liesel-gam 0.0.4__tar.gz

liesel_gam-0.0.4/.gitattributes

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+*.ipynb linguist-vendored

liesel_gam-0.0.4/.github/workflows/pre-commit.yml

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+name: pre-commit
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: "Set up Python"
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: "pyproject.toml"
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 'release'
+          use-public-rspm: true
+
+      - name: Install Package
+        run: uv sync --locked --group dev
+
+      - name: Run pre-commit
+        run: uv run pre-commit run -a

liesel_gam-0.0.4/.github/workflows/pypi.yml

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+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  workflow_dispatch: # trigger manually from GitHub UI
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: "Set up Python"
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: "pyproject.toml"
+
+      - name: Build package
+        run: uv build
+
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@v1.5.0
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_UPLOAD }}

liesel_gam-0.0.4/.github/workflows/pytest-notebooks.yml

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+name: notebooks
+
+on:
+  push:
+    branches: [main]
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+
+    strategy:
+      matrix:
+        python-version: ["3.13"]
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Install uv and set the python version
+        uses: astral-sh/setup-uv@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 'release'
+          use-public-rspm: true
+
+      - name: Install Package
+        run: uv sync --locked --group dev
+
+      - name: Add R shared libraries to LD_LIBRARY_PATH
+        run: |
+          echo "LD_LIBRARY_PATH=$(python -m rpy2.situation LD_LIBRARY_PATH):\$LD_LIBRARY_PATH" >> $GITHUB_ENV
+
+      - name: Debug R environment
+        run: |
+          echo "R_HOME=$(R RHOME)"
+          echo "LD_LIBRARY_PATH=$LD_LIBRARY_PATH"
+          find $(R RHOME) -name methods.so
+          find $(R RHOME) -name libR.so
+
+
+      - name: Run pytest
+        run: uv run pytest tests/notebooks --nbval-lax --nbval-current-env

liesel_gam-0.0.4/.github/workflows/pytest.yml

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+name: pytest
+
+on:
+  push:
+    branches: [main]
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+
+    strategy:
+      matrix:
+        python-version: ["3.13"]
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Install uv and set the python version
+        uses: astral-sh/setup-uv@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 'release'
+          use-public-rspm: true
+
+      - name: Install Package
+        run: uv sync --locked --group dev
+
+      - name: Add R shared libraries to LD_LIBRARY_PATH
+        run: |
+          echo "LD_LIBRARY_PATH=$(python -m rpy2.situation LD_LIBRARY_PATH):\$LD_LIBRARY_PATH" >> $GITHUB_ENV
+
+      - name: Debug R environment
+        run: |
+          echo "R_HOME=$(R RHOME)"
+          echo "LD_LIBRARY_PATH=$LD_LIBRARY_PATH"
+          find $(R RHOME) -name methods.so
+          find $(R RHOME) -name libR.so
+
+
+      - name: Run pytest
+        run: uv run pytest --cov=liesel_gam
+
+      - name: Create coverage badge
+        uses: tj-actions/coverage-badge-py@v2
+        with:
+          output: tests/coverage.svg
+          overwrite: true
+
+      - name: Commit coverage.svg
+        run: |
+          git config --local user.name "github-actions[bot]"
+          git config --local user.email "github-actions[bot]@users.noreply.github.com"
+          git ls-remote | grep refs/heads/pytest-cov && git remote set-branches --add origin pytest-cov && git fetch
+          git add tests/coverage.svg
+          git diff --staged --quiet || git commit -m "Updated coverage.svg"
+
+      - name: Push coverage.svg
+        uses: ad-m/github-push-action@master
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          branch: ${{ github.ref }}

liesel_gam-0.0.4/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+.python-version
+/.vscode
+/tests/data
+.DS_Store

liesel_gam-0.0.4/.pre-commit-config.yaml

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+# see https://pre-commit.com for more information
+# see https://pre-commit.com/hooks.html for more hooks
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-added-large-files
+        args: ["--maxkb=1000"]
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.11.8
+    hooks:
+      # Run the formatter.
+      - id: ruff-format
+      # Run the linter.
+      - id: ruff
+        args: [ --fix ]
+  - repo: local
+    hooks:
+      - id: mypy
+        name: mypy
+        entry: mypy
+        language: python
+        types_or: [python, pyi]
+        args: [--ignore-missing-imports, --scripts-are-modules]
+        require_serial: true
+        exclude: ^docs/

liesel_gam-0.0.4/LICENSE

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+MIT License
+
+Copyright (c) 2025 Liesel
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

liesel_gam-0.0.4/PKG-INFO

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+Metadata-Version: 2.4
+Name: liesel_gam
+Version: 0.0.4
+Summary: Functionality for Generalized Additive Models in Liesel
+Author: Johannes Brachem
+License-File: LICENSE
+Keywords: machine-learning,statistics
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.13
+Requires-Dist: liesel>=0.4
+Description-Content-Type: text/markdown
+
+# Generalized Additive Models Functionality in Liesel
+
+[![pre-commit](https://github.com/liesel-devs/liesel_gam/actions/workflows/pre-commit.yml/badge.svg)](https://github.com/liesel-devs/liesel_gam/actions/workflows/pre-commit.yml)
+[![pytest](https://github.com/liesel-devs/liesel_gam/actions/workflows/pytest.yml/badge.svg)](https://github.com/liesel-devs/liesel_gam/actions/workflows/pytest.yml)
+[![pytest-cov](tests/coverage.svg)](https://github.com/liesel-devs/liesel_gam/actions/workflows/pytest.yml)
+
+This package provides functionality to make the setup of
+semiparametric generalized additive distributional regression models in [Liesel](https://github.com/liesel-devs/liesel)
+convenient. It works nicely with [liesel-devs/smoothcon](https://github.com/liesel-devs/smoothcon),
+which can be used to obtain basis and penalty matrices from the R package [mgcv](https://cran.r-project.org/web/packages/mgcv/index.html).
+
+## Disclaimer
+
+This package is experimental and under active development. That means:
+
+- The API cannot be considered stable. If you depend on this package, pin the version.
+- Testing has not been extensive as of now. Please check and verify!
+- There is currently no documentation beyond this readme.
+
+In any case, this package comes with no warranty or guarantees.
+
+## Installation
+
+You can install the development version from GitHub via pip:
+
+```bash
+pip install git+https://github.com/liesel-devs/liesel_gam.git
+```
+
+## Illustration
+
+This is a short pseudo-code illustration without real data. For full examples, please
+consider the [notebooks](https://github.com/liesel-devs/liesel_gam/blob/main/notebooks).
+
+```python
+import liesel.model as lsl
+import liesel.goose as gs
+
+import liesel_gam as gam
+
+import jax.numpy as jnp
+```
+
+Set up the response model.
+
+```python
+loc = gam.AdditivePredictor("loc")
+scale = gam.AdditivePredictor("scale", inv_link=jnp.exp) # terms will be added on the linked level
+
+y = lsl.Var.new_obs(
+    value=...,
+    distribution=lsl.Dist(..., loc=loc, scale=scale),
+    name="y"
+)
+```
+
+Add intercept terms
+
+```python
+loc += gam.Intercept(
+    value=0.0, # this is the default
+    distribution=None, # this is the default
+    inference=gs.MCMCSpec(gs.IWLSKernel), # supply inference information here
+    name="b0"
+)
+
+scale += gam.Intercept( # this term will be applied on the log link level
+    value=0.0,
+    distribution=None,
+    inference=gs.MCMCSpec(gs.IWLSKernel),
+    name="g0"
+)
+
+```
+
+Add a smooth term, which can be any structured additive term defined by a basis matrix
+and a penalty matrix. A potentially rank-deficient multivariate normal prior will
+be set up for the coefficient of this term.
+
+```python
+loc += gam.SmoothTerm(
+    basis=...,
+    penalty=...,
+    scale=lsl.Var.new_param(..., name="tau"),
+    inference=gs.MCMCSpec(gs.IWLSKernel),
+    name="s(x)"
+)
+```
+
+Add a linear term.
+
+```python
+loc += gam.LinearTerm(
+    x=..., # 1d-array or 2d-array are both allowed
+    distribution=lsl.Dist(...),
+    inference=gs.MCMCSpec(gs.IWLSKernel),
+    name="x"
+)
+```
+
+Get a Liesel EngineBuilder instance to set up MCMC sampling.
+
+```python
+model = lsl.Model([y])
+eb = gs.LieselMCMC(model).get_engine_builder() # get your engine builder instance
+```
+
+## Contents
+
+```python
+import liesel.model as lsl
+import liesel.goose as gs
+
+import liesel_gam as gam
+```
+
+This package provides the following classes and functions:
+
+- `gam.AdditivePredictor`: A `lsl.Var` object that provides a convenient way to define an additive predictor.
+- `gam.SmoothTerm`: A `lsl.Var` object that provides a convenient way to set up a structured additive term with a singular multivariate normal prior, given a basis matrix, a penalty matrix, and a `lsl.Var` representing the prior scale parameter.
+  - The alternative constructor `gam.SmoothTerm.new_ig` can be used to quickly set up a term with an inverse gamma prior on the prior variance parameter. This variance parameter will be initialized with a suitable Gibbs kernel.
+- `gam.LinearTerm`: A `lsl.Var` object that provides a convenient way to set up a linear term.
+- `gam.Intercept`: A `lsl.Var` parameter object that represents an intercept.
+- `gam.Basis`: An observed `lsl.Var` object that represents a basis matrix.
+
+A bit more behind the scenes:
+
+- `gam.MultivariateNormalSingular`: An implementation of the singular multivariate normal distribution in the `tensorflow_probability` interface.
+- `gam.star_ig_gibbs` and `gam.init_star_ig_gibbs`: Shortcuts for setting up a `gs.GibbsKernel` for a variance parameter with an inverse gamma prior.
+
+## Usage
+
+Usage is illustrated in the following notebooks.
+
+- [notebooks/test_gam_gibbs.ipynb](https://github.com/liesel-devs/liesel_gam/blob/main/notebooks/test_gam_gibbs.ipynb): Uses the `gam.SmoothTerm.new_ig` constructor for the quickest and most convenient setup.
+- [notebooks/test_gam_manual.ipynb](https://github.com/liesel-devs/liesel_gam/blob/main/notebooks/test_gam_manual.ipynb): Uses `gam.SmoothTerm` with a manually initialized scale parameter. This is less convenient, but demonstrates how to use any  `lsl.Var` for the scale parameter.
+
+## Usage with bases and penalties from `mgcv` via `smoothcon`
+
+We can get access to a large class of possible basis and penalty matrices by
+interfacing with the wonderful R package [mgcv](https://cran.r-project.org/web/packages/mgcv/index.html)
+via [liesel-devs/smoothcon](https://github.com/liesel-devs/smoothcon).
+
+Example notebooks that illustrate smoothcon usage are provided in the [smoothcon
+repository](https://github.com/liesel-devs/smoothcon/tree/main/notebooks).