From 4534b5a97b78a100e59ba4b35bf42b80e08ce2ef Mon Sep 17 00:00:00 2001 From: "Khalil, Bola [JANBE]" Date: Mon, 8 Dec 2025 11:57:06 +0100 Subject: [PATCH 01/11] Update GitHub Pages dependencies: specify exact versions for improved stability --- .github/workflows/gh-pages.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/gh-pages.yml b/.github/workflows/gh-pages.yml index 2f57236..6111c61 100644 --- a/.github/workflows/gh-pages.yml +++ b/.github/workflows/gh-pages.yml @@ -38,7 +38,7 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install mkdocs-material mkdocstrings[python] mkdocs-git-revision-date-localized-plugin mkdocs-plugin-tags mike + pip install Markdown==3.10 Jinja2==3.1.6 pymdown-extensions==10.18 mkdocs==1.6.1 mkdocstrings==1.0.0 mkdocstrings-python==2.0.1 mike=2.1.3 mkdocs-autorefs==1.4.3 mkdocs-material==8.2.7 mkdocs-git-revision-date-localized-plugin==1.5.0 mkdocs-plugin-tags==1.0.2 - name: Build site run: mkdocs build --strict - name: Upload artifact From 26159761d137ce99d3fd7af01e4ad3e8b426fc62 Mon Sep 17 00:00:00 2001 From: Bola Khalil <49613273+bolak92@users.noreply.github.com> Date: Mon, 8 Dec 2025 12:06:49 +0100 Subject: [PATCH 02/11] Update .github/workflows/gh-pages.yml Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- .github/workflows/gh-pages.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/gh-pages.yml b/.github/workflows/gh-pages.yml index 6111c61..5670fea 100644 --- a/.github/workflows/gh-pages.yml +++ b/.github/workflows/gh-pages.yml @@ -38,7 +38,7 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install Markdown==3.10 Jinja2==3.1.6 pymdown-extensions==10.18 mkdocs==1.6.1 mkdocstrings==1.0.0 mkdocstrings-python==2.0.1 mike=2.1.3 mkdocs-autorefs==1.4.3 mkdocs-material==8.2.7 mkdocs-git-revision-date-localized-plugin==1.5.0 mkdocs-plugin-tags==1.0.2 + pip install Markdown==3.10 Jinja2==3.1.6 pymdown-extensions==10.18 mkdocs==1.6.1 mkdocstrings==1.0.0 mkdocstrings-python==2.0.1 mike=2.1.3 mkdocs-autorefs==1.4.3 mkdocs-material>=9.5.0 mkdocs-git-revision-date-localized-plugin==1.5.0 mkdocs-plugin-tags==1.0.2 - name: Build site run: mkdocs build --strict - name: Upload artifact From abd957ef158cf79d9626edba898dc69663499e39 Mon Sep 17 00:00:00 2001 From: "Khalil, Bola [JANBE]" Date: Mon, 8 Dec 2025 12:11:37 +0100 Subject: [PATCH 03/11] Fix typo in dependency installation command in gh-pages.yml --- .github/workflows/gh-pages.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/gh-pages.yml b/.github/workflows/gh-pages.yml index 5670fea..ad838ff 100644 --- a/.github/workflows/gh-pages.yml +++ b/.github/workflows/gh-pages.yml @@ -38,7 +38,7 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install Markdown==3.10 Jinja2==3.1.6 pymdown-extensions==10.18 mkdocs==1.6.1 mkdocstrings==1.0.0 mkdocstrings-python==2.0.1 mike=2.1.3 mkdocs-autorefs==1.4.3 mkdocs-material>=9.5.0 mkdocs-git-revision-date-localized-plugin==1.5.0 mkdocs-plugin-tags==1.0.2 + pip install Markdown==3.10 Jinja2==3.1.6 pymdown-extensions==10.18 mkdocs==1.6.1 mkdocstrings==1.0.0 mkdocstrings-python==2.0.1 mike==2.1.3 mkdocs-autorefs==1.4.3 mkdocs-material>=9.5.0 mkdocs-git-revision-date-localized-plugin==1.5.0 mkdocs-plugin-tags==1.0.2 - name: Build site run: mkdocs build --strict - name: Upload artifact From 929e897e916d3dfa79bf374cc95bac648d4a79d7 Mon Sep 17 00:00:00 2001 From: "Khalil, Bola [JANBE]" Date: Mon, 8 Dec 2025 12:17:55 +0100 Subject: [PATCH 04/11] Update dependency version for mkdocs-material in gh-pages.yml --- .github/workflows/gh-pages.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/gh-pages.yml b/.github/workflows/gh-pages.yml index ad838ff..b2b2b27 100644 --- a/.github/workflows/gh-pages.yml +++ b/.github/workflows/gh-pages.yml @@ -38,7 +38,7 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install Markdown==3.10 Jinja2==3.1.6 pymdown-extensions==10.18 mkdocs==1.6.1 mkdocstrings==1.0.0 mkdocstrings-python==2.0.1 mike==2.1.3 mkdocs-autorefs==1.4.3 mkdocs-material>=9.5.0 mkdocs-git-revision-date-localized-plugin==1.5.0 mkdocs-plugin-tags==1.0.2 + pip install Markdown==3.10 Jinja2==3.1.6 pymdown-extensions==10.18 mkdocs==1.6.1 mkdocstrings==1.0.0 mkdocstrings-python==2.0.1 mike==2.1.3 mkdocs-autorefs==1.4.3 mkdocs-material==8.2.7 mkdocs-git-revision-date-localized-plugin==1.5.0 mkdocs-plugin-tags==1.0.2 - name: Build site run: mkdocs build --strict - name: Upload artifact From 0a65675058ed720aa67a650cbde1fdb6b99a64b1 Mon Sep 17 00:00:00 2001 From: "Khalil, Bola [JANBE]" Date: Mon, 8 Dec 2025 12:52:10 +0100 Subject: [PATCH 05/11] Update dependency installation in gh-pages.yml: use version ranges for improved compatibility --- .github/workflows/gh-pages.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/gh-pages.yml b/.github/workflows/gh-pages.yml index b2b2b27..1cda05d 100644 --- a/.github/workflows/gh-pages.yml +++ b/.github/workflows/gh-pages.yml @@ -38,7 +38,9 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install Markdown==3.10 Jinja2==3.1.6 pymdown-extensions==10.18 mkdocs==1.6.1 mkdocstrings==1.0.0 mkdocstrings-python==2.0.1 mike==2.1.3 mkdocs-autorefs==1.4.3 mkdocs-material==8.2.7 mkdocs-git-revision-date-localized-plugin==1.5.0 mkdocs-plugin-tags==1.0.2 + pip install "mkdocs>=1.5" "mkdocs-material>=9.5" + pip install "mkdocstrings>=0.25" "mkdocstrings-python>=1.9" "mike>=2.0" "mkdocs-autorefs>=1.0" "mkdocs-git-revision-date-localized-plugin>=1.2" + # pip install Markdown==3.10 Jinja2==3.1.6 pymdown-extensions==10.18 mkdocs==1.6.1 mkdocstrings==1.0.0 mkdocstrings-python==2.0.1 mike==2.1.3 mkdocs-autorefs==1.4.3 mkdocs-material==8.2.7 mkdocs-git-revision-date-localized-plugin==1.5.0 mkdocs-plugin-tags==1.0.2 - name: Build site run: mkdocs build --strict - name: Upload artifact From e73e9b83e62b579c50ed955e8e7555446a78c2fc Mon Sep 17 00:00:00 2001 From: "Khalil, Bola [JANBE]" Date: Mon, 8 Dec 2025 12:56:36 +0100 Subject: [PATCH 06/11] Remove unnecessary condition for git-revision-date-localized in mkdocs.yml --- mkdocs.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/mkdocs.yml b/mkdocs.yml index a5cfdac..12e25de 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -82,7 +82,6 @@ plugins: show_submodules: true - mike - git-revision-date-localized: - enabled_if_env: CI fallback_to_build_date: true enable_creation_date: true enable_git_follow: false From 552d181b3f70fe930c4a241df652fce3a87bd083 Mon Sep 17 00:00:00 2001 From: "Khalil, Bola [JANBE]" Date: Mon, 8 Dec 2025 13:07:49 +0100 Subject: [PATCH 07/11] Enhance documentation: add navigation links to tags page in changelog, index, mind-map, and uqdd files --- docs/api/uqdd.md | 5 +++++ docs/changelog.md | 2 ++ docs/index.md | 3 +++ docs/reference/mind-map.md | 2 +- 4 files changed, 11 insertions(+), 1 deletion(-) diff --git a/docs/api/uqdd.md b/docs/api/uqdd.md index be6f56e..aa351c5 100644 --- a/docs/api/uqdd.md +++ b/docs/api/uqdd.md @@ -7,4 +7,9 @@ tags: # uqdd package +The top-level package overview is provided here. For detailed modules, see: +- [Core Utils](../api/uqdd-utils.md) +- [Data modules](../api/uqdd-data.md) +- [Model modules](../api/uqdd-models.md) + ::: uqdd diff --git a/docs/changelog.md b/docs/changelog.md index d957c31..20e88af 100644 --- a/docs/changelog.md +++ b/docs/changelog.md @@ -17,3 +17,5 @@ tags: - Configured GitHub Pages deployment workflow (`.github/workflows/gh-pages.yml`). - Enabled versioning support via `mike` plugin (optional). - Improved local strict builds by enabling `git-revision-date-localized` only on CI. + +See also the [tags](tags.md) page for topic-based navigation. diff --git a/docs/index.md b/docs/index.md index de519ad..12c333f 100644 --- a/docs/index.md +++ b/docs/index.md @@ -13,9 +13,12 @@ Welcome to the UQDD documentation. This site covers installation, data pipeline, [Combining Bayesian and Evidential Uncertainty Quantification for Improved Bioactivity Modeling](https://pubs.acs.org/doi/10.1021/acs.jcim.5c01597) ## Highlights + - Hybrid UQ models: EOE (Ensemble of Evidential) and EMC (Evidential MC Dropout) - Baselines: Deep ensembles, MC-Dropout, and probabilistic neural networks - Papyrus++ datasets for xC50 and Kx bioactivity endpoints - Comprehensive evaluation: performance, calibration, probabilistic scoring, decision utility +See the [tags](tags.md) page for topics across the documentation. + Use the top navigation to get started. diff --git a/docs/reference/mind-map.md b/docs/reference/mind-map.md index 9a64caa..62a4492 100644 --- a/docs/reference/mind-map.md +++ b/docs/reference/mind-map.md @@ -9,6 +9,6 @@ tags: The following mind map provides a high-level overview of the paper and the UQDD project: -![Mind Map](assets/MindMap.png) +![Mind Map](../assets/MindMap.png) For details, refer to the specific sections throughout the documentation. From 409df98065e50580de29e6df670333b067123f8a Mon Sep 17 00:00:00 2001 From: "Khalil, Bola [JANBE]" Date: Mon, 8 Dec 2025 13:11:18 +0100 Subject: [PATCH 08/11] Update mkdocs.yml: disable showing submodules in the documentation --- mkdocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mkdocs.yml b/mkdocs.yml index 12e25de..bf5cce5 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -79,7 +79,7 @@ plugins: show_root_heading: true show_signature: true heading_level: 2 - show_submodules: true + show_submodules: false - mike - git-revision-date-localized: fallback_to_build_date: true From 710ea397a8078a1616946c5b7b4746e7f2290276 Mon Sep 17 00:00:00 2001 From: "Khalil, Bola [JANBE]" Date: Mon, 8 Dec 2025 13:32:50 +0100 Subject: [PATCH 09/11] Update gh-pages.yml and mkdocs.yml: adjust fetch depth and modify mkdocstrings setup commands --- .github/workflows/gh-pages.yml | 2 ++ mkdocs.yml | 5 ++++- 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/.github/workflows/gh-pages.yml b/.github/workflows/gh-pages.yml index 1cda05d..61e27a6 100644 --- a/.github/workflows/gh-pages.yml +++ b/.github/workflows/gh-pages.yml @@ -27,6 +27,8 @@ jobs: steps: - name: Checkout uses: actions/checkout@v4 + with: + fetch-depth: 0 - name: Setup Python uses: actions/setup-python@v5 with: diff --git a/mkdocs.yml b/mkdocs.yml index bf5cce5..a2579bb 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -66,7 +66,10 @@ plugins: - mkdocstrings: handlers: python: - paths: ["uqdd"] + setup_commands: + - import sys + - sys.path.append('.') + paths: ['.'] options: show_source: false docstring_style: numpy From 7d21feb60b5cdddcd4031728b8bbfd25eec9a5ed Mon Sep 17 00:00:00 2001 From: "Khalil, Bola [JANBE]" Date: Mon, 8 Dec 2025 13:36:45 +0100 Subject: [PATCH 10/11] Update gh-pages.yml and mkdocs.yml: set PYTHONPATH for build environment and remove unnecessary setup commands --- .github/workflows/gh-pages.yml | 2 ++ mkdocs.yml | 3 --- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/workflows/gh-pages.yml b/.github/workflows/gh-pages.yml index 61e27a6..b5c92f4 100644 --- a/.github/workflows/gh-pages.yml +++ b/.github/workflows/gh-pages.yml @@ -44,6 +44,8 @@ jobs: pip install "mkdocstrings>=0.25" "mkdocstrings-python>=1.9" "mike>=2.0" "mkdocs-autorefs>=1.0" "mkdocs-git-revision-date-localized-plugin>=1.2" # pip install Markdown==3.10 Jinja2==3.1.6 pymdown-extensions==10.18 mkdocs==1.6.1 mkdocstrings==1.0.0 mkdocstrings-python==2.0.1 mike==2.1.3 mkdocs-autorefs==1.4.3 mkdocs-material==8.2.7 mkdocs-git-revision-date-localized-plugin==1.5.0 mkdocs-plugin-tags==1.0.2 - name: Build site + env: + PYTHONPATH: ${{ github.workspace }} run: mkdocs build --strict - name: Upload artifact uses: actions/upload-pages-artifact@v3 diff --git a/mkdocs.yml b/mkdocs.yml index a2579bb..9bc23e3 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -66,9 +66,6 @@ plugins: - mkdocstrings: handlers: python: - setup_commands: - - import sys - - sys.path.append('.') paths: ['.'] options: show_source: false From af4d97cf47905d319337d108d50279c84b679628 Mon Sep 17 00:00:00 2001 From: "Khalil, Bola [JANBE]" Date: Mon, 8 Dec 2025 13:40:01 +0100 Subject: [PATCH 11/11] Refactor pnn.py: remove unused aleatoric uncertainty estimation code --- uqdd/models/pnn.py | 30 ------------------------------ 1 file changed, 30 deletions(-) diff --git a/uqdd/models/pnn.py b/uqdd/models/pnn.py index a6e096f..1a49e4e 100644 --- a/uqdd/models/pnn.py +++ b/uqdd/models/pnn.py @@ -259,9 +259,6 @@ def run_pnn(config: Optional[dict] = None) -> nn.Module: # uq: bool = False config : Optional[dict], optional Configuration dictionary for model training, by default None. - uq : bool - Whether to use aleatoric uncertainty estimation, by default - Returns ------- nn.Module @@ -274,33 +271,6 @@ def run_pnn(config: Optional[dict] = None) -> nn.Module: # uq: bool = False logger=LOGGER, ) - # if uq: - # dataloaders = get_dataloader(config, device=DEVICE, logger=LOGGER) - # preds, labels, alea_vars = predict( - # best_model, dataloaders["test"], device=DEVICE - # ) - # # Then comes the predict metrics part - # metrics, plots, uct_logger = evaluate_predictions( - # config, preds, labels, alea_vars, "pnn", LOGGER - # ) - # # RECALIBRATION # Get Calibration / Validation Set - # preds_val, labels_val, alea_vars_val = predict( - # best_model, dataloaders["val"], device=DEVICE - # ) - # iso_recal_model = recalibrate_model( - # preds_val, - # labels_val, - # alea_vars_val, - # preds, - # labels, - # alea_vars, - # config=config, - # uct_logger=uct_logger, - # ) - # uct_logger.wandb_log() - # wandb.finish() - # return best_model, iso_recal_model, metrics, plots - return best_model