From f7a9cb09b7f9f10e41c3666402fbe89f12ddbf65 Mon Sep 17 00:00:00 2001 From: Kai Sommer <89587022+SommerKai@users.noreply.github.com> Date: Tue, 11 Aug 2026 17:07:50 +0200 Subject: [PATCH 01/12] docs: Add initial configuration for Zensical documentation site - Created zensical.toml to define project metadata and navigation structure. - Configured theme features including palette toggle for light and dark modes. - Set up validation for links and included plugins for search and markdown execution. --- .github/skills/update-docs/SKILL.md | 4 +- .github/workflows/workflow.yml | 13 +- .gitignore | 4 +- .pre-commit-config.yaml | 4 +- CLAUDE.md | 2 +- {mkdocs/docs => docs}/Changelog.md | 0 {mkdocs/docs => docs}/chemistry.md | 0 {mkdocs/docs => docs}/development/dev.md | 6 +- .../development/pr_approval_guidelines.md | 0 {mkdocs/docs => docs}/examples.md | 0 {mkdocs/docs => docs}/feature_generation.md | 0 docs/index.md | 1 + {mkdocs/docs => docs}/mother/configurator.md | 0 {mkdocs/docs => docs}/mother/models.md | 0 {mkdocs/docs => docs}/mother/overview.md | 0 {mkdocs/docs => docs}/standardization.md | 0 mkdocs/docs/index.md | 1 - mkdocs/mkdocs.yml | 77 --- pyproject.toml | 13 +- scripts/check_docs_python_fences.py | 6 +- uv.lock | 496 ++---------------- zensical.toml | 57 ++ 22 files changed, 121 insertions(+), 563 deletions(-) rename {mkdocs/docs => docs}/Changelog.md (100%) rename {mkdocs/docs => docs}/chemistry.md (100%) rename {mkdocs/docs => docs}/development/dev.md (98%) rename {mkdocs/docs => docs}/development/pr_approval_guidelines.md (100%) rename {mkdocs/docs => docs}/examples.md (100%) rename {mkdocs/docs => docs}/feature_generation.md (100%) create mode 120000 docs/index.md rename {mkdocs/docs => docs}/mother/configurator.md (100%) rename {mkdocs/docs => docs}/mother/models.md (100%) rename {mkdocs/docs => docs}/mother/overview.md (100%) rename {mkdocs/docs => docs}/standardization.md (100%) delete mode 120000 mkdocs/docs/index.md delete mode 100644 mkdocs/mkdocs.yml create mode 100644 zensical.toml diff --git a/.github/skills/update-docs/SKILL.md b/.github/skills/update-docs/SKILL.md index e28f7e0..c4e11cc 100644 --- a/.github/skills/update-docs/SKILL.md +++ b/.github/skills/update-docs/SKILL.md @@ -26,12 +26,12 @@ description: "Update the documentation and changelog, and reconcile GitHub issue 8. Determine whether changelog entries are managed by CI (for example, `python-semantic-release`). - Check release automation config first (for example, `[tool.semantic_release]` in `pyproject.toml` and release workflow files) to identify the authoritative changelog file path and casing. - If semantic-release (or equivalent) is configured to write changelog entries, **do not manually append a release section**. Instead, verify that the generated/release-bound changelog content is consistent with steps 2-7 and only make non-conflicting adjustments explicitly requested by the user. - - If no automation manages changelog entries, add the changelog to `mkdocs/docs/Changelog.md` (note the path/casing). Follow the existing format. If the file is empty or does not exist, use the Keep a Changelog format (https://keepachangelog.com) with sections: Added, Changed, Deprecated, Removed, Fixed, Security. Include the version number and release date at the top of the new section, and keep the issue/PR links added in step 5. + - If no automation manages changelog entries, add the changelog to `docs/Changelog.md` (note the path/casing). Follow the existing format. If the file is empty or does not exist, use the Keep a Changelog format (https://keepachangelog.com) with sections: Added, Changed, Deprecated, Removed, Fixed, Security. Include the version number and release date at the top of the new section, and keep the issue/PR links added in step 5. 9. Reconcile GitHub issues and milestones per the user's approval in step 7 (skip this step entirely if the GitHub CLI was unavailable in step 4). - Assign approved issues and merged PRs that lack a milestone to the release milestone: `gh issue edit --milestone ""` / `gh pr edit <N> --milestone "<title>"`. - Close each approved open issue with a comment linking the release: `gh issue close <N> --comment "Resolved in <version> release."`. Note that issues referenced with a closing keyword in a PR merged to the default branch are closed automatically by GitHub — do not double-close; only close issues that are still open after the merge. - If the user approved creating a milestone, create it (`gh api repos/:owner/:repo/milestones -f title="<title>" -f state="open"`) and assign the release's issues/PRs to it before closing. - Once every issue in the release milestone is closed, close the milestone: find its number via `gh api repos/:owner/:repo/milestones --jq '.[] | select(.title=="<title>") | .number'` then `gh api repos/:owner/:repo/milestones/<number> -X PATCH -f state="closed"`. - Report the outcome of each action (issues closed, milestone closed/created, anything skipped) back to the user. -10. Now, review the documentation throughout the `mkdocs/docs` folder to ensure any version-specific information is updated for the new version. This includes updating version numbers, dates, and any other relevant details. In case new features are implemented, make sure to add documentation for those features as well into the appropriate sections. In case no sections exists, please create a new section for the new feature and add the documentation there. Make sure to format it properly and include any relevant examples or usage instructions. +10. Now, review the documentation throughout the `docs` folder to ensure any version-specific information is updated for the new version. This includes updating version numbers, dates, and any other relevant details. In case new features are implemented, make sure to add documentation for those features as well into the appropriate sections. In case no sections exists, please create a new section for the new feature and add the documentation there. Make sure to format it properly and include any relevant examples or usage instructions. 11. After updating the documentation, commit the changes to the repository with a clear commit message indicating that the documentation (and changelog verification/update mode) has been completed for the new release. If changelog sections are CI-generated, avoid committing manual duplicate release-note blocks unless explicitly requested. For example, "Update documentation and changelog workflow alignment for version X.Y.Z release." Reference the reconciled issues in the commit body where appropriate (e.g., `Refs #42, #43`). Commit on the current branch. Do not push or create a pull request unless explicitly instructed. If the repository requires pull requests for the main branch, note this to the user and stop. diff --git a/.github/workflows/workflow.yml b/.github/workflows/workflow.yml index bee2a97..57a340c 100644 --- a/.github/workflows/workflow.yml +++ b/.github/workflows/workflow.yml @@ -240,8 +240,8 @@ jobs: with: packages-dir: dist/ - build-mkdocs: - name: Build MkDocs + build-docs: + name: Build Docs runs-on: ubuntu-latest permissions: contents: read @@ -267,17 +267,16 @@ jobs: install-args: "--group docs" - name: Build docs - working-directory: mkdocs - run: uv run mkdocs build + run: uv run zensical build - name: Upload GitHub Pages artifact uses: actions/upload-pages-artifact@v4 with: - path: mkdocs/site/ + path: site/ - deploy-mkdocs: + deploy-docs: name: Publish Docs - needs: build-mkdocs + needs: build-docs if: github.event_name != 'pull_request' && github.ref == 'refs/heads/main' runs-on: ubuntu-latest permissions: diff --git a/.gitignore b/.gitignore index 25505d2..401ba8e 100644 --- a/.gitignore +++ b/.gitignore @@ -44,8 +44,8 @@ ENV/ env.bak/ venv.bak/ -# mkdocs documentation -mkdocs/site +# zensical documentation +site/ # mypy .mypy_cache/ diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index ea9dd6a..a537db9 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,5 +1,5 @@ fail_fast: false -exclude: ^(docs/|examples/|tests/) +exclude: ^(examples/|tests/) repos: - repo: https://github.com/astral-sh/uv-pre-commit rev: "0.11.2" @@ -71,7 +71,7 @@ repos: entry: uv run poe docs-python-fences pass_filenames: false language: system - files: ^mkdocs/docs/.*\.md$ + files: ^docs/.*\.md$ - repo: https://github.com/nbQA-dev/nbQA rev: 1.9.1 hooks: diff --git a/CLAUDE.md b/CLAUDE.md index a3de3ee..229b7de 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -20,7 +20,7 @@ Uses `uv` + `poe` (poethepoet). Run tasks with `uv run poe <task>`. - **Style (check)**: `uv run poe check-style` = `check-sort-imports` (isort, black profile) + `check-format` (ruff format). Apply with `uv run poe style`. - **Static analysis**: `uv run poe check-static-analysis` = `check-lint` (ruff, E+F) + `check-types` (mypy on `src`, strict: `disallow_untyped_defs`). - **Lint autofix**: `uv run poe lint`. -- **Docs**: `uv run poe docs` (build) / `uv run poe serve-docs` (mkdocs serve from `mkdocs/`). +- **Docs**: `uv run poe docs` (build) / `uv run poe serve-docs` (zensical serve; config `zensical.toml` at repo root, content in `docs/`). - **Pre-commit**: `uv run poe install-hook` then `uv run poe check-hook`. Line length: ruff 120, pylint 100. Note: `CONTRIBUTING.md` references some task names (`poe test`, `test-acceptance`, `check-docs`) that do not exist in `pyproject.toml` — use the verified names above. diff --git a/mkdocs/docs/Changelog.md b/docs/Changelog.md similarity index 100% rename from mkdocs/docs/Changelog.md rename to docs/Changelog.md diff --git a/mkdocs/docs/chemistry.md b/docs/chemistry.md similarity index 100% rename from mkdocs/docs/chemistry.md rename to docs/chemistry.md diff --git a/mkdocs/docs/development/dev.md b/docs/development/dev.md similarity index 98% rename from mkdocs/docs/development/dev.md rename to docs/development/dev.md index 0fed58d..c54e025 100644 --- a/mkdocs/docs/development/dev.md +++ b/docs/development/dev.md @@ -55,7 +55,7 @@ Dependency groups are development dependencies that are NOT published with the p | Group | Description | Installation | |-------|-------------|--------------| | `examples` | Dependencies for example notebooks (polaris-lib, shap) | `uv sync --group examples` | -| `docs` | Documentation building tools (mkdocs, etc.) | `uv sync --group docs` | +| `docs` | Documentation building tools (zensical, mkdocstrings, etc.) | `uv sync --group docs` | | `test_duration` | Test performance analysis (pytest-html, pytest-xdist) | `uv sync --group test_duration` | **Install multiple groups:** @@ -259,7 +259,7 @@ upload_to_vcs_release = true [tool.semantic_release.changelog] mode = "update" insertion_flag = "..\n All versions below are listed in reverse chronological order" -changelog_file = "mkdocs/docs/Changelog.md" +changelog_file = "docs/Changelog.md" output_format = "md" ``` @@ -269,7 +269,7 @@ Releases are automatically triggered when commits are pushed to the `main` branc 1. **Analysis**: PSR analyzes commit messages since the last release 2. **Version Calculation**: Determines the next version based on commit types -3. **Changelog Generation**: Updates `mkdocs/docs/Changelog.md` with new changes +3. **Changelog Generation**: Updates `docs/Changelog.md` with new changes 4. **Version Bump**: Updates version in `pyproject.toml` 5. **Build**: Creates distribution packages using uv 6. **Release**: Creates a GitHub release with built artifacts diff --git a/mkdocs/docs/development/pr_approval_guidelines.md b/docs/development/pr_approval_guidelines.md similarity index 100% rename from mkdocs/docs/development/pr_approval_guidelines.md rename to docs/development/pr_approval_guidelines.md diff --git a/mkdocs/docs/examples.md b/docs/examples.md similarity index 100% rename from mkdocs/docs/examples.md rename to docs/examples.md diff --git a/mkdocs/docs/feature_generation.md b/docs/feature_generation.md similarity index 100% rename from mkdocs/docs/feature_generation.md rename to docs/feature_generation.md diff --git a/docs/index.md b/docs/index.md new file mode 120000 index 0000000..32d46ee --- /dev/null +++ b/docs/index.md @@ -0,0 +1 @@ +../README.md \ No newline at end of file diff --git a/mkdocs/docs/mother/configurator.md b/docs/mother/configurator.md similarity index 100% rename from mkdocs/docs/mother/configurator.md rename to docs/mother/configurator.md diff --git a/mkdocs/docs/mother/models.md b/docs/mother/models.md similarity index 100% rename from mkdocs/docs/mother/models.md rename to docs/mother/models.md diff --git a/mkdocs/docs/mother/overview.md b/docs/mother/overview.md similarity index 100% rename from mkdocs/docs/mother/overview.md rename to docs/mother/overview.md diff --git a/mkdocs/docs/standardization.md b/docs/standardization.md similarity index 100% rename from mkdocs/docs/standardization.md rename to docs/standardization.md diff --git a/mkdocs/docs/index.md b/mkdocs/docs/index.md deleted file mode 120000 index fe84005..0000000 --- a/mkdocs/docs/index.md +++ /dev/null @@ -1 +0,0 @@ -../../README.md \ No newline at end of file diff --git a/mkdocs/mkdocs.yml b/mkdocs/mkdocs.yml deleted file mode 100644 index cd4d80d..0000000 --- a/mkdocs/mkdocs.yml +++ /dev/null @@ -1,77 +0,0 @@ -site_name: Mother for Machine Learning -site_url: https://bayer-group.github.io/MotherML/ -theme: - name: "material" - palette: - primary: navy - icon: - repo: fontawesome/brands/github - features: - - content.code.select - - content.code.copy - - content.code.annotate - - content.tabs.link - -repo_url: https://github.com/Bayer-Group/MotherML -repo_name: MotherML - -markdown_extensions: - - admonition - - pymdownx.highlight: - auto_title: true - anchor_linenums: true - line_spans: __span - pygments_lang_class: true - - pymdownx.inlinehilite - - pymdownx.superfences - - pymdownx.snippets - - pymdownx.tabbed: - alternate_style: true - - attr_list - - pymdownx.emoji: - emoji_index: !!python/name:material.extensions.emoji.twemoji - emoji_generator: !!python/name:material.extensions.emoji.to_svg - -validation: - links: - absolute_links: relative_to_docs - anchors: warn - unrecognized_links: warn - -plugins: - - search - - markdown-exec - - mkdocstrings: - handlers: - python: - paths: [..] - - git-revision-date-localized: - fallback_to_build_date: true - - git-authors: - show_contribution: true - sort_authors_by: name - show_line_count: true - count_empty_lines: true - fallback_to_empty: false - # exclude: - # - index.md - enabled: true - - include-markdown - - mkdocs-jupyter - -nav: - - Home: index.md - - Development: - - General Development: development/dev.md - - PR Approval Process: development/pr_approval_guidelines.md - - Usage: - - Overview: mother/overview.md - - Configurator: mother/configurator.md - - Specifics: - - Models: mother/models.md - - Tutorials: examples.md - - Basic Cheminformatics: - - Introduction: chemistry.md - - Molecule Standardisation: standardization.md - - Feature Generation: feature_generation.md - - Changelog: Changelog.md diff --git a/pyproject.toml b/pyproject.toml index d79f75e..0861c19 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -103,14 +103,9 @@ examples = [ "shap>=0.47.2,<0.48", ] docs = [ - "mkdocs", - "mkdocs-git-revision-date-localized-plugin", - "mkdocs-include-markdown-plugin", - "mkdocs-material", + "zensical", "mkdocstrings[python]", "markdown-exec[ansi]>=1.7.0,<2", - "mkdocs-jupyter>=0.25.1,<0.26", - "mkdocs-git-authors-plugin>=0.9.2,<0.10", ] test_duration = [ "pytest-html>=4.0.2,<5", @@ -277,7 +272,7 @@ mode = "update" insertion_flag = "..\n All versions below are listed in reverse chronological order" [tool.semantic_release.changelog.default_templates] -changelog_file = "mkdocs/docs/Changelog.md" +changelog_file = "docs/Changelog.md" output_format = "md" [tool.semantic_release.branches.main] @@ -342,7 +337,7 @@ dist-test = [ "build", { shell = "cd dist && ../test/test-dist.bash `uv run --with tomli python -c \"import tomli; print('mother_ml-' + tomli.load(open('../pyproject.toml','rb'))['project']['version'] + '-py3-none-any.whl')\"`", help = "check build package in its own environment" }, ] -docs = { shell = "cd mkdocs; mkdocs build", help = "Build documentation" } +docs = { cmd = "zensical build", help = "Build documentation" } docs-python-fences = { cmd = "python scripts/check_docs_python_fences.py", help = "Execute python fenced code blocks in docs markdown" } format = { cmd = "ruff format src test examples", help = "Perform code style format" } install-hook = "pre-commit install" @@ -351,7 +346,7 @@ serve-coverage = [ "coverage", { shell = "coverage html -d coverage-html && cd coverage-html; python -m http.server --bind 127.0.0.1", help = "Generate coverage html report" }, ] -serve-docs = { shell = "cd mkdocs; JUPYTER_PLATFORM_DIRS=1 mkdocs serve", help = "Serve project html documentation" } +serve-docs = { cmd = "zensical serve", help = "Serve project html documentation" } sort-imports = { cmd = "isort . --sg=old --profile black", help = "apply import sort ordering" } style = ["sort-imports", "format"] test-unit = { shell = "pytest test -m 'not slow and not serial' -n auto && pytest test -m 'serial and not slow' -n 0" } diff --git a/scripts/check_docs_python_fences.py b/scripts/check_docs_python_fences.py index 789d94f..6a49a3d 100644 --- a/scripts/check_docs_python_fences.py +++ b/scripts/check_docs_python_fences.py @@ -1,7 +1,7 @@ #!/usr/bin/env python3 """Validate executable Python code fences in docs markdown files. -This script scans mkdocs/docs/**/*.md for fenced blocks with the `python` language, +This script scans docs/**/*.md for fenced blocks with the `python` language, executes them sequentially per file, and fails if any block raises an exception. 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https://github.com/astral-sh/uv-pre-commit rev: "0.11.2" From 3a18f47863eb5b56b41a5a5a74b11893b8e13dd5 Mon Sep 17 00:00:00 2001 From: Kai Sommer <89587022+SommerKai@users.noreply.github.com> Date: Tue, 18 Aug 2026 11:54:50 +0200 Subject: [PATCH 04/12] docs: Add markdown extensions and update mkdocstrings configuration - Introduced several markdown extensions for enhanced functionality, including attr_list, snippets, admonition, highlight, superfences, tabbed, and emoji support. - Configured mkdocstrings for Python with a specified inventory URL, updated paths, and set options for docstring style, inherited members, and source visibility. --- README.md | 7 +- docs/mother/configurator.md | 4 +- docs/mother/models.md | 4 +- pyproject.toml | 2 +- uv.lock | 648 ++++++++++++++++++------------------ zensical.toml | 14 + 6 files changed, 353 insertions(+), 326 deletions(-) diff --git a/README.md b/README.md index b9f786e..c6f8bed 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ Mother is a machine-learning framework for predicting properties from chemical m - 🔬 **SMILES** preprocessing - 💾 Generating of **feature vectors** from molecules - 📈 Grouping and cross-validation, based on chemical similarity -- 💻 Model Training: Standard catboost models, and feature selection methods +- 💻 Model Training: Standard models like catboost, lasso, or random forest, and custom models (e.g.: TabPFN), and feature selection methods - 🚴 Training, cross-validation, and hyperparameter optimization of machine-learning models - 🌀 Handling Gene expression data from transcriptomics experiments including different normalisation techniques - ✨ ~~Explainability analysis with *SHAP*~~ (Currently not supported, will be added in a later release) @@ -16,7 +16,7 @@ Mother is a machine-learning framework for predicting properties from chemical m Mother provides methods for each of these steps in the form of sklearn transformer objects. By that, all methods are designed to be easily accessible and usable in a modular way. The methods can be combined to ML workflows with [sklearn pipelines, column transformers, and feature unions](https://scikit-learn.org/dev/modules/compose.html). -All methods can be used as sklearn `transformer` or `estimator`. Combination with other methods, or own methods and models (e.g. using mother preprocessing with other model) is therefore straightforward. To be as compatible as possible, every transformer can be constructed using a dictionary containing the required parameters. However, to provide some convenience to the users, a settings class [MotherSettings](https://github.com/Bayer-Group/MotherML/blob/main/src/mother/settings.py). This class can be used to store all relevant settings for your ML project. +All methods can be used as sklearn `transformer` or `estimator`. Combination with other methods, or own methods and models (e.g. using mother preprocessing with other model) is therefore straightforward. To be as compatible as possible, every transformer can be constructed using a dictionary containing the required parameters. However, to provide some convenience to the users, a settings class [MotherSettings](https://github.com/Bayer-Group/MotherML/blob/main/src/mother/settings.py) is provided. This class can be used to store all relevant settings for your ML project. ## Usage @@ -166,6 +166,9 @@ model.fit(features, targets) Here, we use the extended sklearn pipeline `PipelineWithHyperparameterRooting` for some additional methods for hyperparameter tuning. +!!! note + + Without feature selection, this is simplified: ```python diff --git a/docs/mother/configurator.md b/docs/mother/configurator.md index d98678c..0c7b9ee 100644 --- a/docs/mother/configurator.md +++ b/docs/mother/configurator.md @@ -116,7 +116,5 @@ To dump the default configuration as yaml file and to be able to modify it to yo In the following every highlighted subsection represents the settings for a different transformer. A specialty is the `model` section which contains also the information for feature selection which can be used to create a more complex feature selection pipeline. For example, `pipeline` contains all the required parameters to configure a scikit learn pipeline. Thus, parameters can be set once and reused at different stages of your pipeline. ~~~yaml hl_lines="8 15 18 31 36 45" title="mother/data/mother_config.yaml" -{% - include "../../../src/mother/data/mother_config.yaml" -%} +--8<-- "src/mother/data/mother_config.yaml" ~~~ diff --git a/docs/mother/models.md b/docs/mother/models.md index dcc751d..822ffe8 100644 --- a/docs/mother/models.md +++ b/docs/mother/models.md @@ -130,9 +130,7 @@ To provide your own model and make this step as easy as possible, we provide the Your own model just has to inherit from that class and implement the required functions that provide the hyperparameters you want to tune. For example, see the implementation of the Lasso model. Since lasso basically has one parameter to be tuned, the implementation is fairly easy. ~~~python title="Lasso with Hyperparameter Tuning" -{% - include "../../../src/mother/ml/models/m_lasso.py" -%} +--8<-- "src/mother/ml/models/m_lasso.py" ~~~ ## Registering your model using MotherModelRegistry diff --git a/pyproject.toml b/pyproject.toml index 0861c19..c09b7ad 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -105,7 +105,7 @@ examples = [ docs = [ "zensical", "mkdocstrings[python]", - "markdown-exec[ansi]>=1.7.0,<2", + "markdown-exec[ansi]>=1.7.0,<2" ] test_duration = [ "pytest-html>=4.0.2,<5", diff --git a/uv.lock b/uv.lock index 4f09ff7..ac32b18 100644 --- a/uv.lock +++ b/uv.lock @@ -341,15 +341,6 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/fb/95/adcb68e20c34162e9135f370d6e31737719c2b6f94bc953fe7ed1f10fe21/authlib-1.7.2-py2.py3-none-any.whl", hash = "sha256:3e1faedc9d87e7d56a164eca3ccb6ace0d61b94abe83e92242f8dc8bba9b4a9f", size = 259548, upload-time = 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a/zensical.toml +++ b/zensical.toml @@ -53,5 +53,19 @@ not_found = "warn" search = {} "markdown-exec" = {} +[project.markdown_extensions] +attr_list = {} +pymdownx.snippets = { base_path = ["."], check_paths = true } +admonition = {} +pymdownx.highlight = {auto_title = true, anchor_linenums = true, line_spans = "__span", pygments_lang_class = true} +pymdownx.superfences = {} +pymdownx.tabbed = {alternate_style = true} +pymdownx.emoji.emoji_generator = "zensical.extensions.emoji.to_svg" +pymdownx.emoji.emoji_index = "zensical.extensions.emoji.twemoji" + [project.plugins.mkdocstrings.handlers.python] +inventories = ["https://docs.python.org/3/objects.inv"] paths = ["src"] +options.docstring_style = "google" +options.inherited_members = true +options.show_source = false From c396ccf28a85f921807e95506868758e24561a8a Mon Sep 17 00:00:00 2001 From: Kai Sommer <89587022+SommerKai@users.noreply.github.com> Date: Tue, 18 Aug 2026 12:04:27 +0200 Subject: [PATCH 05/12] docs: Update README to include 'Why Mother?" section --- README.md | 20 +++++++++++++------- 1 file changed, 13 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index c6f8bed..3e4a61b 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,6 @@ -# Mother-ML +# Mother-ML - A ML framework that takes care. -A ML framework that takes care. - -Mother is a machine-learning framework for predicting properties from chemical molecules. The major features are: +Mother is a machine-learning framework for predicting properties from mainly chemical molecules. The major features are: - 🔬 **SMILES** preprocessing - 💾 Generating of **feature vectors** from molecules @@ -18,6 +16,17 @@ Mother provides methods for each of these steps in the form of sklearn transform All methods can be used as sklearn `transformer` or `estimator`. Combination with other methods, or own methods and models (e.g. using mother preprocessing with other model) is therefore straightforward. To be as compatible as possible, every transformer can be constructed using a dictionary containing the required parameters. However, to provide some convenience to the users, a settings class [MotherSettings](https://github.com/Bayer-Group/MotherML/blob/main/src/mother/settings.py) is provided. This class can be used to store all relevant settings for your ML project. +## Why Mother? + +Mother keeps the parts of a molecular ML workflow connected without requiring you to leave the scikit-learn ecosystem. + +- **Tune an entire workflow from one place.** Mother model wrappers define their own Optuna search spaces, and `PipelineWithHyperparameterRooting`, `ColumnTransformerWithHyperparameterRooting`, and `FeatureUnionWithHyperparameterRooting` collect them across nested steps using familiar `step__parameter` names. You can therefore tune preprocessing, feature selection, and the final estimator together while retaining scikit-learn composition. +- **Exchange compatible transformers and estimators.** Preprocessing, molecular feature generation, feature selection, cross-validation grouping, and models follow scikit-learn's estimator and transformer interfaces. Mother components work in `Pipeline`, `ColumnTransformer`, and `FeatureUnion`, and can be combined with your own scikit-learn components. +- **Use consistent, analysis-ready outputs.** Components preserve pandas-friendly tabular data where appropriate. `predict_uncertainty(...)` exposes a common prediction and uncertainty schema across model backends, while `mother_cv(...)` returns fold-level predictions together with evaluation metadata for straightforward comparison and downstream analysis. +- **Evaluate chemical models more realistically.** Chemistry-aware grouping, including Tanimoto-similarity groups, makes it practical to use group-aware splits that better test generalisation to dissimilar compounds. +- **Choose models without rewriting the workflow.** The model registry discovers integrated model wrappers and presents a common interface for CatBoost, random forest, lasso, TabPFN when installed, and compatible custom models. +- **Make workflows reproducible and configurable.** `MotherSettings` keeps input, preprocessing, feature generation, cross-validation, model, and tuning configuration in one validated object that can be loaded from or written to YAML. + ## Usage A basic example can be found in the [example regression notebook](https://github.com/Bayer-Group/MotherML/blob/main/examples/notebooks/02_regression/01_basic_regression.ipynb). Other @@ -166,9 +175,6 @@ model.fit(features, targets) Here, we use the extended sklearn pipeline `PipelineWithHyperparameterRooting` for some additional methods for hyperparameter tuning. -!!! note - - Without feature selection, this is simplified: ```python From 54b61a5e791a249752936e7831200a97a3b1fd1d Mon Sep 17 00:00:00 2001 From: Kai Sommer <89587022+SommerKai@users.noreply.github.com> Date: Fri, 21 Aug 2026 08:25:09 +0200 Subject: [PATCH 06/12] docs: Add changelog file configuration to pyproject.toml --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index c09b7ad..5f2e61d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -269,6 +269,7 @@ exclude_commit_patterns = [ '''Initial [Cc]ommit.*''', ] mode = "update" +changelog_file = "docs/Changelog.md" insertion_flag = "..\n All versions below are listed in reverse chronological order" [tool.semantic_release.changelog.default_templates] From 1d59e3b0b2378f997a1df5eac52edbbc1bb87775 Mon Sep 17 00:00:00 2001 From: Kai Sommer <89587022+SommerKai@users.noreply.github.com> Date: Fri, 21 Aug 2026 14:27:41 +0200 Subject: [PATCH 07/12] feat: Add release preflight workflow and reporting script - Implemented a new GitHub Actions workflow for release preflight checks that runs on pull requests and main branch pushes. - Added a script to generate a release preflight report, validating commit messages against conventional standards. - Updated documentation to reflect the new preflight process and its integration with the release workflow. --- .github/workflows/workflow.yml | 86 ++++++++++++++++- .pre-commit-config.yaml | 2 +- docs/development/dev.md | 51 ++++++++--- release-preflight-report.md | 28 ++++++ scripts/release_preflight.py | 162 +++++++++++++++++++++++++++++++++ 5 files changed, 313 insertions(+), 16 deletions(-) create mode 100644 release-preflight-report.md create mode 100644 scripts/release_preflight.py diff --git a/.github/workflows/workflow.yml b/.github/workflows/workflow.yml index 57a340c..27b764c 100644 --- a/.github/workflows/workflow.yml +++ b/.github/workflows/workflow.yml @@ -139,9 +139,93 @@ jobs: run: | uv run poe test-slow + release-preflight: + name: Release Preflight + needs: test-slow + runs-on: ubuntu-latest + if: + ${{ success() && (github.ref == 'refs/heads/main' || github.event_name == + 'pull_request') }} + permissions: + contents: read + pull-requests: write + issues: write + steps: + - name: Checkout 🛎 + uses: actions/checkout@v7 + with: + fetch-depth: 0 + + - name: Run release preflight report + id: preflight + run: | + set +e + python3 scripts/release_preflight.py --strict --output release-preflight-report.md + exit_code=$? + echo "exit_code=$exit_code" >> "$GITHUB_OUTPUT" + exit 0 + + - name: Upload preflight artifact + uses: actions/upload-artifact@v4 + with: + name: release-preflight-report + path: release-preflight-report.md + if-no-files-found: error + + - name: Comment preflight report on PR + if: always() && github.event_name == 'pull_request' + uses: actions/github-script@v8 + with: + script: | + const fs = require('fs'); + const path = 'release-preflight-report.md'; + const marker = '<!-- release-preflight-report -->'; + const report = fs.existsSync(path) + ? fs.readFileSync(path, 'utf8') + : 'Preflight report file was not generated.'; + const body = `${marker}\n## Release Preflight\n\n\ + _Automated check that complements semantic-release changelog generation._\n\n\ + \`\`\`markdown\n${report}\n\`\`\``; + + const { owner, repo } = context.repo; + const issue_number = context.issue.number; + + const comments = await github.paginate(github.rest.issues.listComments, { + owner, + repo, + issue_number, + per_page: 100, + }); + + const existing = comments.find( + (c) => c.user?.type === 'Bot' && c.body?.includes(marker), + ); + + if (existing) { + await github.rest.issues.updateComment({ + owner, + repo, + comment_id: existing.id, + body, + }); + } else { + await github.rest.issues.createComment({ + owner, + repo, + issue_number, + body, + }); + } + + - name: Fail on preflight violations + if: steps.preflight.outputs.exit_code != '0' + run: | + echo "Release preflight failed with exit code ${{ steps.preflight.outputs.exit_code }}." + exit 1 + release: name: Create Release package - needs: test-slow + needs: release-preflight if: success() && github.ref == 'refs/heads/main' && !contains(github.event.head_commit.message, '[skip release]') runs-on: ubuntu-latest diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index a18b5dc..c510f52 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -2,7 +2,7 @@ fail_fast: false exclude: ^(examples/|test/) repos: - repo: https://github.com/astral-sh/uv-pre-commit - rev: "0.11.2" + rev: "0.12.5" hooks: - id: uv-lock diff --git a/docs/development/dev.md b/docs/development/dev.md index c54e025..ad23cc7 100644 --- a/docs/development/dev.md +++ b/docs/development/dev.md @@ -151,19 +151,18 @@ from pathlib import Path durations_path = Path("durations.json") if durations_path.exists(): - with durations_path.open("r", encoding="utf-8") as json_file: - data = json.load(json_file) + with durations_path.open("r", encoding="utf-8") as json_file: + data = json.load(json_file) else: - # Example fallback so the snippet can run as-is. - data = [ - {"nodeid": "test/unit/test_core.py::test_fit", "duration": 0.12}, - {"nodeid": "test/unit/test_ml.py::test_predict", "duration": 0.08}, - ] + # Example fallback so the snippet can run as-is. + data = [ + {"nodeid": "test/unit/test_core.py::test_fit", "duration": 0.12}, + {"nodeid": "test/unit/test_ml.py::test_predict", "duration": 0.08}, + ] test_durations = {item["nodeid"]: item["duration"] for item in data} for test_name, duration in test_durations.items(): print(f"Test {test_name} took {duration:.2f} seconds") - ``` ## Credential Handling @@ -268,12 +267,36 @@ output_format = "md" Releases are automatically triggered when commits are pushed to the `main` branch: 1. **Analysis**: PSR analyzes commit messages since the last release -2. **Version Calculation**: Determines the next version based on commit types -3. **Changelog Generation**: Updates `docs/Changelog.md` with new changes -4. **Version Bump**: Updates version in `pyproject.toml` -5. **Build**: Creates distribution packages using uv -6. **Release**: Creates a GitHub release with built artifacts -7. **Publish**: Uploads packages to the configured repository +2. **Preflight Audit**: CI runs `scripts/release_preflight.py` to create a release report artifact and fail on non-conventional commit subjects +3. **Version Calculation**: Determines the next version based on commit types +4. **Changelog Generation**: Updates `docs/Changelog.md` with new changes +5. **Version Bump**: Updates version in `pyproject.toml` +6. **Build**: Creates distribution packages using uv +7. **Release**: Creates a GitHub release with built artifacts +8. **Publish**: Uploads packages to the configured repository + +The preflight report is designed to complement the `update-docs` skill. It does not replace the skill's issue and milestone reconciliation, but it ensures contributors get an automatic reminder and an auditable report on every PR and on main. + +### PR Preflight Comment + +On pull requests, the `Release Preflight` workflow posts (and updates) a sticky bot comment that includes the full `release-preflight-report.md` output. + +Expected behavior: + +- The comment is updated on each workflow run instead of creating duplicates. +- The report artifact is uploaded even if strict checks fail. +- The job fails at the end if non-conventional commits are detected. + +Typical failure causes: + +- Commit subject does not follow Conventional Commits (for example `feat: ...`, `fix: ...`, `docs: ...`). +- Unsupported commit type in the subject. + +How to resolve failures: + +1. Rewrite or squash commit subjects to Conventional Commit format. +2. Re-run CI by pushing the updated branch. +3. Verify the updated PR comment no longer lists non-conventional commits. ### Manual Release (if needed) diff --git a/release-preflight-report.md b/release-preflight-report.md new file mode 100644 index 0000000..0105475 --- /dev/null +++ b/release-preflight-report.md @@ -0,0 +1,28 @@ +# Release Preflight Report + +Base tag: v1.0.6 +Commit count: 6 + +## Conventional commit summary + +- chore: 1 +- docs: 3 + +## Non-conventional or unsupported commits + +- 7228faa1 Add markdown extensions and update mkdocstrings configuration +- 876a5aab Potential fix for pull request finding + +## Commits missing issue or PR reference + +- f75e34f0 docs: Add changelog file configuration to pyproject.toml +- 21325232 docs: Update README to include 'Why Mother?" section +- 7228faa1 Add markdown extensions and update mkdocstrings configuration +- 876a5aab Potential fix for pull request finding +- 97f43c4d chore: uv audit +- 2c886f7f docs: Add initial configuration for Zensical documentation site + +## Suggested manual follow-up + +- Run the update-docs skill before release for issue and milestone reconciliation. +- Confirm docs updates for release-specific changes. diff --git a/scripts/release_preflight.py b/scripts/release_preflight.py new file mode 100644 index 0000000..b7a2205 --- /dev/null +++ b/scripts/release_preflight.py @@ -0,0 +1,162 @@ +#!/usr/bin/env python3 +"""Release preflight checks that complement semantic-release. + +This script does not write changelog entries. It validates the commit range since +last tag and produces a markdown report to support manual release review steps. +""" + +from __future__ import annotations + +import argparse +import re +import subprocess +import sys +from collections import defaultdict +from dataclasses import dataclass +from pathlib import Path + +CONVENTIONAL_RE = re.compile(r"^(?P<type>[a-z]+)(\([^)]+\))?(!)?:\s+.+") +ISSUE_RE = re.compile(r"#(?P<num>\d+)") + +ALLOWED_TYPES = { + "feat", + "fix", + "perf", + "docs", + "style", + "refactor", + "test", + "build", + "ci", + "chore", + "revert", +} + + +@dataclass +class Commit: + sha: str + subject: str + + +def run_git(args: list[str]) -> str: + result = subprocess.run(["git", *args], capture_output=True, text=True, check=False) + if result.returncode != 0: + raise RuntimeError(result.stderr.strip() or "git command failed") + return result.stdout.strip() + + +def get_last_tag() -> str: + return run_git(["describe", "--tags", "--abbrev=0"]) + + +def get_commits(base_tag: str) -> list[Commit]: + raw = run_git(["log", f"{base_tag}..HEAD", "--pretty=format:%H%x09%s"]) + if not raw: + return [] + commits: list[Commit] = [] + for line in raw.splitlines(): + sha, subject = line.split("\t", 1) + commits.append(Commit(sha=sha, subject=subject)) + return commits + + +def classify(commit: Commit) -> str | None: + match = CONVENTIONAL_RE.match(commit.subject) + if not match: + return None + commit_type = match.group("type") + if commit_type not in ALLOWED_TYPES: + return None + return commit_type + + +def build_report(base_tag: str, commits: list[Commit]) -> tuple[str, int]: + categorized: dict[str, list[Commit]] = defaultdict(list) + unknown: list[Commit] = [] + missing_issue_refs: list[Commit] = [] + + for commit in commits: + commit_type = classify(commit) + if commit_type is None: + unknown.append(commit) + else: + categorized[commit_type].append(commit) + + if not ISSUE_RE.search(commit.subject): + missing_issue_refs.append(commit) + + lines: list[str] = [] + lines.append("# Release Preflight Report") + lines.append("") + lines.append(f"Base tag: {base_tag}") + lines.append(f"Commit count: {len(commits)}") + lines.append("") + + if not commits: + lines.append("No commits found since the last tag. Release is likely unnecessary.") + return "\n".join(lines), 0 + + lines.append("## Conventional commit summary") + lines.append("") + for key in sorted(categorized.keys()): + lines.append(f"- {key}: {len(categorized[key])}") + lines.append("") + + if unknown: + lines.append("## Non-conventional or unsupported commits") + lines.append("") + for commit in unknown: + lines.append(f"- {commit.sha[:8]} {commit.subject}") + lines.append("") + + if missing_issue_refs: + lines.append("## Commits missing issue or PR reference") + lines.append("") + for commit in missing_issue_refs: + lines.append(f"- {commit.sha[:8]} {commit.subject}") + lines.append("") + + lines.append("## Suggested manual follow-up") + lines.append("") + lines.append("- Run the update-docs skill before release for issue and milestone reconciliation.") + lines.append("- Confirm docs updates for release-specific changes.") + + return "\n".join(lines), len(unknown) + + +def parse_args() -> argparse.Namespace: + parser = argparse.ArgumentParser(description="Release preflight helper") + parser.add_argument("--base-tag", default="auto", help="Tag to compare against, or 'auto'") + parser.add_argument("--output", default="release-preflight-report.md", help="Output markdown file") + parser.add_argument( + "--strict", + action="store_true", + help="Exit non-zero if non-conventional commits are found", + ) + return parser.parse_args() + + +def main() -> int: + args = parse_args() + + try: + base_tag = get_last_tag() if args.base_tag == "auto" else args.base_tag + commits = get_commits(base_tag) + report, unknown_count = build_report(base_tag, commits) + Path(args.output).write_text(report + "\n", encoding="utf-8") + + print(report) + + if args.strict and unknown_count > 0: + print("\nPreflight failed: non-conventional commits found.", file=sys.stderr) + return 2 + except Exception as exc: # pragma: no cover - runtime safety + print(f"Preflight failed: {exc}", file=sys.stderr) + return 1 + + return 0 + + +if __name__ == "__main__": + raise SystemExit(main()) From 2e71ab29111109d176467fa780464291eb3279b9 Mon Sep 17 00:00:00 2001 From: Kai Sommer <89587022+SommerKai@users.noreply.github.com> Date: Fri, 21 Aug 2026 15:33:44 +0200 Subject: [PATCH 08/12] fix: Update release preflight script to validate commits against the main branch and remove outdated report file --- .github/workflows/workflow.yml | 6 +++--- release-preflight-report.md | 28 ---------------------------- scripts/release_preflight.py | 34 ++++++++++++++++++++++------------ 3 files changed, 25 insertions(+), 43 deletions(-) delete mode 100644 release-preflight-report.md diff --git a/.github/workflows/workflow.yml b/.github/workflows/workflow.yml index 27b764c..6cded88 100644 --- a/.github/workflows/workflow.yml +++ b/.github/workflows/workflow.yml @@ -173,7 +173,7 @@ jobs: if-no-files-found: error - name: Comment preflight report on PR - if: always() && github.event_name == 'pull_request' + if: always() && github.event_name == 'pull_request' && github.event.pull_request.head.repo.full_name == github.repository uses: actions/github-script@v8 with: script: | @@ -304,8 +304,8 @@ jobs: publish-pypi: name: Publish to PyPI - needs: release - if: needs.release.outputs.released == 'true' + needs: [release, test-pypi-publish] + if: needs.release.outputs.released == 'true' && needs.test-pypi-publish.result == 'success' environment: name: pypi url: https://pypi.org/project/mother-ml/ diff --git a/release-preflight-report.md b/release-preflight-report.md deleted file mode 100644 index 0105475..0000000 --- a/release-preflight-report.md +++ /dev/null @@ -1,28 +0,0 @@ -# Release Preflight Report - -Base tag: v1.0.6 -Commit count: 6 - -## Conventional commit summary - -- chore: 1 -- docs: 3 - -## Non-conventional or unsupported commits - -- 7228faa1 Add markdown extensions and update mkdocstrings configuration -- 876a5aab Potential fix for pull request finding - -## Commits missing issue or PR reference - -- f75e34f0 docs: Add changelog file configuration to pyproject.toml -- 21325232 docs: Update README to include 'Why Mother?" section -- 7228faa1 Add markdown extensions and update mkdocstrings configuration -- 876a5aab Potential fix for pull request finding -- 97f43c4d chore: uv audit -- 2c886f7f docs: Add initial configuration for Zensical documentation site - -## Suggested manual follow-up - -- Run the update-docs skill before release for issue and milestone reconciliation. -- Confirm docs updates for release-specific changes. diff --git a/scripts/release_preflight.py b/scripts/release_preflight.py index b7a2205..dd9e6fe 100644 --- a/scripts/release_preflight.py +++ b/scripts/release_preflight.py @@ -1,8 +1,8 @@ #!/usr/bin/env python3 """Release preflight checks that complement semantic-release. -This script does not write changelog entries. It validates the commit range since -last tag and produces a markdown report to support manual release review steps. +This script does not write changelog entries. It validates commits added after +the main branch and produces a markdown report to support manual release review. """ from __future__ import annotations @@ -46,12 +46,22 @@ def run_git(args: list[str]) -> str: return result.stdout.strip() -def get_last_tag() -> str: - return run_git(["describe", "--tags", "--abbrev=0"]) +def resolve_base_ref(base_ref: str) -> str: + candidates = (f"origin/{base_ref}", base_ref) if base_ref == "main" else (base_ref,) + for candidate in candidates: + result = subprocess.run( + ["git", "rev-parse", "--verify", candidate], + capture_output=True, + text=True, + check=False, + ) + if result.returncode == 0: + return candidate + raise RuntimeError(f"could not resolve base ref: {base_ref}") -def get_commits(base_tag: str) -> list[Commit]: - raw = run_git(["log", f"{base_tag}..HEAD", "--pretty=format:%H%x09%s"]) +def get_commits(base_ref: str) -> list[Commit]: + raw = run_git(["log", "--no-merges", f"{base_ref}..HEAD", "--pretty=format:%H%x09%s"]) if not raw: return [] commits: list[Commit] = [] @@ -71,7 +81,7 @@ def classify(commit: Commit) -> str | None: return commit_type -def build_report(base_tag: str, commits: list[Commit]) -> tuple[str, int]: +def build_report(base_ref: str, commits: list[Commit]) -> tuple[str, int]: categorized: dict[str, list[Commit]] = defaultdict(list) unknown: list[Commit] = [] missing_issue_refs: list[Commit] = [] @@ -89,7 +99,7 @@ def build_report(base_tag: str, commits: list[Commit]) -> tuple[str, int]: lines: list[str] = [] lines.append("# Release Preflight Report") lines.append("") - lines.append(f"Base tag: {base_tag}") + lines.append(f"Base ref: {base_ref}") lines.append(f"Commit count: {len(commits)}") lines.append("") @@ -127,7 +137,7 @@ def build_report(base_tag: str, commits: list[Commit]) -> tuple[str, int]: def parse_args() -> argparse.Namespace: parser = argparse.ArgumentParser(description="Release preflight helper") - parser.add_argument("--base-tag", default="auto", help="Tag to compare against, or 'auto'") + parser.add_argument("--base-ref", default="main", help="Branch or ref to compare against") parser.add_argument("--output", default="release-preflight-report.md", help="Output markdown file") parser.add_argument( "--strict", @@ -141,9 +151,9 @@ def main() -> int: args = parse_args() try: - base_tag = get_last_tag() if args.base_tag == "auto" else args.base_tag - commits = get_commits(base_tag) - report, unknown_count = build_report(base_tag, commits) + base_ref = resolve_base_ref(args.base_ref) + commits = get_commits(base_ref) + report, unknown_count = build_report(base_ref, commits) Path(args.output).write_text(report + "\n", encoding="utf-8") print(report) From 378bfd4275cecc3e9f89d625ea33e2d11d4c62c7 Mon Sep 17 00:00:00 2001 From: Kai Sommer <89587022+SommerKai@users.noreply.github.com> Date: Fri, 21 Aug 2026 15:59:52 +0200 Subject: [PATCH 09/12] fix: Remove changelog file reference from semantic release configuration --- pyproject.toml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 5f2e61d..a18da9e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -253,7 +253,7 @@ warn_no_return = true extend_skip = [".gitignore", ".pylintrc", "sonar-project.properties"] [tool.semantic_release] -version_toml = ["pyproject.toml:project.version"] # changelog file +version_toml = ["pyproject.toml:project.version"] tag_format = "v{version}" upload_to_vcs_release = true @@ -269,7 +269,6 @@ exclude_commit_patterns = [ '''Initial [Cc]ommit.*''', ] mode = "update" -changelog_file = "docs/Changelog.md" insertion_flag = "..\n All versions below are listed in reverse chronological order" [tool.semantic_release.changelog.default_templates] From cde8d649890fde320d4e19baff678a8a49c47f36 Mon Sep 17 00:00:00 2001 From: Kai Sommer <89587022+SommerKai@users.noreply.github.com> Date: Mon, 31 Aug 2026 10:41:18 +0200 Subject: [PATCH 10/12] ci: Enhance release workflow with preflight checks and reporting --- .github/dependabot.yml | 4 ++++ .github/workflows/workflow.yml | 44 ++++++++++++++++++++++++---------- 2 files changed, 36 insertions(+), 12 deletions(-) diff --git a/.github/dependabot.yml b/.github/dependabot.yml index f8dfa18..2f87ab5 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -6,6 +6,10 @@ version: 2 updates: + - package-ecosystem: "github-actions" + directory: "/" + schedule: + interval: weekly - package-ecosystem: "devcontainers" directory: "/" schedule: diff --git a/.github/workflows/workflow.yml b/.github/workflows/workflow.yml index 6cded88..e2cca4f 100644 --- a/.github/workflows/workflow.yml +++ b/.github/workflows/workflow.yml @@ -146,10 +146,12 @@ jobs: if: ${{ success() && (github.ref == 'refs/heads/main' || github.event_name == 'pull_request') }} + # Least privilege: this job checks out and runs untrusted PR code + # (scripts/release_preflight.py), so it must never hold a write-scoped token. + # Posting the report comment is handled by the separate comment-preflight + # job below, which never executes PR code. permissions: contents: read - pull-requests: write - issues: write steps: - name: Checkout 🛎 uses: actions/checkout@v7 @@ -172,8 +174,32 @@ jobs: path: release-preflight-report.md if-no-files-found: error + - name: Fail on preflight violations + if: steps.preflight.outputs.exit_code != '0' + run: | + echo "Release preflight failed with exit code ${{ steps.preflight.outputs.exit_code }}." + exit 1 + + comment-preflight: + name: Comment Preflight Report + needs: release-preflight + runs-on: ubuntu-latest + # Isolated commenting job: it does NOT check out or execute any PR code, it + # only downloads the report artifact and posts it. This is the only job that + # holds a write-scoped token, and it is gated to same-repo PRs (fork PRs + # receive a read-only token from GitHub regardless). always() lets the + # comment post even when the preflight check fails upstream. + if: always() && github.event_name == 'pull_request' && github.event.pull_request.head.repo.full_name == github.repository + permissions: + pull-requests: write + steps: + - name: Download preflight artifact + uses: actions/download-artifact@v4 + continue-on-error: true + with: + name: release-preflight-report + - name: Comment preflight report on PR - if: always() && github.event_name == 'pull_request' && github.event.pull_request.head.repo.full_name == github.repository uses: actions/github-script@v8 with: script: | @@ -217,12 +243,6 @@ jobs: }); } - - name: Fail on preflight violations - if: steps.preflight.outputs.exit_code != '0' - run: | - echo "Release preflight failed with exit code ${{ steps.preflight.outputs.exit_code }}." - exit 1 - release: name: Create Release package needs: release-preflight @@ -253,7 +273,7 @@ jobs: install-args: "--extra report --extra rna --extra tabpfn --extra tabicl" - name: Python Semantic Release - uses: python-semantic-release/python-semantic-release@v10.2.0 + uses: python-semantic-release/python-semantic-release@2896129e02bb7809d2cf0c1b8e9e795ee27acbcf # v10.2.0 id: release with: github_token: ${{ secrets.PAT_RELEASE_PIPELINE }} @@ -296,7 +316,7 @@ jobs: path: dist - name: Upload package to Test PyPI - uses: pypa/gh-action-pypi-publish@release/v1 + uses: pypa/gh-action-pypi-publish@76f52bc884231f62b9a034ebfe128415bbaabdfc # v1.12.4 with: repository-url: https://test.pypi.org/legacy/ skip-existing: true @@ -320,7 +340,7 @@ jobs: path: dist/ - name: Publish package distributions to PyPI - uses: pypa/gh-action-pypi-publish@release/v1 + uses: pypa/gh-action-pypi-publish@76f52bc884231f62b9a034ebfe128415bbaabdfc # v1.12.4 with: packages-dir: dist/ From c134a87fcaebf4d3b2f24bb1c20e1ece7cb7df4d Mon Sep 17 00:00:00 2001 From: Kai Sommer <89587022+SommerKai@users.noreply.github.com> Date: Mon, 31 Aug 2026 11:33:34 +0200 Subject: [PATCH 11/12] fix: Update actions to latest versions in workflow and sync package version in uv.lock --- .github/workflows/workflow.yml | 6 +++--- pyproject.toml | 6 ++++++ 2 files changed, 9 insertions(+), 3 deletions(-) diff --git a/.github/workflows/workflow.yml b/.github/workflows/workflow.yml index e2cca4f..f3bec35 100644 --- a/.github/workflows/workflow.yml +++ b/.github/workflows/workflow.yml @@ -85,7 +85,7 @@ jobs: run: | uv run poe coverage - - uses: actions/upload-artifact@v4 + - uses: actions/upload-artifact@v7 with: name: coverage-py${{ matrix.python-version }} path: ./coverage.xml @@ -168,7 +168,7 @@ jobs: exit 0 - name: Upload preflight artifact - uses: actions/upload-artifact@v4 + uses: actions/upload-artifact@v7 with: name: release-preflight-report path: release-preflight-report.md @@ -194,7 +194,7 @@ jobs: pull-requests: write steps: - name: Download preflight artifact - uses: actions/download-artifact@v4 + uses: actions/download-artifact@v8 continue-on-error: true with: name: release-preflight-report diff --git a/pyproject.toml b/pyproject.toml index a18da9e..736fd41 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -256,6 +256,12 @@ extend_skip = [".gitignore", ".pylintrc", "sonar-project.properties"] version_toml = ["pyproject.toml:project.version"] tag_format = "v{version}" upload_to_vcs_release = true +# Keep uv.lock's own-package version in sync with the bump. build_command runs +# after the version is written and before the release commit; assets adds the +# regenerated lock to that same commit. uv is not present in the PSR action +# container, so it is installed here first. +build_command = "python3 -m pip install uv && uv lock" +assets = ["uv.lock"] [tool.semantic_release.changelog] # Recommended patterns for conventional commits parser that is scope aware From 5c2a0e8cf8ff90155ce12de5cbb9bebafcc4a1d1 Mon Sep 17 00:00:00 2001 From: Kai Sommer <89587022+SommerKai@users.noreply.github.com> Date: Mon, 31 Aug 2026 11:52:55 +0200 Subject: [PATCH 12/12] docs: Add missing changelog entries for v1.1.1, v1.1.2, and v1.1.3 --- docs/Changelog.md | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/docs/Changelog.md b/docs/Changelog.md index f895e5a..857b7f8 100644 --- a/docs/Changelog.md +++ b/docs/Changelog.md @@ -6,6 +6,34 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## v1.1.3 (2026-08-31) + +### Bug Fixes + +- Fix use count based fingerprints as default, including TabPFN precision handling and test updates + ([#75](https://github.com/Bayer-Group/MotherML/pull/75), + [`74cac2ec`](https://github.com/Bayer-Group/MotherML/commit/74cac2ec0f93fa7f436c5fc6f4f5c8f711ae1a8a)) + +- (tabpfn) Restore upstream TabPFN precision handling with float32 for all operations + + +## v1.1.2 (2026-08-25) + +### Bug Fixes + +- Solving the `max_features` parameter not being correctly passed to the superclass + ([#40](https://github.com/Bayer-Group/MotherML/pull/40), + [`4fd6869c`](https://github.com/Bayer-Group/MotherML/commit/4fd6869c3b3218cedf96060bcf4afe84ba70ece5)) + + +## v1.1.1 (2026-08-21) + +### Chores + +- Update changelog for version 1.1.0 with bug fixes and new features + ([`8a69fa24`](https://github.com/Bayer-Group/MotherML/commit/8a69fa246b449f257dacd93d0cbbd28b28090532)) + + ## v1.1.0 (2026-08-20) ### Bug Fixes