lassoinf 0.1.1__tar.gz

lassoinf-0.1.1/.github/workflows/build_wheel.yml

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+name: Build Wheels
+
+on:
+  push:
+    tags:
+      - 'v*'
+  workflow_dispatch:
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        # Add windows-latest to the build matrix
+        os: [ubuntu-latest, macos-latest]
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v3.3.1 # Use the latest version
+
+      - name: Upload wheel artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-${{ matrix.os }}
+          path: ./wheelhouse/*.whl # cibuildwheel puts wheels in this directory
+
+  build_windows_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        # Add windows-latest to the build matrix
+        os: [windows-latest]
+
+    steps:
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          architecture: "x64"
+
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v3.3.1 # Use the latest version
+        env:
+          # Only build 64-bit wheels (skips the broken win32 build)
+          CIBW_ARCHS: auto64
+
+      - name: Upload wheel artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-${{ matrix.os }}
+          path: ./wheelhouse/*.whl # cibuildwheel puts wheels in this directory
+
+  make_sdist:
+    name: Make SDist
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+    
+    - name: Build SDist
+      run: pipx run build --sdist
+
+    - uses: actions/upload-artifact@v4
+      with:
+        name: sdist
+        path: dist/*.tar.gz

lassoinf-0.1.1/.github/workflows/docs.yml

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+# This file was created automatically with `myst init --gh-pages` 
+
+name: Docs
+on:
+  workflow_dispatch:
+    inputs:
+      tag_name:
+        description: 'The tag or commit to build docs from'
+        required: true
+        default: 'main'
+        type: string
+
+env:
+  # `BASE_URL` determines the website is served from, including CSS & JS assets
+  # You may need to change this to `BASE_URL: ''`
+  BASE_URL: /${{ github.event.repository.name }}
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: 'pages'
+  cancel-in-progress: false
+jobs:
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          # This logic uses the input if it exists, otherwise defaults to the current ref (main)
+          ref: ${{ github.event.inputs.tag_name || github.ref }}
+          fetch-depth: 0 # Important for your get-version.py script to see tags!
+          submodules: recursive
+
+      - name: Setup Pages
+        uses: actions/configure-pages@v3
+
+      - uses: actions/setup-node@v4
+        with:
+          node-version: 18.x
+
+      - name: Install MyST Markdown
+        run: npm install -g mystmd
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+
+      - name: Install package
+        run: |
+          pip install --upgrade pip
+          pip install meson-python ninja meson pybind11 setuptools_scm pytest pandas joblib jupyterlab
+          pip install .[test]
+
+      - name: Build HTML Assets
+        run: cd docs && myst build --html  --execute
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: 'docs/_build/html'
+
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

lassoinf-0.1.1/.github/workflows/test.yml

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+# Run all tests
+
+name: Run tests (Linux)
+
+# Controls when the workflow will run
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.12"]
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+        fetch-depth: 0
+
+    - name: Set up Python  ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install lassoinf
+      run: |
+        pip install --upgrade pip
+        pip install meson-python ninja meson pybind11 setuptools_scm pytest pandas joblib
+        pip install .[test]
+
+    - name: Verify installed source
+      run: |
+        cd /tmp
+        python -c "import lassoinf.affine_constraints; import inspect; print(inspect.getsourcefile(lassoinf.affine_constraints)); print(''.join(open(inspect.getsourcefile(lassoinf.affine_constraints)).readlines()[:20]))"
+
+    - name: Debug Installation
+      run: |
+        cd /tmp
+        python -c "import lassoinf; print(f'Location: {lassoinf.__file__}'); import os; print(f'Contents: {os.listdir(os.path.dirname(lassoinf.__file__))}')"
+
+    - name: Test lassoinf
+      run: |
+        mkdir empty_dir
+        cd empty_dir
+        python -m pytest ../tests

lassoinf-0.1.1/.gitignore

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+*result*.csv
+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# docs/*.ipynb
+
+# Virtual Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# Meson / Ninja Build
+build/
+builddir/
+meson-logs/
+meson-private/
+.ninja_deps
+.ninja_log
+compile_commands.json
+
+# C/C++
+*.o
+*.obj
+*.dll
+*.dylib
+*.exe
+*.out
+*.app
+
+# OS generated files
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+
+# Subprojects
+subprojects/*
+!subprojects/eigen/
+!subprojects/*.wrap

lassoinf-0.1.1/.gitmodules

@@ -0,0 +1,3 @@
+[submodule "subprojects/eigen"]
+	path = subprojects/eigen
+	url = https://gitlab.com/libeigen/eigen.git

lassoinf-0.1.1/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2026, Jonathan Taylor
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

lassoinf-0.1.1/PKG-INFO

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+Metadata-Version: 2.1
+Name: lassoinf
+Version: 0.1.1
+Summary: Selective inference tools
+Keywords: Selective inference for LASSO
+Author-Email: Jonathan Taylor <jonathan.taylor@stanford.edu>
+Maintainer-Email: Jonathan Taylor <jonathan.taylor@stanford.edu>
+License: BSD-3-Clause
+Classifier: Development Status :: 3 - Alpha
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.10
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: matplotlib
+Requires-Dist: pandas
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pandas; extra == "test"
+Requires-Dist: joblib; extra == "test"
+Requires-Dist: cvxpy; extra == "test"
+Requires-Dist: coxdev==0.1.4; extra == "test"
+Requires-Dist: glmstar; extra == "test"
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: scipy; extra == "dev"
+Requires-Dist: ninja; extra == "dev"
+Requires-Dist: meson; extra == "dev"
+Requires-Dist: meson-python; extra == "dev"
+Requires-Dist: pybind11; extra == "dev"
+Requires-Dist: setuptools_scm; extra == "dev"
+Provides-Extra: doc
+Requires-Dist: jupytext; extra == "doc"
+Requires-Dist: jupyter-book; extra == "doc"
+Requires-Dist: matplotlib; extra == "doc"
+Requires-Dist: rpy2; extra == "doc"
+Requires-Dist: cvxpy; extra == "doc"
+Description-Content-Type: text/markdown
+
+# lassoinf
+
+`lassoinf` provides selective inference tools leveraging a high-performance C++ backend. It is a hybrid codebase written in Python and C++, utilizing `pybind11` for bindings and the `Eigen` library for fast linear algebra.
+
+## Features
+
+- **Affine Constraints**: Core numerical tools for inference tasks.
+- **Dual Implementation**: Logic provided in pure Python (`lassoinf.affine_constraints`) and fast C++ counterparts (`lassoinf_cpp`).
+- **High Performance**: The C++ extensions target C++14 and integrate seamlessly with numpy and scipy.
+
+## Requirements
+
+### Python
+- Python >= 3.10
+- `numpy`, `scipy`, `matplotlib`
+- `meson-python`, `ninja`, `pybind11` (for building the extension)
+
+### R
+- R >= 4.0
+- `Rcpp`, `RcppEigen`
+
+### General
+- A C++14 compliant compiler
+
+## Installation
+
+### Python
+
+You can install `lassoinf` and build its C++ extension directly using `pip`:
+
+```bash
+pip install .
+```
+
+For an editable install during development (using the `meson-python` backend):
+
+```bash
+pip install --no-build-isolation -Csetup-args=-Dbuildtype=debug -e .
+```
+
+### R
+
+The R package `lassoinf` requires `Rcpp`, `RcppEigen`, and `R6`. You can install the package from the terminal or directly from the source directory.
+
+**From the terminal:**
+
+```bash
+# Build and install the package
+R CMD INSTALL R_pkg
+```
+
+**From within an R session:**
+
+```R
+# Install required dependencies if not already present
+install.packages(c("Rcpp", "RcppEigen", "R6", "mvtnorm"))
+
+# Install the package from the source directory
+install.packages("R_pkg", repos = NULL, type = "source")
+```
+
+Or using `devtools`:
+
+```R
+devtools::install("R_pkg")
+```
+
+### Testing the R Package
+
+To run the R test suite, you can use the `testthat` package from the command line:
+
+```bash
+cd R_pkg
+Rscript -e 'testthat::test_dir("tests/testthat")'
+```
+
+## Documentation
+
+For more information, refer to the documentation in the `docs/` folder. For the R package, you can view the vignette:
+
+```R
+vignette("gaussian_lasso_boot", package = "lassoinf")
+```
+
+Alternatively, you can browse the `pkgdown` documentation site in `R_pkg/docs/index.html`.
+
+## License
+
+This project is licensed under the BSD 3-Clause License. See the `LICENSE` file for details.

lassoinf-0.1.1/README.md

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+# lassoinf
+
+`lassoinf` provides selective inference tools leveraging a high-performance C++ backend. It is a hybrid codebase written in Python and C++, utilizing `pybind11` for bindings and the `Eigen` library for fast linear algebra.
+
+## Features
+
+- **Affine Constraints**: Core numerical tools for inference tasks.
+- **Dual Implementation**: Logic provided in pure Python (`lassoinf.affine_constraints`) and fast C++ counterparts (`lassoinf_cpp`).
+- **High Performance**: The C++ extensions target C++14 and integrate seamlessly with numpy and scipy.
+
+## Requirements
+
+### Python
+- Python >= 3.10
+- `numpy`, `scipy`, `matplotlib`
+- `meson-python`, `ninja`, `pybind11` (for building the extension)
+
+### R
+- R >= 4.0
+- `Rcpp`, `RcppEigen`
+
+### General
+- A C++14 compliant compiler
+
+## Installation
+
+### Python
+
+You can install `lassoinf` and build its C++ extension directly using `pip`:
+
+```bash
+pip install .
+```
+
+For an editable install during development (using the `meson-python` backend):
+
+```bash
+pip install --no-build-isolation -Csetup-args=-Dbuildtype=debug -e .
+```
+
+### R
+
+The R package `lassoinf` requires `Rcpp`, `RcppEigen`, and `R6`. You can install the package from the terminal or directly from the source directory.
+
+**From the terminal:**
+
+```bash
+# Build and install the package
+R CMD INSTALL R_pkg
+```
+
+**From within an R session:**
+
+```R
+# Install required dependencies if not already present
+install.packages(c("Rcpp", "RcppEigen", "R6", "mvtnorm"))
+
+# Install the package from the source directory
+install.packages("R_pkg", repos = NULL, type = "source")
+```
+
+Or using `devtools`:
+
+```R
+devtools::install("R_pkg")
+```
+
+### Testing the R Package
+
+To run the R test suite, you can use the `testthat` package from the command line:
+
+```bash
+cd R_pkg
+Rscript -e 'testthat::test_dir("tests/testthat")'
+```
+
+## Documentation
+
+For more information, refer to the documentation in the `docs/` folder. For the R package, you can view the vignette:
+
+```R
+vignette("gaussian_lasso_boot", package = "lassoinf")
+```
+
+Alternatively, you can browse the `pkgdown` documentation site in `R_pkg/docs/index.html`.
+
+## License
+
+This project is licensed under the BSD 3-Clause License. See the `LICENSE` file for details.

lassoinf-0.1.1/R_pkg/.Rbuildignore

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+^_pkgdown\.yml$
+^docs$
+^pkgdown$

lassoinf-0.1.1/R_pkg/.gitignore

@@ -0,0 +1 @@
+docs

lassoinf-0.1.1/R_pkg/DESCRIPTION

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+Package: lassoinf
+Title: Selective Inference Tools
+Version: 0.1.0
+Authors@R: person("Jonathan", "Taylor", email = "someone@example.com", role = c("aut", "cre"))
+Description: Computes post-selection inference for the lasso leveraging a high-performance C++ backend.
+License: BSD_3_clause + file LICENSE
+Encoding: UTF-8
+LinkingTo: Rcpp, RcppEigen
+Imports: Rcpp, mvtnorm, R6
+RoxygenNote: 7.3.3

lassoinf-0.1.1/R_pkg/NAMESPACE

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+useDynLib(lassoinf, .registration = TRUE)
+importFrom(Rcpp, sourceCpp)
+importFrom(Rcpp, loadModule)
+export(LassoInference)
+export(AffineConstraints)
+export(DiscreteFamily)
+export(TruncatedGaussian)
+export(WeightedGaussianFamily)
+export(TruncBivariateNormal)