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 d35884a4..c0cd0358 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
-[](https://opensource.org/license/mit)
-[](https://pypi.org/project/pyfixest/)
+[](https://opensource.org/license/mit)
-[](https://pepy.tech/project/pyfixest)
-[](https://pepy.tech/project/pyfixest)
+[](https://pypi.org/project/pyfixest/)
[](https://codecov.io/gh/py-econometrics/pyfixest)
[](https://github.com/astral-sh/ruff)
-[](#contributors-)
+[![Pixi Badge][pixi-badge]][pixi-url]
+[](#contributors-)
+[](https://pepy.tech/project/pyfixest)
+[](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 @@
[](https://pepy.tech/project/pyfixest)
[](https://codecov.io/gh/py-econometrics/pyfixest)
[](https://github.com/astral-sh/ruff)
-[](#contributors-)
+[![Pixi Badge][pixi-badge]][pixi-url]
+[](#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 @@
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-]
-
-[package.dependencies]
-idna = ">=2.0"
-multidict = ">=4.0"
-
-[[package]]
-name = "zipp"
-version = "3.20.2"
-description = "Backport of pathlib-compatible object wrapper for zip files"
-category = "main"
-optional = false
-python-versions = ">=3.8"
-files = [
- {file = "zipp-3.20.2-py3-none-any.whl", hash = "sha256:a817ac80d6cf4b23bf7f2828b7cabf326f15a001bea8b1f9b49631780ba28350"},
- {file = "zipp-3.20.2.tar.gz", hash = "sha256:bc9eb26f4506fda01b81bcde0ca78103b6e62f991b381fec825435c836edbc29"},
-]
-
-[package.extras]
-check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
-cover = ["pytest-cov"]
-doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-enabler = ["pytest-enabler (>=2.2)"]
-test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"]
-type = ["pytest-mypy"]
-
-[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(