From ea12dd25f22e4a760029be0343208c719a2aca94 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Fri, 27 Sep 2024 21:46:09 +0200 Subject: [PATCH] Move from `poetry` and `just` to `pixi` (#595) --- .gitattributes | 2 + .github/workflows/ci-tests.yaml | 109 +- .github/workflows/extended-tests.yml | 24 +- .github/workflows/publish-to-pypi.yml | 22 +- .gitignore | 8 +- .pre-commit-config.yaml | 2 +- README.md | 14 +- coverage.xml | 4078 ++++++++ docs/contributing.qmd | 173 +- docs/pyfixest.md | 7 +- pixi.lock | 12407 ++++++++++++++++++++++++ poetry.lock | 5027 ---------- pyfixest/utils/set_rpy2_path.py | 35 + pyproject.toml | 129 +- r_test_requirements.R | 9 + tests/test_did.py | 3 + tests/test_i.py | 3 + tests/test_iv.py | 18 +- tests/test_multcomp.py | 3 + tests/test_poisson.py | 3 + tests/test_predict_resid_fixef.py | 3 + tests/test_vcov.py | 3 + tests/test_vs_fixest.py | 3 + tests/test_wald_test.py | 74 +- 24 files changed, 16834 insertions(+), 5325 deletions(-) create mode 100644 .gitattributes create mode 100644 coverage.xml create mode 100644 pixi.lock delete mode 100644 poetry.lock create mode 100644 pyfixest/utils/set_rpy2_path.py create mode 100644 r_test_requirements.R diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 00000000..07fe41c5 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,2 @@ +# GitHub syntax highlighting +pixi.lock linguist-language=YAML linguist-generated=true diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index d205ac37..2f21c2e5 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -27,10 +27,11 @@ jobs: with: python-version: ${{ matrix.python-version }} architecture: x64 - - name: Set up poetry - uses: snok/install-poetry@v1 - - name: Install - run: poetry install --without docs + + - uses: prefix-dev/setup-pixi@v0.8.1 + with: + pixi-version: v0.29.0 + cache: true - name: set numba parallel flags run: | @@ -39,13 +40,21 @@ jobs: - name: Setup r2u uses: eddelbuettel/github-actions/r2u-setup@master - - name: install R packages - run: Rscript -e 'install.packages(c("fixest", "broom", "did2s", "clubSandwich", "wildrwolf", "ivDiag"))' - shell: bash + - name: Print R version + run: | + Rscript -e 'R.version' + + - name: Install R packages + run: | + R_LIB_PATH="${{ github.workspace }}/.pixi/envs/dev/lib/R/library" + mkdir -p $R_LIB_PATH + Rscript -e ".libPaths('$R_LIB_PATH'); install.packages(c('fixest', 'broom', 'did2s', 'wildrwolf', 'ivDiag', 'car'), lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library')" + Rscript -e ".libPaths('$R_LIB_PATH'); install.packages('ritest', lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos = c('https://grantmcdermott.r-universe.dev'))" - - name: Run tests + - name: Run 'regular 'tests run: | - poetry run pytest tests -m "not (extended or slow or plots)" --cov=pyfixest --cov-report=xml + pixi run tests-regular + - name: Upload to Codecov uses: codecov/codecov-action@v4 with: @@ -71,10 +80,12 @@ jobs: with: python-version: ${{ matrix.python-version }} architecture: x64 - - name: Set up poetry - uses: snok/install-poetry@v1 - - name: Install - run: poetry install --without docs + + - uses: prefix-dev/setup-pixi@v0.8.1 + with: + pixi-version: v0.29.0 + cache: true + - name: set numba parallel flags run: | @@ -83,13 +94,16 @@ jobs: - name: Setup r2u uses: eddelbuettel/github-actions/r2u-setup@master - - name: install R packages - run: Rscript -e 'install.packages(c("fixest", "broom", "did2s", "clubSandwich", "wildrwolf", "ivDiag"))' - shell: bash + - name: Install R packages + run: | + R_LIB_PATH="${{ github.workspace }}/.pixi/envs/dev/lib/R/library" + mkdir -p $R_LIB_PATH + Rscript -e ".libPaths('$R_LIB_PATH'); install.packages(c('fixest', 'broom','did2s', 'wildrwolf', 'ivDiag', 'car'), lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library')" + Rscript -e ".libPaths('$R_LIB_PATH'); install.packages('ritest', lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos = c('https://grantmcdermott.r-universe.dev'))" - - name: Run tests + - name: Run 'slow 'tests run: | - poetry run pytest tests -m slow --cov=./ --cov-report=xml + pixi run tests-slow #- name: Upload to Codecov # uses: codecov/codecov-action@v4 @@ -99,47 +113,6 @@ jobs: # flags: tests-vs-fixest - test_notebooks: - name: "Test Notebooks" - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v3 - - - name: Set up Python - uses: actions/setup-python@v3 - with: - python-version: "3.12" - - - name: Set up poetry - uses: snok/install-poetry@v1 - - - name: Install dependencies - run: poetry install - - - name: Set up poetry - uses: snok/install-poetry@v1 - - - name: Install - run: poetry install --without docs - - name: set numba parallel flags - run: | - echo "NUMBA_NUM_THREADS=1" >> $GITHUB_ENV - - - name: Setup r2u - uses: eddelbuettel/github-actions/r2u-setup@master - - - name: install R packages - run: Rscript -e 'install.packages(c("fixest", "broom", "did2s", "clubSandwich", "wildrwolf", "ivDiag"))' - shell: bash - - - name: Install TeXlive - run: sudo apt-get update && sudo apt-get install texlive texlive-publishers texlive-science latexmk cm-super - - - name: Run notebooks - run: | - poetry install --with docs - poetry run python scripts/run_notebooks.py - build-docs: name: "Build Docs" @@ -152,26 +125,32 @@ jobs: uses: actions/setup-python@v5 with: python-version: "3.11" - - name: Set up poetry - uses: snok/install-poetry@v1 - - name: Install dependencies - run: poetry install --with docs + + - uses: prefix-dev/setup-pixi@v0.8.1 + with: + pixi-version: v0.29.0 + cache: true + - name: Set up Quarto uses: quarto-dev/quarto-actions/setup@v2 + - name: install tinytex run: | quarto install tinytex + - name: Compile docstrings with quartodoc run : | - poetry run quartodoc build --verbose --config docs/_quarto.yml + pixi run docs-build - name: Render docs run: | - poetry run quarto render docs + pixi run docs-render - name: Save docs artifact uses: actions/upload-artifact@v4 with: name: docs-html path: docs/_site + + publish-docs: name: "Publish Docs" runs-on: ubuntu-latest diff --git a/.github/workflows/extended-tests.yml b/.github/workflows/extended-tests.yml index 4492a18a..df115b76 100644 --- a/.github/workflows/extended-tests.yml +++ b/.github/workflows/extended-tests.yml @@ -31,13 +31,10 @@ jobs: with: python-version: ${{ matrix.python-version }} - # Set up poetry (common to both scenarios) - - name: Set up poetry - uses: snok/install-poetry@v1 - - # Install dependencies (common to both scenarios) - - name: Install dependencies - run: poetry install --without docs + - uses: prefix-dev/setup-pixi@v0.8.1 + with: + pixi-version: v0.29.0 + cache: true # Set numba parallel flags (common to both scenarios) - name: Set numba parallel flags @@ -46,16 +43,19 @@ jobs: - name: Setup r2u uses: eddelbuettel/github-actions/r2u-setup@master - - name: install R packages - run: Rscript -e 'install.packages(c("fixest", "broom", "did2s", "clubSandwich", "wildrwolf", "ivDiag"))' - shell: bash + - name: Install R packages + run: | + R_LIB_PATH="${{ github.workspace }}/.pixi/envs/dev/lib/R/library" + mkdir -p $R_LIB_PATH + Rscript -e ".libPaths('$R_LIB_PATH'); install.packages(c('fixest', 'broom','clubSandwich', 'did2s', 'wildrwolf', 'ivDiag', 'car'), lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library')" + Rscript -e ".libPaths('$R_LIB_PATH'); install.packages('ritest', lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos = c('https://grantmcdermott.r-universe.dev', 'https://cloud.r-project.org'))" # Run tests for PRs with the label "extended" - name: Run tests for plots (only on PRs with the 'tests-extended' label) if: github.event_name == 'pull_request' && contains(github.event.label.name, 'tests-extended') - run: poetry run pytest tests -m "extended" --cov=pyfixest --cov-report=xml + run: pixi run tests-extended # Run tests for push to master - name: Run tests for push to master if: github.event_name == 'push' && github.ref == 'refs/heads/master' - run: poetry run pytest tests -m "extended" --cov=pyfixest --cov-report=xml + run: pixi run tests-extended diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml index ef71e2eb..d407563a 100644 --- a/.github/workflows/publish-to-pypi.yml +++ b/.github/workflows/publish-to-pypi.yml @@ -10,20 +10,14 @@ jobs: - name: Set up Python 3.10 uses: actions/setup-python@v5 with: - python-version: '3.10' - - name: Install pypa/build - run: >- - python -m - pip install - build - --user - - name: Build a binary wheel and a source tarball - run: >- - python -m - build - --sdist - --wheel - --outdir dist/ + python-version: '3.11' + - uses: prefix-dev/setup-pixi@v0.8.1 + with: + pixi-version: v0.29.0 + cache: true + - name: Install R packages + run: | + pixi run build-pip - name: Publish distribution 📦 to PyPI if: startsWith(github.ref, 'refs/tags') uses: pypa/gh-action-pypi-publish@release/v1 diff --git a/.gitignore b/.gitignore index 4b0b2e0e..8176c49d 100644 --- a/.gitignore +++ b/.gitignore @@ -23,5 +23,9 @@ readme.ipynb #docs/site_libs #site_libs tests/.coverage -.venv/ -docs/regression-compression.ipynb +.venv/# pixi environments +.pixi +*.egg-info +# pixi environments +.pixi +*.egg-info diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index a5071fe9..cdaed7b5 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -12,7 +12,7 @@ repos: args: [--allow-multiple-documents] - id: check-toml - id: check-added-large-files - + exclude: pixi.lock - repo: https://github.com/python-jsonschema/check-jsonschema rev: 0.29.2 hooks: diff --git a/README.md b/README.md index 483fdb71..bdaf7c60 100644 --- a/README.md +++ b/README.md @@ -2,14 +2,18 @@ # PyFixest: Fast High-Dimensional Fixed Effects Regression in Python -[![License](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/license/mit) -[![PyPI -Version](https://img.shields.io/pypi/v/pyfixest.svg)](https://pypi.org/project/pyfixest/) +[![License](https://img.shields.io/badge/License-MIT-green.svg)](https://opensource.org/license/mit) ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/pyfixest.svg) -[![Downloads](https://static.pepy.tech/badge/pyfixest)](https://pepy.tech/project/pyfixest) -[![Downloads](https://static.pepy.tech/badge/pyfixest/month)](https://pepy.tech/project/pyfixest) +[![PyPI -Version](https://img.shields.io/pypi/v/pyfixest.svg)](https://pypi.org/project/pyfixest/) [![image](https://codecov.io/gh/py-econometrics/pyfixest/branch/master/graph/badge.svg)](https://codecov.io/gh/py-econometrics/pyfixest) [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) -[![All Contributors](https://img.shields.io/badge/all_contributors-5-orange.svg?style=flat-square)](#contributors-) +[![Pixi Badge][pixi-badge]][pixi-url] +[![All Contributors](https://img.shields.io/badge/all_contributors-18-green.svg?style=flat-square)](#contributors-) +[![Downloads](https://static.pepy.tech/badge/pyfixest)](https://pepy.tech/project/pyfixest) +[![Downloads](https://static.pepy.tech/badge/pyfixest/month)](https://pepy.tech/project/pyfixest) + +[pixi-badge]:https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/prefix-dev/pixi/main/assets/badge/v0.json&style=flat-square +[pixi-url]: https://pixi.sh `PyFixest` is a Python implementation of the formidable [fixest](https://github.com/lrberge/fixest) package for fast high-dimensional fixed effects regression. diff --git a/coverage.xml b/coverage.xml new file mode 100644 index 00000000..c3551824 --- /dev/null +++ b/coverage.xml @@ -0,0 +1,4078 @@ + + + + + + C:\Users\alexa\Documents\pyfixest\pyfixest + + + + + + + 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/docs/contributing.qmd b/docs/contributing.qmd index b35e1dc2..5c9ae52a 100644 --- a/docs/contributing.qmd +++ b/docs/contributing.qmd @@ -30,180 +30,153 @@ Please describe the behavior you want and why, and provide examples of how pyfix ### Setting up your local environment -`pyfixest` development flow relies on Python. Testing statistical and econometric -models is implement using Python and R. Documents are written with Quarto and -Jupyter. +Would you like to contribute to pyfixest, or run some of the unit tests locally? Awesome! +Here's how you can get started: -Start by forking the pyfixest GitHub repository, then clone your forked repository -using `git`: +First, you'll want to fork the pyfixest GitHub repository. Then, clone your forked repo with git: ```{.bash .code-copy} git clone https://github.com//pyfixest.git cd pyfixest ``` -In order to work of `pyfixest`, you will need Python and R installed. If working -on documentation, you will need Quarto installed. +To work on pyfixest, you'll need Python and R installed. If you're planning to work on the documentation, be sure to have Quarto installed as well. +Note: an R installation is only needed if you plan to run the unit tests locally. -There are multiple ways of installing Python and R, but if you need to install -them prior to development the following are potential options: +For guidance on installing R and Python, check out the sections below. -#### Installing Python - -On Mac/Linux via [Hombrew](https://brew.sh/): +### Package Management via `pixi` -```{.bash .code-copy} -brew install python@3.11 # specify the version of python you prefer -``` -On Windows via [Winget](https://winget.run/pkg/Python/Python.3.11): -```{.bash .code-copy} -winget install -e --id Python.Python.3.11 -``` +`PyFixest` is using [pixi](https://pixi.sh/latest/). -### Installing R +Just follow the [installation instructions](https://pixi.sh/latest/#installation) from the `pixi` documentation +to set up `pixi`. -Note that installing R and the R packages listed below is only necessary if you want to test against R in your local installation. -You can also test against R by using github actions. +Once `pixi` is installed, initialize the project environment and install all dependencies with: -On Mac/Linux: ```{.bash .code-copy} -brew install r +cd path-to-pyfixest +pixi install ``` -Depending on your local set up, you may need to install additional libraries, for -example: +After installation, activate your custom `pixi` environment for `pyfixest` by typing: ```{.bash .code-copy} -sudo apt install gcc-11 cmake +pixi shell ``` -On Windows using [Winget](https://winget.run/pkg/RProject/R): +You'll now be in the `pixi` environment and ready to go! -```{.bash .code-copy} -winget install -e --id RProject.R -``` +### `Pixi` tasks -Tests run with R require the following packages: +To help with development, we've included several handy pixi tasks. -- base -- broom -- clubSandwich -- did2s -- fixest -- stats -- wildrwolf -- ritest -- ivDiag +To avtivate relevant pixi environments, you can type ```{.bash .code-copy} -Rscript -e 'install.packages(c("broom", "clubSandwich", "did2s", "fixest", "wildrwolf"), repos="https://cran.rstudio.com"); install.packages('ritest', repos = c('https://grantmcdermott.r-universe.dev', 'https://cloud.r-project.org'))' +pixi shell # open the base environment +pixi shell --environment dev # open the dev environment ``` -Documentation for `pyfixest` is written, compiled, and published using Quarto. +For most development tasks, it’s best to activate the development environment since it includes all the necessary dependencies for development. -To install Quarto, run: +For example, we use `ruff` and `pre-commit` to ensure code consistency across the project. -On MacOS via [Homebrew](https://formulae.brew.sh/cask/quarto#default): +To install the required hooks, simply run ```{.bash .code-copy} -brew install --cask quarto +pixi run lint ``` -On Linux (Ubuntu using `gdebi`): +and you're ready to go! + +We’ve also included additional tasks to help you install the necessary R packages for running unit tests or to run different test suites, whether they’re lightweight or more computationally demanding: ```{.bash .code-copy} -sudo curl -o quarto-linux-amd64.deb -L -sudo gdebi quarto-linux-amd64.deb +# install all R development dependencies +pixi run install-r +# run all tests via pytest +pixi run tests +# run all tests excluding very computationally demanding tests +pixi run tests-regular +# rerun failed tests +pixi run tests-rerun ``` -On Windows: +Building the documentation is also straightforward. We’ve got tasks to build, render, and preview the docs: ```{.bash .code-copy} -scoop bucket add extras -scoop install extras/quarto +# Build documentation and website +pixi run docs-build +# render the docs +pixi run docs-render +# preview the docs +pixi run docs-preview ``` -### Package Management +Keep in mind that you’ll need quarto installed to build the documentation locally. -`PyFixest` is using [poetry](https://github.com/python-poetry/poetry). +## Installing Python, R and Quarto -Please follow the [installation instructions](https://python-poetry.org/docs/#installing-with-the-official-installer) from the poetry documentation. +#### Installing Python -Afterwards, you can initiate the project environment and install all dependencies by running +The minimal Python version to develop `pyfixest` is `3.9`. You can installed it on Mac/Linux via [Hombrew](https://brew.sh/): ```{.bash .code-copy} -cd path-to-pyfixest -poetry install +brew install python@3.11 # specify the version of python you prefer ``` -If you type +On Windows via [Winget](https://winget.run/pkg/Python/Python.3.11): ```{.bash .code-copy} -poetry shell +winget install -e --id Python.Python.3.11 ``` -you will see that you have activated a custom poetry environment for pyfixest. - -### Code Style - -We use `ruff` and `pre-commit` to ensure a consistent code style. +### Installing R -You can install `pre-commit` from `pip` by running +Note that installing R and the R packages listed below is only necessary if you want to test against R in your local installation. +You can also test against R by using github actions. +On Mac/Linux: ```{.bash .code-copy} -pip install pre-commit +brew install r ``` -To install the required hooks, run +Depending on your local set up, you may need to install additional libraries, for +example: ```{.bash .code-copy} -pre-commit install +sudo apt install gcc-11 cmake ``` -and you're ready to go! +On Windows using [Winget](https://winget.run/pkg/RProject/R): -### Justfile +```{.bash .code-copy} +winget install -e --id RProject.R +``` -There are several command line targets that assist with development included in the -`justfile`. [Just](https://just.systems/) can be installed to help run these -command line targets. Installing `just` is only recommended and not needed for -development of pyfixest. +### Installing Quarto -On Mac/Linux via [Homebrew](https://formulae.brew.sh/formula/just#default): +Documentation for `pyfixest` is written, compiled, and published using Quarto. -```{.bash .code-copy} -brew install just -``` +To install Quarto, run: -On Windows: +On MacOS via [Homebrew](https://formulae.brew.sh/cask/quarto#default): ```{.bash .code-copy} -scoop bucket add main -scoop install main/just +brew install --cask quarto ``` -The justfile includes multiple helpful shorthands to help with development. Note that -if you are not using windows/powershell, you will have to uncomment the first line of the justfile -`set shell := ["powershell.exe", "-c"]`. +On Linux (Ubuntu using `gdebi`): ```{.bash .code-copy} -# install all development dependencies -just install-dev -# install all R development dependencies -just install-r -# run all tests via pytest -just tests +sudo curl -o quarto-linux-amd64.deb -L +sudo gdebi quarto-linux-amd64.deb ``` -To rebuild the documentation locally, you can run +On Windows: ```{.bash .code-copy} -# Build documentation and website -just docs-build -# render the docs -just render -# preview the docs -just preview +scoop bucket add extras +scoop install extras/quarto ``` - -To re-create the csv files in `tests/data` that contain results from R packages for testing, you can run `just update-tests-data`. diff --git a/docs/pyfixest.md b/docs/pyfixest.md index 328eedb2..c598c2e6 100644 --- a/docs/pyfixest.md +++ b/docs/pyfixest.md @@ -9,7 +9,12 @@ [![Downloads](https://static.pepy.tech/badge/pyfixest/month)](https://pepy.tech/project/pyfixest) [![image](https://codecov.io/gh/py-econometrics/pyfixest/branch/master/graph/badge.svg)](https://codecov.io/gh/py-econometrics/pyfixest) [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) -[![All Contributors](https://img.shields.io/badge/all_contributors-5-orange.svg?style=flat-square)](#contributors-) +[![Pixi Badge][pixi-badge]][pixi-url] +[![All Contributors](https://img.shields.io/badge/all_contributors-18-orange.svg?style=flat-square)](#contributors-) + +[pixi-badge]:https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/prefix-dev/pixi/main/assets/badge/v0.json&style=flat-square +[pixi-url]: https://pixi.sh + `PyFixest` is a Python implementation of the formidable [fixest](https://github.com/lrberge/fixest) package for fast high-dimensional fixed effects regression. diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 00000000..59f92755 --- /dev/null +++ b/pixi.lock @@ -0,0 +1,12407 @@ +version: 5 +environments: + build: + channels: + - 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-[metadata] -lock-version = "2.0" -python-versions = ">=3.9,<4.0" -content-hash = "d2fdaaea63fa7c9ce606686fd2764ecdeebad38c294ea77d57e641ef26ed959e" diff --git a/pyfixest/utils/set_rpy2_path.py b/pyfixest/utils/set_rpy2_path.py new file mode 100644 index 00000000..d2ea6d52 --- /dev/null +++ b/pyfixest/utils/set_rpy2_path.py @@ -0,0 +1,35 @@ +import rpy2.robjects as robjects +from rpy2.robjects.packages import importr + + +def update_r_paths(): + "Get current R library paths." + current_r_paths = robjects.r(".libPaths()") + + # Define your custom paths + custom_paths = robjects.StrVector( + [ + "/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library", + "/usr/local/lib/R/site-library", + "/usr/lib/R/site-library", + "/usr/lib/R/library", + ] + ) + + # Combine current R paths with custom paths (avoiding duplicates) + new_lib_paths = robjects.StrVector(list(set(custom_paths).union(current_r_paths))) + + # Set the combined library paths in the R environment + robjects.r[".libPaths"](new_lib_paths) + + +def _check_update_r_paths(): + update_r_paths() + try: + importr("did2s") + print("did2s package imported successfully.") + except Exception as e: + print(f"Error importing did2s: {e}") + + +_check_update_r_paths() diff --git a/pyproject.toml b/pyproject.toml index 8f672b46..a928a963 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,52 +1,87 @@ -[tool.poetry] +[project] name = "pyfixest" +description = "Fast high dimensional fixed effect estimation following syntax of the fixest R package." +requires-python = ">= 3.9" version = "0.24.3" +authors = [{name = "Alexander Fischer", email = "alexander-fischer1801@t-online.de"}, {name = "Styfen Schär"}] -description = "Fast high dimensional fixed effect estimation following syntax of the fixest R package. Supports OLS, IV and Poisson regression and a range of inference procedures (HC1-3, CRV1 & CRV3, wild bootstrap, randomization inference, simultaneous CIs, Romano-Wolf's multiple testing correction). Additionally, supports (some of) the regression based new Difference-in-Differences Estimators (Did2s, Linear Projections)." -authors = [ - "Alexander Fischer ", - "Styfen Schär", +dependencies = [ + "lets-plot>=4.0.0", + "scipy>=1.6", + "formulaic>=1.0.0", + "pandas>=1.1.0", + "numba>=0.58.0", + "seaborn>=0.13.2", + "tabulate>=0.9.0", + "polars>=0.20.1", + "tqdm==4.66.4", + "great-tables>=0.10.0", + "numpy>=1.19.0", + "jinja2>=3.1.4,<4" ] -license = "MIT" -readme = "README.md" -homepage = "https://py-econometrics.github.io/pyfixest/" -repository = "https://github.com/py-econometrics/pyfixest" - -[tool.poetry.dependencies] -python = ">=3.9,<4.0" -pandas = ">=1.1.0" -numpy = ">=1.19.0" -scipy = ">=1.6" -formulaic = ">=1.0.0" -lets-plot = ">=4.0.1" -seaborn = ">=0.13.2" -numba = ">=0.58.0" -tabulate = ">=0.9.0" -polars = ">=0.20.1" -tqdm = "^4.66.4" -great-tables = ">=0.10.0" - -[tool.poetry.group.dev.dependencies] -pytest = ">=7.0.0" -rpy2 = "3.5.15" -pytest-cov = "^4.1.0" -pytest-xdist = ">=3.5.0" -pyhdfe = ">=0.2.0" -pyarrow = ">=14.0.2" -wildboottest = ">=0.2.0" -pre-commit = "^3.6.0" -doubleml = "^0.7.1" -marginaleffects = "^0.0.10" - -[tool.poetry.group.docs.dependencies] -causaldata = "*" -quartodoc = ">=0.7.2" -jupyterlab = "^4.0.12" -jupytext = "^1.16.1" -papermill = "*" -pylatex = "*" -stargazer = "*" -watermark = "^2.4.3" + +[tool.pixi.feature.dev.dependencies] +rpy2 = ">=3.5.11,<4" + +[project.optional-dependencies] +dev = [ + "pytest>=7.2.0", + "pytest-cov>=4.1.0", + "pytest-xdist>=3.5.0", + "pyhdfe>=0.2.0", + "pyarrow>=17.0.0", + "pre-commit==3.6.0", + "doubleml==0.7.1", + "wildboottest>=0.3.2" +] + +docs = [ + "quartodoc>=0.7.2", + "jupyterlab>=4.0.12", + "jupytext==1.16.1", + "watermark==2.4.3", + "wildboottest>=0.3.2" +] + +[tool.pixi.feature.build.dependencies] +python-build = ">=1.2.2,<2" + +[build-system] +build-backend = "hatchling.build" +requires = ["hatchling"] + +[tool.pixi.project] +channels = ["conda-forge"] +platforms = ["linux-64", "win-64", "osx-arm64", "osx-64"] + +[tool.pixi.pypi-dependencies] +pyfixest = { path = ".", editable = true } + +[tool.pixi.environments] +default = { solve-group = "default" } +dev = { features = ["dev"], solve-group = "default" } +docs = { features = ["docs"], solve-group = "default" } +build = { features = ["build"], solve-group = "default" } + +[tool.pixi.feature.dev.tasks] +tests = "pytest -n 4 --cov-report=term tests" +tests-regular = "pytest tests -n 4 -m \"not (extended or slow or plots)\" --cov=pyfixest --cov-report=xml" +tests-extended = "pytest tests -n 4 -m \"tests-extended\" --cov=pyfixest --cov-report=xml" +tests-slow = "pytest tests -n 4 -m slow --cov=./ --cov-report=xml" +tests-rerun = "pytest --lf -n 4" +debug = "python pyfixest/debug.py" +lint = "pre-commit run ruff --all-files" +update-test-data = "Rscript tests/r_test_comparisons.R" +install-r = "Rscript r_test_requirements.R" +render-notebooks = "python scripts/run_notebooks.py" + +[tool.pixi.feature.build.tasks] +build-pip = 'python -m build .' + +[tool.pixi.feature.docs.tasks] +docs-build = "quartodoc build --verbose --config docs/_quarto.yml" +docs-render = "quarto render docs" +docs-preview = "quarto preview docs" [tool.pytest.ini_options] addopts = [ @@ -123,7 +158,3 @@ convention = "numpy" [tool.ruff.format] docstring-code-format = true docstring-code-line-length = 88 - -[build-system] -requires = ["poetry-core"] -build-backend = "poetry.core.masonry.api" diff --git a/r_test_requirements.R b/r_test_requirements.R new file mode 100644 index 00000000..4e4b3846 --- /dev/null +++ b/r_test_requirements.R @@ -0,0 +1,9 @@ +# note: fixest and broom are installed via conda +install.packages( + c('fixest', 'broom','clubSandwich', 'did2s', 'wildrwolf', 'reticulate', 'ivDiag', 'stats', 'base', 'car'), + repos='https://cran.rstudio.com' +); +install.packages( + 'ritest', + repos = c('https://grantmcdermott.r-universe.dev', 'https://cloud.r-project.org') +); diff --git a/tests/test_did.py b/tests/test_did.py index b749bf91..a2434c8a 100644 --- a/tests/test_did.py +++ b/tests/test_did.py @@ -10,6 +10,9 @@ from pyfixest.did.estimation import did2s as did2s_pyfixest from pyfixest.did.estimation import event_study, lpdid +from pyfixest.utils.set_rpy2_path import update_r_paths + +update_r_paths() pandas2ri.activate() did2s = importr("did2s") diff --git a/tests/test_i.py b/tests/test_i.py index 3240ca9c..511588cd 100644 --- a/tests/test_i.py +++ b/tests/test_i.py @@ -8,6 +8,9 @@ from rpy2.robjects.packages import importr from pyfixest.estimation.estimation import feols +from pyfixest.utils.set_rpy2_path import update_r_paths + +update_r_paths() pandas2ri.activate() diff --git a/tests/test_iv.py b/tests/test_iv.py index 91fcdf71..eb5275da 100644 --- a/tests/test_iv.py +++ b/tests/test_iv.py @@ -6,8 +6,11 @@ from rpy2.robjects.packages import importr from pyfixest.estimation.estimation import feols +from pyfixest.utils.set_rpy2_path import update_r_paths from pyfixest.utils.utils import get_data +update_r_paths() + # Activate pandas2ri to enable conversion between pandas DataFrames and R DataFrames pandas2ri.activate() @@ -86,10 +89,21 @@ def r_results(): data=data_r, weights="weights", cl=cl_r, + run_AR=False, + parallel=False, + bootstrap=False, ) result_without_weights = ivDiag.ivDiag( - Y=Y_r, D=D_r, Z=Z_r, controls=controls_r, data=data_r, cl=cl_r + Y=Y_r, + D=D_r, + Z=Z_r, + controls=controls_r, + data=data_r, + cl=cl_r, + run_AR=False, + parallel=False, + bootstrap=False, ) return { @@ -141,7 +155,7 @@ def test_iv_Fstat_ivDiag(has_weight, adj_vcov, r_results): _N = fit_iv._N if adj_vcov == {"CRV1": "cluster"}: F_stat_R = F_cl - F_eff_R = result[4] + F_eff_R = result[3] elif adj_vcov == "iid": F_stat_R = F_naive F_eff_R = result[1] # * _N / (_N - 1) diff --git a/tests/test_multcomp.py b/tests/test_multcomp.py index 2da65272..6a3e6daa 100644 --- a/tests/test_multcomp.py +++ b/tests/test_multcomp.py @@ -7,8 +7,11 @@ from pyfixest.estimation.estimation import feols from pyfixest.estimation.multcomp import _get_rwolf_pval, bonferroni, rwolf +from pyfixest.utils.set_rpy2_path import update_r_paths from pyfixest.utils.utils import get_data +update_r_paths() + pandas2ri.activate() fixest = importr("fixest") diff --git a/tests/test_poisson.py b/tests/test_poisson.py index 545d2b70..33460672 100644 --- a/tests/test_poisson.py +++ b/tests/test_poisson.py @@ -9,6 +9,9 @@ import pyfixest as pf from pyfixest.estimation.estimation import fepois +from pyfixest.utils.set_rpy2_path import update_r_paths + +update_r_paths() pandas2ri.activate() diff --git a/tests/test_predict_resid_fixef.py b/tests/test_predict_resid_fixef.py index 265e202e..019e1928 100644 --- a/tests/test_predict_resid_fixef.py +++ b/tests/test_predict_resid_fixef.py @@ -10,8 +10,11 @@ from pyfixest.errors import NotImplementedError from pyfixest.estimation.estimation import feols, fepois from pyfixest.utils.dev_utils import _extract_variable_level +from pyfixest.utils.set_rpy2_path import update_r_paths from pyfixest.utils.utils import get_data +update_r_paths() + pandas2ri.activate() fixest = importr("fixest") diff --git a/tests/test_vcov.py b/tests/test_vcov.py index d9021c08..487952c7 100644 --- a/tests/test_vcov.py +++ b/tests/test_vcov.py @@ -7,8 +7,11 @@ from rpy2.robjects.packages import importr import pyfixest as pf +from pyfixest.utils.set_rpy2_path import update_r_paths from pyfixest.utils.utils import ssc +update_r_paths() + pandas2ri.activate() fixest = importr("fixest") diff --git a/tests/test_vs_fixest.py b/tests/test_vs_fixest.py index 9f4be4d5..5ae71438 100644 --- a/tests/test_vs_fixest.py +++ b/tests/test_vs_fixest.py @@ -11,8 +11,11 @@ import pyfixest as pf from pyfixest.estimation.estimation import feols +from pyfixest.utils.set_rpy2_path import update_r_paths from pyfixest.utils.utils import get_data, ssc +update_r_paths() + pandas2ri.activate() fixest = importr("fixest") diff --git a/tests/test_wald_test.py b/tests/test_wald_test.py index b01fef70..1041adef 100644 --- a/tests/test_wald_test.py +++ b/tests/test_wald_test.py @@ -9,12 +9,13 @@ import pyfixest as pf from pyfixest.estimation.estimation import feols +from pyfixest.utils.set_rpy2_path import update_r_paths from pyfixest.utils.utils import ssc -pandas2ri.activate() +update_r_paths() +pandas2ri.activate() -clubSandwich = importr("clubSandwich") fixest = importr("fixest") stats = importr("stats") broom = importr("broom") @@ -57,19 +58,10 @@ def test_F_test_single_equation_no_clustering(R): # Compare with R r_fit = stats.lm(fml, data=data) + r_wald = car.linearHypothesis(r_fit, base.matrix(R, 3, 3), test="F") - unique_cluster = base.seq_len(len(data)) - - r_wald = clubSandwich.Wald_test( - r_fit, - constraints=base.matrix(R, 3, 3), - vcov="CR0", - cluster=unique_cluster, - test="Naive-F", - ) - - r_fstat = pd.DataFrame(r_wald).T[1].values[0] - r_pvalue = pd.DataFrame(r_wald).T[5].values[0] + r_fstat = r_wald.rx2("F")[1] + r_pvalue = r_wald.rx2("Pr(>F)")[1] np.testing.assert_allclose(f_stat, r_fstat, rtol=1e-03, atol=1e-02) np.testing.assert_allclose(p_stat, r_pvalue, rtol=1e-03, atol=1e-02) @@ -98,16 +90,14 @@ def test_F_test_single_equation(R): p_value = fit._p_value # Compare with R - r_fit = stats.lm(fml, data=data) - r_wald = clubSandwich.Wald_test( - r_fit, - constraints=base.matrix(R, 1, 2), - vcov="CR1", - cluster=data["year"], - test="Naive-F", + r_fit = fixest.feols( + ro.Formula(fml), data=data, vcov=ro.Formula("~year"), ssc=fixest.ssc(adj=False) ) - r_fstat = pd.DataFrame(r_wald).T[1].values[0] - r_pvalue = pd.DataFrame(r_wald).T[5].values[0] + + r_wald = car.linearHypothesis(r_fit, base.matrix(R, 1, 2), test="F") + + r_fstat = r_wald.rx2("F")[1] + r_pvalue = r_wald.rx2("Pr(>F)")[1] np.testing.assert_allclose(f_stat, r_fstat, rtol=1e-03, atol=1e-03) np.testing.assert_allclose(p_value, r_pvalue, rtol=1e-03, atol=1e-03) @@ -130,7 +120,7 @@ def test_F_test_multiple_equation(seedn): n = 3000 treat = np.random.choice([0, 1], size=n) X1 = 1 + np.random.randn(n) - dep_var = 0.0 + 0.0 * treat + 0.0 * X1 + np.random.randn(n) + dep_var = 0.0 + 1.0 * treat + 0.0 * X1 + np.random.randn(n) data = pd.DataFrame( { @@ -149,17 +139,14 @@ def test_F_test_multiple_equation(seedn): f_stat = fit._f_statistic p_value = fit._p_value - # Compare with R - r_fit = stats.lm(fml, data=data) - r_wald = clubSandwich.Wald_test( - r_fit, - constraints=base.matrix(R, 3, 3), - vcov="CR1", - cluster=data["year"], - test="Naive-F", + r_fit = fixest.feols( + ro.Formula(fml), data=data, vcov=ro.Formula("~year"), ssc=fixest.ssc(adj=False) ) - r_fstat = pd.DataFrame(r_wald).T[1].values[0] - r_pvalue = pd.DataFrame(r_wald).T[5].values[0] + + r_wald = car.linearHypothesis(r_fit, base.matrix(R, 3, 3), test="F") + + r_fstat = r_wald.rx2("F")[1] + r_pvalue = r_wald.rx2("Pr(>F)")[1] np.testing.assert_allclose(f_stat, r_fstat, rtol=1e-03, atol=1e-03) np.testing.assert_allclose(p_value, r_pvalue, rtol=1e-03, atol=1e-03) @@ -213,22 +200,15 @@ def test_F_test_multiple_equations_pvalue(R, fml): fit.wald_test(R=R) f_stat = fit._f_statistic - # Compare with R - r_fit = stats.lm(fml, data=data) - r_wald = clubSandwich.Wald_test( - r_fit, - constraints=base.matrix(R, Rsize1, Rsize2), - vcov="CR1", - cluster=data["year"], - test="Naive-F", + r_fit = fixest.feols( + ro.Formula(fml), data=data, vcov=ro.Formula("~year"), ssc=fixest.ssc(adj=False) ) - r_fstat = pd.DataFrame(r_wald).T[1].values[0] - np.testing.assert_allclose(f_stat, r_fstat, rtol=1e-02, atol=1e-02) + r_wald = car.linearHypothesis(r_fit, base.matrix(R, Rsize1, Rsize2), test="F") -# We test "Wald-test" cases, where R and q are not trivial -# Note that clubSandwich R package does not allow non-zero q vector -car = importr("car") + r_fstat = r_wald.rx2("F")[1] + + np.testing.assert_allclose(f_stat, r_fstat, rtol=1e-02, atol=1e-02) @pytest.mark.parametrize(