b88e0be9446cb9f2028fc808dac7cc9a1b3320dc Mon Sep 17 00:00:00 2001 From: Tam Huynh Date: Thu, 26 Sep 2024 17:13:44 +0200 Subject: [PATCH 6/9] Bump version v0.2.1 > v0.2.2 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index e423aaf..fab3268 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -32,7 +32,7 @@ classifiers = [ "Topic :: Software Development :: Libraries", "Topic :: Software Development :: Libraries :: Python Modules", ] -version = "0.2.1" +version = "0.2.2" license = {file="LICENSE.md"} description = "UNIQUE is a Python package for benchmarking uncertainty estimation and quantification methods for Machine Learning models predictions." requires-python = ">=3.8,<=3.12.1" From 4dec6476cd52ab6ffd9747c2b51e0610045a81cf Mon Sep 17 00:00:00 2001 From: Tam Huynh Date: Mon, 30 Sep 2024 09:36:34 +0200 Subject: [PATCH 7/9] Update Makefile --- Makefile | 1 - 1 file changed, 1 deletion(-) diff --git a/Makefile b/Makefile index 1e3b0b4..cd5439e 100644 --- a/Makefile +++ b/Makefile @@ -30,7 +30,6 @@ print-info: # Install environment 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 From 36a7d57ff2c7728ca90386594c0828b83810e34e Mon Sep 17 00:00:00 2001 From: Tam Huynh Date: Mon, 30 Sep 2024 09:37:52 +0200 Subject: [PATCH 8/9] Update logging in pipeline.py --- unique/pipeline.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/unique/pipeline.py b/unique/pipeline.py index 8de29c1..dc79fa8 100644 --- a/unique/pipeline.py +++ b/unique/pipeline.py @@ -1113,7 +1113,7 @@ def evaluate_uq_metrics( ).reset_index(drop=True) if (i + 1) % np.floor(len(self.all_metrics) / 3) == 0: self.logger.info( - f"Evaluated {i + 1} UQ methods out of {len(self.all_metrics)}..." + f"Evaluated {i + 1} UQ methods out of {len(self.all_metrics)}{'...' if i+1 Date: Mon, 30 Sep 2024 10:27:18 +0200 Subject: [PATCH 9/9] Update logging in pipeline.py --- unique/pipeline.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/unique/pipeline.py b/unique/pipeline.py index dc79fa8..825305c 100644 --- a/unique/pipeline.py +++ b/unique/pipeline.py @@ -1115,6 +1115,10 @@ def evaluate_uq_metrics( self.logger.info( f"Evaluated {i + 1} UQ methods out of {len(self.all_metrics)}{'...' if i+1= len(self.all_metrics): + self.logger.info( + f"Evaluated {i + 1} UQ methods out of {len(self.all_metrics)}." + ) if self._bootstrap: best_methods = self._stat_analysis_bootstrapping(eval_dfs, eval_bs_dfs)