From c403860cd00c1b5a6dce54faf549278b69d546bd Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Thu, 29 Aug 2024 22:40:06 +0200 Subject: [PATCH 001/102] move to pixi, first commit --- .coverage.DESKTOP-K05JQ94.23872.XnqWxQfx | 0 .gitattributes | 2 + .gitignore | 4 +- .pre-commit-config.yaml | 2 +- =0.1.0 | 0 =14.0.2 | 0 .../quarto_example/QuartoExample.quarto_ipynb | 116 - pixi.lock | 21494 ++++++++++++++++ poetry.lock | 4945 ---- pyproject.toml | 150 +- r_test_requirements.R | 11 + 11 files changed, 21570 insertions(+), 5154 deletions(-) create mode 100644 .coverage.DESKTOP-K05JQ94.23872.XnqWxQfx create mode 100644 .gitattributes create mode 100644 =0.1.0 create mode 100644 =14.0.2 delete mode 100644 docs/quarto_example/QuartoExample.quarto_ipynb create mode 100644 pixi.lock delete mode 100644 poetry.lock create mode 100644 r_test_requirements.R diff --git a/.coverage.DESKTOP-K05JQ94.23872.XnqWxQfx b/.coverage.DESKTOP-K05JQ94.23872.XnqWxQfx new file mode 100644 index 00000000..e69de29b 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/.gitignore b/.gitignore index c3d23333..5d05e6f4 100644 --- a/.gitignore +++ b/.gitignore @@ -23,4 +23,6 @@ readme.ipynb #docs/site_libs #site_libs tests/.coverage -.venv/ \ No newline at end of file +.venv/# pixi environments +.pixi +*.egg-info diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index f19d0e83..bc53da25 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -11,7 +11,7 @@ repos: - id: check-yaml args: [--allow-multiple-documents] - id: check-toml - - id: check-added-large-files + #- id: check-added-large-files - repo: https://github.com/python-jsonschema/check-jsonschema rev: 0.29.2 diff --git a/=0.1.0 b/=0.1.0 new file mode 100644 index 00000000..e69de29b diff --git a/=14.0.2 b/=14.0.2 new file mode 100644 index 00000000..e69de29b diff --git a/docs/quarto_example/QuartoExample.quarto_ipynb b/docs/quarto_example/QuartoExample.quarto_ipynb deleted file mode 100644 index 9dc50b19..00000000 --- a/docs/quarto_example/QuartoExample.quarto_ipynb +++ /dev/null @@ -1,116 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "---\n", - "title: \"Quarto and PyFixest\"\n", - "jupyter: python3\n", - "format:\n", - " pdf:\n", - " number-sections: true\n", - " include-in-header:\n", - " - text: |\n", - " \\usepackage{booktabs}\n", - " \\usepackage{makecell}\n", - " \\usepackage{threeparttable}\n", - "execute:\n", - " echo: false\n", - " warning: false\n", - "author:\n", - "- Peter Pan^[University of Neverland]\n", - "date: last-modified\n", - "abstract: |\n", - " \\\n", - " \\\n", - " We study the effect of X1 and X2 on Y and Y2 using PyFixest. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet.\n", - " \\\n", - " \\\n", - " **Keywords**: Regressions, PyFixest, Tables, Quarto\n", - "---\n", - "\n", - "{{< pagebreak >}}\n", - "\n", - "\n", - "# Introduction\n", - "\n", - "Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet.\"\n" - ], - "id": "78e2a9c8" - }, - { - "cell_type": "code", - "metadata": {}, - "source": [ - "#| echo: false\n", - "#| output: false\n", - "import pandas as pd\n", - "import pyfixest as pf\n", - "\n", - "data = pf.get_data()\n", - "\n", - "fit1 = pf.feols(\"Y ~ X1 + X2 | f1\", data = data)\n", - "fit2 = pf.feols(\"Y ~ X1 + X2 | f1 + f2\", data = data)\n", - "fit3 = pf.feols(\"Y ~ X1 *X2 | f1 + f2\", data = data)\n", - "fit4 = pf.feols(\"Y2 ~ X1 + X2 | f1\", data = data)\n", - "fit5 = pf.feols(\"Y2 ~ X1 + X2 | f1 + f2\", data = data)\n", - "fit6 = pf.feols(\"Y2 ~ X1 *X2 | f1 + f2\", data = data)\n", - "\n", - "labels={\n", - " \"Y\": \"Wage\",\n", - " \"Y2\": \"Wealth\",\n", - " \"X1\": \"Age\",\n", - " \"X2\": \"Years of Schooling\",\n", - " \"f1\": \"Industry\",\n", - " \"f2\": \"Year\"\n", - "}" - ], - "id": "c444d358", - "execution_count": null, - "outputs": [] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# A PyFixest Regression Table\n", - "As @tbl-main shows, LaTex Tables generated by PyFixest can be easily integrated into Quarto document when rendered as pdf.\n" - ], - "id": "4fc14b82" - }, - { - "cell_type": "code", - "metadata": { - "tbl-pos": "H" - }, - "source": [ - "#| label: tbl-main\n", - "#| tbl-cap: A PyFixest Regression Table\n", - "#| output: asis\n", - "#| echo: false\n", - "\n", - "mynotes=\"Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet.\"\n", - "\n", - "tab=pf.etable([fit1, fit2, fit4, fit5],\n", - " labels=labels, notes=mynotes, type=\"tex\",\n", - " model_heads=[\"US\", \"China\", \"US\", \"China\"])\n", - "\n", - "print(tab)" - ], - "id": "tbl-main", - "execution_count": null, - "outputs": [] - } - ], - "metadata": { - "kernelspec": { - "name": "python3", - "language": "python", - "display_name": "Python 3 (ipykernel)", - "path": "C:\\Users\\dirks\\AppData\\Roaming\\Python\\share\\jupyter\\kernels\\python3" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 00000000..f9071ed6 --- /dev/null +++ b/pixi.lock @@ -0,0 +1,21494 @@ +version: 5 +environments: + default: + channels: + - url: https://conda.anaconda.org/conda-forge/ + indexes: + - https://pypi.org/simple + packages: + linux-64: + - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 + - 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-[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 = "e609fccc5b60ea2d206376264d30ff2072f70d59d00ec0f5b8bf10c6b83c749c" diff --git a/pyproject.toml b/pyproject.toml index 868750c5..81019e6d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,45 +1,76 @@ -[tool.poetry] +[project] +authors = [{name = "Alexander Fischer", email = "alexander-fischer1801@t-online.de"}] +description = "Fast high dimensional fixed effect estimation following syntax of the fixest R package." name = "pyfixest" +requires-python = ">= 3.9" version = "0.24.1" +dependencies = ["lets-plot>=4.0.1"] -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"] -license = "MIT" -readme = "README.md" -homepage = "https://py-econometrics.github.io/pyfixest/" -repository = "https://github.com/py-econometrics/pyfixest" +[project.optional-dependencies] +test = ["pytest>=7.2.0"] -[tool.poetry.dependencies] -python = ">=3.9,<4.0" -pandas = ">=1.1.0" -numpy = ">=1.19.0" +[build-system] +build-backend = "hatchling.build" +requires = ["hatchling"] + +[tool.pixi.project] +channels = ["conda-forge"] +platforms = ["linux-64", "win-64", "osx-64", "osx-arm64"] + +[tool.pixi.pypi-dependencies] +pyfixest = { path = ".", editable = true } + +[tool.pixi.tasks] +debug = "python pyfixest/debug.py" + +[tool.pixi.dependencies] scipy = ">=1.6" formulaic = ">=1.0.0" -lets-plot = ">=4.0.1" -seaborn = ">=0.13.2" +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" +tqdm = "==4.66.4" +great_tables = ">=0.10.0,<0.11" +numpy = ">=1.19.0" -[tool.poetry.group.dev.dependencies] -pytest=">=7.0.0" -rpy2 = "3.5.15" -pytest-cov = "^4.1.0" +[tool.pixi.environments] +default = { solve-group = "default" } +test = { features = ["test"], solve-group = "default" } +docs = { features = ["docs"], solve-group = "default" } + +[tool.pixi.feature.test.dependencies] +pytest = ">=7.0.0" +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" +pyarrow = ">=17.0.0,<18" +pre-commit = "==3.6.0" +doubleml = "==0.7.1" +r-fixest = ">=0.12.1,<0.13" +r-broom = ">=1.0.5,<2" + +[tool.pixi.feature.test.tasks] +test = "pytest" +tests = "pytest -n 4 --cov-report=term tests" +tests-regular = "pytest tests -m 'not extended' -n 4" +tests-rerun = "pytest --lf -n 4" -[tool.poetry.group.docs.dependencies] +[tool.pixi.feature.docs.dependencies] quartodoc = ">=0.7.2" -jupyterlab = "^4.0.12" -jupytext = "^1.16.1" -watermark = "^2.4.3" +jupyterlab = "4.0.12.*" +jupytext = "==1.16.1" +watermark = "==2.4.3" + +[tool.pixi.feature.docs.tasks] +build-docs = "run quartodoc build --verbose --config docs/_quarto.yml" +build-docs2 = "quartodoc build --verbose --config docs/_quarto.yml" +render-docs2 = "quarto render docs" +preview2 = "quarto preview docs" + +[tool.pixi.feature.tests.dependencies] +rpy2 = "==3.5.15" [tool.pytest.ini_options] addopts = [ @@ -53,66 +84,3 @@ addopts = [ markers = [ "extended: mark test to be part of the extended test suite" ] -filterwarnings =[ - "ignore::FutureWarning:rpy2", - "ignore::DeprecationWarning:rpy2" -] - -[tool.ruff] -line-length = 88 -fix = true - -# Assume Python 3.9 -target-version = "py39" - -[tool.ruff.lint] -# docs: https://docs.astral.sh/ruff/rules/ -select = [ - "F", # Pyflakes - "E", # pycodestyle errors - "W", # pycodestyle warnings - "I", # isort - "D", # flake8-docstrings - "UP", # pyupgrade - "SIM", # flake8-simplify - "TRY", # tryceratops -] - -ignore = [ -# do not enable if formatting -# docs: https://docs.astral.sh/ruff/formatter/#conflicting-lint-rules - "W191", # tab indentation - "E111", # indentation - "E114", # indentation - "E117", # over indented - "D206", # indent with spaces - "D300", # triple single quotes - "E501", # line length regulated by formatter - "D105", # missing docstring in magic method - "D100", # missing docstring in public module - "D104", # missing docstring in public package - "SIM110", # Use all instead of `for` loop - "TRY003", # Avoid specifying long messages outside the exception class - "D205", # 1 blank line required between summary line and description - "W505", # Doc line too long -] - -[tool.ruff.lint.per-file-ignores] -"tests/**/*.py" = ["D100", "D103"] -"pyfixest/multcomp.py" = ["D103"] -"pyfixest/summarize.py" = ["D103"] -"pyfixest/visualize.py" = ["D103"] - -[tool.ruff.lint.pycodestyle] -max-doc-length = 88 - -[tool.ruff.lint.pydocstyle] -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..964a77d6 --- /dev/null +++ b/r_test_requirements.R @@ -0,0 +1,11 @@ +# note: fixest and broom are installed via conda +install.packages( + c('clubSandwich', 'did2s', 'wildrwolf', 'reticulate', 'ivDiag'), + repos='https://cran.rstudio.com', + type = "binary" +); +install.packages( + 'ritest', + repos = c('https://grantmcdermott.r-universe.dev', 'https://cloud.r-project.org'), + type = "binary" +); From 5672f7ca7bbfc9056c4b8ff55d9946faf0c83b24 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Fri, 30 Aug 2024 12:54:18 +0200 Subject: [PATCH 002/102] bring back ruff to pyproject.toml --- pixi.lock | 2 +- pyproject.toml | 55 ++++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 56 insertions(+), 1 deletion(-) diff --git a/pixi.lock b/pixi.lock index f9071ed6..e9967348 100644 --- a/pixi.lock +++ b/pixi.lock @@ -14927,7 +14927,7 @@ packages: name: pyfixest version: 0.24.1 path: . - sha256: ca2c1e59e37962de1788a1086100a690082f9cf93739bc722226d2a6f072a1e9 + sha256: dbc58c12854c7866134d196f4484179dc63b1c65e7f232750f50774982ebe656 requires_dist: - lets-plot>=4.0.1 - pytest>=7.2.0 ; extra == 'test' diff --git a/pyproject.toml b/pyproject.toml index 81019e6d..f871d884 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -84,3 +84,58 @@ addopts = [ markers = [ "extended: mark test to be part of the extended test suite" ] + +[tool.ruff] +line-length = 88 +fix = true + +# Assume Python 3.9 +target-version = "py39" + +[tool.ruff.lint] +# docs: https://docs.astral.sh/ruff/rules/ +select = [ + "F", # Pyflakes + "E", # pycodestyle errors + "W", # pycodestyle warnings + "I", # isort + "D", # flake8-docstrings + "UP", # pyupgrade + "SIM", # flake8-simplify + "TRY", # tryceratops +] + +ignore = [ +# do not enable if formatting +# docs: https://docs.astral.sh/ruff/formatter/#conflicting-lint-rules + "W191", # tab indentation + "E111", # indentation + "E114", # indentation + "E117", # over indented + "D206", # indent with spaces + "D300", # triple single quotes + "E501", # line length regulated by formatter + "D105", # missing docstring in magic method + "D100", # missing docstring in public module + "D104", # missing docstring in public package + "SIM110", # Use all instead of `for` loop + "TRY003", # Avoid specifying long messages outside the exception class + "D205", # 1 blank line required between summary line and description + "W505", # Doc line too long +] + +[tool.ruff.lint.per-file-ignores] +"tests/**/*.py" = ["D100", "D103"] +"pyfixest/multcomp.py" = ["D103"] +"pyfixest/summarize.py" = ["D103"] +"pyfixest/visualize.py" = ["D103"] + +[tool.ruff.lint.pycodestyle] +max-doc-length = 88 + +[tool.ruff.lint.pydocstyle] +convention = "numpy" + +[tool.ruff.format] +docstring-code-format = true +docstring-code-line-length = 88 From c95368f753bc25ab25f46a945603e6f4f97dd5aa Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Fri, 30 Aug 2024 13:57:47 +0200 Subject: [PATCH 003/102] bring back size checks --- .pre-commit-config.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index bc53da25..75a4ddda 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -11,8 +11,8 @@ repos: - id: check-yaml args: [--allow-multiple-documents] - id: check-toml - #- id: check-added-large-files - + - id: check-added-large-files + exclude: pixi.lock - repo: https://github.com/python-jsonschema/check-jsonschema rev: 0.29.2 hooks: From bc52b40cf6c203a599b22e86e566310a86a90b47 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Fri, 30 Aug 2024 14:05:44 +0200 Subject: [PATCH 004/102] update ci --- .github/workflows/ci-tests.yaml | 19 ++++++++----------- 1 file changed, 8 insertions(+), 11 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index 7c0d65c8..58992be8 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -27,10 +27,9 @@ 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 + + - name: Set up pixi + uses: prefix-dev/setup-pixi@v0.8.1 - name: set numba parallel flags run: | @@ -45,7 +44,7 @@ jobs: - name: Run tests run: | - poetry run pytest tests -m "not extended" --cov=./ --cov-report=xml + pixi run tests-regular - name: Upload to Codecov uses: codecov/codecov-action@v4 @@ -60,10 +59,8 @@ 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 + - name: Set up pixi + uses: prefix-dev/setup-pixi@v0.8.1 - name: Set up Quarto uses: quarto-dev/quarto-actions/setup@v2 - name: install tinytex @@ -71,10 +68,10 @@ jobs: quarto install tinytex - name: Compile docstrings with quartodoc run : | - poetry run quartodoc build --verbose --config docs/_quarto.yml + pixi run build-docs2 - name: Render docs run: | - poetry run quarto render docs + pixi run render-docs2 - name: Save docs artifact uses: actions/upload-artifact@v4 with: From 83d621e554444831bb0c8ebd6c07c48f2cbe3fcf Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Fri, 30 Aug 2024 14:13:33 +0200 Subject: [PATCH 005/102] update env file --- pixi.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pixi.lock b/pixi.lock index e9967348..ed66b7f0 100644 --- a/pixi.lock +++ b/pixi.lock @@ -14927,7 +14927,7 @@ packages: name: pyfixest version: 0.24.1 path: . - sha256: dbc58c12854c7866134d196f4484179dc63b1c65e7f232750f50774982ebe656 + sha256: 53d9db31ca5da7b98277fffe021893878bd8ac3cad99a9bd70a810fb59f41ce9 requires_dist: - lets-plot>=4.0.1 - pytest>=7.2.0 ; extra == 'test' From e23457d2d89cfb1bf84b17f4cc8f7c2bf932a753 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Fri, 30 Aug 2024 16:14:35 +0200 Subject: [PATCH 006/102] small toml updates --- pyproject.toml | 21 +++++---------------- r_test_requirements.R | 2 +- 2 files changed, 6 insertions(+), 17 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index f871d884..264bc5c0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,17 +6,13 @@ requires-python = ">= 3.9" version = "0.24.1" dependencies = ["lets-plot>=4.0.1"] -[project.optional-dependencies] -test = ["pytest>=7.2.0"] - [build-system] build-backend = "hatchling.build" requires = ["hatchling"] [tool.pixi.project] channels = ["conda-forge"] -platforms = ["linux-64", "win-64", "osx-64", "osx-arm64"] - +platforms = ["win-64"] [tool.pixi.pypi-dependencies] pyfixest = { path = ".", editable = true } @@ -37,22 +33,19 @@ numpy = ">=1.19.0" [tool.pixi.environments] default = { solve-group = "default" } -test = { features = ["test"], solve-group = "default" } +dev = { features = ["dev"], solve-group = "default" } docs = { features = ["docs"], solve-group = "default" } -[tool.pixi.feature.test.dependencies] -pytest = ">=7.0.0" +[tool.pixi.feature.dev.dependencies] +pytest = ">=7.0.0, <8.0.0" pytest-cov = "==4.1.0" pytest-xdist = ">=3.5.0" pyhdfe = ">=0.2.0" pyarrow = ">=17.0.0,<18" pre-commit = "==3.6.0" doubleml = "==0.7.1" -r-fixest = ">=0.12.1,<0.13" -r-broom = ">=1.0.5,<2" -[tool.pixi.feature.test.tasks] -test = "pytest" +[tool.pixi.feature.dev.tasks] tests = "pytest -n 4 --cov-report=term tests" tests-regular = "pytest tests -m 'not extended' -n 4" tests-rerun = "pytest --lf -n 4" @@ -64,14 +57,10 @@ jupytext = "==1.16.1" watermark = "==2.4.3" [tool.pixi.feature.docs.tasks] -build-docs = "run quartodoc build --verbose --config docs/_quarto.yml" build-docs2 = "quartodoc build --verbose --config docs/_quarto.yml" render-docs2 = "quarto render docs" preview2 = "quarto preview docs" -[tool.pixi.feature.tests.dependencies] -rpy2 = "==3.5.15" - [tool.pytest.ini_options] addopts = [ "-v", diff --git a/r_test_requirements.R b/r_test_requirements.R index 964a77d6..0629f90f 100644 --- a/r_test_requirements.R +++ b/r_test_requirements.R @@ -1,6 +1,6 @@ # note: fixest and broom are installed via conda install.packages( - c('clubSandwich', 'did2s', 'wildrwolf', 'reticulate', 'ivDiag'), + c('fixest', 'broom','clubSandwich', 'did2s', 'wildrwolf', 'reticulate', 'ivDiag'), repos='https://cran.rstudio.com', type = "binary" ); From 365b07a151f719061bd049ac0cbcf7aeaf9715e6 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sat, 31 Aug 2024 18:42:29 +0200 Subject: [PATCH 007/102] rename docs tasks, rename test env to dev --- .github/workflows/ci-tests.yaml | 4 +- pixi.lock | 9565 ++++++------------------------- pyproject.toml | 11 +- 3 files changed, 1681 insertions(+), 7899 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index 58992be8..29fe877f 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -68,10 +68,10 @@ jobs: quarto install tinytex - name: Compile docstrings with quartodoc run : | - pixi run build-docs2 + pixi run build-docs - name: Render docs run: | - pixi run render-docs2 + pixi run render-docs - name: Save docs artifact uses: actions/upload-artifact@v4 with: diff --git a/pixi.lock b/pixi.lock index ed66b7f0..621609d4 100644 --- a/pixi.lock +++ b/pixi.lock @@ -14,7 +14,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-1.1.0-hd590300_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-bin-1.1.0-hd590300_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.8.30-hbcca054_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/cached_property-1.5.2-pyha770c72_1.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2024.7.4-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_0.tar.bz2 @@ -116,7 +116,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/osx-64/brotli-1.1.0-h0dc2134_1.conda - conda: https://conda.anaconda.org/conda-forge/osx-64/brotli-bin-1.1.0-h0dc2134_1.conda - conda: https://conda.anaconda.org/conda-forge/osx-64/bzip2-1.0.8-hfdf4475_7.conda - - conda: https://conda.anaconda.org/conda-forge/osx-64/ca-certificates-2024.7.4-h8857fd0_0.conda + - conda: https://conda.anaconda.org/conda-forge/osx-64/ca-certificates-2024.8.30-h8857fd0_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/cached_property-1.5.2-pyha770c72_1.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2024.7.4-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_0.tar.bz2 @@ -210,7 +210,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/osx-arm64/brotli-1.1.0-hb547adb_1.conda - conda: https://conda.anaconda.org/conda-forge/osx-arm64/brotli-bin-1.1.0-hb547adb_1.conda - conda: https://conda.anaconda.org/conda-forge/osx-arm64/bzip2-1.0.8-h99b78c6_7.conda - - conda: https://conda.anaconda.org/conda-forge/osx-arm64/ca-certificates-2024.7.4-hf0a4a13_0.conda + - conda: https://conda.anaconda.org/conda-forge/osx-arm64/ca-certificates-2024.8.30-hf0a4a13_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/cached_property-1.5.2-pyha770c72_1.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2024.7.4-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_0.tar.bz2 @@ -309,9 +309,9 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2024.7.4-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_0.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/noarch/commonmark-0.9.1-py_0.tar.bz2 - - conda: https://conda.anaconda.org/conda-forge/win-64/contourpy-1.3.0-py310hc19bc0b_0.conda + - conda: https://conda.anaconda.org/conda-forge/win-64/contourpy-1.3.0-py312hd5eb7cc_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/cycler-0.12.1-pyhd8ed1ab_0.conda - - conda: https://conda.anaconda.org/conda-forge/win-64/fonttools-4.53.1-py310ha8f682b_0.conda + - conda: https://conda.anaconda.org/conda-forge/win-64/fonttools-4.53.1-py312h4389bb4_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/formulaic-1.0.2-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/win-64/freetype-2.12.1-hdaf720e_2.conda - conda: https://conda.anaconda.org/conda-forge/noarch/future-1.0.0-pyhd8ed1ab_0.conda @@ -323,7 +323,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/importlib_resources-6.4.4-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/win-64/intel-openmp-2024.2.1-h57928b3_1083.conda - conda: https://conda.anaconda.org/conda-forge/noarch/interface_meta-1.3.0-pyhd8ed1ab_0.tar.bz2 - - conda: https://conda.anaconda.org/conda-forge/win-64/kiwisolver-1.4.5-py310h232114e_1.conda + - conda: https://conda.anaconda.org/conda-forge/win-64/kiwisolver-1.4.5-py312hd5eb7cc_2.conda - conda: https://conda.anaconda.org/conda-forge/win-64/lcms2-2.16-h67d730c_0.conda - conda: https://conda.anaconda.org/conda-forge/win-64/lerc-4.0.0-h63175ca_0.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/win-64/libblas-3.9.0-23_win64_mkl.conda @@ -332,6 +332,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/win-64/libbrotlienc-1.1.0-hcfcfb64_1.conda - conda: https://conda.anaconda.org/conda-forge/win-64/libcblas-3.9.0-23_win64_mkl.conda - conda: https://conda.anaconda.org/conda-forge/win-64/libdeflate-1.21-h2466b09_0.conda + - conda: https://conda.anaconda.org/conda-forge/win-64/libexpat-2.6.2-h63175ca_0.conda - conda: https://conda.anaconda.org/conda-forge/win-64/libffi-3.4.2-h8ffe710_5.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/win-64/libhwloc-2.11.1-default_h8125262_1000.conda - conda: https://conda.anaconda.org/conda-forge/win-64/libiconv-1.17-hcfcfb64_2.conda @@ -344,40 +345,40 @@ environments: - conda: https://conda.anaconda.org/conda-forge/win-64/libxcb-1.16-h013a479_1.conda - conda: https://conda.anaconda.org/conda-forge/win-64/libxml2-2.12.7-h0f24e4e_4.conda - conda: https://conda.anaconda.org/conda-forge/win-64/libzlib-1.3.1-h2466b09_1.conda - - conda: https://conda.anaconda.org/conda-forge/win-64/llvmlite-0.43.0-py310h0288bfe_0.conda + - conda: https://conda.anaconda.org/conda-forge/win-64/llvmlite-0.43.0-py312h1f7db74_0.conda - conda: 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"0.24.1" -dependencies = ["lets-plot>=4.0.1"] [project.optional-dependencies] -test = ["wildboottest==0.3.1"] +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"] +docs = ["quartodoc>=0.7.2", "jupyterlab>=4.0.12", "jupytext==1.16.1", "watermark==2.4.3"] [build-system] build-backend = "hatchling.build" @@ -16,53 +17,27 @@ requires = ["hatchling"] [tool.pixi.project] channels = ["conda-forge"] platforms = ["linux-64", "win-64", "osx-64", "osx-arm64"] + [tool.pixi.pypi-dependencies] pyfixest = { path = ".", editable = true } [tool.pixi.tasks] debug = "python pyfixest/debug.py" -[tool.pixi.dependencies] -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,<0.11" -numpy = ">=1.19.0" - [tool.pixi.environments] default = { solve-group = "default" } dev = { features = 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17 00:00:00 2001 From: Alexander Fischer Date: Sat, 31 Aug 2024 23:29:04 +0200 Subject: [PATCH 010/102] add other authors --- pixi.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index e1c16fd7..9a1b6471 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4665,7 +4665,7 @@ packages: name: pyfixest version: 0.24.1 path: . - sha256: 5af70520144d3a7943e9e2c146854f93b5a42ac450a93c4b06f7857b61a563ed + sha256: 64efcdab55743bce02c30f9db51b5184cd1fd40b63db7fdd4378113d504490ea requires_dist: - lets-plot>=4.0.0 - scipy>=1.6 diff --git a/pyproject.toml b/pyproject.toml index c484b6c6..e1c56501 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,5 +1,5 @@ [project] -authors = [{name = "Alexander Fischer", email = "alexander-fischer1801@t-online.de"}] +authors = [{name = "Alexander Fischer", email = "alexander-fischer1801@t-online.de"}, {name = "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"] description = "Fast high dimensional fixed effect estimation following syntax of the fixest R package." name = "pyfixest" From 9a4e1452a24984b2697cce8d60293313c32b67be Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sat, 31 Aug 2024 23:29:48 +0200 Subject: [PATCH 011/102] update description --- pixi.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index 9a1b6471..e5996073 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4665,7 +4665,7 @@ packages: name: pyfixest version: 0.24.1 path: . - sha256: 64efcdab55743bce02c30f9db51b5184cd1fd40b63db7fdd4378113d504490ea + sha256: 96275f6093abffcfc9a41beef0f9ffa15bf53ac6feebe4de953a3f83de150a10 requires_dist: - lets-plot>=4.0.0 - scipy>=1.6 diff --git a/pyproject.toml b/pyproject.toml index e1c56501..08958b3b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,7 @@ [project] authors = [{name = "Alexander Fischer", email = "alexander-fischer1801@t-online.de"}, {name = "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"] -description = "Fast high dimensional fixed effect estimation following syntax of the fixest R package." +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)." name = "pyfixest" requires-python = ">= 3.9" version = "0.24.1" From 77b1a5bc7952d9c118fc48c52e08ad56c37db8d3 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sat, 31 Aug 2024 23:32:12 +0200 Subject: [PATCH 012/102] tweaks --- pixi.lock | 2 +- pyproject.toml | 6 ++---- 2 files changed, 3 insertions(+), 5 deletions(-) diff --git a/pixi.lock b/pixi.lock index e5996073..2457d17e 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4665,7 +4665,7 @@ packages: name: pyfixest version: 0.24.1 path: . - sha256: 96275f6093abffcfc9a41beef0f9ffa15bf53ac6feebe4de953a3f83de150a10 + sha256: ce956937e96a91f2861a34ecc528637b6d9a030a5e8a555552aef5a1c1b801d1 requires_dist: - lets-plot>=4.0.0 - scipy>=1.6 diff --git a/pyproject.toml b/pyproject.toml index 08958b3b..2fbba14e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,7 @@ [project] authors = [{name = "Alexander Fischer", email = "alexander-fischer1801@t-online.de"}, {name = "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"] -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)." +description = "Fast high dimensional fixed effect estimation following syntax of the fixest R package." name = "pyfixest" requires-python = ">= 3.9" version = "0.24.1" @@ -21,9 +21,6 @@ platforms = ["linux-64", "win-64", "osx-64", "osx-arm64"] [tool.pixi.pypi-dependencies] pyfixest = { path = ".", editable = true } -[tool.pixi.tasks] -debug = "python pyfixest/debug.py" - [tool.pixi.environments] default = { solve-group = "default" } dev = { features = ["dev"], solve-group = "default" } @@ -33,6 +30,7 @@ docs = { features = ["docs"], solve-group = "default" } tests = "pytest -n 4 --cov-report=term tests" tests-regular = "pytest tests -m 'not extended' -n 4" tests-rerun = "pytest --lf -n 4" +debug = "python pyfixest/debug.py" [tool.pixi.feature.docs.tasks] docs-build = "quartodoc build --verbose --config docs/_quarto.yml" From 32f4a4ba4bb6042f61233103a5ab545320176d97 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sat, 31 Aug 2024 23:34:07 +0200 Subject: [PATCH 013/102] even more tweaks --- pixi.lock | 2 +- pyproject.toml | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/pixi.lock b/pixi.lock index 2457d17e..4d4e8589 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4665,7 +4665,7 @@ packages: name: pyfixest version: 0.24.1 path: . - 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pixi.lock | 4 +- poetry.lock | 4970 ------------------------------------------------ pyproject.toml | 2 + 4 files changed, 4 insertions(+), 5037 deletions(-) delete mode 100644 justfile delete mode 100644 poetry.lock diff --git a/justfile b/justfile deleted file mode 100644 index 1f74e2c7..00000000 --- a/justfile +++ /dev/null @@ -1,65 +0,0 @@ -# uncomment for windows -set shell := ["powershell.exe", "-c"] - -# docs: justfile docs: https://just.systems/man/en/ -default: - just --list --unsorted - -# Clean environment -[confirm] -clean: - rm -rf .venv/ - -# Update dependencies in pyproject.toml -poetry-update: - poetry update - -# Install development dependencies -install-dev: - poetry env use 3.11 - poetry config virtualenvs.in-project true - poetry install - -# Install R dependencies -install-r: - Rscript -e "install.packages(c('broom', 'clubSandwich', 'did2s', 'fixest', 'wildrwolf', 'reticulate'), repos='https://cran.rstudio.com'); install.packages('ritest', repos = c('https://grantmcdermott.r-universe.dev', 'https://cloud.r-project.org')); install.packages('ivDiag', repos='http://cran.us.r-project.org')" -# Create R test data sets -update-tests-data: - poetry run Rscript tests/r_test_comparisons.R - -# Run pytest -tests: - poetry run pytest -n 4 --cov-report=term tests - -rerun-tests: - poetry run pytest --lf -n 4 - -# Build the package -build: tests - poetry build - -# Build documentation and website -docs-build: - poetry run quartodoc build --verbose --config docs/_quarto.yml - -# Render documentation and website -render: docs-build - poetry run quarto render docs - -# Build the documentation and watch for changes -docs-watch: - poetry run poetry run quartodoc build --watch --verbose --config docs/_quarto.yml - -# Preview the docs -preview: - poetry run quarto preview docs - -# Clean docs build -docs-clean: - rm -rf docs/_build docs/api/api_card - -lint: - poetry run pre-commit run ruff --all-files - -debug: - python pyfixest/debug.py diff --git a/pixi.lock b/pixi.lock index 4d4e8589..e2185133 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4663,9 +4663,9 @@ packages: requires_python: '>=3.8' - kind: pypi name: pyfixest - version: 0.24.1 + version: 0.24.3 path: . - 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-[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 = "e609fccc5b60ea2d206376264d30ff2072f70d59d00ec0f5b8bf10c6b83c749c" diff --git a/pyproject.toml b/pyproject.toml index 0fa57153..d45a6805 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -31,6 +31,8 @@ tests = "pytest -n 4 --cov-report=term tests" tests-regular = "pytest tests -m 'not extended' -n 4" 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" [tool.pixi.feature.docs.tasks] docs-build = "quartodoc build --verbose --config docs/_quarto.yml" From 815a37669407695a1f9cda61359f58b0314bfdbe Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 1 Sep 2024 09:47:23 +0200 Subject: [PATCH 015/102] update contributing md --- docs/contributing.qmd | 86 ++++++++++++++----------------------------- 1 file changed, 28 insertions(+), 58 deletions(-) diff --git a/docs/contributing.qmd b/docs/contributing.qmd index b35e1dc2..ae60222c 100644 --- a/docs/contributing.qmd +++ b/docs/contributing.qmd @@ -42,7 +42,7 @@ git clone https://github.com//pyfixest.git cd pyfixest ``` -In order to work of `pyfixest`, you will need Python and R installed. If working +In order to work on `pyfixest`, you will need Python and R installed. If working on documentation, you will need Quarto installed. There are multiple ways of installing Python and R, but if you need to install @@ -50,7 +50,7 @@ them prior to development the following are potential options: #### Installing Python -On Mac/Linux via [Hombrew](https://brew.sh/): +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} brew install python@3.11 # specify the version of python you prefer @@ -84,22 +84,6 @@ On Windows using [Winget](https://winget.run/pkg/RProject/R): winget install -e --id RProject.R ``` -Tests run with R require the following packages: - -- base -- broom -- clubSandwich -- did2s -- fixest -- stats -- wildrwolf -- ritest -- ivDiag - -```{.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'))' -``` - Documentation for `pyfixest` is written, compiled, and published using Quarto. To install Quarto, run: @@ -126,84 +110,70 @@ scoop install extras/quarto ### Package Management -`PyFixest` is using [poetry](https://github.com/python-poetry/poetry). +`PyFixest` is using [pixi](https://pixi.sh/latest/). -Please follow the [installation instructions](https://python-poetry.org/docs/#installing-with-the-official-installer) from the poetry documentation. +Please follow the [installation instructions](https://pixi.sh/latest/#installation) from the `pixi` documentation. Afterwards, you can initiate the project environment and install all dependencies by running ```{.bash .code-copy} cd path-to-pyfixest -poetry install +pixi install ``` If you type ```{.bash .code-copy} -poetry shell +pixi shell ``` -you will see that you have activated a custom poetry environment for pyfixest. +you will see that you have activated a custom `pixi` environment for `pyfixest`. ### Code Style We use `ruff` and `pre-commit` to ensure a consistent code style. -You can install `pre-commit` from `pip` by running - -```{.bash .code-copy} -pip install pre-commit -``` - To install the required hooks, run ```{.bash .code-copy} -pre-commit install +pixi run lint ``` and you're ready to go! -### Justfile +### `Pixi` tasks -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. +There are several command line targets that assist with development included +as `pixi` tasks. -On Mac/Linux via [Homebrew](https://formulae.brew.sh/formula/just#default): ```{.bash .code-copy} -brew install just +# install all R development dependencies +pixi r install-r +# run all tests via pytest +pixi r tests +# run all tests excluding very computationally demanding tests +pixi r tests-regular ``` -On Windows: +To rebuild the documentation locally, you can run ```{.bash .code-copy} -scoop bucket add main -scoop install main/just +# Build documentation and website +pixi r docs-build +# render the docs +pixi r docs-render +# preview the docs +pixi r docs-preview ``` -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"]`. +To run the linter, you can run ```{.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 +just r lint ``` -To rebuild the documentation locally, you can run +To re-create the csv files in `tests/data` that contain results from R packages for testing, you can run ```{.bash .code-copy} -# Build documentation and website -just docs-build -# render the docs -just render -# preview the docs -just preview +`just update-tests-data` ``` - -To re-create the csv files in `tests/data` that contain results from R packages for testing, you can run `just update-tests-data`. 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extra == 'dev' + - wildboottest>=0.3.2 ; extra == 'dev' - quartodoc>=0.7.2 ; extra == 'docs' - jupyterlab>=4.0.12 ; extra == 'docs' - jupytext==1.16.1 ; extra == 'docs' @@ -6236,6 +6241,18 @@ packages: - wsaccel ; extra == 'optional' - websockets ; extra == 'test' requires_python: '>=3.8' +- kind: pypi + name: wildboottest + version: 0.3.2 + url: https://files.pythonhosted.org/packages/b2/75/419e54d92b1b97128a12f8dcd53b40b5144a33a69026496287a3ab7557e4/wildboottest-0.3.2-py3-none-any.whl + sha256: 886762642098358ddeb190656fc05c17e26d5c024ccff9f8863627ce3392902f + requires_dist: + - numba>=0.57 + - numpy>=1.18 + - pandas>=1.4 + - statsmodels>=0.13 + - tabulate>=0.9.0 + requires_python: '>=3.8,<4.0' - kind: pypi name: wrapt version: 1.16.0 diff --git a/pyproject.toml b/pyproject.toml index d45a6805..3eb96f4d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,7 +7,7 @@ authors = [{name = "Alexander Fischer", email = "alexander-fischer1801@t-online. dependencies = ["lets-plot>=4.0.0", 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a/.gitattributes +++ b/.gitattributes @@ -1,4 +1,2 @@ # GitHub syntax highlighting pixi.lock linguist-language=YAML linguist-generated=true -# GitHub syntax highlighting -pixi.lock linguist-language=YAML linguist-generated=true diff --git a/pyproject.toml b/pyproject.toml index 3eb96f4d..7398fc05 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -106,3 +106,8 @@ convention = "numpy" [tool.ruff.format] docstring-code-format = true docstring-code-line-length = 88 + +filterwarnings =[ + "ignore::FutureWarning:rpy2", + "ignore::DeprecationWarning:rpy2" +] From 0c02911bc865a1eb4d614e7d79027f92cc20a878 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 1 Sep 2024 15:04:43 +0200 Subject: [PATCH 018/102] add badges to readmes --- README.md | 6 +++++- docs/pyfixest.md | 7 ++++++- pixi.lock | 2 +- 3 files changed, 12 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 483fdb71..b1b7cd43 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,11 @@ [![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/docs/pyfixest.md b/docs/pyfixest.md index e767034d..1b7024ca 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 index 1abe59e8..1df041d6 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4669,7 +4669,7 @@ packages: name: pyfixest version: 0.24.3 path: . - sha256: 0e6deaafd1144766a556fbfa26558e53e277fed762b5a14be867872f9bbe88d1 + sha256: e762acc437fc6d0ce0203b3d5a488a03458544e887b546ab7f5de19978683ca8 requires_dist: - lets-plot>=4.0.0 - scipy>=1.6 From f48bcd6299f64fa093626f910a7224439c32ea8e Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 1 Sep 2024 15:10:07 +0200 Subject: [PATCH 019/102] move filterwarnings to correct section --- pixi.lock | 2 +- pyproject.toml | 9 ++++----- 2 files changed, 5 insertions(+), 6 deletions(-) diff --git a/pixi.lock b/pixi.lock index 1df041d6..ea6c1ae9 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4669,7 +4669,7 @@ packages: name: pyfixest version: 0.24.3 path: . - sha256: 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docs-build = "quartodoc build --verbose --config docs/_quarto.yml" docs-render = "quarto render docs" From 6fc256daf77484109cdc43a443550efdc033aaeb Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 1 Sep 2024 16:09:55 +0200 Subject: [PATCH 022/102] update lock file --- pixi.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pixi.lock b/pixi.lock index 6d360991..92547ff4 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5098,7 +5098,7 @@ packages: name: pyfixest version: 0.24.3 path: . - sha256: 66f2a31b8e555ff88b7ecb9f2c5032da205411a9cf143643c8cc1c3541240ca6 + sha256: 68a461751271fc230804dc1fd05b2344b73ecabb893a25b6822e437b43634b11 requires_dist: - lets-plot>=4.0.0 - scipy>=1.6 From 7cb23b59f12c4d375638fb1b11673c78afafd06c Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 1 Sep 2024 18:11:25 +0200 Subject: [PATCH 023/102] install r packages via pixi --- .github/workflows/ci-tests.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index 6b4940b1..fdefe90e 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -39,12 +39,13 @@ jobs: 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 + run: | + pixi run install-r - name: Run tests run: | pixi run tests-regular + - name: Upload to Codecov uses: codecov/codecov-action@v4 From 22f96900509fcf88972746f64bfe6cc26d80b86b Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 1 Sep 2024 18:13:30 +0200 Subject: [PATCH 024/102] define install-r --- pixi.lock | 2 +- pyproject.toml | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/pixi.lock b/pixi.lock index 92547ff4..a9b5870a 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5098,7 +5098,7 @@ packages: name: pyfixest version: 0.24.3 path: . - sha256: 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3.20.1 - url: https://files.pythonhosted.org/packages/07/9e/c96f7a4cd0bf5625bb409b7e61e99b1130dc63a98cb8b24aeabae62d43e8/zipp-3.20.1-py3-none-any.whl - sha256: 9960cd8967c8f85a56f920d5d507274e74f9ff813a0ab8889a5b5be2daf44064 + version: 3.20.2 + url: https://files.pythonhosted.org/packages/62/8b/5ba542fa83c90e09eac972fc9baca7a88e7e7ca4b221a89251954019308b/zipp-3.20.2-py3-none-any.whl + sha256: a817ac80d6cf4b23bf7f2828b7cabf326f15a001bea8b1f9b49631780ba28350 requires_dist: - pytest-checkdocs>=2.4 ; extra == 'check' - pytest-ruff>=0.2.1 ; sys_platform != 'cygwin' and extra == 'check' From 64423e690912c8138c7b11aa7475c208d86f1f2c Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Wed, 18 Sep 2024 22:56:40 +0200 Subject: [PATCH 026/102] do not install r binaries --- r_test_requirements.R | 2 -- 1 file changed, 2 deletions(-) diff --git a/r_test_requirements.R b/r_test_requirements.R index 0629f90f..7a94e4ab 100644 --- a/r_test_requirements.R +++ b/r_test_requirements.R @@ -2,10 +2,8 @@ install.packages( c('fixest', 'broom','clubSandwich', 'did2s', 'wildrwolf', 'reticulate', 'ivDiag'), repos='https://cran.rstudio.com', - type = "binary" ); install.packages( 'ritest', repos = c('https://grantmcdermott.r-universe.dev', 'https://cloud.r-project.org'), - type = "binary" ); From 6f1b35402c21f15df80fb56b1edc3bb7fb910514 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Thu, 19 Sep 2024 19:55:12 +0200 Subject: [PATCH 027/102] test --- .github/workflows/ci-tests.yaml | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index 32ae98a9..112a6fe8 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -35,13 +35,21 @@ jobs: run: | echo "NUMBA_NUM_THREADS=1" >> $GITHUB_ENV - - name: Setup r2u - uses: eddelbuettel/github-actions/r2u-setup@master + - name: Setup r2u + uses: eddelbuettel/github-actions/r2u-setup@master - - name: install R packages + # Set the R_LIBS_USER to a specific location and install R packages there + - name: Install R packages run: | - pixi run install-r + mkdir -p ~/.R/library + echo 'R_LIBS_USER="~/.R/library"' >> ~/.Renviron + Rscript -e 'install.packages(c("fixest", "broom", "did2s", "clubSandwich", "wildrwolf", "ivDiag"))' + shell: bash + # Ensure pixi knows about the R library path + - name: Export R library path + run: | + echo "R_LIBS_USER=~/.R/library" >> $GITHUB_ENV - name: Run tests run: | pixi run tests-regular From 346902c362435677c57000698c1b1fc35747bf74 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Thu, 19 Sep 2024 19:56:18 +0200 Subject: [PATCH 028/102] fix syntax error --- .github/workflows/ci-tests.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index 112a6fe8..3ef954cf 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -35,8 +35,8 @@ jobs: run: | echo "NUMBA_NUM_THREADS=1" >> $GITHUB_ENV - - name: Setup r2u - uses: eddelbuettel/github-actions/r2u-setup@master + - name: Setup r2u + uses: eddelbuettel/github-actions/r2u-setup@master # Set the R_LIBS_USER to a specific location and install R packages there - name: Install R packages From 71bd8f42b4e7ae676126cd9fb0960a132339e9dd Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Thu, 19 Sep 2024 19:56:51 +0200 Subject: [PATCH 029/102] fail fast --- .github/workflows/ci-tests.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index 3ef954cf..a1388871 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -13,7 +13,7 @@ jobs: name: "Tests Core" runs-on: ${{ matrix.os }} strategy: - fail-fast: false + fail-fast: true matrix: os: ["ubuntu-latest"] python-version: ["3.9", "3.12"] @@ -63,7 +63,7 @@ jobs: name: "Tests vs fixest" runs-on: ${{ matrix.os }} strategy: - fail-fast: false + fail-fast: true matrix: os: ["ubuntu-latest"] python-version: ["3.9", "3.12"] From ef0d2ff946124150eb4e20c69ff15e6c557ce445 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Thu, 19 Sep 2024 20:02:35 +0200 Subject: [PATCH 030/102] tweak --- .github/workflows/ci-tests.yaml | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index a1388871..b5903bce 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -38,7 +38,7 @@ jobs: - name: Setup r2u uses: eddelbuettel/github-actions/r2u-setup@master - # Set the R_LIBS_USER to a specific location and install R packages there + - name: Install R packages run: | mkdir -p ~/.R/library @@ -46,10 +46,15 @@ jobs: Rscript -e 'install.packages(c("fixest", "broom", "did2s", "clubSandwich", "wildrwolf", "ivDiag"))' shell: bash - # Ensure pixi knows about the R library path - name: Export R library path run: | echo "R_LIBS_USER=~/.R/library" >> $GITHUB_ENV + + # Verify that the R packages are installed + - name: Verify R packages + run: | + Rscript -e 'print(installed.packages()[,c(1,3)])' + - name: Run tests run: | pixi run tests-regular From e44b4b7b610ca50ab3681809d3610541fd92f7d8 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Thu, 19 Sep 2024 20:25:56 +0200 Subject: [PATCH 031/102] export r library paths --- .github/workflows/ci-tests.yaml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index b5903bce..3182742f 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -50,6 +50,10 @@ jobs: run: | echo "R_LIBS_USER=~/.R/library" >> $GITHUB_ENV + - name: Set R environment for testing + run: | + export R_LIBS_USER=~/.R/library + echo "R environment set: $R_LIBS_USER" # Verify that the R packages are installed - name: Verify R packages run: | @@ -57,6 +61,7 @@ jobs: - name: Run tests run: | + export R_LIBS_USER=~/.R/library pixi run tests-regular - name: Upload to Codecov From 75c69228e9c366feb1ea65e53bdd718705543bfe Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Thu, 19 Sep 2024 20:32:00 +0200 Subject: [PATCH 032/102] another test --- .github/workflows/ci-tests.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index 3182742f..288b08af 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -103,7 +103,10 @@ jobs: - name: Run tests run: | + export R_LIBS_USER=~/.R/library + echo "R environment set: $R_LIBS_USER" pixi run tests-slow + - name: Upload to Codecov uses: codecov/codecov-action@v4 From edc160e6d3abfffdde82c9358d87e7b948e770ad Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Thu, 19 Sep 2024 20:32:52 +0200 Subject: [PATCH 033/102] set r home --- .github/workflows/ci-tests.yaml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index 288b08af..8b8f1874 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -101,6 +101,11 @@ jobs: run: Rscript -e 'install.packages(c("fixest", "broom", "did2s", "clubSandwich", "wildrwolf", "ivDiag"))' shell: bash + - name: Set R_HOME + run: | + export R_HOME=$(R RHOME) + echo "R_HOME=$R_HOME" + - name: Run tests run: | export R_LIBS_USER=~/.R/library From 79f5e5fa68f71dd205ec2eba492a2d938bb42e22 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Thu, 19 Sep 2024 20:48:16 +0200 Subject: [PATCH 034/102] another attempt --- .github/workflows/ci-tests.yaml | 27 +++++++++++++++++++-------- 1 file changed, 19 insertions(+), 8 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index 8b8f1874..ada07caf 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -97,19 +97,30 @@ jobs: - name: Setup r2u uses: eddelbuettel/github-actions/r2u-setup@master - - name: install R packages - run: Rscript -e 'install.packages(c("fixest", "broom", "did2s", "clubSandwich", "wildrwolf", "ivDiag"))' - shell: bash + - name: Install R and setup environment + run: | + mkdir -p ~/.R/library + echo 'R_LIBS_USER="~/.R/library"' >> ~/.Renviron + echo 'R_LIBS_USER="~/.R/library"' >> ~/.bashrc + export R_LIBS_USER=~/.R/library + Rscript -e 'install.packages(c("fixest", "broom", "did2s", "clubSandwich", "wildrwolf", "ivDiag"), repos="http://cran.us.r-project.org")' - - name: Set R_HOME + # Check which R packages are installed + - name: Verify installed R packages run: | - export R_HOME=$(R RHOME) - echo "R_HOME=$R_HOME" + Rscript -e 'installed.packages()[, c("Package", "Version")]' + + # Export the R_LIBS_USER path to make it available in the next steps + - name: Export R library path + run: | + echo "R_LIBS_USER=~/.R/library" >> $GITHUB_ENV + + - name: Run tests + run: | + pixi run tests-regular - name: Run tests run: | - export R_LIBS_USER=~/.R/library - echo "R environment set: $R_LIBS_USER" pixi run tests-slow - name: Upload to Codecov From 7974bc9a52ce57d7829a0f1e3d20e2ab13ed3059 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Thu, 19 Sep 2024 21:04:02 +0200 Subject: [PATCH 035/102] another attempt --- .github/workflows/ci-tests.yaml | 150 +- coverage.xml | 3729 +++++++++++++++++++++++++++++++ 2 files changed, 3730 insertions(+), 149 deletions(-) create mode 100644 coverage.xml diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index ada07caf..79f3a199 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -38,65 +38,7 @@ jobs: - name: Setup r2u uses: eddelbuettel/github-actions/r2u-setup@master - - - name: Install R packages - run: | - mkdir -p ~/.R/library - echo 'R_LIBS_USER="~/.R/library"' >> ~/.Renviron - Rscript -e 'install.packages(c("fixest", "broom", "did2s", "clubSandwich", "wildrwolf", "ivDiag"))' - shell: bash - - - name: Export R library path - run: | - echo "R_LIBS_USER=~/.R/library" >> $GITHUB_ENV - - - name: Set R environment for testing - run: | - export R_LIBS_USER=~/.R/library - echo "R environment set: $R_LIBS_USER" - # Verify that the R packages are installed - - name: Verify R packages - run: | - Rscript -e 'print(installed.packages()[,c(1,3)])' - - - name: Run tests - run: | - export R_LIBS_USER=~/.R/library - pixi run tests-regular - - - name: Upload to Codecov - uses: codecov/codecov-action@v4 - with: - token: ${{ secrets.CODECOV_TOKEN }} - - test_slow: - name: "Tests vs fixest" - runs-on: ${{ matrix.os }} - strategy: - fail-fast: true - matrix: - os: ["ubuntu-latest"] - python-version: ["3.9", "3.12"] - pytest_opts: ["--workers 4 --tests-per-worker 1"] - - steps: - - name: Checkout source - uses: actions/checkout@v4 - - name: Setup python - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} - architecture: x64 - - name: Set up pixi - uses: prefix-dev/setup-pixi@v0.8.1 - - - name: set numba parallel flags - run: | - echo "NUMBA_NUM_THREADS=1" >> $GITHUB_ENV - - - name: Setup r2u - uses: eddelbuettel/github-actions/r2u-setup@master - + # Set up R base using system package manager (or conda) - name: Install R and setup environment run: | mkdir -p ~/.R/library @@ -118,93 +60,3 @@ jobs: - name: Run tests run: | pixi run tests-regular - - - name: Run tests - run: | - pixi run tests-slow - - - name: Upload to Codecov - uses: codecov/codecov-action@v4 - - 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 pixi - uses: prefix-dev/setup-pixi@v0.8.1 - - - - 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: | - pixi run render-notebooks - - build-docs: - name: "Build Docs" - runs-on: ubuntu-latest - needs: ["test"] - steps: - - name: Checkout source - uses: actions/checkout@v4 - - name: Setup python - uses: actions/setup-python@v5 - with: - python-version: "3.11" - - name: Set up pixi - uses: prefix-dev/setup-pixi@v0.8.1 - - name: Set up Quarto - uses: quarto-dev/quarto-actions/setup@v2 - - name: install tinytex - run: | - quarto install tinytex - - name: Compile docstrings with quartodoc - run : | - pixi run docs-build - - name: Render docs - run: | - 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" 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From ba49144b72ea7a24040ab709e76fffb62a81b328 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Thu, 19 Sep 2024 21:14:13 +0200 Subject: [PATCH 036/102] tweak --- .github/workflows/ci-tests.yaml | 21 ++++++++++----------- 1 file changed, 10 insertions(+), 11 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index 79f3a199..50eab01e 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -17,46 +17,45 @@ jobs: matrix: os: ["ubuntu-latest"] python-version: ["3.9", "3.12"] - pytest_opts: ["--workers 4 --tests-per-worker 1"] steps: - name: Checkout source uses: actions/checkout@v4 + - name: Setup python uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - architecture: x64 - name: Set up pixi uses: prefix-dev/setup-pixi@v0.8.1 - - name: set numba parallel flags - run: | - echo "NUMBA_NUM_THREADS=1" >> $GITHUB_ENV + - name: Set numba parallel flags + run: echo "NUMBA_NUM_THREADS=1" >> $GITHUB_ENV - name: Setup r2u uses: eddelbuettel/github-actions/r2u-setup@master - # Set up R base using system package manager (or conda) + # Set up R and R environment - name: Install R and setup environment run: | mkdir -p ~/.R/library echo 'R_LIBS_USER="~/.R/library"' >> ~/.Renviron - echo 'R_LIBS_USER="~/.R/library"' >> ~/.bashrc - export R_LIBS_USER=~/.R/library Rscript -e 'install.packages(c("fixest", "broom", "did2s", "clubSandwich", "wildrwolf", "ivDiag"), repos="http://cran.us.r-project.org")' - # Check which R packages are installed + # Check installed R packages - name: Verify installed R packages run: | Rscript -e 'installed.packages()[, c("Package", "Version")]' - # Export the R_LIBS_USER path to make it available in the next steps - - name: Export R library path + # Set environment variables for R and rpy2 + - name: Export R and rpy2 environment run: | echo "R_LIBS_USER=~/.R/library" >> $GITHUB_ENV + echo "R_HOME=$(R RHOME)" >> $GITHUB_ENV + echo "R_LIBS_SITE=$(Rscript -e '.libPaths()[1]')" >> $GITHUB_ENV + # Run tests - name: Run tests run: | pixi run tests-regular From 665d88d7ebde1b53934d9b88c4ac9c2b8a845362 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Thu, 19 Sep 2024 21:20:14 +0200 Subject: [PATCH 037/102] tweak --- .github/workflows/ci-tests.yaml | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index 50eab01e..e997f7b7 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -48,6 +48,13 @@ jobs: run: | Rscript -e 'installed.packages()[, c("Package", "Version")]' + # Check R environment details (debugging step) + - name: Debug R environment + run: | + echo "R_HOME: $(R RHOME)" + echo "R_LIBS_USER: $R_LIBS_USER" + Rscript -e 'cat(.libPaths(), "\n")' + # Set environment variables for R and rpy2 - name: Export R and rpy2 environment run: | @@ -55,6 +62,12 @@ jobs: echo "R_HOME=$(R RHOME)" >> $GITHUB_ENV echo "R_LIBS_SITE=$(Rscript -e '.libPaths()[1]')" >> $GITHUB_ENV + # Force print rpy2 environment paths (debugging step) + - name: Check rpy2 configuration + run: | + python -c "import rpy2.robjects as ro; print(ro.r('R.home()'))" + python -c "import os; print('R_HOME:', os.getenv('R_HOME')); print('R_LIBS_USER:', os.getenv('R_LIBS_USER'))" + # Run tests - name: Run tests run: | From 44bc91c64793bcd44384793bc7f6ef929ca913b5 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Thu, 19 Sep 2024 21:24:45 +0200 Subject: [PATCH 038/102] pixi install --- .github/workflows/ci-tests.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index e997f7b7..5f03b1f0 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -62,6 +62,10 @@ jobs: echo "R_HOME=$(R RHOME)" >> $GITHUB_ENV echo "R_LIBS_SITE=$(Rscript -e '.libPaths()[1]')" >> $GITHUB_ENV + - name: run pixi install + run: | + pixi install + # Force print rpy2 environment paths (debugging step) - name: Check rpy2 configuration run: | From f3d5bc93e4532edf115b8d76549f8a371ad2f2c8 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Thu, 19 Sep 2024 21:44:00 +0200 Subject: [PATCH 039/102] tweak --- .github/workflows/ci-tests.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index 5f03b1f0..94d216be 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -55,12 +55,12 @@ jobs: echo "R_LIBS_USER: $R_LIBS_USER" Rscript -e 'cat(.libPaths(), "\n")' - # Set environment variables for R and rpy2 - - name: Export R and rpy2 environment + - name: Activate Pixi Environment and Set R Paths run: | - echo "R_LIBS_USER=~/.R/library" >> $GITHUB_ENV - echo "R_HOME=$(R RHOME)" >> $GITHUB_ENV - echo "R_LIBS_SITE=$(Rscript -e '.libPaths()[1]')" >> $GITHUB_ENV + eval "$(pixi shell-hook)" + export R_LIBS_USER="$CONDA_PREFIX/lib/R/library" + export R_HOME="$(R RHOME)" + echo "Pixi environment activated with R_HOME: $R_HOME and R_LIBS_USER: $R_LIBS_USER" - name: run pixi install run: | From 4eb1afc51e274c99cd7899458effd57a95a06de7 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 22 Sep 2024 11:16:15 +0200 Subject: [PATCH 040/102] another attempt --- .github/workflows/ci-tests.yaml | 39 ++++++++++----------------------- 1 file changed, 12 insertions(+), 27 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index 94d216be..5665a65a 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -36,41 +36,26 @@ jobs: - name: Setup r2u uses: eddelbuettel/github-actions/r2u-setup@master - # Set up R and R environment + # Set up R and install base R packages - name: Install R and setup environment run: | mkdir -p ~/.R/library - echo 'R_LIBS_USER="~/.R/library"' >> ~/.Renviron Rscript -e 'install.packages(c("fixest", "broom", "did2s", "clubSandwich", "wildrwolf", "ivDiag"), repos="http://cran.us.r-project.org")' - # Check installed R packages - - name: Verify installed R packages + # Set R_HOME and R_LIBS to base R path + - name: Set R_HOME and R_LIBS environment variables run: | - Rscript -e 'installed.packages()[, c("Package", "Version")]' + echo "R_HOME=$(R RHOME)" >> $GITHUB_ENV + echo "R_LIBS=~/.R/library" >> $GITHUB_ENV - # Check R environment details (debugging step) - - name: Debug R environment + # Activate pixi environment and set R paths for rpy2 + - name: Activate pixi environment and set R paths run: | - echo "R_HOME: $(R RHOME)" - echo "R_LIBS_USER: $R_LIBS_USER" - Rscript -e 'cat(.libPaths(), "\n")' - - - name: Activate Pixi Environment and Set R Paths - run: | - eval "$(pixi shell-hook)" - export R_LIBS_USER="$CONDA_PREFIX/lib/R/library" - export R_HOME="$(R RHOME)" - echo "Pixi environment activated with R_HOME: $R_HOME and R_LIBS_USER: $R_LIBS_USER" - - - name: run pixi install - run: | - pixi install - - # Force print rpy2 environment paths (debugging step) - - name: Check rpy2 configuration - run: | - python -c "import rpy2.robjects as ro; print(ro.r('R.home()'))" - python -c "import os; print('R_HOME:', os.getenv('R_HOME')); print('R_LIBS_USER:', os.getenv('R_LIBS_USER'))" + pixi env activate # Activate the conda environment created by Pixi + export R_HOME=$(R RHOME) # Ensure R_HOME is set to the base R installation + export R_LIBS=~/.R/library # Set R_LIBS to use the base R package library + echo "R_HOME is set to: $R_HOME" + echo "R_LIBS is set to: $R_LIBS" # Run tests - name: Run tests From 695d71b501446630e66315e544161d1f6db721e4 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 22 Sep 2024 11:20:38 +0200 Subject: [PATCH 041/102] update pixi lock --- pixi.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pixi.lock b/pixi.lock index b74c5b2d..b5bcaf3d 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5106,7 +5106,7 @@ packages: name: pyfixest version: 0.24.3 path: . - sha256: 2ea7c8743b640e970ca14a40051c1fc6fd4a6fda23f7d6e306396e81439e2c3f + sha256: acb866dc21dc21d693355b5a0d66708607999936156b81007e73fa3251cc4447 requires_dist: - lets-plot>=4.0.0 - scipy>=1.6 From 10ec65892dcec602c6560671300bd50eee1ea007 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 22 Sep 2024 11:32:11 +0200 Subject: [PATCH 042/102] add r dependencies to toml --- .github/workflows/ci-tests.yaml | 26 +- pixi.lock | 1975 ++++++++++++++++++++++++++++++- pyproject.toml | 2 + 3 files changed, 1977 insertions(+), 26 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index 5665a65a..400221cf 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -33,31 +33,7 @@ jobs: - name: Set numba parallel flags run: echo "NUMBA_NUM_THREADS=1" >> $GITHUB_ENV - - name: Setup r2u - uses: eddelbuettel/github-actions/r2u-setup@master - - # Set up R and install base R packages - - name: Install R and setup environment - run: | - mkdir -p ~/.R/library - Rscript -e 'install.packages(c("fixest", "broom", "did2s", "clubSandwich", "wildrwolf", "ivDiag"), repos="http://cran.us.r-project.org")' - - # Set R_HOME and R_LIBS to base R path - - name: Set R_HOME and R_LIBS environment variables - run: | - echo "R_HOME=$(R RHOME)" >> $GITHUB_ENV - echo "R_LIBS=~/.R/library" >> $GITHUB_ENV - - # Activate pixi environment and set R paths for rpy2 - - name: Activate pixi environment and set R paths - run: | - pixi env activate # Activate the conda environment created by Pixi - export R_HOME=$(R RHOME) # Ensure R_HOME is set to the base R installation - export R_LIBS=~/.R/library # Set R_LIBS to use the base R package library - echo "R_HOME is set to: $R_HOME" - echo "R_LIBS is set to: $R_LIBS" - # Run tests - name: Run tests run: | - pixi run tests-regular + pixi run tests-slow diff --git a/pixi.lock b/pixi.lock index b5bcaf3d..b04f641d 100644 --- a/pixi.lock +++ b/pixi.lock @@ -213,7 +213,54 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.12.5-h2ad013b_0_cpython.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-5_cp312.conda - conda: https://conda.anaconda.org/conda-forge/noarch/pytz-2024.2-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/r-backports-1.5.0-r43hb1dbf0f_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/r-base-4.3.3-h9967228_14.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/r-broom-1.0.6-r43hc72bb7e_1.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/r-cli-3.6.3-r43h0d4f4ea_1.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/r-colorspace-2.1_1-r43hdb488b9_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/r-crayon-1.5.3-r43hc72bb7e_1.conda + - conda: 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diff --git a/pyproject.toml b/pyproject.toml index e8badf17..7f08a9a8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -41,6 +41,8 @@ render-notebooks = "python scripts/run_notebooks.py" [tool.pixi.feature.dev.dependencies] rpy2 = ">=3.5.11,<4" +r-fixest = ">=0.12.1,<0.13" +r-broom = ">=1.0.5,<2" [tool.pixi.feature.docs.tasks] docs-build = "quartodoc build --verbose --config docs/_quarto.yml" From aa243d09b60445a80b766fe8af1d45820e00a3f3 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 22 Sep 2024 11:40:34 +0200 Subject: [PATCH 043/102] switch back to install-r --- .github/workflows/ci-tests.yaml | 10 +- pixi.lock | 1975 +------------------------------ pyproject.toml | 2 - 3 files changed, 10 insertions(+), 1977 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index 400221cf..b71127f7 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -33,7 +33,15 @@ jobs: - name: Set numba parallel flags run: echo "NUMBA_NUM_THREADS=1" >> $GITHUB_ENV + - name: Setup r2u + uses: eddelbuettel/github-actions/r2u-setup@master + + # Set up R and install base R packages + - name: Install R and setup environment + run: | + pixi run install-r + # Run tests - name: Run tests run: | - pixi run tests-slow + pixi run tests-regular diff --git a/pixi.lock b/pixi.lock index b04f641d..b5bcaf3d 100644 --- a/pixi.lock +++ b/pixi.lock @@ -213,54 +213,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.12.5-h2ad013b_0_cpython.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-5_cp312.conda - conda: https://conda.anaconda.org/conda-forge/noarch/pytz-2024.2-pyhd8ed1ab_0.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/r-backports-1.5.0-r43hb1dbf0f_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/r-base-4.3.3-h9967228_14.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/r-broom-1.0.6-r43hc72bb7e_1.conda - - 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c10148d59300b7b97026d5a4b586844dd83d0e21165da94ed40262a93f936631 - md5: 952e1c80dccc51f914f821157b2a67e8 - depends: - - libgcc-ng >=12 - - r-base >=4.3,<4.4.0a0 - - r-lattice >=0.20_27 - license: GPL-2.0-or-later - license_family: GPL3 - purls: [] - size: 1005058 - timestamp: 1719765989086 - kind: conda name: readline version: '8.2' diff --git a/pyproject.toml b/pyproject.toml index 7f08a9a8..e8badf17 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -41,8 +41,6 @@ render-notebooks = "python scripts/run_notebooks.py" [tool.pixi.feature.dev.dependencies] rpy2 = ">=3.5.11,<4" -r-fixest = ">=0.12.1,<0.13" -r-broom = ">=1.0.5,<2" [tool.pixi.feature.docs.tasks] docs-build = "quartodoc build --verbose --config docs/_quarto.yml" From d75c928c20679441d4a552f8b3785a63719d8a99 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 22 Sep 2024 11:50:58 +0200 Subject: [PATCH 044/102] test on windows --- .github/workflows/ci-tests.yaml | 2 +- coverage.xml | 64076 ++++++++++++++++++++++++++++-- 2 files changed, 61163 insertions(+), 2915 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index b71127f7..6134f25d 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -15,7 +15,7 @@ jobs: strategy: fail-fast: true matrix: - os: ["ubuntu-latest"] + os: ["windows-latest"] python-version: ["3.9", "3.12"] steps: diff --git a/coverage.xml b/coverage.xml index f193856c..7021d191 100644 --- a/coverage.xml +++ b/coverage.xml @@ -1,12 +1,13 @@ - + + C:\Users\alexa\Documents\pyfixest C:\Users\alexa\Documents\pyfixest\pyfixest - + @@ -32,665 +33,1877 @@ - - - + + - + - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - - - - - - - - - + + - - + + + + + + + + + + + + + - + - - - + + + + - + + + + + + + + + + + + + + - - - + + + + + + + + - + + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - + + + + + + + - - - - - 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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + @@ -3420,7 +61668,7 @@ - + @@ -3431,42 +61679,42 @@ - - - + + + - - - + + + - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + @@ -3495,23 +61743,23 @@ - - - - - + + + + + - - - + + + - + - - - + + + @@ -3520,54 +61768,54 @@ - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + - - - - - - + + + + + + - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + - + @@ -3618,7 +61866,7 @@ - + @@ -3714,13 +61962,13 @@ - - - - - - - + + + + + + + From fe71422f9ef2c1bb1001f370887ad501c9067c7e Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 22 Sep 2024 11:52:31 +0200 Subject: [PATCH 045/102] mac --- .github/workflows/ci-tests.yaml | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index 6134f25d..9683b534 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -15,7 +15,7 @@ jobs: strategy: fail-fast: true matrix: - os: ["windows-latest"] + os: ["mac-latest"] python-version: ["3.9", "3.12"] steps: @@ -33,9 +33,6 @@ jobs: - name: Set numba parallel flags run: echo "NUMBA_NUM_THREADS=1" >> $GITHUB_ENV - - name: Setup r2u - uses: eddelbuettel/github-actions/r2u-setup@master - # Set up R and install base R packages - name: Install R and setup environment run: | From 394a14d9c9e53a3f443f747a9fad25ee121e5f98 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 22 Sep 2024 11:53:58 +0200 Subject: [PATCH 046/102] cache pixi --- .github/workflows/ci-tests.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index 9683b534..77cc39ac 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -27,8 +27,11 @@ jobs: with: python-version: ${{ matrix.python-version }} - - name: Set up pixi - uses: prefix-dev/setup-pixi@v0.8.1 + - uses: prefix-dev/setup-pixi@v0.8.1 + with: + pixi-version: v0.29.0 + cache: true + auth-host: prefix.dev - name: Set numba parallel flags run: echo "NUMBA_NUM_THREADS=1" >> $GITHUB_ENV From 18a54af3c9cd574fe67bdf8cda04fd244f0eb478 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 22 Sep 2024 11:56:07 +0200 Subject: [PATCH 047/102] back to windows --- .github/workflows/ci-tests.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index 77cc39ac..1ade0275 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -15,8 +15,8 @@ jobs: strategy: fail-fast: true matrix: - os: ["mac-latest"] - python-version: ["3.9", "3.12"] + os: ["windows-latest"] + python-version: ["3.12"] steps: - name: Checkout source From bb8adbd379529246fa9c83bcba66e64011c63db0 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 22 Sep 2024 11:57:00 +0200 Subject: [PATCH 048/102] no host --- .github/workflows/ci-tests.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index 1ade0275..c3175330 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -31,7 +31,6 @@ jobs: with: pixi-version: v0.29.0 cache: true - auth-host: prefix.dev - name: Set numba parallel flags run: echo "NUMBA_NUM_THREADS=1" >> $GITHUB_ENV From fddc0dad670617536913c4ed15b3cd16bf6af1b0 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 22 Sep 2024 12:03:29 +0200 Subject: [PATCH 049/102] install compiled linux from r universe --- .github/workflows/ci-tests.yaml | 2 +- r_test_requirements.R | 10 +++------- 2 files changed, 4 insertions(+), 8 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index c3175330..785cc258 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -15,7 +15,7 @@ jobs: strategy: fail-fast: true matrix: - os: ["windows-latest"] + os: ["ubuntu-latest"] python-version: ["3.12"] steps: diff --git a/r_test_requirements.R b/r_test_requirements.R index 7a94e4ab..e4656be7 100644 --- a/r_test_requirements.R +++ b/r_test_requirements.R @@ -1,9 +1,5 @@ # note: fixest and broom are installed via conda install.packages( - c('fixest', 'broom','clubSandwich', 'did2s', 'wildrwolf', 'reticulate', 'ivDiag'), - repos='https://cran.rstudio.com', -); -install.packages( - 'ritest', - repos = c('https://grantmcdermott.r-universe.dev', 'https://cloud.r-project.org'), -); + c('fixest', 'broom','clubSandwich', 'did2s', 'wildrwolf', 'reticulate', 'ivDiag', 'ritest'), + repos = c('https://ropensci.r-universe.dev') +) From ec435b370f0b658e62272a09c3beb957ab9632c7 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 22 Sep 2024 12:11:52 +0200 Subject: [PATCH 050/102] update r installs --- r_test_requirements.R | 20 +++++++++++++++----- 1 file changed, 15 insertions(+), 5 deletions(-) diff --git a/r_test_requirements.R b/r_test_requirements.R index e4656be7..ddbfae9e 100644 --- a/r_test_requirements.R +++ b/r_test_requirements.R @@ -1,5 +1,15 @@ -# note: fixest and broom are installed via conda -install.packages( - c('fixest', 'broom','clubSandwich', 'did2s', 'wildrwolf', 'reticulate', 'ivDiag', 'ritest'), - repos = c('https://ropensci.r-universe.dev') -) +install.packages('fixest', repos = c('https://lrberge.r-universe.dev', 'https://cloud.r-project.org')) + +install.packages('broom', repos = c('https://tidymodels.r-universe.dev', 'https://cloud.r-project.org')) + +install.packages('clubSandwich', repos = c('https://jepusto.r-universe.dev', 'https://cloud.r-project.org')) + +install.packages('did2s', repos = c('https://kylebutts.r-universe.dev', 'https://cloud.r-project.org')) + +install.packages('wildrwolf', repos = c('https://s3alfisc.r-universe.dev', 'https://cloud.r-project.org')) + +install.packages('reticulate', repos = c('https://rstudio.r-universe.dev', 'https://cloud.r-project.org')) + +install.packages('ivDiag', repos = 'https://cloud.r-project.org') + +install.packages('ritest', repos = c('https://grantmcdermott.r-universe.dev', 'https://cloud.r-project.org')) From ffe75a541d9a24fa460f8cca9a795166f62ddca3 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 22 Sep 2024 12:13:47 +0200 Subject: [PATCH 051/102] install binary --- r_test_requirements.R | 2 ++ 1 file changed, 2 insertions(+) diff --git a/r_test_requirements.R b/r_test_requirements.R index ddbfae9e..4c43afef 100644 --- a/r_test_requirements.R +++ b/r_test_requirements.R @@ -1,3 +1,5 @@ +options(pkgType = "binary") + install.packages('fixest', repos = c('https://lrberge.r-universe.dev', 'https://cloud.r-project.org')) install.packages('broom', repos = c('https://tidymodels.r-universe.dev', 'https://cloud.r-project.org')) From 506ca756dc8ffe0e2db85a21ba8e578e888ecb6a Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 22 Sep 2024 12:16:49 +0200 Subject: [PATCH 052/102] try rstudio pkg manager --- r_test_requirements.R | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/r_test_requirements.R b/r_test_requirements.R index 4c43afef..8f95f9aa 100644 --- a/r_test_requirements.R +++ b/r_test_requirements.R @@ -1,6 +1,7 @@ -options(pkgType = "binary") - -install.packages('fixest', repos = c('https://lrberge.r-universe.dev', 'https://cloud.r-project.org')) +install.packages( + "fixest", + repos = "https://packagemanager.rstudio.com/all/__linux__/focal/latest" +) install.packages('broom', repos = c('https://tidymodels.r-universe.dev', 'https://cloud.r-project.org')) From caee64c1e99346fcfef96fde21b281b3b1ecb234 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 22 Sep 2024 12:28:59 +0200 Subject: [PATCH 053/102] revert to r2u --- .github/workflows/ci-tests.yaml | 3 +++ r_test_requirements.R | 27 ++++++++++----------------- 2 files changed, 13 insertions(+), 17 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index 785cc258..4f668d97 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -35,6 +35,9 @@ jobs: - name: Set numba parallel flags run: echo "NUMBA_NUM_THREADS=1" >> $GITHUB_ENV + - name: Setup r2u + uses: eddelbuettel/github-actions/r2u-setup@master + # Set up R and install base R packages - name: Install R and setup environment run: | diff --git a/r_test_requirements.R b/r_test_requirements.R index 8f95f9aa..0629f90f 100644 --- a/r_test_requirements.R +++ b/r_test_requirements.R @@ -1,18 +1,11 @@ +# note: fixest and broom are installed via conda install.packages( - "fixest", - repos = "https://packagemanager.rstudio.com/all/__linux__/focal/latest" -) - -install.packages('broom', repos = c('https://tidymodels.r-universe.dev', 'https://cloud.r-project.org')) - -install.packages('clubSandwich', repos = c('https://jepusto.r-universe.dev', 'https://cloud.r-project.org')) - -install.packages('did2s', repos = c('https://kylebutts.r-universe.dev', 'https://cloud.r-project.org')) - -install.packages('wildrwolf', repos = c('https://s3alfisc.r-universe.dev', 'https://cloud.r-project.org')) - -install.packages('reticulate', repos = c('https://rstudio.r-universe.dev', 'https://cloud.r-project.org')) - -install.packages('ivDiag', repos = 'https://cloud.r-project.org') - -install.packages('ritest', repos = c('https://grantmcdermott.r-universe.dev', 'https://cloud.r-project.org')) + c('fixest', 'broom','clubSandwich', 'did2s', 'wildrwolf', 'reticulate', 'ivDiag'), + repos='https://cran.rstudio.com', + type = "binary" +); +install.packages( + 'ritest', + repos = c('https://grantmcdermott.r-universe.dev', 'https://cloud.r-project.org'), + type = "binary" +); From 207263d19f25c586872930ed17502c28e2660e74 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 22 Sep 2024 12:31:52 +0200 Subject: [PATCH 054/102] install r packages by hand --- .github/workflows/ci-tests.yaml | 5 +++-- r_test_requirements.R | 6 ++---- 2 files changed, 5 insertions(+), 6 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index 4f668d97..a7b9f550 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -39,9 +39,10 @@ jobs: uses: eddelbuettel/github-actions/r2u-setup@master # Set up R and install base R packages - - name: Install R and setup environment + - name: Install R packages run: | - pixi run install-r + Rscript -e "install.packages(c('fixest', 'broom','clubSandwich', 'did2s', 'wildrwolf', 'reticulate', 'ivDiag'), repos='https://cran.rstudio.com')" + Rscript -e "install.packages('ritest', repos = c('https://grantmcdermott.r-universe.dev', 'https://cloud.r-project.org'))" # Run tests - name: Run tests diff --git a/r_test_requirements.R b/r_test_requirements.R index 0629f90f..0380e7bc 100644 --- a/r_test_requirements.R +++ b/r_test_requirements.R @@ -1,11 +1,9 @@ # note: fixest and broom are installed via conda install.packages( c('fixest', 'broom','clubSandwich', 'did2s', 'wildrwolf', 'reticulate', 'ivDiag'), - repos='https://cran.rstudio.com', - type = "binary" + repos='https://cran.rstudio.com' ); install.packages( 'ritest', - repos = c('https://grantmcdermott.r-universe.dev', 'https://cloud.r-project.org'), - type = "binary" + repos = c('https://grantmcdermott.r-universe.dev', 'https://cloud.r-project.org') ); From 7460366750c4fce9b0e6634cee28e9eacabbb419 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 22 Sep 2024 12:59:29 +0200 Subject: [PATCH 055/102] install fixest and broom from conda --- .github/workflows/ci-tests.yaml | 10 +- pixi.lock | 1973 +++++++++++++++++++++++++++++++ pyproject.toml | 2 + 3 files changed, 1977 insertions(+), 8 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index a7b9f550..08e1e36c 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -35,14 +35,8 @@ jobs: - name: Set numba parallel flags run: echo "NUMBA_NUM_THREADS=1" >> $GITHUB_ENV - - name: Setup r2u - uses: eddelbuettel/github-actions/r2u-setup@master - - # Set up R and install base R packages - - name: Install R packages - run: | - Rscript -e "install.packages(c('fixest', 'broom','clubSandwich', 'did2s', 'wildrwolf', 'reticulate', 'ivDiag'), repos='https://cran.rstudio.com')" - Rscript -e "install.packages('ritest', repos = c('https://grantmcdermott.r-universe.dev', 'https://cloud.r-project.org'))" + - name: install other r dependencies + run: pixi r install-r # Run tests - name: Run tests diff --git a/pixi.lock b/pixi.lock index b5bcaf3d..99625175 100644 --- a/pixi.lock +++ b/pixi.lock @@ -213,7 +213,54 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.12.5-h2ad013b_0_cpython.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-5_cp312.conda - conda: https://conda.anaconda.org/conda-forge/noarch/pytz-2024.2-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/r-backports-1.5.0-r43hb1dbf0f_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/r-base-4.3.3-h9967228_14.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/r-broom-1.0.6-r43hc72bb7e_1.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/r-cli-3.6.3-r43h0d4f4ea_1.conda + - conda: 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diff --git a/pyproject.toml b/pyproject.toml index e8badf17..7f08a9a8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -41,6 +41,8 @@ render-notebooks = "python scripts/run_notebooks.py" [tool.pixi.feature.dev.dependencies] rpy2 = ">=3.5.11,<4" +r-fixest = ">=0.12.1,<0.13" +r-broom = ">=1.0.5,<2" [tool.pixi.feature.docs.tasks] docs-build = "quartodoc build --verbose --config docs/_quarto.yml" From 35debebff493d5b75ac129db328cf3940a0107de Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 22 Sep 2024 13:00:21 +0200 Subject: [PATCH 056/102] update pixi lock --- pixi.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pixi.lock b/pixi.lock index 99625175..b04f641d 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5218,7 +5218,7 @@ packages: name: pyfixest version: 0.24.3 path: . - sha256: acb866dc21dc21d693355b5a0d66708607999936156b81007e73fa3251cc4447 + sha256: 6b0dae1ae42626f8d8f6a7f99b05eee9ff24cb4ea2d69c902cf399e0ee451da1 requires_dist: - lets-plot>=4.0.0 - scipy>=1.6 From a9b562ca23e4be6697faa09cb746e2bfd363200b Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 22 Sep 2024 13:05:22 +0200 Subject: [PATCH 057/102] install in pixi path --- .github/workflows/ci-tests.yaml | 19 +++++++++++++++++-- 1 file changed, 17 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index 08e1e36c..d6fbb181 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -35,8 +35,23 @@ jobs: - name: Set numba parallel flags run: echo "NUMBA_NUM_THREADS=1" >> $GITHUB_ENV - - name: install other r dependencies - run: pixi r install-r + # Set R library path to pixi's environment + - name: Set R library path for pixi environment + run: | + # Assuming pixi's R library path is this; adapt if needed + R_LIB_PATH="${{ github.workspace }}/.pixi/envs/dev/lib/R/library" + echo "R_LIBS_USER=$R_LIB_PATH" >> $GITHUB_ENV + + # Install R packages into pixi's R library path + - name: Install R packages + run: | + R_LIB_PATH="${{ 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', 'reticulate', 'ivDiag'), repos='https://cran.rstudio.com')" + Rscript -e ".libPaths('$R_LIB_PATH'); install.packages('ritest', repos = c('https://grantmcdermott.r-universe.dev', 'https://cloud.r-project.org'))" + + #- name: install other r dependencies + # run: pixi r install-r # Run tests - name: Run tests From bd10055db1d609fe84bfe7e38818f5e5220b10d8 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 22 Sep 2024 13:09:12 +0200 Subject: [PATCH 058/102] add r2u --- .github/workflows/ci-tests.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index d6fbb181..68d954a6 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -35,7 +35,10 @@ jobs: - name: Set numba parallel flags run: echo "NUMBA_NUM_THREADS=1" >> $GITHUB_ENV - # Set R library path to pixi's environment + - name: Setup r2u + uses: eddelbuettel/github-actions/r2u-setup@master + + # Set R library path to pixi's environment - name: Set R library path for pixi environment run: | # Assuming pixi's R library path is this; adapt if needed From e67bcb616bfbe8b1f3ff736fac6f1c33973d24b6 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 22 Sep 2024 13:14:22 +0200 Subject: [PATCH 059/102] debug --- .github/workflows/ci-tests.yaml | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index 68d954a6..e2d7a8ca 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -38,7 +38,8 @@ jobs: - name: Setup r2u uses: eddelbuettel/github-actions/r2u-setup@master - # Set R library path to pixi's environment + + # Set R library path to pixi's environment - name: Set R library path for pixi environment run: | # Assuming pixi's R library path is this; adapt if needed @@ -53,6 +54,19 @@ jobs: Rscript -e ".libPaths('$R_LIB_PATH'); install.packages(c('fixest', 'broom','clubSandwich', 'did2s', 'wildrwolf', 'reticulate', 'ivDiag'), repos='https://cran.rstudio.com')" Rscript -e ".libPaths('$R_LIB_PATH'); install.packages('ritest', repos = c('https://grantmcdermott.r-universe.dev', 'https://cloud.r-project.org'))" + + # Verify where R packages are installed + - name: Verify R package installation path + run: | + Rscript -e "print(.libPaths())" + Rscript -e "installed.packages()[, c('Package', 'LibPath')]" + + # Print R library paths that rpy2 is using + - name: Debug rpy2 R library paths + run: | + python -c "import rpy2.robjects as robjects; print(robjects.r('.libPaths()'))" + + #- name: install other r dependencies # run: pixi r install-r From ec292f4c449a143acb1a2748ea08a60637c8b490 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 22 Sep 2024 13:19:02 +0200 Subject: [PATCH 060/102] update debug env --- .github/workflows/ci-tests.yaml | 3 +-- pixi.lock | 2 +- pyproject.toml | 1 + 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index e2d7a8ca..9b3bbeac 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -64,8 +64,7 @@ jobs: # Print R library paths that rpy2 is using - name: Debug rpy2 R library paths run: | - python -c "import rpy2.robjects as robjects; print(robjects.r('.libPaths()'))" - + pixi r debug-env #- name: install other r dependencies # run: pixi r install-r diff --git a/pixi.lock b/pixi.lock index b04f641d..91411de9 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5218,7 +5218,7 @@ packages: name: pyfixest version: 0.24.3 path: . - sha256: 6b0dae1ae42626f8d8f6a7f99b05eee9ff24cb4ea2d69c902cf399e0ee451da1 + sha256: 2466d8aa5a1db321382382a0e733aaa8b56d344fff757dd5d9ee9374f6a78c7d requires_dist: - lets-plot>=4.0.0 - scipy>=1.6 diff --git a/pyproject.toml b/pyproject.toml index 7f08a9a8..6ca1c90f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -33,6 +33,7 @@ tests-regular = "pytest tests -m \"not (extended or slow or plots)\" --cov=pyfix tests-extended = "pytest tests -m \"tests-extended\" --cov=pyfixest --cov-report=xml" tests-slow = "pytest tests -m slow --cov=./ --cov-report=xml" tests-rerun = "pytest --lf -n 4" +debug-env = "python -c \"import rpy2.robjects as robjects; print(robjects.r('.libPaths()'))\"" debug = "python pyfixest/debug.py" lint = "pre-commit run ruff --all-files" update-test-data = "Rscript tests/r_test_comparisons.R" From 4357a74498c6374acb2843ca99a2663fcf903140 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 22 Sep 2024 13:25:01 +0200 Subject: [PATCH 061/102] set r lib to install to --- .github/workflows/ci-tests.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index 9b3bbeac..d3467c5e 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -51,8 +51,8 @@ jobs: 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', 'reticulate', 'ivDiag'), repos='https://cran.rstudio.com')" - Rscript -e ".libPaths('$R_LIB_PATH'); install.packages('ritest', repos = c('https://grantmcdermott.r-universe.dev', 'https://cloud.r-project.org'))" + Rscript -e ".libPaths('$R_LIB_PATH'); install.packages(c('fixest', 'broom','clubSandwich', 'did2s', 'wildrwolf', 'reticulate', 'ivDiag'), lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos='https://cran.rstudio.com')" + Rscript -e ".libPaths('$R_LIB_PATH'); install.packages('ritest', lib = lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos = c('https://grantmcdermott.r-universe.dev', 'https://cloud.r-project.org'))" # Verify where R packages are installed From 98ebbfd59da9b92b0f514b7467a0c03f4eb57449 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 22 Sep 2024 13:27:53 +0200 Subject: [PATCH 062/102] fix typo --- .github/workflows/ci-tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index d3467c5e..472dd002 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -52,7 +52,7 @@ jobs: R_LIB_PATH="${{ 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', 'reticulate', 'ivDiag'), lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos='https://cran.rstudio.com')" - Rscript -e ".libPaths('$R_LIB_PATH'); install.packages('ritest', lib = lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos = c('https://grantmcdermott.r-universe.dev', 'https://cloud.r-project.org'))" + Rscript -e ".libPaths('$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'))" # Verify where R packages are installed From 2ba76bb5c43190e1a6fb0dd23abaf469a134019a Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 22 Sep 2024 13:34:00 +0200 Subject: [PATCH 063/102] one more time --- .github/workflows/ci-tests.yaml | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index 472dd002..536bf442 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -69,6 +69,17 @@ jobs: #- name: install other r dependencies # run: pixi r install-r + - name: Ensure rpy2 uses all R library paths + run: | + python -c " + import rpy2.robjects as robjects; + new_lib_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']); + robjects.r('.libPaths(new_lib_paths)'); + print('Updated R library paths:', robjects.r('.libPaths()')); + from rpy2.robjects.packages import importr; + did2s = importr('did2s') + " + # Run tests - name: Run tests run: | From fc8039a2cb1a378471b4a4f8ec77a586ba885797 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 22 Sep 2024 13:44:41 +0200 Subject: [PATCH 064/102] More debugging --- .github/workflows/ci-tests.yaml | 9 +-------- pixi.lock | 2 +- pyfixest/utils/set_rpy2_path.py | 21 +++++++++++++++++++++ pyproject.toml | 1 + 4 files changed, 24 insertions(+), 9 deletions(-) create mode 100644 pyfixest/utils/set_rpy2_path.py diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index 536bf442..c09f240e 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -71,14 +71,7 @@ jobs: - name: Ensure rpy2 uses all R library paths run: | - python -c " - import rpy2.robjects as robjects; - new_lib_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']); - robjects.r('.libPaths(new_lib_paths)'); - print('Updated R library paths:', robjects.r('.libPaths()')); - from rpy2.robjects.packages import importr; - did2s = importr('did2s') - " + pixi r set-rpy2-path # Run tests - name: Run tests diff --git a/pixi.lock b/pixi.lock index 91411de9..e25fdb45 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5218,7 +5218,7 @@ packages: name: pyfixest version: 0.24.3 path: . - sha256: 2466d8aa5a1db321382382a0e733aaa8b56d344fff757dd5d9ee9374f6a78c7d + sha256: 40b9f2de43473c966860e51ff4e9c3b78abace632ee7b7f1a10c4313d9c9af47 requires_dist: - lets-plot>=4.0.0 - scipy>=1.6 diff --git a/pyfixest/utils/set_rpy2_path.py b/pyfixest/utils/set_rpy2_path.py new file mode 100644 index 00000000..0c210acc --- /dev/null +++ b/pyfixest/utils/set_rpy2_path.py @@ -0,0 +1,21 @@ +import rpy2.robjects as robjects +from rpy2.robjects.packages import importr + +# Define the list of R library paths in Python +new_lib_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", + ] +) + +# Set the library paths in the R environment +robjects.r[".libPaths"](new_lib_paths) + +# Verify that the paths have been set correctly +print("Updated R library paths:", robjects.r(".libPaths()")) + +# Now attempt to import the did2s package +did2s = importr("did2s") diff --git a/pyproject.toml b/pyproject.toml index 6ca1c90f..671bbf8c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -33,6 +33,7 @@ tests-regular = "pytest tests -m \"not (extended or slow or plots)\" --cov=pyfix tests-extended = "pytest tests -m \"tests-extended\" --cov=pyfixest --cov-report=xml" tests-slow = "pytest tests -m slow --cov=./ --cov-report=xml" tests-rerun = "pytest --lf -n 4" +set-rpy2-path = "python pyfixest/utils/set_rpy2_path.py" debug-env = "python -c \"import rpy2.robjects as robjects; print(robjects.r('.libPaths()'))\"" debug = "python pyfixest/debug.py" lint = "pre-commit run ruff --all-files" From ee859ee97c90e20045f36aec4c3936a388439c80 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 22 Sep 2024 13:49:19 +0200 Subject: [PATCH 065/102] one more time --- pyfixest/utils/set_rpy2_path.py | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/pyfixest/utils/set_rpy2_path.py b/pyfixest/utils/set_rpy2_path.py index 0c210acc..1ad0c7e0 100644 --- a/pyfixest/utils/set_rpy2_path.py +++ b/pyfixest/utils/set_rpy2_path.py @@ -1,7 +1,7 @@ import rpy2.robjects as robjects from rpy2.robjects.packages import importr -# Define the list of R library paths in Python +# Set the R library paths again new_lib_paths = robjects.StrVector( [ "/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library", @@ -10,12 +10,11 @@ "/usr/lib/R/library", ] ) - -# Set the library paths in the R environment robjects.r[".libPaths"](new_lib_paths) -# Verify that the paths have been set correctly -print("Updated R library paths:", robjects.r(".libPaths()")) - -# Now attempt to import the did2s package -did2s = importr("did2s") +# Check if did2s is installed +try: + did2s = importr("did2s") + print("did2s package imported successfully.") +except Exception as e: + print(f"Error importing did2s: {e}") From cb714bdadc02070b50e2d7e648135bb057892fad Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 22 Sep 2024 13:59:04 +0200 Subject: [PATCH 066/102] Udpate r paths in scripts --- pyfixest/utils/set_rpy2_path.py | 49 ++++++++++++++++++++----------- tests/test_did.py | 3 ++ tests/test_i.py | 3 ++ tests/test_iv.py | 3 ++ tests/test_multcomp.py | 3 ++ tests/test_poisson.py | 3 ++ tests/test_predict_resid_fixef.py | 3 ++ tests/test_vs_fixest.py | 3 ++ tests/test_wald_test.py | 3 ++ 9 files changed, 56 insertions(+), 17 deletions(-) diff --git a/pyfixest/utils/set_rpy2_path.py b/pyfixest/utils/set_rpy2_path.py index 1ad0c7e0..d2ea6d52 100644 --- a/pyfixest/utils/set_rpy2_path.py +++ b/pyfixest/utils/set_rpy2_path.py @@ -1,20 +1,35 @@ import rpy2.robjects as robjects from rpy2.robjects.packages import importr -# Set the R library paths again -new_lib_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", - ] -) -robjects.r[".libPaths"](new_lib_paths) - -# Check if did2s is installed -try: - did2s = importr("did2s") - print("did2s package imported successfully.") -except Exception as e: - print(f"Error importing did2s: {e}") + +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/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..669e1302 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() 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_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..e8599fc2 100644 --- a/tests/test_wald_test.py +++ b/tests/test_wald_test.py @@ -9,8 +9,11 @@ import pyfixest as pf from pyfixest.estimation.estimation import feols +from pyfixest.utils.set_rpy2_path 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100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -26,6 +26,7 @@ pyfixest = { path = ".", editable = true } 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" @@ -41,10 +42,14 @@ 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.build.dependencies] +python-build = ">=1.2.2,<2" + [tool.pixi.feature.dev.dependencies] rpy2 = ">=3.5.11,<4" -r-fixest = ">=0.12.1,<0.13" -r-broom = ">=1.0.5,<2" [tool.pixi.feature.docs.tasks] docs-build = "quartodoc build --verbose --config docs/_quarto.yml" 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") From c242d6cfc4b50054c36ec61417575429ceafbacf Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 22 Sep 2024 14:18:37 +0200 Subject: [PATCH 068/102] wfl cleanup --- .github/workflows/ci-tests.yaml | 27 --------------------------- pyproject.toml | 2 -- 2 files changed, 29 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index c09f240e..65c37f36 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -38,14 +38,6 @@ jobs: - name: Setup r2u uses: eddelbuettel/github-actions/r2u-setup@master - - # Set R library path to pixi's environment - - name: Set R library path for pixi environment - run: | - # Assuming pixi's R library path is this; adapt if needed - R_LIB_PATH="${{ github.workspace }}/.pixi/envs/dev/lib/R/library" - echo "R_LIBS_USER=$R_LIB_PATH" >> $GITHUB_ENV - # Install R packages into pixi's R library path - name: Install R packages run: | @@ -54,25 +46,6 @@ jobs: Rscript -e ".libPaths('$R_LIB_PATH'); install.packages(c('fixest', 'broom','clubSandwich', 'did2s', 'wildrwolf', 'reticulate', 'ivDiag'), lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos='https://cran.rstudio.com')" 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'))" - - # Verify where R packages are installed - - name: Verify R package installation path - run: | - Rscript -e "print(.libPaths())" - Rscript -e "installed.packages()[, c('Package', 'LibPath')]" - - # Print R library paths that rpy2 is using - - name: Debug rpy2 R library paths - run: | - pixi r debug-env - - #- name: install other r dependencies - # run: pixi r install-r - - - name: Ensure rpy2 uses all R library paths - run: | - pixi r set-rpy2-path - # Run tests - name: Run tests run: | diff --git a/pyproject.toml b/pyproject.toml index 61c238e2..f4b7c4e2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -34,8 +34,6 @@ tests-regular = "pytest tests -m \"not (extended or slow or plots)\" --cov=pyfix tests-extended = "pytest tests -m \"tests-extended\" --cov=pyfixest --cov-report=xml" tests-slow = "pytest tests -m slow --cov=./ --cov-report=xml" tests-rerun = "pytest --lf -n 4" -set-rpy2-path = "python pyfixest/utils/set_rpy2_path.py" -debug-env = "python -c \"import rpy2.robjects as robjects; print(robjects.r('.libPaths()'))\"" debug = "python pyfixest/debug.py" lint = "pre-commit run ruff --all-files" update-test-data = "Rscript tests/r_test_comparisons.R" From 9c7077f1eab1e884e0d3f7c6a429903d9cecb300 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 22 Sep 2024 14:19:37 +0200 Subject: [PATCH 069/102] 4 threads --- pyproject.toml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index f4b7c4e2..b09e084a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -30,9 +30,9 @@ build = { features = ["build"], solve-group = "default" } [tool.pixi.feature.dev.tasks] tests = "pytest -n 4 --cov-report=term tests" -tests-regular = "pytest tests -m \"not (extended or slow or plots)\" --cov=pyfixest --cov-report=xml" -tests-extended = "pytest tests -m \"tests-extended\" --cov=pyfixest --cov-report=xml" -tests-slow = "pytest tests -m slow --cov=./ --cov-report=xml" +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" From e149e0c9bdd3ce6989db9ee4ffd3106559529f8a Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 22 Sep 2024 16:14:39 +0200 Subject: [PATCH 070/102] bring back full ci --- .github/workflows/ci-tests.yaml | 72 +++++++++++++++++++++++++++------ pixi.lock | 2 +- 2 files changed, 61 insertions(+), 13 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index 65c37f36..52aab1ed 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -13,32 +13,78 @@ jobs: name: "Tests Core" runs-on: ${{ matrix.os }} strategy: - fail-fast: true + fail-fast: false matrix: os: ["ubuntu-latest"] - python-version: ["3.12"] + python-version: ["3.9", "3.12"] + pytest_opts: ["--workers 4 --tests-per-worker 1"] steps: - name: Checkout source uses: actions/checkout@v4 - - name: Setup python uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} + architecture: x64 + - 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" >> $GITHUB_ENV + + - name: Setup r2u + uses: eddelbuettel/github-actions/r2u-setup@master + + - name: Install R packages + run: | + R_LIB_PATH="${{ 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', 'reticulate', 'ivDiag'), lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos='https://cran.rstudio.com')" + 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'))" + + - name: Run 'regular 'tests + run: | + pixi run tests-regular - - uses: prefix-dev/setup-pixi@v0.8.1 + - name: Upload to Codecov + uses: codecov/codecov-action@v4 with: - pixi-version: v0.29.0 - cache: true + token: ${{ secrets.CODECOV_TOKEN }} - - name: Set numba parallel flags - run: echo "NUMBA_NUM_THREADS=1" >> $GITHUB_ENV + test_slow: + name: "Tests vs fixest" + runs-on: ${{ matrix.os }} + strategy: + fail-fast: false + matrix: + os: ["ubuntu-latest"] + python-version: ["3.9", "3.12"] + pytest_opts: ["--workers 4 --tests-per-worker 1"] + + steps: + - name: Checkout source + uses: actions/checkout@v4 + - name: Setup python + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + architecture: x64 + - 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" >> $GITHUB_ENV - name: Setup r2u uses: eddelbuettel/github-actions/r2u-setup@master - # Install R packages into pixi's R library path - name: Install R packages run: | R_LIB_PATH="${{ github.workspace }}/.pixi/envs/dev/lib/R/library" @@ -46,7 +92,9 @@ jobs: Rscript -e ".libPaths('$R_LIB_PATH'); install.packages(c('fixest', 'broom','clubSandwich', 'did2s', 'wildrwolf', 'reticulate', 'ivDiag'), lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos='https://cran.rstudio.com')" Rscript -e ".libPaths('$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 - - name: Run tests + - name: Run 'slow 'tests run: | - pixi run tests-regular + pixi run tests-slow + + - name: Upload to Codecov + uses: codecov/codecov-action@v4 diff --git a/pixi.lock b/pixi.lock index fed4410e..18ac700b 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5232,7 +5232,7 @@ packages: name: pyfixest version: 0.24.3 path: . - sha256: 2426947b0a3a1aa86ecc6d37af91290592e742787f8391ed5d6523d79eafbfd6 + sha256: 53002350204189022b0606c2c5cd3bf1d59785b8e062a0a52a8b1713fcdd33df requires_dist: - lets-plot>=4.0.0 - scipy>=1.6 From 7334f1bb1319a1198b3889a1f84e0834673921ce Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 22 Sep 2024 16:18:30 +0200 Subject: [PATCH 071/102] Install pixi --- .github/workflows/ci-tests.yaml | 19 +++++++++++-------- 1 file changed, 11 insertions(+), 8 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index 52aab1ed..9fdaad30 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: | @@ -73,10 +74,12 @@ jobs: with: python-version: ${{ matrix.python-version }} 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Testing statistical and econometric -models is implement using Python and R. Documents are written with Quarto and -Jupyter. - Start by forking the pyfixest GitHub repository, then clone your forked repository using `git`: @@ -43,137 +39,150 @@ cd pyfixest ``` In order to work on `pyfixest`, you will need Python and R installed. If working -on documentation, you will need Quarto installed. +on documentation, you will need Quarto installed. Note that you only need +a local R installation if you want to run 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 suggestions on how to install R and Python, see the sections below. -#### Installing Python -The minimal Python version to develop `pyfixest` is `3.9`. You can installed it on Mac/Linux via [Hombrew](https://brew.sh/): +### Package Management via `pixi` + +`PyFixest` is using [pixi](https://pixi.sh/latest/). + +Please follow the [installation instructions](https://pixi.sh/latest/#installation) from the `pixi` documentation. + +Afterwards, you can initiate the project environment and install all dependencies by running ```{.bash .code-copy} -brew install python@3.11 # specify the version of python you prefer +cd path-to-pyfixest +pixi install ``` -On Windows via [Winget](https://winget.run/pkg/Python/Python.3.11): +If you type ```{.bash .code-copy} -winget install -e --id Python.Python.3.11 +pixi shell ``` -### Installing R +you will see that you have activated a custom `pixi` environment for `pyfixest`. -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. +### Code Style + +We use `ruff` and `pre-commit` to ensure a consistent code style. + +To install the required hooks, run -On Mac/Linux: ```{.bash .code-copy} -brew install r +pixi run lint ``` -Depending on your local set up, you may need to install additional libraries, for -example: +and you're ready to go! + +### `Pixi` tasks + +There are several command line targets that assist with development included +as `pixi` tasks. + ```{.bash .code-copy} -sudo apt install gcc-11 cmake +# 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 ``` -On Windows using [Winget](https://winget.run/pkg/RProject/R): +To rebuild the documentation locally, you can run ```{.bash .code-copy} -winget install -e --id RProject.R +# Build documentation and website +pixi run docs-build +# render the docs +pixi run docs-render +# preview the docs +pixi run docs-preview ``` -Documentation for `pyfixest` is written, compiled, and published using Quarto. +Note that you need to have `quarto` installed in order to build the documentation locally. -To install Quarto, run: - -On MacOS via [Homebrew](https://formulae.brew.sh/cask/quarto#default): +To run the linter, you can run ```{.bash .code-copy} -brew install --cask quarto +pixi run lint ``` -On Linux (Ubuntu using `gdebi`): +To build the package for PyPi, you can run ```{.bash .code-copy} -sudo curl -o quarto-linux-amd64.deb -L -sudo gdebi quarto-linux-amd64.deb +pixi run build-pip ``` -On Windows: +To re-create the csv files in `tests/data` that contain results from R packages for testing, you can run ```{.bash .code-copy} -scoop bucket add extras -scoop install extras/quarto +`pixi run update-tests-data` ``` -### Package Management - -`PyFixest` is using [pixi](https://pixi.sh/latest/). +## Installing Python, R and Quarto -Please follow the [installation instructions](https://pixi.sh/latest/#installation) from the `pixi` 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 -pixi 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} -pixi shell +winget install -e --id Python.Python.3.11 ``` -you will see that you have activated a custom `pixi` environment for `pyfixest`. +### Installing R -### Code Style +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. -We use `ruff` and `pre-commit` to ensure a consistent code style. +On Mac/Linux: +```{.bash .code-copy} +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} -pixi run lint +sudo apt install gcc-11 cmake ``` -and you're ready to go! +On Windows using [Winget](https://winget.run/pkg/RProject/R): -### `Pixi` tasks +```{.bash .code-copy} +winget install -e --id RProject.R +``` -There are several command line targets that assist with development included -as `pixi` tasks. +### Installing Quarto +Documentation for `pyfixest` is written, compiled, and published using Quarto. -```{.bash .code-copy} -# install all R development dependencies -pixi r install-r -# run all tests via pytest -pixi r tests -# run all tests excluding very computationally demanding tests -pixi r tests-regular -``` +To install Quarto, run: -To rebuild the documentation locally, you can run +On MacOS via [Homebrew](https://formulae.brew.sh/cask/quarto#default): ```{.bash .code-copy} -# Build documentation and website -pixi r docs-build -# render the docs -pixi r docs-render -# preview the docs -pixi r docs-preview +brew install --cask quarto ``` -To run the linter, you can run +On Linux (Ubuntu using `gdebi`): ```{.bash .code-copy} -just r lint +sudo curl -o quarto-linux-amd64.deb -L +sudo gdebi quarto-linux-amd64.deb ``` -To re-create the csv files in `tests/data` that contain results from R packages for testing, you can run +On Windows: ```{.bash .code-copy} -`just update-tests-data` +scoop bucket add extras +scoop install extras/quarto ``` From f31b96102c253a9a687990cb7be564070228ee47 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 22 Sep 2024 16:56:01 +0200 Subject: [PATCH 074/102] add publish step for docs --- .github/workflows/ci-tests.yaml | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index b9fa72f6..dc6bdb67 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -144,3 +144,25 @@ jobs: with: name: docs-html path: docs/_site + + + publish-docs: + name: "Publish Docs" + runs-on: ubuntu-latest + permissions: + contents: write + concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + needs: ["build-docs", "test"] + if: github.ref == 'refs/heads/master' + steps: + - 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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) [![Pixi Badge][pixi-badge]][pixi-url] -[![All Contributors](https://img.shields.io/badge/all_contributors-18-orange.svg?style=flat-square)](#contributors-) +[![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 From 19635968c709ffca76fb9b2d7605d9169a0c0787 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Wed, 25 Sep 2024 22:30:51 +0200 Subject: [PATCH 078/102] rebuild pixi lock file --- pixi.lock | 679 +++++++++++++++++++++++++++++++++++------------------- 1 file changed, 437 insertions(+), 242 deletions(-) diff --git a/pixi.lock b/pixi.lock index 18ac700b..13f84661 100644 --- a/pixi.lock +++ b/pixi.lock @@ -14,7 +14,7 @@ environments: - 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- libgcc-ng >=12 + - __glibc >=2.17,<3.0.a0 + - libgcc >=13 license: MIT license_family: MIT purls: [] - size: 30270 - timestamp: 1677036833037 + size: 73315 + timestamp: 1726845753874 - kind: conda name: xorg-xproto version: 7.0.31 - build: h7f98852_1007 + build: hcd874cb_1007 build_number: 1007 - subdir: linux-64 - url: https://conda.anaconda.org/conda-forge/linux-64/xorg-xproto-7.0.31-h7f98852_1007.tar.bz2 - sha256: f197bb742a17c78234c24605ad1fe2d88b1d25f332b75d73e5ba8cf8fbc2a10d - md5: b4a4381d54784606820704f7b5f05a15 + subdir: win-64 + url: https://conda.anaconda.org/conda-forge/win-64/xorg-xproto-7.0.31-hcd874cb_1007.tar.bz2 + sha256: b84cacba8479fa14199c9255fb62e005cacc619e90198c53b1653973709ec331 + md5: 88f3c65d2ad13826a9e0b162063be023 depends: - - libgcc-ng >=9.3.0 + - m2w64-gcc-libs license: MIT license_family: MIT purls: [] - size: 74922 - timestamp: 1607291557628 + size: 75708 + timestamp: 1607292254607 - kind: conda name: xz version: 5.2.6 From 0f5e8f9989b34f6dd803c1fc629f35275622c40c Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Wed, 25 Sep 2024 22:44:15 +0200 Subject: [PATCH 079/102] print r version --- .github/workflows/ci-tests.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index fb2dab5e..c0640c95 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -40,6 +40,10 @@ jobs: - name: Setup r2u uses: eddelbuettel/github-actions/r2u-setup@master + - 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" From e0bb41125f3763266da49ac9b0d83449753da5a8 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Wed, 25 Sep 2024 22:50:56 +0200 Subject: [PATCH 080/102] install r version --- .github/workflows/ci-tests.yaml | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index c0640c95..f6d9e533 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -13,7 +13,7 @@ jobs: name: "Tests Core" runs-on: ${{ matrix.os }} strategy: - fail-fast: false + fail-fast: true matrix: os: ["ubuntu-latest"] python-version: ["3.9", "3.12"] @@ -37,6 +37,11 @@ jobs: run: | echo "NUMBA_NUM_THREADS=1" >> $GITHUB_ENV + - name: Install R + uses: r-lib/actions/setup-r@v2 + with: + r-version: "4.2.0" # You can specify the R version you need here + - name: Setup r2u uses: eddelbuettel/github-actions/r2u-setup@master From 3c555019818dc9b905444f188fc568b9e6035c95 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Wed, 25 Sep 2024 22:53:57 +0200 Subject: [PATCH 081/102] r2u before r --- .github/workflows/ci-tests.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index f6d9e533..42e2391d 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -37,14 +37,14 @@ jobs: run: | echo "NUMBA_NUM_THREADS=1" >> $GITHUB_ENV + - name: Setup r2u + uses: eddelbuettel/github-actions/r2u-setup@master + - name: Install R uses: r-lib/actions/setup-r@v2 with: r-version: "4.2.0" # You can specify the R version you need here - - name: Setup r2u - uses: eddelbuettel/github-actions/r2u-setup@master - - name: Print R version run: | Rscript -e 'R.version' From c6eb06fc0043999ad97f447be83f91402155e055 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Wed, 25 Sep 2024 23:27:26 +0200 Subject: [PATCH 082/102] try cleanup --- .github/workflows/ci-tests.yaml | 2 - coverage.xml | 64435 ++---------------------------- 2 files changed, 3268 insertions(+), 61169 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index 42e2391d..db91dd21 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -101,8 +101,6 @@ jobs: - name: Install R packages run: | - R_LIB_PATH="${{ 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', 'reticulate', 'ivDiag'), lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos='https://cran.rstudio.com')" 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'))" diff --git a/coverage.xml b/coverage.xml index 7021d191..c3551824 100644 --- a/coverage.xml +++ b/coverage.xml @@ -1,9 +1,8 @@ - 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+ - - - - - - - - - - - - - - - + + + + + + - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + - + - + - - - - - - - - - + + + - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + @@ -61668,7 +3749,7 @@ - + @@ -61679,42 +3760,42 @@ - - - + + + - - - + + + - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + @@ -61743,18 +3824,18 @@ - - - - - + + + + + - - - + + + - + @@ -61771,49 +3852,49 @@ - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + - - - - - - + + + + + + - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + @@ -61866,7 +3947,27 @@ - + + + + + + + + + + + + + + + + + + + + + @@ -61962,13 +4063,13 @@ - - - - - - - + + + + + + + From 7e98b1b14863f165fd9aa2db068e530317b95205 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Wed, 25 Sep 2024 23:28:29 +0200 Subject: [PATCH 083/102] try cleanup --- .github/workflows/ci-tests.yaml | 7 ------- 1 file changed, 7 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index db91dd21..ae73cb7f 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -40,19 +40,12 @@ jobs: - name: Setup r2u uses: eddelbuettel/github-actions/r2u-setup@master - - name: Install R - uses: r-lib/actions/setup-r@v2 - with: - r-version: "4.2.0" # You can specify the R version you need here - - 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','clubSandwich', 'did2s', 'wildrwolf', 'reticulate', 'ivDiag'), lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos='https://cran.rstudio.com')" Rscript -e ".libPaths('$R_LIB_PATH'); install.packages('ritest', lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos = c('https://grantmcdermott.r-universe.dev', 'https://cloud.r-project.org'))" From 020ffa88ebbda876b0407efcb22262eedc15658a Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Wed, 25 Sep 2024 23:33:23 +0200 Subject: [PATCH 084/102] revert and install r version --- .github/workflows/ci-tests.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index ae73cb7f..8d97a83f 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -46,6 +46,8 @@ jobs: - name: Install R packages run: | + R_LIB_PATH="${{ 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', 'reticulate', 'ivDiag'), lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos='https://cran.rstudio.com')" Rscript -e ".libPaths('$R_LIB_PATH'); install.packages('ritest', lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos = c('https://grantmcdermott.r-universe.dev', 'https://cloud.r-project.org'))" @@ -94,6 +96,8 @@ jobs: - name: Install R packages run: | + R_LIB_PATH="${{ 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', 'reticulate', 'ivDiag'), lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos='https://cran.rstudio.com')" 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'))" From 733e3d6ccf83b0b9969c9f6c7866e4cd28ae929b Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Thu, 26 Sep 2024 20:44:20 +0200 Subject: [PATCH 085/102] install r and test on windows --- .github/workflows/ci-tests.yaml | 17 ++++++++++++----- 1 file changed, 12 insertions(+), 5 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index 8d97a83f..e2fb54bc 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -15,7 +15,7 @@ jobs: strategy: fail-fast: true matrix: - os: ["ubuntu-latest"] + os: ["windows-latest"] python-version: ["3.9", "3.12"] pytest_opts: ["--workers 4 --tests-per-worker 1"] @@ -37,8 +37,13 @@ jobs: run: | echo "NUMBA_NUM_THREADS=1" >> $GITHUB_ENV - - name: Setup r2u - uses: eddelbuettel/github-actions/r2u-setup@master + #- name: Setup r2u + # uses: eddelbuettel/github-actions/r2u-setup@master + + - name: Set up R + uses: r-lib/actions/setup-r@v2 + with: + r-version: '4.3.0' # Install only R 4.2.0 - name: Print R version run: | @@ -91,8 +96,10 @@ jobs: run: | echo "NUMBA_NUM_THREADS=1" >> $GITHUB_ENV - - name: Setup r2u - uses: eddelbuettel/github-actions/r2u-setup@master + - name: Set up R + uses: r-lib/actions/setup-r@v2 + with: + r-version: '4.3.0' # Install only R 4.2.0 - name: Install R packages run: | From b22b3b972ab45a23ab553f989c37a288e78d3c85 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Thu, 26 Sep 2024 20:57:34 +0200 Subject: [PATCH 086/102] fix path for windows --- .github/workflows/ci-tests.yaml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index e2fb54bc..0b0aa2cb 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -51,8 +51,7 @@ jobs: - name: Install R packages run: | - R_LIB_PATH="${{ github.workspace }}/.pixi/envs/dev/lib/R/library" - mkdir -p $R_LIB_PATH + $env:R_LIB_PATH="D:\a\pyfixest\pyfixest/.pixi/envs/dev/lib/R/library" Rscript -e ".libPaths('$R_LIB_PATH'); install.packages(c('fixest', 'broom','clubSandwich', 'did2s', 'wildrwolf', 'reticulate', 'ivDiag'), lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos='https://cran.rstudio.com')" Rscript -e ".libPaths('$R_LIB_PATH'); install.packages('ritest', lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos = c('https://grantmcdermott.r-universe.dev', 'https://cloud.r-project.org'))" @@ -103,8 +102,7 @@ jobs: - name: Install R packages run: | - R_LIB_PATH="${{ github.workspace }}/.pixi/envs/dev/lib/R/library" - mkdir -p $R_LIB_PATH + $env:R_LIB_PATH="D:\a\pyfixest\pyfixest/.pixi/envs/dev/lib/R/library" Rscript -e ".libPaths('$R_LIB_PATH'); install.packages(c('fixest', 'broom','clubSandwich', 'did2s', 'wildrwolf', 'reticulate', 'ivDiag'), lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos='https://cran.rstudio.com')" 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'))" From b0324e3cf4303db21344a51a1be7d0c1f2097c13 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Thu, 26 Sep 2024 21:33:27 +0200 Subject: [PATCH 087/102] revert ubuntu --- .github/workflows/ci-tests.yaml | 25 ++++++++++--------------- 1 file changed, 10 insertions(+), 15 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index 0b0aa2cb..c0640c95 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -13,9 +13,9 @@ jobs: name: "Tests Core" runs-on: ${{ matrix.os }} strategy: - fail-fast: true + fail-fast: false matrix: - os: ["windows-latest"] + os: ["ubuntu-latest"] python-version: ["3.9", "3.12"] pytest_opts: ["--workers 4 --tests-per-worker 1"] @@ -37,13 +37,8 @@ jobs: run: | echo "NUMBA_NUM_THREADS=1" >> $GITHUB_ENV - #- name: Setup r2u - # uses: eddelbuettel/github-actions/r2u-setup@master - - - name: Set up R - uses: r-lib/actions/setup-r@v2 - with: - r-version: '4.3.0' # Install only R 4.2.0 + - name: Setup r2u + uses: eddelbuettel/github-actions/r2u-setup@master - name: Print R version run: | @@ -51,7 +46,8 @@ jobs: - name: Install R packages run: | - $env:R_LIB_PATH="D:\a\pyfixest\pyfixest/.pixi/envs/dev/lib/R/library" + R_LIB_PATH="${{ 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', 'reticulate', 'ivDiag'), lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos='https://cran.rstudio.com')" 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'))" @@ -95,14 +91,13 @@ jobs: run: | echo "NUMBA_NUM_THREADS=1" >> $GITHUB_ENV - - name: Set up R - uses: r-lib/actions/setup-r@v2 - with: - r-version: '4.3.0' # Install only R 4.2.0 + - name: Setup r2u + uses: eddelbuettel/github-actions/r2u-setup@master - name: Install R packages run: | - $env:R_LIB_PATH="D:\a\pyfixest\pyfixest/.pixi/envs/dev/lib/R/library" + R_LIB_PATH="${{ 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', 'reticulate', 'ivDiag'), lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos='https://cran.rstudio.com')" Rscript -e ".libPaths('$R_LIB_PATH'); install.packages('ritest', lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos = c('https://grantmcdermott.r-universe.dev', 'https://cloud.r-project.org'))" From 7e86d994b7e110cdd92837ae390f46011bb9fef6 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Thu, 26 Sep 2024 21:49:27 +0200 Subject: [PATCH 088/102] tweaks --- .github/workflows/ci-tests.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index c0640c95..e1f83b64 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -48,8 +48,8 @@ jobs: run: | R_LIB_PATH="${{ 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', 'reticulate', 'ivDiag'), lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos='https://cran.rstudio.com')" - Rscript -e ".libPaths('$R_LIB_PATH'); install.packages('ritest', lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos = c('https://grantmcdermott.r-universe.dev', 'https://cloud.r-project.org'))" + Rscript -e ".libPaths('$R_LIB_PATH'); install.packages(c('fixest', 'broom','clubSandwich', 'did2s', 'wildrwolf', 'reticulate'), lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library')" + Rscript -e ".libPaths('$R_LIB_PATH'); install.packages('ritest', lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos = c('https://grantmcdermott.r-universe.dev'))" - name: Run 'regular 'tests run: | @@ -98,8 +98,8 @@ jobs: run: | R_LIB_PATH="${{ 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', 'reticulate', 'ivDiag'), lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos='https://cran.rstudio.com')" - Rscript -e ".libPaths('$R_LIB_PATH'); install.packages('ritest', lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos = c('https://grantmcdermott.r-universe.dev', 'https://cloud.r-project.org'))" + Rscript -e ".libPaths('$R_LIB_PATH'); install.packages(c('fixest', 'broom','clubSandwich', 'did2s', 'wildrwolf', 'reticulate'), 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 'slow 'tests run: | From dbcdecebacc784270bfc8b450fbcc33c3a6b99cd Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Thu, 26 Sep 2024 21:57:04 +0200 Subject: [PATCH 089/102] dont run bootstrap ivdiag --- tests/test_iv.py | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/tests/test_iv.py b/tests/test_iv.py index 669e1302..6a36efdf 100644 --- a/tests/test_iv.py +++ b/tests/test_iv.py @@ -89,10 +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 { From 37ea3d3b1f77c1a6cfc11a0bf7101c0d71b33639 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Thu, 26 Sep 2024 22:52:21 +0200 Subject: [PATCH 090/102] move wald testing to car::linearHypothesis --- r_test_requirements.R | 2 +- tests/test_wald_test.py | 71 ++++++++++++++--------------------------- 2 files changed, 25 insertions(+), 48 deletions(-) diff --git a/r_test_requirements.R b/r_test_requirements.R index f064d2c1..4e4b3846 100644 --- a/r_test_requirements.R +++ b/r_test_requirements.R @@ -1,6 +1,6 @@ # note: fixest and broom are installed via conda install.packages( - c('fixest', 'broom','clubSandwich', 'did2s', 'wildrwolf', 'reticulate', 'ivDiag', 'stats', 'base'), + c('fixest', 'broom','clubSandwich', 'did2s', 'wildrwolf', 'reticulate', 'ivDiag', 'stats', 'base', 'car'), repos='https://cran.rstudio.com' ); install.packages( diff --git a/tests/test_wald_test.py b/tests/test_wald_test.py index e8599fc2..1041adef 100644 --- a/tests/test_wald_test.py +++ b/tests/test_wald_test.py @@ -16,8 +16,6 @@ pandas2ri.activate() - -clubSandwich = importr("clubSandwich") fixest = importr("fixest") stats = importr("stats") broom = importr("broom") @@ -60,19 +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) @@ -101,16 +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) @@ -133,7 +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( { @@ -152,17 +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) @@ -216,22 +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( From 8756dc2a52a4113ec8968cb2355733933dfd43dc Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Thu, 26 Sep 2024 22:55:33 +0200 Subject: [PATCH 091/102] update readme --- docs/contributing.qmd | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/docs/contributing.qmd b/docs/contributing.qmd index 580e9711..2dea6938 100644 --- a/docs/contributing.qmd +++ b/docs/contributing.qmd @@ -82,6 +82,14 @@ and you're ready to go! There are several command line targets that assist with development included as `pixi` tasks. +To avtivate relevant pixi environments, you can type + +```{.bash .code-copy} +pixi shell # open the base environment +pixi shell --environment dev # open the dev environment +``` + +For development, it is recommended to activate the dev environment (as it includes all development dependencies). ```{.bash .code-copy} # install all R development dependencies From 0eef3300b9473f026d296c9c7b5d371cd74fccd4 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Thu, 26 Sep 2024 23:02:16 +0200 Subject: [PATCH 092/102] install all relevant packages --- .github/workflows/ci-tests.yaml | 4 ++-- .github/workflows/extended-tests.yml | 3 +-- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index e1f83b64..a12a6191 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -48,7 +48,7 @@ jobs: 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', 'reticulate'), lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library')" + 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 'regular 'tests @@ -98,7 +98,7 @@ jobs: 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', 'reticulate'), lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library')" + 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 'slow 'tests diff --git a/.github/workflows/extended-tests.yml b/.github/workflows/extended-tests.yml index af899936..df115b76 100644 --- a/.github/workflows/extended-tests.yml +++ b/.github/workflows/extended-tests.yml @@ -47,7 +47,7 @@ jobs: 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', 'reticulate', 'ivDiag'), lib='/home/runner/work/pyfixest/pyfixest/.pixi/envs/dev/lib/R/library', repos='https://cran.rstudio.com')" + 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" @@ -59,4 +59,3 @@ jobs: - name: Run tests for push to master if: github.event_name == 'push' && github.ref == 'refs/heads/master' run: pixi run tests-extended - \ No newline at end of file From 0e5274d961803f80b48bc6468c8b3a1eaabdf231 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Thu, 26 Sep 2024 23:30:27 +0200 Subject: [PATCH 093/102] fix IV tests --- tests/test_iv.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/test_iv.py b/tests/test_iv.py index 6a36efdf..eb5275da 100644 --- a/tests/test_iv.py +++ b/tests/test_iv.py @@ -89,7 +89,7 @@ def r_results(): data=data_r, weights="weights", cl=cl_r, - run_ar=False, + run_AR=False, parallel=False, bootstrap=False, ) @@ -101,7 +101,7 @@ def r_results(): controls=controls_r, data=data_r, cl=cl_r, - run_ar=False, + run_AR=False, parallel=False, bootstrap=False, ) @@ -155,7 +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) From 10f7fa1ca3f753c3aa788a2ca2e100e8424b9d78 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Thu, 26 Sep 2024 23:38:07 +0200 Subject: [PATCH 094/102] do not install poetry for docs --- .github/workflows/ci-tests.yaml | 6 ------ 1 file changed, 6 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index a12a6191..574f2901 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -131,12 +131,6 @@ jobs: pixi-version: v0.29.0 cache: true - - name: Set up poetry - uses: snok/install-poetry@v1 - - - name: Install dependencies - run: poetry install --with docs - - name: Set up Quarto uses: quarto-dev/quarto-actions/setup@v2 From c3a94d0e46a61f3e29df6a419c5f0b5446ef89ac Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Thu, 26 Sep 2024 23:46:30 +0200 Subject: [PATCH 095/102] fix typo --- .github/workflows/ci-tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index 574f2901..c0cd0358 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -143,7 +143,7 @@ jobs: pixi run docs-build - 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__glibc >=2.17,<3.0.a0 + - libgcc >=13 + license: MIT + license_family: MIT + purls: [] + size: 565425 + timestamp: 1726846388217 - kind: conda name: xorg-xproto version: 7.0.31 @@ -7190,6 +7480,32 @@ packages: purls: [] size: 217804 timestamp: 1660346976440 +- kind: pypi + name: zipp + version: 3.20.2 + url: https://files.pythonhosted.org/packages/62/8b/5ba542fa83c90e09eac972fc9baca7a88e7e7ca4b221a89251954019308b/zipp-3.20.2-py3-none-any.whl + sha256: a817ac80d6cf4b23bf7f2828b7cabf326f15a001bea8b1f9b49631780ba28350 + requires_dist: + - pytest-checkdocs>=2.4 ; extra == 'check' + - pytest-ruff>=0.2.1 ; sys_platform != 'cygwin' and extra == 'check' + - pytest-cov ; extra == 'cover' + - sphinx>=3.5 ; extra == 'doc' + - jaraco-packaging>=9.3 ; extra == 'doc' + - rst-linker>=1.9 ; extra == 'doc' + - furo ; extra == 'doc' + - sphinx-lint ; extra == 'doc' + - jaraco-tidelift>=1.4 ; extra == 'doc' + - pytest-enabler>=2.2 ; extra == 'enabler' + - pytest!=8.1.*,>=6 ; extra == 'test' + - jaraco-itertools ; extra == 'test' + - jaraco-functools ; extra == 'test' + - more-itertools ; extra == 'test' + - big-o ; extra == 'test' + - pytest-ignore-flaky ; extra == 'test' + - jaraco-test ; extra == 'test' + - importlib-resources ; python_full_version < '3.9' and extra == 'test' + - pytest-mypy ; extra == 'type' + requires_python: '>=3.8' - kind: conda name: zipp version: 3.20.2 From f9d7ec460f11fc031124bfb5fdcc555d0f51e8d3 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Fri, 27 Sep 2024 20:21:54 +0200 Subject: [PATCH 098/102] slight reorg of lock file --- pixi.lock | 2 +- pyproject.toml | 46 +++++++++++++++++++++++++++++++++++++--------- 2 files changed, 38 insertions(+), 10 deletions(-) diff --git a/pixi.lock b/pixi.lock index 816f8582..1707ec7b 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5514,7 +5514,7 @@ packages: name: pyfixest version: 0.24.3 path: . - sha256: d7c337db43a17939075fcc80c170280502b1026e7eb60e881d11cf5082c7da2a + sha256: f697d8aaaad791e13bb3049ba33028ce7c8a2b989d1c021a8fa1f11f8cc2fe4b requires_dist: - lets-plot>=4.0.0 - scipy>=1.6 diff --git a/pyproject.toml b/pyproject.toml index 854fdace..7bf2b7c8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,12 +4,46 @@ description = "Fast high dimensional fixed effect estimation following syntax of requires-python = ">= 3.9" version = "0.24.3" authors = [{name = "Alexander Fischer", email = "alexander-fischer1801@t-online.de"}, {name = "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"] +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" +] + +[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"] +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" +] + +[tool.pixi.feature.build.dependencies] +python-build = ">=1.2.2,<2" [build-system] build-backend = "hatchling.build" @@ -43,12 +77,6 @@ render-notebooks = "python scripts/run_notebooks.py" [tool.pixi.feature.build.tasks] build-pip = 'python -m build .' -[tool.pixi.feature.build.dependencies] -python-build = ">=1.2.2,<2" - -[tool.pixi.feature.dev.dependencies] -rpy2 = ">=3.5.11,<4" - [tool.pixi.feature.docs.tasks] docs-build = "quartodoc build --verbose --config docs/_quarto.yml" docs-render = "quarto render docs" From dbe2eb9904e4fa3ce3a4b9b2f75f9baccc9cc6ef Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Fri, 27 Sep 2024 20:40:08 +0200 Subject: [PATCH 099/102] Update lock --- docs/compare-fixest-pyfixest.html | 1860 ++++++++++++++++ docs/contributing.html | 735 +++++++ docs/difference-in-differences.html | 1871 +++++++++++++++++ .../figure-html/cell-5-output-1.png | Bin 0 -> 11809 bytes .../figure-html/cell-6-output-1.png | Bin 0 -> 12334 bytes .../figure-html/cell-7-output-1.png | Bin 0 -> 16273 bytes docs/marginaleffects.html | 937 +++++++++ docs/news.html | 1483 +++++++++++++ docs/pyfixest.html | 795 +++++++ pixi.lock | 375 +--- pyproject.toml | 5 +- 11 files changed, 7727 insertions(+), 334 deletions(-) create mode 100644 docs/compare-fixest-pyfixest.html create mode 100644 docs/contributing.html create mode 100644 docs/difference-in-differences.html create mode 100644 docs/difference-in-differences_files/figure-html/cell-5-output-1.png create mode 100644 docs/difference-in-differences_files/figure-html/cell-6-output-1.png create mode 100644 docs/difference-in-differences_files/figure-html/cell-7-output-1.png create mode 100644 docs/marginaleffects.html create mode 100644 docs/news.html create mode 100644 docs/pyfixest.html diff --git a/docs/compare-fixest-pyfixest.html b/docs/compare-fixest-pyfixest.html new file mode 100644 index 00000000..b295c09a --- /dev/null +++ b/docs/compare-fixest-pyfixest.html @@ -0,0 +1,1860 @@ + + + + + + + + + +Does PyFixest match fixest? + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+
+ +
+ +
+ + + + +
+ +
+
+

Does PyFixest match fixest?

+
+ + + +
+ + + + +
+ + + +
+ + +

This vignette compares estimation results from fixest with pyfixest via the rpy2 package.

+
+
import pandas as pd
+import rpy2.robjects as ro
+from rpy2.robjects import pandas2ri
+from rpy2.robjects.packages import importr
+
+import pyfixest as pf
+
+# Activate pandas2ri
+pandas2ri.activate()
+
+# Import R packages
+fixest = importr("fixest")
+stats = importr("stats")
+
+# IPython magic commands for autoreloading
+%load_ext autoreload
+%autoreload 2
+
+# Get data using pyfixest
+data = pf.get_data(model="Feols", N=10_000, seed=99292)
+
+ +
+ + +
+
+ +
+ + +
+
+
+

Ordinary Least Squares (OLS)

+
+

IID Inference

+

First, we estimate a model via `pyfixest. We compute “iid” standard errors.

+
+
fit = pf.feols(fml="Y ~ X1 + X2 | f1 + f2", data=data, vcov="iid")
+
+

We estimate the same model with weights:

+
+
fit_weights = pf.feols(
+    fml="Y ~ X1 + X2 | f1 + f2", data=data, weights="weights", vcov="iid"
+)
+
+

Via r-fixest and rpy2, we get

+
+
r_fit = fixest.feols(
+    ro.Formula("Y ~ X1 + X2 | f1 + f2"),
+    data=data,
+    vcov="iid",
+    ssc=fixest.ssc(True, "none", True, "min", "min", False),
+)
+
+r_fit_weights = fixest.feols(
+    ro.Formula("Y ~ X1 + X2 | f1 + f2"),
+    data=data,
+    weights=ro.Formula("~weights"),
+    vcov="iid",
+    ssc=fixest.ssc(True, "none", True, "min", "min", False),
+)
+
+
R[write to console]: NOTE: 3 observations removed because of NA values (LHS: 1, RHS: 1, Fixed-effects: 1).
+
+R[write to console]: NOTE: 3 observations removed because of NA values (LHS: 1, RHS: 1, Fixed-effects: 1).
+
+
+
+

Let’s compare how close the covariance matrices are:

+
+
fit_vcov = fit._vcov
+r_vcov = stats.vcov(r_fit)
+fit_vcov - r_vcov
+
+
array([[-7.04731412e-19, -3.34180967e-22],
+       [-3.34594558e-22, -1.38913403e-19]])
+
+
+

And for WLS:

+
+
fit_weights._vcov - stats.vcov(r_fit_weights)
+
+
array([[ 1.68051337e-18, -1.69406589e-21],
+       [-1.69406589e-21, -1.49077799e-19]])
+
+
+

We conclude by comparing all estimation results via the etable function:

+
+
pf.etable([fit, fit_weights], digits=6)
+
+
+ + + +++++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Y
(1)(2)
coef
X10.112019***
+(0.016947)		0.123687***
+(0.016880)
X20.732788***
+(0.004595)		0.732244***
+(0.004584)
fe
f1xx
f2xx
modelstats
Observations99979997
S.E. typeiidiid
R20.774375-
Significance levels: * p < 0.05, ** p < 0.01, *** p < 0.001. Format of coefficient cell: Coefficient (Std. Error)
+ + +
+ +
+
+
+
pd.DataFrame(fixest.etable(r_fit, r_fit_weights, digits=6)).T
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
012
0Dependent Var.:YY
1
2X10.112019*** (0.016947)0.123687*** (0.016880)
3X20.732788*** (0.004595)0.732244*** (0.004584)
4Fixed-Effects:--------------------------------------------
5f1YesYes
6f2YesYes
7___________________________________________________________
8S.E. typeIIDIID
9Observations9,9979,997
10R20.774380.77526
11Within R20.718220.71886
+ +
+
+
+
+
+

Heteroskedastic Errors

+

We repeat the same exercise with heteroskedastic (HC1) errors:

+
+
fit = pf.feols(fml="Y ~ X1 + X2 | f1 + f2", data=data, vcov="hetero")
+fit_weights = pf.feols(
+    fml="Y ~ X1 + X2 | f1 + f2", data=data, vcov="hetero", weights="weights"
+)
+
+
+
fit_r = fixest.feols(
+    ro.Formula("Y ~ X1 + X2 | f1 + f2"),
+    data=data,
+    vcov="hetero",
+    ssc=fixest.ssc(True, "none", True, "min", "min", False),
+)
+
+fit_weights_r = fixest.feols(
+    ro.Formula("Y ~ X1 + X2 | f1 + f2"),
+    data=data,
+    weights=ro.Formula("~weights"),
+    vcov="hetero",
+    ssc=fixest.ssc(True, "none", True, "min", "min", False),
+)
+
+
R[write to console]: NOTE: 3 observations removed because of NA values (LHS: 1, RHS: 1, Fixed-effects: 1).
+
+R[write to console]: NOTE: 3 observations removed because of NA values (LHS: 1, RHS: 1, Fixed-effects: 1).
+
+
+
+

As before, we compare the variance covariance matrices:

+
+
fit._vcov - stats.vcov(fit_r)
+
+
array([[-1.61925594e-16, -2.13306719e-17],
+       [-2.13306719e-17, -5.39593869e-17]])
+
+
+
+
fit_weights._vcov - stats.vcov(fit_weights_r)
+
+
array([[-2.04968421e-16, -9.53780274e-18],
+       [-9.53780274e-18, -3.03136151e-17]])
+
+
+
+
pf.etable([fit, fit_weights], digits=6)
+
+
+ + + +++++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Y
(1)(2)
coef
X10.112019***
+(0.017009)		0.123687***
+(0.019361)
X20.732788***
+(0.004553)		0.732244***
+(0.005140)
fe
f1xx
f2xx
modelstats
Observations99979997
S.E. typeheterohetero
R20.774375-
Significance levels: * p < 0.05, ** p < 0.01, *** p < 0.001. Format of coefficient cell: Coefficient (Std. Error)
+ + +
+ +
+
+
+
pd.DataFrame(fixest.etable(fit_r, fit_weights_r, digits=6)).T
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
012
0Dependent Var.:YY
1
2X10.112019*** (0.017009)0.123687*** (0.019361)
3X20.732788*** (0.004553)0.732244*** (0.005140)
4Fixed-Effects:--------------------------------------------
5f1YesYes
6f2YesYes
7___________________________________________________________
8S.E. typeHeteroskedastici.-rob.Heteroskedastici.-rob.
9Observations9,9979,997
10R20.774380.77526
11Within R20.718220.71886
+ +
+
+
+
+
+

Cluster-Robust Errors

+

We conclude with cluster robust errors.

+
+
fit = pf.feols(fml="Y ~ X1 + X2 | f1 + f2", data=data, vcov={"CRV1": "f1"})
+fit_weights = pf.feols(
+    fml="Y ~ X1 + X2 | f1 + f2", data=data, vcov={"CRV1": "f1"}, weights="weights"
+)
+
+fit_r = fixest.feols(
+    ro.Formula("Y ~ X1 + X2 | f1 + f2"),
+    data=data,
+    vcov=ro.Formula("~f1"),
+    ssc=fixest.ssc(True, "none", True, "min", "min", False),
+)
+fit_r_weights = fixest.feols(
+    ro.Formula("Y ~ X1 + X2 | f1 + f2"),
+    data=data,
+    weights=ro.Formula("~weights"),
+    vcov=ro.Formula("~f1"),
+    ssc=fixest.ssc(True, "none", True, "min", "min", False),
+)
+
+
R[write to console]: NOTE: 3 observations removed because of NA values (LHS: 1, RHS: 1, Fixed-effects: 1).
+
+R[write to console]: NOTE: 3 observations removed because of NA values (LHS: 1, RHS: 1, Fixed-effects: 1).
+
+
+
+
+
fit._vcov - stats.vcov(fit_r)
+
+
array([[ 4.20345182e-16, -6.97387636e-17],
+       [-6.97404577e-17, -1.42166010e-17]])
+
+
+
+
fit_weights._vcov - stats.vcov(fit_weights_r)
+
+
array([[-3.95318402e-05,  2.05473422e-05],
+       [ 2.05473422e-05,  1.13249200e-06]])
+
+
+
+
pf.etable([fit, fit_weights], digits=6)
+
+
+ + + +++++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Y
(1)(2)
coef
X10.112019***
+(0.015816)		0.123687***
+(0.018311)
X20.732788***
+(0.004476)		0.732244***
+(0.005249)
fe
f1xx
f2xx
modelstats
Observations99979997
S.E. typeby: f1by: f1
R20.774375-
Significance levels: * p < 0.05, ** p < 0.01, *** p < 0.001. Format of coefficient cell: Coefficient (Std. Error)
+ + +
+ +
+
+
+
pd.DataFrame(fixest.etable(fit_r, fit_r_weights, digits=6)).T
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
012
0Dependent Var.:YY
1
2X10.112019*** (0.015816)0.123687*** (0.018311)
3X20.732788*** (0.004476)0.732244*** (0.005249)
4Fixed-Effects:--------------------------------------------
5f1YesYes
6f2YesYes
7___________________________________________________________
8S.E.: Clusteredby: f1by: f1
9Observations9,9979,997
10R20.774380.77526
11Within R20.718220.71886
+ +
+
+
+
+
+
+

Poisson Regression

+
+
data = pf.get_data(model="Fepois")
+
+
+
fit_iid = pf.fepois(fml="Y ~ X1 + X2 | f1 + f2", data=data, vcov="iid", iwls_tol=1e-10)
+fit_hetero = pf.fepois(
+    fml="Y ~ X1 + X2 | f1 + f2", data=data, vcov="hetero", iwls_tol=1e-10
+)
+fit_crv = pf.fepois(
+    fml="Y ~ X1 + X2 | f1 + f2", data=data, vcov={"CRV1": "f1"}, iwls_tol=1e-10
+)
+
+fit_r_iid = fixest.fepois(
+    ro.Formula("Y ~ X1 + X2 | f1 + f2"),
+    data=data,
+    vcov="iid",
+    ssc=fixest.ssc(True, "none", True, "min", "min", False),
+)
+
+fit_r_hetero = fixest.fepois(
+    ro.Formula("Y ~ X1 + X2 | f1 + f2"),
+    data=data,
+    vcov="hetero",
+    ssc=fixest.ssc(True, "none", True, "min", "min", False),
+)
+
+fit_r_crv = fixest.fepois(
+    ro.Formula("Y ~ X1 + X2 | f1 + f2"),
+    data=data,
+    vcov=ro.Formula("~f1"),
+    ssc=fixest.ssc(True, "none", True, "min", "min", False),
+)
+
+
R[write to console]: NOTE: 3 observations removed because of NA values (LHS: 1, RHS: 1, Fixed-effects: 1).
+
+R[write to console]: NOTE: 3 observations removed because of NA values (LHS: 1, RHS: 1, Fixed-effects: 1).
+
+R[write to console]: NOTE: 3 observations removed because of NA values (LHS: 1, RHS: 1, Fixed-effects: 1).
+
+
+
+
+
fit_iid._vcov - stats.vcov(fit_r_iid)
+
+
array([[ 1.20791284e-08, -6.55604931e-10],
+       [-6.55604931e-10,  1.69958097e-09]])
+
+
+
+
fit_hetero._vcov - stats.vcov(fit_r_hetero)
+
+
array([[ 2.18101847e-08, -7.38711972e-10],
+       [-7.38711972e-10,  3.07587753e-09]])
+
+
+
+
fit_crv._vcov - stats.vcov(fit_r_crv)
+
+
array([[ 1.58300904e-08, -1.20806815e-10],
+       [-1.20806815e-10,  3.17512746e-09]])
+
+
+
+
pf.etable([fit_iid, fit_hetero, fit_crv], digits=6)
+
+
+ + + ++++++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Y
(1)(2)(3)
coef
X1-0.006591
+(0.040758)		-0.006591
+(0.039145)		-0.006591
+(0.034745)
X2-0.014924
+(0.010994)		-0.014924
+(0.010501)		-0.014924
+(0.010303)
fe
f1xxx
f2xxx
modelstats
Observations997997997
S.E. typeiidheteroby: f1
R2---
Significance levels: * p < 0.05, ** p < 0.01, *** p < 0.001. Format of coefficient cell: Coefficient (Std. Error)
+ + +
+ +
+
+
+
pd.DataFrame(fixest.etable(fit_r_iid, fit_r_hetero, fit_r_crv, digits=6)).T
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
0123
0Dependent Var.:YYY
1
2X1-0.006591 (0.040758)-0.006591 (0.039145)-0.006591 (0.034745)
3X2-0.014924 (0.010994)-0.014924 (0.010501)-0.014924 (0.010302)
4Fixed-Effects:------------------------------------------------------------
5f1YesYesYes
6f2YesYesYes
7___________________________________________________________________________
8S.E. typeIIDHeteroskedasti.-rob.by: f1
9Observations997997997
10Squared Cor.0.076870.076870.07687
11Pseudo R20.028660.028660.02866
12BIC2,934.72,934.72,934.7
+ +
+
+
+ + +
+ +
+ +
+ + + + + diff --git a/docs/contributing.html b/docs/contributing.html new file mode 100644 index 00000000..cfc7b1d8 --- /dev/null +++ b/docs/contributing.html @@ -0,0 +1,735 @@ + + + + + + + + + +Contributing + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ +
+ +
+ + + + +
+ +
+
+

Contributing

+
+ + + +
+ + + + +
+ + + +
+ + +
+

Overview

+

Thanks for showing interest in contributing to pyfixest! We appreciate all contributions and constructive feedback, whether that be reporting bugs, requesting new features, or suggesting improvements to documentation.

+

If you’d like to get involved, but are not yet sure how, please feel free to send us an email. Some familiarity with either Python or econometrics will help, but you really don’t need to be a numpy core developer or have published in Econometrica =) We’d be more than happy to invest time to help you get started!

+
+

Reporting bugs

+

We use GitHub issues to track bugs. You can report a bug by opening a new issue or contribute to an existing issue if related to the bug you are reporting.

+

Before creating a bug report, please check that your bug has not already been reported, and that your bug exists on the latest version of pyfixest. If you find a closed issue that seems to report the same bug you’re experiencing, open a new issue and include a link to the original issue in your issue description.

+

Please include as many details as possible in your bug report. The information helps the maintainers resolve the issue faster.

+
+
+

Suggesting enhancements

+

We use GitHub issues to track bugs and suggested enhancements. You can suggest an enhancement by opening a new feature request. Before creating an enhancement suggestion, please check that a similar issue does not already exist.

+

Please describe the behavior you want and why, and provide examples of how pyfixest would be used if your feature were added.

+
+
+

Contributing to the codebase

+
+

Setting up your local environment

+

Start by forking the pyfixest GitHub repository, then clone your forked repository using git:

+
git clone https://github.com/<username>/pyfixest.git
+cd pyfixest
+

In order to work on pyfixest, you will need Python and R installed. If working on documentation, you will need Quarto installed. Note that you only need a local R installation if you want to run unit tests locally.

+

For suggestions on how to install R and Python, see the sections below.

+
+
+

Package Management via pixi

+

PyFixest is using pixi.

+

Please follow the installation instructions from the pixi documentation.

+

Afterwards, you can initiate the project environment and install all dependencies by running

+
cd path-to-pyfixest
+pixi install
+

If you type

+
pixi shell
+

you will see that you have activated a custom pixi environment for pyfixest.

+
+
+

Code Style

+

We use ruff and pre-commit to ensure a consistent code style.

+

To install the required hooks, run

+
pixi run lint
+

and you’re ready to go!

+
+
+

Pixi tasks

+

There are several command line targets that assist with development included as pixi tasks.

+

To avtivate relevant pixi environments, you can type

+
pixi shell                      # open the base environment
+pixi shell --environment dev    # open the dev environment
+

For development, it is recommended to activate the dev environment (as it includes all development dependencies).

+
# 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
+

To rebuild the documentation locally, you can run

+
# Build documentation and website
+pixi run docs-build
+# render the docs
+pixi run docs-render
+# preview the docs
+pixi run docs-preview
+

Note that you need to have quarto installed in order to build the documentation locally.

+

To run the linter, you can run

+
pixi run lint
+

To build the package for PyPi, you can run

+
pixi run build-pip
+

To re-create the csv files in tests/data that contain results from R packages for testing, you can run

+
`pixi run update-tests-data`
+
+
+
+

Installing Python, R and Quarto

+
+

Installing Python

+

The minimal Python version to develop pyfixest is 3.9. You can installed it on Mac/Linux via Hombrew:

+
brew install python@3.11 # specify the version of python you prefer
+

On Windows via Winget:

+
winget install -e --id Python.Python.3.11
+
+
+

Installing R

+

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:

+
brew install r
+

Depending on your local set up, you may need to install additional libraries, for example:

+
sudo apt install gcc-11 cmake
+

On Windows using Winget:

+
winget install -e --id RProject.R
+
+
+

Installing Quarto

+

Documentation for pyfixest is written, compiled, and published using Quarto.

+

To install Quarto, run:

+

On MacOS via Homebrew:

+
brew install --cask quarto
+

On Linux (Ubuntu using gdebi):

+
sudo curl -o quarto-linux-amd64.deb -L <https://github.com/quarto-dev/quarto-cli/releases/download/v${QUARTO_VERSION}/quarto-${QUARTO_VERSION}-linux-amd64.deb>
+sudo gdebi quarto-linux-amd64.deb
+

On Windows:

+
scoop bucket add extras
+scoop install extras/quarto
+ + +
+
+
+ +
+ +
+ + + + + diff --git a/docs/difference-in-differences.html b/docs/difference-in-differences.html new file mode 100644 index 00000000..8ca682d6 --- /dev/null +++ b/docs/difference-in-differences.html @@ -0,0 +1,1871 @@ + + + + + + + + + +Difference-in-Differences Estimation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ +
+ +
+ + + + +
+ +
+
+

Difference-in-Differences Estimation

+
+ + + +
+ + + + +
+ + + +
+ + +

PyFixest supports event study designs via the canonical two-way fixed effects design, the 2-Step imputation estimator, and local projections.

+

See also NBER SI methods lectures on Linear Panel Event Studies.

+
+
from importlib import resources
+
+import pandas as pd
+
+import pyfixest as pf
+from pyfixest.did.estimation import did2s, lpdid
+from pyfixest.did.visualize import panelview
+from pyfixest.report.utils import rename_event_study_coefs
+from pyfixest.utils.dgps import get_sharkfin
+
+%load_ext watermark
+%watermark --iversions
+
+ +
+ + +
+
+ +
+ + +
+
+
pandas  : 2.2.2
+pyfixest: 0.24.2
+
+
+
+
+
# one-shot adoption data - parallel trends is true
+df_one_cohort = get_sharkfin()
+df_one_cohort.head()
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
unityeartreatYever_treated
00001.6293070
10100.8259020
20200.2089880
3030-0.2447390
40400.8046650
+ +
+
+
+
+
# multi-cohort adoption data
+df_multi_cohort = pd.read_csv(
+    resources.files("pyfixest.did.data").joinpath("df_het.csv")
+)
+df_multi_cohort.head()
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
unitstategroupunit_fegyearyear_fetreatrel_yearrel_year_binnederrortete_dynamicdep_var
0133Group 27.043016201019900.066159False-20.0-6-0.08646600.07.022709
1133Group 27.04301620101991-0.030980False-19.0-60.76659300.07.778628
2133Group 27.04301620101992-0.119607False-18.0-61.51296800.08.436377
3133Group 27.043016201019930.126321False-17.0-60.02187000.07.191207
4133Group 27.04301620101994-0.106921False-16.0-6-0.01760300.06.918492
+ +
+
+
+
+

Examining Treatment Timing

+

Before any DiD estimation, we need to examine the treatment timing, since it is crucial to our choice of estimator.

+
+
panelview(
+    df_one_cohort,
+    unit="unit",
+    time="year",
+    treat="treat",
+    collapse_to_cohort=True,
+    sort_by_timing=True,
+    ylab="Cohort",
+    xlab="Year",
+    title="Treatment Assignment Cohorts",
+)
+
+
+
+

+
+
+
+
+
+
panelview(
+    df_multi_cohort,
+    unit="unit",
+    time="year",
+    treat="treat",
+    collapse_to_cohort=True,
+    sort_by_timing=True,
+    ylab="Cohort",
+    xlab="Year",
+    title="Treatment Assignment Cohorts",
+)
+
+
+
+

+
+
+
+
+

We immediately see that we have staggered adoption of treatment in the second case, which implies that a naive application of 2WFE might yield biased estimates under substantial effect heterogeneity.

+

We can also plot treatment assignment in a disaggregated fashion, which gives us a sense of cohort sizes.

+
+
panelview(
+    df_multi_cohort,
+    unit="unit",
+    time="year",
+    treat="treat",
+    sort_by_timing=True,
+    ylab="Unit",
+    xlab="Year",
+    title="Treatment Assignment (all units)",
+)
+
+
+
+

+
+
+
+
+
+
+

One-shot adoption: Static and Dynamic Specifications

+
+
fit_static_twfe = pf.feols(
+    "Y ~ treat | unit + year",
+    df_one_cohort,
+    vcov={"CRV1": "unit"},
+)
+fit_static_twfe.summary()
+
+
###
+
+Estimation:  OLS
+Dep. var.: Y, Fixed effects: unit+year
+Inference:  CRV1
+Observations:  30000
+
+| Coefficient   |   Estimate |   Std. Error |   t value |   Pr(>|t|) |   2.5% |   97.5% |
+|:--------------|-----------:|-------------:|----------:|-----------:|-------:|--------:|
+| treat         |      0.206 |        0.052 |     3.929 |      0.000 |  0.103 |   0.308 |
+---
+RMSE: 0.701 R2: 0.905 R2 Within: 0.003
+
+
+

Since this is a single-cohort dataset, this estimate is consistent for the ATT under parallel trends. We can estimate heterogeneous effects by time by interacting time with the treated group:

+
+
fit_dynamic_twfe = pf.feols(
+    "Y ~ i(year, ever_treated,  ref = 14) | unit + year",
+    df_one_cohort,
+    vcov={"CRV1": "unit"},
+)
+
+
+
fit_dynamic_twfe.iplot(
+    coord_flip=False,
+    title="Event Study",
+    figsize=[1200, 400],
+    yintercept=0,
+    xintercept=13.5,
+    labels=rename_event_study_coefs(fit_dynamic_twfe._coefnames),
+)
+
+
+ +
+
+

Event study plots like this are very informative, as they allow us to visually inspect the parallel trends assumption and also the dynamic effects of the treatment.

+

Based on a cursory glance, one would conclude that parallel trends does not hold because one of the pre-treatment coefficient has a confidence interval that does not include zero. However, we know that parallel trends is true because the treatment is randomly assigned in the underlying DGP.

+
+

Pointwise vs Simultaneous Inference in Event Studies

+

This is an example of a false positive in testing for pre-trends produced by pointwise inference (where each element of the coefficient vector is tested separately).

+

As an alternative, we can use simultaneous confidence bands of the form \([a, b] = ([a_k, b_k])_{k=1}^K\) such that

+

\[ +P(\beta \in [a, b]) = P(\beta_k \in [a_k, b_k] \forall k) \rightarrow 1 - \alpha +\]

+

These bands can be constructed by using a carefully chosen critical value \(c\) that accounts for the covariance between coefficients using the multiplier bootstrap. In pointwise inference, the critical value is \(c = z_{1 - \alpha/2} = 1.96\) for \(\alpha = 0.05\); the corresponding critical value for simultaneous inference is typically larger. These are also known as sup-t bands in the literature (see lec 3 of the NBER SI methods lectures linked above).

+

This is implemented in the confint(joint=True) method in the feols class. If we pass the joint='both' argument to iplot, we get the simultaneous confidence bands (for all event study coefficients) in addition to the pointwise confidence intervals. Note that simultaneous inference for all event study coefficients may be overly conservative, especially when the number of coefficients is large; one may instead choose to perform joint inference for all pre-treatment coefficients and all post-treatment coefficients separately.

+
+
fit_dynamic_twfe.iplot(
+    coord_flip=False,
+    title="Event Study",
+    figsize=[1200, 400],
+    yintercept=0,
+    xintercept=13.5,
+    joint="both",
+    labels=rename_event_study_coefs(fit_dynamic_twfe._coefnames),
+)
+
+
+ +
+
+

The joint confidence bands are wider than the pointwise confidence intervals, and they include zero for all pre-treatment coefficients. This is consistent with the parallel trends assumption.

+
+
+
+

Event Study under Staggered Adoption via feols(), did2s() and lpdid()

+

We can estimate a simple two-way fixed effects DiD regression via feols():

+
+
fit_twfe = pf.feols(
+    "dep_var ~ i(rel_year, ref=-1.0) | state + year",
+    df_multi_cohort,
+    vcov={"CRV1": "state"},
+)
+
+

To do the same via Gardners 2-stage estimator, we employ the the did2s() function:

+
+
fit_did2s = did2s(
+    df_multi_cohort,
+    yname="dep_var",
+    first_stage="~ 0 | state + year",
+    second_stage="~i(rel_year,ref=-1.0)",
+    treatment="treat",
+    cluster="state",
+)
+
+

Last, we can estimate the ATT for each time period via local projections by using the lpdid() function:

+
+
fit_lpdid = lpdid(
+    data=df_multi_cohort,
+    yname="dep_var",
+    gname="g",
+    tname="year",
+    idname="unit",
+    vcov={"CRV1": "state"},
+    pre_window=-20,
+    post_window=20,
+    att=False,
+)
+
+

Let’s look at some results:

+
+
figsize = [1200, 400]
+
+
+
fit_twfe.iplot(
+    coord_flip=False,
+    title="TWFE-Estimator",
+    figsize=figsize,
+    xintercept=18.5,
+    yintercept=0,
+    labels=rename_event_study_coefs(fit_twfe._coefnames),  # rename coefficients
+).show()
+
+
+ +
+
+
+
fit_did2s.iplot(
+    coord_flip=False,
+    title="DID2s-Estimator",
+    figsize=figsize,
+    xintercept=18.5,
+    yintercept=0,
+    labels=rename_event_study_coefs(fit_twfe._coefnames),
+).show()
+
+
+ +
+
+
+
fit_lpdid.iplot(
+    coord_flip=False,
+    title="Local-Projections-Estimator",
+    figsize=figsize,
+    yintercept=0,
+    xintercept=18.5,
+).show()
+
+
+ +
+
+

What if we are not interested in the ATT per treatment period, but in a pooled effects?

+
+
fit_twfe = pf.feols(
+    "dep_var ~ i(treat) | unit + year",
+    df_multi_cohort,
+    vcov={"CRV1": "state"},
+)
+
+fit_did2s = did2s(
+    df_multi_cohort,
+    yname="dep_var",
+    first_stage="~ 0 | unit + year",
+    second_stage="~i(treat)",
+    treatment="treat",
+    cluster="state",
+)
+
+fit_lpdid = lpdid(
+    data=df_multi_cohort,
+    yname="dep_var",
+    gname="g",
+    tname="year",
+    idname="unit",
+    vcov={"CRV1": "state"},
+    pre_window=-20,
+    post_window=20,
+    att=True,
+)
+pd.concat(
+    [
+        fit_twfe.tidy().assign(estimator="TWFE"),
+        fit_did2s.tidy().assign(estimator="DID2s"),
+        fit_lpdid.tidy().assign(estimator="LPDID").drop("N", axis=1),
+    ],
+    axis=0,
+)
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
EstimateStd. Errort valuePr(>|t|)2.5%97.5%estimator
C(treat)[T.True]1.9825400.019331102.5561800.01.9434392.021642TWFE
C(treat)[T.True]2.2304820.02470990.2714370.02.1820542.278910DID2s
treat_diff2.5067460.07135735.1296480.02.3624132.651080LPDID
+ +
+
+
+ + +
+ +
+ +
+ + + + + diff --git a/docs/difference-in-differences_files/figure-html/cell-5-output-1.png b/docs/difference-in-differences_files/figure-html/cell-5-output-1.png new file mode 100644 index 0000000000000000000000000000000000000000..cf2f5200061ff82e6358f94441db6d1157151908 GIT binary patch literal 11809 zcmeHtcT|&mw`SC1gCiUZB1Q01LLodey3eu}|5ow{9fOH#jl&16|O-cw==^cav z9O)2>5FjE#2r*JaC<3!zzdPUDxp(fmb7##TGi!Zo$#NOP`~J$_&wid~?-yDcw~jDz zGNDkYBPzFV>Yz}21yHCxU55_9CtIyg-@{+ho=SH;bzN*cy)E6XQRFMerBO>DTk1q(jxZ8^SO=I6EJmj$JZ6gm9iq#VN*^{e? zvqzzXB2;c((|h=aHsNUdd}>g?q4F$EN*P~M~*6M?Kwz( zs=zyfHgxOl?oRe|o}tJyer2%=JBmU*3ihv)hgCIEeuM2c89##qcy}^mFA7zllnb9b z9Q_YJuDjoteogiE?ZvfI?1jz~HFzv_c#>zIl;HLK!|qbt`Za~7)ys8V;(lw6^_%ng zT}}CH{d@z;bfjWY;p^Vf?-R9Xw=Xx(^YP_65i2Hn4q|`J z*y}J6xJ7g34cexUY<`W_6u7K7^xmpnuQ70YjGOkP+;+>7&Ac0GlKGJqBr1|Tt%yzE~c-k81=(uaQ zU6kuWVgGz*+0um%aU3Z!Q&&}eX;kT)LK(;o#TyoXthMm7|R6eaksS??1C2%zb^BnOWSM6i|6dKtQZY3Z>h->KwTBO@ zR5Udunc0OsCoJyXwNnn~v__UrpjG3{wfB!n77b~~aJ?F-4 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z;%piF0|9hYIMidKb^OGMAEms>(Lfavpe2bt9J6pE4K^6Ned$d}c3qs4!HG;B5>W*A z#Pv~95a>_2WZU*0#RAJ7n*%M&Q+?`Jfm!Q2`$w@L)~OMuMa4yHMo@TpB@!{k6lm8K_X@ z2Y(I@{q$&=4~RG4LY#;k#yg5b4`gBwF@0x~;0=@>a0TZ24`dZMkV{1hlf*x)>-BAA rv(4qb?%76wczu8HU$+)0i}abPS)V7i^n~MhJVjpi literal 0 HcmV?d00001 diff --git a/docs/marginaleffects.html b/docs/marginaleffects.html new file mode 100644 index 00000000..1edb1677 --- /dev/null +++ b/docs/marginaleffects.html @@ -0,0 +1,937 @@ + + + + + + + + + +Marginal Effects and Hypothesis Tests via marginaleffects + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ +
+ +
+ + + + +
+ +
+
+

Marginal Effects and Hypothesis Tests via marginaleffects

+
+ + + +
+ + + + +
+ + + +
+ + +

We can compute marginal effects and linear and non-linear hypothesis tests via the excellent marginaleffects package.

+
+
from marginaleffects import hypotheses
+
+import pyfixest as pf
+
+data = pf.get_data()
+fit = pf.feols("Y ~ X1 + X2", data=data)
+
+fit.tidy()
+
+ +
+ + +
+
+ +
+ + +
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
EstimateStd. Errort valuePr(>|t|)2.5%97.5%
Coefficient
Intercept0.8887790.1084228.1973748.881784e-160.6760161.101542
X1-0.9929360.082117-12.0916500.000000e+00-1.154079-0.831792
X2-0.1763420.021766-8.1017431.554312e-15-0.219055-0.133630
+ +
+
+
+

Suppose we were interested in testing the hypothesis that \(X_{1} = X_{2}\). Given the relatively large differences in coefficients and small standard errors, we will likely reject the null that the two parameters are equal.

+

We can run the formal test via the hypotheses function from the marginaleffects package.

+
+
hypotheses(fit, "X1 - X2 = 0")
+
+
+shape: (1, 8) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
termestimatestd_errorstatisticp_values_valueconf_lowconf_high
strf64f64f64f64f64f64f64
"X1-X2=0"-0.8165930.085179-9.5867970.0inf-0.983541-0.649646
+
+
+
+

And indeed, we reject the null of equality of coefficients: we get a p-value of zero and a confidence interval that does not contain 0.

+
+

Ratio Estimates

+

We can also test run-linear hypotheses, in which case marginaleffects will automatically compute correct standard errors based on the estimated covariance matrix and the Delta method. This is for example useful for computing inferential statistics for the “relative uplift” in an AB test.

+

For the moment, let’s assume that \(X1\) is a randomly assigned treatment variable. As before, \(Y\) is our variable / KPI of interest.

+

Under randomization, the model intercept measures the “baseline”, i.e. the population average of \(Y\) in the absence of treatment. To compute a relative uplift, we might compute

+
+
(fit.coef().xs("X1") / fit.coef().xs("Intercept") - 1) * 100
+
+
-211.71906665561212
+
+
+

So we have a really big negative treatment effect of around minus 212%! To conduct correct inference on this ratio statistic, we need to use the delta method.

+
+

The Multivariate Delta Method

+

In a nutshell, the delta method provides a way to approximate the asympotic distribution of any non-linear transformation \(g()\) or one or more random variables.

+

In the case of the ratio statistics, this non-linear transformation can be denoted as \(g(\theta_{1}, \theta_{2}) = \theta_{1} / \theta_{2}\).

+

Here’s the Delta Method theorem:

+

First, we define \(\theta = (\theta_{1}, \theta_{2})'\) and \(\mu = (\mu_{1}, \mu_{2})'\).

+

By the law of large numbers, we know that

+

\[ +\sqrt{N} (\theta - \mu) \rightarrow_{d} N(0_{2}, \Sigma_{2,2}) \text{ if } N \rightarrow \infty. +\]

+

By the Delta Method, we can then approximate the limit distribution of \(g(\theta)\) as

+

\[ +\sqrt{N} (g(\theta) - g(\mu)) \rightarrow_{d} N(0_{1}, g'(\theta) \times \Sigma \times g(\theta)) \text{ if } N \rightarrow \infty. +\].

+

Here’s a long derivation of how to use the the delta method for inference of ratio statistics.. The key steps from the formula above is to derive the expression for the asymptotic variance $ g’() g()$.

+

But hey - we’re lucky, because marginaleffects will do all this work for us: we don’t have to derive analytic gradients ourselves =)

+
+
+

Using the Delta Method via marginaleffects:

+

We can employ the Delta Method via marginaleffects via the hypotheses function:

+
+
hypotheses(fit, "(X1 / Intercept - 1) * 100 = 0")
+
+
+shape: (1, 8) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
termestimatestd_errorstatisticp_values_valueconf_lowconf_high
strf64f64f64f64f64f64f64
"(X1/Intercept-…-211.7190678.478682-24.9707510.0inf-228.336979-195.101155
+
+
+
+

As before, we get an estimate of around -212%. Additionally, we obtain a 95% CI via the Delta Method of [-228%, -195%].

+

Besides hypopotheses testing, you can do a range of other cool things with the marginaleffects package. For example (and likely unsurprisingly), you can easily compute all sorts of marginal effects for your regression models. For all the details, we highly recommend to take a look at the marginaleffects zoo book!.

+ + +
+
+ +
+ +
+ + + + + diff --git a/docs/news.html b/docs/news.html new file mode 100644 index 00000000..22c4ed97 --- /dev/null +++ b/docs/news.html @@ -0,0 +1,1483 @@ + + + + + + + + + +news + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ +
+ +
+ + + + +
+ +
+
+

News

+
+ + + +
+ + + + +
+ + + +
+ + +
+

PyFixest 0.22.0

+
+

Changes

+
    +
  • Fix bug in wildboottest method @s3alfisc (#506)
    • +
  • docs: add sanskriti2005 as a contributor for infra @allcontributors (#503)
    • +
  • Infra: added the release-drafter for automation of release notes @sanskriti2005 (#502)
    • +
  • Fix broken link in contributing.md @s3alfisc (#499)
    • +
  • docs: add leostimpfle as a contributor for bug @allcontributors (#495)
    • +
  • Update justfile @leostimpfle (#494)
    • +
  • docs: add baggiponte as a contributor for doc @allcontributors (#490)
    • +
  • docs: improve installation section @baggiponte (#489)
    • +
  • Bump tornado from 6.4 to 6.4.1 @dependabot (#487)
    • +
  • docs: add leostimpfle as a contributor for code @allcontributors (#478)
    • +
  • Feols: speed up the creation of interacted fixed effects via fe1^fe2 syntax @leostimpfle (#475)
    • +
  • rename resampling iterations to ‘reps’ in all methods @s3alfisc (#474)
    • +
  • fix a lot of broken links throught the repo @s3alfisc (#472)
    • +
  • Multiple readme fixes required after package was moved to py-econometrics project @s3alfisc (#450)
    • +
+
+
+

Infrastructure

+
    +
  • infrastructure: fix minor release drafter bugs @s3alfisc (#504)
    • +
+
+
+
+

PyFixest 0.21.0

+
    +
  • Add support for randomization inference via the ritest() method:
    • +
+
+
import pyfixest as pf
+data = pf.get_data()
+
+fit = pf.feols("Y ~ X1", data = data)
+fit.ritest(resampvar="X1=0", reps = 1000)
+
+
+
+

PyFixest 0.20.0

+
    +
  • This version introduces MyPy type checks to the entire pyfixest codebase. Thanks to @juanitorduz for nudging me to get started with this =). It also fixes a handful of smaller bugs.
    • +
+
+
+

PyFixest 0.19.0

+
    +
  • Fixes multiple smaller and larger performance regressions. The NYC-Taxi example regression now takes approximately 22 seconds to run (… if my laptopt is connected to a power charger)!
    • +
+
+
%load_ext autoreload
+%autoreload 2
+
+import duckdb
+import time
+import numpy as np
+import pyfixest as pf
+
+# %%
+nyc = duckdb.sql(
+    '''
+    FROM 'C:/Users/alexa/Documents/nyc-taxi/**/*.parquet'
+    SELECT
+        tip_amount, trip_distance, passenger_count,
+        vendor_id, payment_type, dropoff_at,
+        dayofweek(dropoff_at) AS dofw
+    WHERE year = 2012 AND month <= 3
+    '''
+    ).df()
+
+# convert dowf, vendor_id, payment_type to categorical
+tic = time.time()
+nyc["dofw"] = nyc["dofw"].astype(int)
+nyc["vendor_id"] = nyc["vendor_id"].astype("category")
+nyc["payment_type"] = nyc["payment_type"].astype("category")
+print(f"""
+    I am convering columns of type 'objects' to 'categories' and 'int'data types outside
+    of the regression, hence I am cheating a bit. This saves {np.round(time.time() - tic)} seconds.
+    """
+)
+#    I am convering columns of type 'objects' to 'categories' and 'int'data types outside
+#    of the regression, hence I am cheating a bit. This saves 7.0 seconds.
+
+run = True
+if run:
+
+    # mock regression for JIT compilation
+    fit = pf.feols(
+        fml = "tip_amount ~ trip_distance + passenger_count | vendor_id + payment_type + dofw",
+        data = nyc.iloc[1:10_000],
+        copy_data = False,
+        store_data = False
+        )
+
+    import time
+    tic = time.time()
+    fit = pf.feols(
+        fml = "tip_amount ~ trip_distance + passenger_count | vendor_id + payment_type + dofw",
+        data = nyc,
+        copy_data = False, # saves a few seconds
+        store_data = False # saves a few second
+        )
+    passed = time.time() - tic
+    print(f"Passed time is {np.round(passed)}.")
+    # Passed time is 22.
+
+
    +
  • Adds three new function arguments to feols() and fepois(): copy_data, store_data, and fixef_tol.
    • +
  • Adds support for frequency weights with the weights_type function argument.
    • +
+
+
import pyfixest as pf
+
+data = pf.get_data(N = 10000, model = "Fepois")
+df_weighted = data[["Y", "X1", "f1"]].groupby(["Y", "X1", "f1"]).size().reset_index().rename(columns={0: "count"})
+df_weighted["id"] = list(range(df_weighted.shape[0]))
+
+print("Dimension of the aggregated df:", df_weighted.shape)
+print(df_weighted.head())
+
+fit = pf.feols(
+    "Y ~ X1 | f1",
+    data = data
+)
+fit_weighted = pf.feols(
+    "Y ~ X1 | f1",
+    data = df_weighted,
+    weights = "count",
+    weights_type = "fweights"
+)
+pf.etable([fit, fit_weighted], coef_fmt = "b(se) \n (t) \n (p)")
+
+ +
+ + +
+
+ +
+ + +
+
+
Dimension of the aggregated df: (1278, 5)
+     Y   X1   f1  count  id
+0  0.0  0.0  0.0     17   0
+1  0.0  0.0  1.0     11   1
+2  0.0  0.0  2.0     10   2
+3  0.0  0.0  3.0     17   3
+4  0.0  0.0  4.0     14   4
+
+
+
+ + + +++++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Y
(1)(2)
coef
X10.001(0.012)
+(0.092)
+(0.927)		0.001(0.012)
+(0.092)
+(0.927)
fe
f1xx
stats
Observations99979997
S.E. typeby: f1by: f1
R20.011-
+ + +
+ +
+
+
    +
  • Bugfix: Wild Cluster Bootstrap Inference with Weights would compute unweighted standard errors. Sorry about that! WLS is not supported for the WCB.
    • +
  • Adds support for CRV3 inference with weights.
    • +
+
+
+

PyFixest 0.18.0

+
    +
  • Large Refactoring of Interal Processing of Model Formulas, in particular FixestFormulaParser and model_matrix_fixest. As a results, the code should be cleaner and more robust.
    • +
  • Thanks to the refactoring, we can now bump the required formulaic version to the stable 1.0.0 release.
    • +
  • The fml argument of model_matrix_fixest is deprecated. Instead, model_matrix_fixest now asks for a FixestFormula, which is essentially a dictionary with information on model specifications like a first stage formula (if applicable), dependent variables, fixed effects, etc.
    • +
  • Additionally, model_matrix_fixest now returns a dictionary instead of a tuple.
    • +
  • Brings back fixed effects reference setting via i(var1, var2, ref) syntax. Deprecates the i_ref1, i_ref2 function arguments. I.e. it is again possible to e.g. run
    • +
+
+
import pyfixest as pf
+data = pf.get_data()
+
+fit1 = pf.feols("Y ~ i(f1, X2)", data=data)
+fit1.coef()[0:8]
+
+

Via the ref syntax, via can set the reference level:

+
+
fit2 = pf.feols("Y ~ i(f1, X2, ref = 1)", data=data)
+fit2.coef()[0:8]
+
+
+
+

PyFixest 0.17.0

+
    +

  • Restructures the codebase and reorganizes how users can interact with the pyfixest API. It is now recommended to use pyfixest in the following way:

    +
    +
    import numpy as np
+import pyfixest as pf
+data = pf.get_data()
+data["D"] = data["X1"] > 0
+fit = pf.feols("Y ~ D + f1", data = data)
+fit.tidy()
    +
    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    EstimateStd. Errort valuePr(>|t|)2.5%97.5%
    Coefficient
    Intercept0.7788490.1702614.5744370.0000050.4447371.112961
    D-1.4026170.152224-9.2141400.000000-1.701335-1.103899
    f10.0047740.0080580.5925080.553645-0.0110380.020587
    + +
    +
    +
    +

    The update should not inroduce any breaking changes. Thanks to @Wenzhi-Ding for the PR!

    • +

  • Adds support for simultaneous confidence intervals via a multiplier bootstrap. Thanks to @apoorvalal for the contribution!

    +
    +
    fit.confint(joint = True)
    +
    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    2.5%97.5%
    Intercept0.3826591.175039
    D-1.756836-1.048397
    f1-0.0139760.023525
    + +
    +
    +
    • +

  • Adds support for the causal cluster variance estimator by Abadie et al. (QJE, 2023) for OLS via the .ccv() method.

    +
    +
    fit.ccv(treatment = "D", cluster = "group_id")
    +
    +
    C:\Users\alexa\Documents\pyfixest\pyfixest\estimation\feols_.py:1364: UserWarning: The initial model was not clustered. CRV1 inference is computed and stored in the model object.
+  warnings.warn(
    +
    +
    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    EstimateStd. Errort valuePr(>|t|)2.5%97.5%
    CCV-1.40261686221799290.28497-4.9219840.00011-2.001316-0.803917
    CRV1-1.4026170.205132-6.8376210.000002-1.833584-0.97165
    + +
    +
    +
    • +
+
+
+

PyFixest 0.16.0

+
    +
  • Adds multiple quality of life improvements for developers, thanks to NKeleher.
    • +
  • Adds more options to customize etable() output thanks to Wenzhi-Ding.
    • +
  • Implements Romano-Wolf and Bonferroni corrections for multiple testing in the multcomp module.
    • +
+
+
+

PyFixest 0.15.

+
    +
  • Adds support for weighted least squares for feols().
    • +
  • Reduces testing time drastically by running tests on fewer random data samples. Qualitatively, the set of test remains identical.
    • +
  • Some updates for future pandas compatibility.
    • +
+
+
+

PyFixest 0.14.0

+
    +
  • Moves the documentation to quartodoc.
    • +
  • Changes all docstrings to numpy format.
    • +
  • Difference-in-differences estimation functions now need to be imported via the pyfixest.did.estimation module:
    • +
+
+
from pyfixest.did.estimation import did2s, lpdid, event_study
+
+
+
+

PyFixest 0.13.5

+
    +
  • Fixes a bug that lead to incorrect results when the dependent variable and all covariates (excluding the fixed effects) where integers.
    • +
+
+
+

PyFixest 0.13.4

+
    +
  • Fixes a bug in etable() with IV’s that occurred because feols() does not report R2 statistics for IVs.
    • +
+
+
+

PyFixest 0.13.2

+
    +
  • Fixes a bug in etable() and a warning in fixest_model_matrix that arose with higher pandas versions. Thanks to @aeturrell for reporting!
    • +
+
+
+

PyFixest 0.13.0

+
+

New Features

+
    +
  • Introduces a new pyfixest.did module which contains routines for Difference-in-Differences estimation.
    • +
  • Introduces support for basic versions of the local projections DiD estimator following Dube et al (2023)
    • +
  • Adds a new vignette for Difference-in-Differences estimation.
    • +
  • Reports R2 values in etable().
    • +
+
+
+
+

PyFixest 0.12.0

+
+

Enhancements:

+
    +
  • Good performance improvements for singleton fixed effects detection. Thanks to @styfenschaer for the PR! See #229.
    • +
  • Uses the r2u project for installing R and R packages on github actions, with great performance improvements.
    • +
  • Allows to pass polars data frames to feols(), fepois() and predict(). #232. Thanks to @vincentarelbundock for the suggestion!
    • +
+
+
+

Bug Fixes:

+
    +
  • Missing variables in features were not always handled correctly in predict() with newdata not None in the presence of missing data, which would lead to an error. See #246 for details.
    • +
  • Categorical variables were not always handled correctly in predict() with newdata not None, because the number of fixed effects levels in newdata might be smaller than in data. In consequence, some levels were not found, which lead to an error. See #245 for details. Thanks to @jiafengkevinchen for the pointer!
    • +
  • Multicollinearity checks for over-identified IV was not implemented correctly, which lead to a dimension error. See #236 for details. Thanks to @jiafengkevinchen for the pointer!
    • +
  • The number of degrees of freedom k was computed incorrectly if columns were dropped from the design matrix X in the presence of multicollinearity. See #235 for details. Thanks to @jiafengkevinchen for the pointer!
    • +
  • If all variables were dropped due to multicollinearity, an unclear and imprecise error message was produced. See #228 for details. Thanks to @manferdinig for the pointer!
    • +
  • If selection fixef_rm = 'singleton', feols() and fepois() would fail, which has been fixed. #192
    • +
+
+
+

Dependency Requirements

+
    +
  • For now, sets formulaic versions to be 0.6.6 or lower as version 1.0.0 seems to have introduced a problem with the i() operator, See #244 for details.
    • +
  • Drops dependency on pyhdfe.
    • +
+
+
+
+

PyFixest 0.11.1

+
    +
  • Fixes some bugs around the computation of R-squared values (see issue #103).
    • +
  • Reports R-squared values again when calling .summary().
    • +
+
+
+

PyFixest 0.11.0

+
    +
  • Significant speedups for CRV1 inference.
    • +
+
+
+

PyFixest 0.10.12

+

Fixes a small bug with the separation check for poisson regression #138.

+
+
+

PyFixest 0.10.11

+

Fixes bugs with i(var1, var2) syntax introduced with PyFixest 0.10.10.

+
+
+

PyFixest 0.10.10

+

Fixes a bug with variable interactions via i(var) syntax. See issue #221.

+
+
+

PyFixest 0.10.9

+

Makes etable() prettier and more informative.

+
+
+

PyFixest 0.10.8

+
+

Breaking changes

+

Reference levels for the i() formula syntax can no longer be set within the formula, but need to be added via the i_ref1 function argument to either feols() and fepois().

+
+
+

New feature

+

A dids2() function is added, which implements the 2-stage difference-in-differences procedure à la Gardner and follows the syntax of @kylebutts did2s R package.

+
from pyfixest.did.did import did2s
+from pyfixest.estimation import feols
+from pyfixest.visualize import iplot
+import pandas as pd
+import numpy as np
+
+df_het = pd.read_csv("https://raw.githubusercontent.com/py-econometrics/pyfixest/master/pyfixest/did/data/df_het.csv")
+
+fit = did2s(
+    df_het,
+    yname = "dep_var",
+    first_stage = "~ 0 | state + year",
+    second_stage = "~i(rel_year)",
+    treatment = "treat",
+    cluster = "state",
+    i_ref1 = [-1.0, np.inf],
+)
+
+fit_twfe = feols(
+    "dep_var ~ i(rel_year) | state + year",
+    df_het,
+    i_ref1 = [-1.0, np.inf]
+)
+
+iplot([fit, fit_twfe], coord_flip=False, figsize = (900, 400), title = "TWFE vs DID2S")
+

+
+
+
+

PyFixest 0.10.7

+
    +
  • Adds basic support for event study estimation via two-way fixed effects and Gardner’s two-stage “Did2s” approach. This is a beta version and experimental. Further updates (i.e. proper event studies vs “only” ATTs) and a more flexible did2s front end will follow in future releases.
    • +
+
%load_ext autoreload
+%autoreload 2
+
+from pyfixest.did.did import event_study
+import pyfixest as pf
+import pandas as pd
+df_het = pd.read_csv("pyfixest/did/data/df_het.csv")
+
+fit_twfe = event_study(
+    data = df_het,
+    yname = "dep_var",
+    idname= "state",
+    tname = "year",
+    gname = "g",
+    estimator = "twfe"
+)
+
+fit_did2s = event_study(
+    data = df_het,
+    yname = "dep_var",
+    idname= "state",
+    tname = "year",
+    gname = "g",
+    estimator = "did2s"
+)
+
+pf.etable([fit_twfe, fit_did2s])
+# | Coefficient   | est1             | est2             |
+# |:--------------|:-----------------|:-----------------|
+# | ATT           | 2.135*** (0.044) | 2.152*** (0.048) |
+# Significance levels: * p < 0.05, ** p < 0.01, *** p < 0.001
+
+
+

PyFixest 0.10.6

+
    +
  • Adds an etable() function that outputs markdown, latex or a pd.DataFrame.
    • +
+
+
+

PyFixest 0.10.5

+
    +
  • Fixes a big in IV estimation that would trigger an error. See here for details. Thanks to @aeturrell for reporting!
    • +
+
+
+

PyFixest 0.10.4

+
    +
  • Implements a custom function to drop singleton fixed effects.
    • +
  • Additional small performance improvements.
    • +
+
+
+

PyFixest 0.10.3

+
    +
  • Allows for white space in the multiway clustering formula.
    • +
  • Adds documentation for multiway clustering.
    • +
+
+
+

PyFixest 0.10.2

+
    +
  • Adds support for two-way clustering.
    • +
  • Adds support for CRV3 inference for Poisson regression.
    • +
+
+
+

PyFixest 0.10.1

+
    +
  • Adapts the internal fixed effects demeaning criteron to match `PyHDFE’s default.
    • +
  • Adds Styfen as coauthor.
    • +
+
+
+

PyFixest 0.10

+
    +
  • Multiple performance improvements.
    • +
  • Most importantly, implements a custom demeaning algorithm in numba - thanks to Styfen Schaer (@styfenschaer), which leads to performance improvements of 5x or more:
    • +
+
%load_ext autoreload
+%autoreload 2
+
+import numpy as np
+import time
+import pyhdfe
+from pyfixest.demean import demean
+
+np.random.seed(1238)
+N = 10_000_000
+x = np.random.normal(0, 1, 10*N).reshape((N,10))
+f1 = np.random.choice(list(range(1000)), N).reshape((N,1))
+f2 = np.random.choice(list(range(1000)), N).reshape((N,1))
+
+flist = np.concatenate((f1, f2), axis = 1)
+weights = np.ones(N)
+
+algorithm = pyhdfe.create(flist)
+
+start_time = time.time()
+res_pyhdfe = algorithm.residualize(x)
+end_time = time.time()
+print(end_time - start_time)
+# 26.04527711868286
+
+
+start_time = time.time()
+res_pyfixest, success = demean(x, flist, weights, tol = 1e-10)
+# Calculate the execution time
+end_time = time.time()
+print(end_time - start_time)
+#4.334428071975708
+
+np.allclose(res_pyhdfe , res_pyfixest)
+# True
+
+
+

PyFixest 0.9.11

+
    +
  • Bump required formulaic version to 0.6.5.
    • +
  • Stop copying the data frame in fixef().
    • +
+
+
+

PyFixest 0.9.10

+
    +
  • Fixes a big in the wildboottest method (see #158).
    • +
  • Allows to run a wild bootstrap after fixed effect estimation.
    • +
+
+
+

PyFixest 0.9.9

+
    +
  • Adds support for wildboottest for Python 3.11.
    • +
+
+
+

PyFixest 0.9.8

+
    +
  • Fixes a couple more bugs in the predict() and fixef() methods.
    • +
  • The predict() argument data is renamed to newdata.
    • +
+
+
+

PyFixest 0.9.7

+

Fixes a bug in predict() produced when multicollinear variables are dropped.

+
+
+

PyFixest 0.9.6

+

Improved Collinearity handling. See #145

+
+
+

PyFixest 0.9.5

+
    +
  • Moves plotting from matplotlib to lets-plot.
    • +
  • Fixes a few minor bugs in plotting and the fixef() method.
    • +
+
+
+

PyFixest 0.9.1

+
+

Breaking API changes

+

It is no longer required to initiate an object of type Fixest prior to running [Feols(/reference/Feols.qmd) or fepois. Instead, you can now simply use feols() and fepois() as functions, just as in fixest. Both function can be found in an estimation module and need to obtain a pd.DataFrame as a function argument:

+
from pyfixest.estimation import fixest, fepois
+from pyfixest.utils import get_data
+
+data = get_data()
+fit = feols("Y ~ X1 | f1", data = data, vcov = "iid")
+

Calling feols() will return an instance of class [Feols(/reference/Feols.qmd), while calling fepois() will return an instance of class Fepois. Multiple estimation syntax will return an instance of class FixestMulti.

+

Post processing works as before via .summary(), .tidy() and other methods.

+
+
+

New Features

+

A summary function allows to compare multiple models:

+
from pyfixest.summarize import summary
+fit2 = feols("Y ~ X1 + X2| f1", data = data, vcov = "iid")
+summary([fit, fit2])
+

Visualization is possible via custom methods (.iplot() & .coefplot()), but a new module allows to visualize a list of [Feols(/reference/Feols.qmd) and/or Fepois instances:

+
from pyfixest.visualize import coefplot, iplot
+coefplot([fit, fit2])
+

The documentation has been improved (though there is still room for progress), and the code has been cleaned up a bit (also lots of room for improvements).

+ + +
+
+ +
+ +
+ + + + + diff --git a/docs/pyfixest.html b/docs/pyfixest.html new file mode 100644 index 00000000..c7bc3dd6 --- /dev/null +++ b/docs/pyfixest.html @@ -0,0 +1,795 @@ + + + + + + + + + +pyfixest + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ +
+ +
+ + + + +
+ + + + +

+
+

PyFixest: Fast High-Dimensional Fixed Effects Regression in Python

+

License PyPI -Version PyPI - Python Version Downloads Downloads image Ruff Pixi Badge All Contributors

+

PyFixest is a Python implementation of the formidable fixest package for fast high-dimensional fixed effects regression.

+

The package aims to mimic fixest syntax and functionality as closely as Python allows: if you know fixest well, the goal is that you won’t have to read the docs to get started! In particular, this means that all of fixest's defaults are mirrored by PyFixest - currently with only one small exception.

+

Nevertheless, for a quick introduction, you can take a look at the quickstart or the regression chapter of Arthur Turrell’s book on Coding for Economists.

+
+

Features

+
    +
  • OLS, WLS and IV Regression
    • +
  • Poisson Regression following the pplmhdfe algorithm
    • +
  • Multiple Estimation Syntax
    • +
  • Several Robust and Cluster Robust Variance-Covariance Estimators
    • +
  • Wild Cluster Bootstrap Inference (via wildboottest)
    • +
  • Difference-in-Differences Estimators: +
    • +
  • Multiple Hypothesis Corrections following the Procedure by Romano and Wolf and Simultaneous Confidence Intervals using a Multiplier Bootstrap
    • +
  • The Causal Cluster Variance Estimator (CCV) following Abadie et al.
    • +
  • Publication-ready tables with Great Tables or LaTex booktabs
    • +
+
+
+

Installation

+

You can install the release version from PyPi by running

+
pip install -U pyfixest
+

or the development version from github by running

+
pip install git+https://github.com/py-econometrics/pyfixest.git
+
+
+

Benchmarks

+

All benchmarks follow the fixest benchmarks. All non-pyfixest timings are taken from the fixest benchmarks.

+

+
+
+

Quickstart

+
import pyfixest as pf
+
+data = pf.get_data()
+pf.feols("Y ~ X1 | f1 + f2", data=data).summary()
+
###
+
+Estimation:  OLS
+Dep. var.: Y, Fixed effects: f1+f2
+Inference:  CRV1
+Observations:  997
+
+| Coefficient   |   Estimate |   Std. Error |   t value |   Pr(>|t|) |   2.5% |   97.5% |
+|:--------------|-----------:|-------------:|----------:|-----------:|-------:|--------:|
+| X1            |     -0.919 |        0.065 |   -14.057 |      0.000 | -1.053 |  -0.786 |
+---
+RMSE: 1.441   R2: 0.609   R2 Within: 0.2
+
+

Multiple Estimation

+

You can estimate multiple models at once by using multiple estimation syntax:

+
# OLS Estimation: estimate multiple models at once
+fit = pf.feols("Y + Y2 ~X1 | csw0(f1, f2)", data = data, vcov = {'CRV1':'group_id'})
+# Print the results
+fit.etable()
+
                           est1               est2               est3               est4               est5               est6
+------------  -----------------  -----------------  -----------------  -----------------  -----------------  -----------------
+depvar                        Y                 Y2                  Y                 Y2                  Y                 Y2
+------------------------------------------------------------------------------------------------------------------------------
+Intercept      0.919*** (0.121)   1.064*** (0.232)
+X1            -1.000*** (0.117)  -1.322*** (0.211)  -0.949*** (0.087)  -1.266*** (0.212)  -0.919*** (0.069)  -1.228*** (0.194)
+------------------------------------------------------------------------------------------------------------------------------
+f2                            -                  -                  -                  -                  x                  x
+f1                            -                  -                  x                  x                  x                  x
+------------------------------------------------------------------------------------------------------------------------------
+R2                        0.123              0.037              0.437              0.115              0.609              0.168
+S.E. type          by: group_id       by: group_id       by: group_id       by: group_id       by: group_id       by: group_id
+Observations                998                999                997                998                997                998
+------------------------------------------------------------------------------------------------------------------------------
+Significance levels: * p < 0.05, ** p < 0.01, *** p < 0.001
+Format of coefficient cell:
+Coefficient (Std. Error)
+
+
+

Adjust Standard Errors “on-the-fly”

+

Standard Errors can be adjusted after estimation, “on-the-fly”:

+
fit1 = fit.fetch_model(0)
+fit1.vcov("hetero").summary()
+
Model:  Y~X1
+###
+
+Estimation:  OLS
+Dep. var.: Y
+Inference:  hetero
+Observations:  998
+
+| Coefficient   |   Estimate |   Std. Error |   t value |   Pr(>|t|) |   2.5% |   97.5% |
+|:--------------|-----------:|-------------:|----------:|-----------:|-------:|--------:|
+| Intercept     |      0.919 |        0.112 |     8.223 |      0.000 |  0.699 |   1.138 |
+| X1            |     -1.000 |        0.082 |   -12.134 |      0.000 | -1.162 |  -0.838 |
+---
+RMSE: 2.158   R2: 0.123
+
+
+

Poisson Regression via fepois()

+

You can estimate Poisson Regressions via the fepois() function:

+
poisson_data = pf.get_data(model = "Fepois")
+pf.fepois("Y ~ X1 + X2 | f1 + f2", data = poisson_data).summary()
+
###
+
+Estimation:  Poisson
+Dep. var.: Y, Fixed effects: f1+f2
+Inference:  CRV1
+Observations:  997
+
+| Coefficient   |   Estimate |   Std. Error |   t value |   Pr(>|t|) |   2.5% |   97.5% |
+|:--------------|-----------:|-------------:|----------:|-----------:|-------:|--------:|
+| X1            |     -0.007 |        0.035 |    -0.190 |      0.850 | -0.075 |   0.062 |
+| X2            |     -0.015 |        0.010 |    -1.449 |      0.147 | -0.035 |   0.005 |
+---
+Deviance: 1068.169
+
+
+

IV Estimation via three-part formulas

+

Last, PyFixest also supports IV estimation via three part formula syntax:

+
fit_iv = pf.feols("Y ~ 1 | f1 | X1 ~ Z1", data = data)
+fit_iv.summary()
+
###
+
+Estimation:  IV
+Dep. var.: Y, Fixed effects: f1
+Inference:  CRV1
+Observations:  997
+
+| Coefficient   |   Estimate |   Std. Error |   t value |   Pr(>|t|) |   2.5% |   97.5% |
+|:--------------|-----------:|-------------:|----------:|-----------:|-------:|--------:|
+| X1            |     -1.025 |        0.115 |    -8.930 |      0.000 | -1.259 |  -0.790 |
+---
+
+
+
+

Call for Contributions

+

Thanks for showing interest in contributing to pyfixest! We appreciate all contributions and constructive feedback, whether that be reporting bugs, requesting new features, or suggesting improvements to documentation.

+

If you’d like to get involved, but are not yet sure how, please feel free to send us an email. Some familiarity with either Python or econometrics will help, but you really don’t need to be a numpy core developer or have published in Econometrica =) We’d be more than happy to invest time to help you get started!

+
+
+

Contributors ✨

+

Thanks goes to these wonderful people:

+ + + + + + + + + + + + + + + +
+styfenschaer
styfenschaer
💻 +		 +Niall Keleher
Niall Keleher
🚇 💻 +		 +Wenzhi Ding
Wenzhi Ding
💻 +		 +Apoorva Lal
Apoorva Lal
💻 🐛 +		 +Juan Orduz
Juan Orduz
🚇 💻 +		 +Alexander Fischer
Alexander Fischer
💻 🚇 +		 +aeturrell
aeturrell
✅ 📖 📣 +
+ + + +

This project follows the all-contributors specification. Contributions of any kind welcome!

+ + +
+
+ +
+ +
+ + + + + diff --git a/pixi.lock b/pixi.lock index 1707ec7b..be0da573 100644 --- a/pixi.lock +++ b/pixi.lock @@ -608,6 +608,10 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.8.30-hbcca054_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/cffi-1.17.1-py312h06ac9bb_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_0.tar.bz2 + - conda: https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-8.5.0-pyha770c72_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.4-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.43-h712a8e2_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.3-h5888daf_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2 @@ -619,13 +623,19 @@ environments: - 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license: MIT - license_family: MIT - purls: [] - size: 569140 - timestamp: 1726846656126 - kind: conda name: xorg-xorgproto version: '2024.1' @@ -7480,32 +7217,6 @@ packages: purls: [] size: 217804 timestamp: 1660346976440 -- kind: pypi - name: zipp - version: 3.20.2 - url: https://files.pythonhosted.org/packages/62/8b/5ba542fa83c90e09eac972fc9baca7a88e7e7ca4b221a89251954019308b/zipp-3.20.2-py3-none-any.whl - sha256: a817ac80d6cf4b23bf7f2828b7cabf326f15a001bea8b1f9b49631780ba28350 - requires_dist: - - pytest-checkdocs>=2.4 ; extra == 'check' - - pytest-ruff>=0.2.1 ; sys_platform != 'cygwin' and extra == 'check' - - pytest-cov ; extra == 'cover' - - sphinx>=3.5 ; extra == 'doc' - - jaraco-packaging>=9.3 ; extra == 'doc' - - rst-linker>=1.9 ; extra == 'doc' - - furo ; extra == 'doc' - - sphinx-lint ; extra == 'doc' - - jaraco-tidelift>=1.4 ; extra == 'doc' - - pytest-enabler>=2.2 ; extra == 'enabler' - - pytest!=8.1.*,>=6 ; extra == 'test' - - jaraco-itertools ; extra == 'test' - - jaraco-functools ; extra == 'test' - - more-itertools ; extra == 'test' - - big-o ; extra == 'test' - - pytest-ignore-flaky ; extra == 'test' - - jaraco-test ; extra == 'test' - - importlib-resources ; python_full_version < '3.9' and extra == 'test' - - pytest-mypy ; extra == 'type' - requires_python: '>=3.8' - kind: conda name: zipp version: 3.20.2 diff --git a/pyproject.toml b/pyproject.toml index 7bf2b7c8..7ef25d8f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -39,7 +39,8 @@ docs = [ "quartodoc>=0.7.2", "jupyterlab>=4.0.12", "jupytext==1.16.1", - "watermark==2.4.3" + "watermark==2.4.3", + "wildboottest>=0.3.2" ] [tool.pixi.feature.build.dependencies] @@ -59,7 +60,7 @@ pyfixest = { path = ".", editable = true } [tool.pixi.environments] default = { solve-group = "default" } dev = { features = ["dev"], solve-group = "default" } -docs = { features = ["docs"], solve-group = "dev" } +docs = { features = ["docs"], solve-group = "default" } build = { features = ["build"], solve-group = "default" } [tool.pixi.feature.dev.tasks] From eb164d2200c7c2634fe5e9c9cffa5696e3cf65a8 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Fri, 27 Sep 2024 20:43:56 +0200 Subject: [PATCH 100/102] update lock --- docs/compare-fixest-pyfixest.html | 1860 ---------------- docs/contributing.html | 735 ------- docs/difference-in-differences.html | 1871 ----------------- .../figure-html/cell-5-output-1.png | Bin 11809 -> 0 bytes .../figure-html/cell-6-output-1.png | Bin 12334 -> 0 bytes .../figure-html/cell-7-output-1.png | Bin 16273 -> 0 bytes docs/marginaleffects.html | 937 --------- docs/news.html | 1483 ------------- docs/pyfixest.html | 795 ------- 9 files changed, 7681 deletions(-) delete mode 100644 docs/compare-fixest-pyfixest.html delete mode 100644 docs/contributing.html delete mode 100644 docs/difference-in-differences.html delete mode 100644 docs/difference-in-differences_files/figure-html/cell-5-output-1.png delete mode 100644 docs/difference-in-differences_files/figure-html/cell-6-output-1.png delete mode 100644 docs/difference-in-differences_files/figure-html/cell-7-output-1.png delete mode 100644 docs/marginaleffects.html delete mode 100644 docs/news.html delete mode 100644 docs/pyfixest.html diff --git a/docs/compare-fixest-pyfixest.html b/docs/compare-fixest-pyfixest.html deleted file mode 100644 index b295c09a..00000000 --- a/docs/compare-fixest-pyfixest.html +++ /dev/null @@ -1,1860 +0,0 @@ - - - - - - - - - -Does PyFixest match fixest? - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Does PyFixest match fixest?

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This vignette compares estimation results from fixest with pyfixest via the rpy2 package.

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-
import pandas as pd
-import rpy2.robjects as ro
-from rpy2.robjects import pandas2ri
-from rpy2.robjects.packages import importr
-
-import pyfixest as pf
-
-# Activate pandas2ri
-pandas2ri.activate()
-
-# Import R packages
-fixest = importr("fixest")
-stats = importr("stats")
-
-# IPython magic commands for autoreloading
-%load_ext autoreload
-%autoreload 2
-
-# Get data using pyfixest
-data = pf.get_data(model="Feols", N=10_000, seed=99292)
-
- -
- - -
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- -
- - -
-
-
-

Ordinary Least Squares (OLS)

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-

IID Inference

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First, we estimate a model via `pyfixest. We compute “iid” standard errors.

-
-
fit = pf.feols(fml="Y ~ X1 + X2 | f1 + f2", data=data, vcov="iid")
-
-

We estimate the same model with weights:

-
-
fit_weights = pf.feols(
-    fml="Y ~ X1 + X2 | f1 + f2", data=data, weights="weights", vcov="iid"
-)
-
-

Via r-fixest and rpy2, we get

-
-
r_fit = fixest.feols(
-    ro.Formula("Y ~ X1 + X2 | f1 + f2"),
-    data=data,
-    vcov="iid",
-    ssc=fixest.ssc(True, "none", True, "min", "min", False),
-)
-
-r_fit_weights = fixest.feols(
-    ro.Formula("Y ~ X1 + X2 | f1 + f2"),
-    data=data,
-    weights=ro.Formula("~weights"),
-    vcov="iid",
-    ssc=fixest.ssc(True, "none", True, "min", "min", False),
-)
-
-
R[write to console]: NOTE: 3 observations removed because of NA values (LHS: 1, RHS: 1, Fixed-effects: 1).
-
-R[write to console]: NOTE: 3 observations removed because of NA values (LHS: 1, RHS: 1, Fixed-effects: 1).
-
-
-
-

Let’s compare how close the covariance matrices are:

-
-
fit_vcov = fit._vcov
-r_vcov = stats.vcov(r_fit)
-fit_vcov - r_vcov
-
-
array([[-7.04731412e-19, -3.34180967e-22],
-       [-3.34594558e-22, -1.38913403e-19]])
-
-
-

And for WLS:

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fit_weights._vcov - stats.vcov(r_fit_weights)
-
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array([[ 1.68051337e-18, -1.69406589e-21],
-       [-1.69406589e-21, -1.49077799e-19]])
-
-
-

We conclude by comparing all estimation results via the etable function:

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pf.etable([fit, fit_weights], digits=6)
-
-
- - - ----- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Y
(1)(2)
coef
X10.112019***
-(0.016947)		0.123687***
-(0.016880)
X20.732788***
-(0.004595)		0.732244***
-(0.004584)
fe
f1xx
f2xx
modelstats
Observations99979997
S.E. typeiidiid
R20.774375-
Significance levels: * p < 0.05, ** p < 0.01, *** p < 0.001. Format of coefficient cell: Coefficient (Std. Error)
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- -
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-
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pd.DataFrame(fixest.etable(r_fit, r_fit_weights, digits=6)).T
-
-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
012
0Dependent Var.:YY
1
2X10.112019*** (0.016947)0.123687*** (0.016880)
3X20.732788*** (0.004595)0.732244*** (0.004584)
4Fixed-Effects:--------------------------------------------
5f1YesYes
6f2YesYes
7___________________________________________________________
8S.E. typeIIDIID
9Observations9,9979,997
10R20.774380.77526
11Within R20.718220.71886
- -
-
-
-
-
-

Heteroskedastic Errors

-

We repeat the same exercise with heteroskedastic (HC1) errors:

-
-
fit = pf.feols(fml="Y ~ X1 + X2 | f1 + f2", data=data, vcov="hetero")
-fit_weights = pf.feols(
-    fml="Y ~ X1 + X2 | f1 + f2", data=data, vcov="hetero", weights="weights"
-)
-
-
-
fit_r = fixest.feols(
-    ro.Formula("Y ~ X1 + X2 | f1 + f2"),
-    data=data,
-    vcov="hetero",
-    ssc=fixest.ssc(True, "none", True, "min", "min", False),
-)
-
-fit_weights_r = fixest.feols(
-    ro.Formula("Y ~ X1 + X2 | f1 + f2"),
-    data=data,
-    weights=ro.Formula("~weights"),
-    vcov="hetero",
-    ssc=fixest.ssc(True, "none", True, "min", "min", False),
-)
-
-
R[write to console]: NOTE: 3 observations removed because of NA values (LHS: 1, RHS: 1, Fixed-effects: 1).
-
-R[write to console]: NOTE: 3 observations removed because of NA values (LHS: 1, RHS: 1, Fixed-effects: 1).
-
-
-
-

As before, we compare the variance covariance matrices:

-
-
fit._vcov - stats.vcov(fit_r)
-
-
array([[-1.61925594e-16, -2.13306719e-17],
-       [-2.13306719e-17, -5.39593869e-17]])
-
-
-
-
fit_weights._vcov - stats.vcov(fit_weights_r)
-
-
array([[-2.04968421e-16, -9.53780274e-18],
-       [-9.53780274e-18, -3.03136151e-17]])
-
-
-
-
pf.etable([fit, fit_weights], digits=6)
-
-
- - - ----- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Y
(1)(2)
coef
X10.112019***
-(0.017009)		0.123687***
-(0.019361)
X20.732788***
-(0.004553)		0.732244***
-(0.005140)
fe
f1xx
f2xx
modelstats
Observations99979997
S.E. typeheterohetero
R20.774375-
Significance levels: * p < 0.05, ** p < 0.01, *** p < 0.001. Format of coefficient cell: Coefficient (Std. Error)
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- -
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pd.DataFrame(fixest.etable(fit_r, fit_weights_r, digits=6)).T
-
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
012
0Dependent Var.:YY
1
2X10.112019*** (0.017009)0.123687*** (0.019361)
3X20.732788*** (0.004553)0.732244*** (0.005140)
4Fixed-Effects:--------------------------------------------
5f1YesYes
6f2YesYes
7___________________________________________________________
8S.E. typeHeteroskedastici.-rob.Heteroskedastici.-rob.
9Observations9,9979,997
10R20.774380.77526
11Within R20.718220.71886
- -
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-
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-

Cluster-Robust Errors

-

We conclude with cluster robust errors.

-
-
fit = pf.feols(fml="Y ~ X1 + X2 | f1 + f2", data=data, vcov={"CRV1": "f1"})
-fit_weights = pf.feols(
-    fml="Y ~ X1 + X2 | f1 + f2", data=data, vcov={"CRV1": "f1"}, weights="weights"
-)
-
-fit_r = fixest.feols(
-    ro.Formula("Y ~ X1 + X2 | f1 + f2"),
-    data=data,
-    vcov=ro.Formula("~f1"),
-    ssc=fixest.ssc(True, "none", True, "min", "min", False),
-)
-fit_r_weights = fixest.feols(
-    ro.Formula("Y ~ X1 + X2 | f1 + f2"),
-    data=data,
-    weights=ro.Formula("~weights"),
-    vcov=ro.Formula("~f1"),
-    ssc=fixest.ssc(True, "none", True, "min", "min", False),
-)
-
-
R[write to console]: NOTE: 3 observations removed because of NA values (LHS: 1, RHS: 1, Fixed-effects: 1).
-
-R[write to console]: NOTE: 3 observations removed because of NA values (LHS: 1, RHS: 1, Fixed-effects: 1).
-
-
-
-
-
fit._vcov - stats.vcov(fit_r)
-
-
array([[ 4.20345182e-16, -6.97387636e-17],
-       [-6.97404577e-17, -1.42166010e-17]])
-
-
-
-
fit_weights._vcov - stats.vcov(fit_weights_r)
-
-
array([[-3.95318402e-05,  2.05473422e-05],
-       [ 2.05473422e-05,  1.13249200e-06]])
-
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pf.etable([fit, fit_weights], digits=6)
-
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- - - ----- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Y
(1)(2)
coef
X10.112019***
-(0.015816)		0.123687***
-(0.018311)
X20.732788***
-(0.004476)		0.732244***
-(0.005249)
fe
f1xx
f2xx
modelstats
Observations99979997
S.E. typeby: f1by: f1
R20.774375-
Significance levels: * p < 0.05, ** p < 0.01, *** p < 0.001. Format of coefficient cell: Coefficient (Std. Error)
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- -
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pd.DataFrame(fixest.etable(fit_r, fit_r_weights, digits=6)).T
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
012
0Dependent Var.:YY
1
2X10.112019*** (0.015816)0.123687*** (0.018311)
3X20.732788*** (0.004476)0.732244*** (0.005249)
4Fixed-Effects:--------------------------------------------
5f1YesYes
6f2YesYes
7___________________________________________________________
8S.E.: Clusteredby: f1by: f1
9Observations9,9979,997
10R20.774380.77526
11Within R20.718220.71886
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Poisson Regression

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-
data = pf.get_data(model="Fepois")
-
-
-
fit_iid = pf.fepois(fml="Y ~ X1 + X2 | f1 + f2", data=data, vcov="iid", iwls_tol=1e-10)
-fit_hetero = pf.fepois(
-    fml="Y ~ X1 + X2 | f1 + f2", data=data, vcov="hetero", iwls_tol=1e-10
-)
-fit_crv = pf.fepois(
-    fml="Y ~ X1 + X2 | f1 + f2", data=data, vcov={"CRV1": "f1"}, iwls_tol=1e-10
-)
-
-fit_r_iid = fixest.fepois(
-    ro.Formula("Y ~ X1 + X2 | f1 + f2"),
-    data=data,
-    vcov="iid",
-    ssc=fixest.ssc(True, "none", True, "min", "min", False),
-)
-
-fit_r_hetero = fixest.fepois(
-    ro.Formula("Y ~ X1 + X2 | f1 + f2"),
-    data=data,
-    vcov="hetero",
-    ssc=fixest.ssc(True, "none", True, "min", "min", False),
-)
-
-fit_r_crv = fixest.fepois(
-    ro.Formula("Y ~ X1 + X2 | f1 + f2"),
-    data=data,
-    vcov=ro.Formula("~f1"),
-    ssc=fixest.ssc(True, "none", True, "min", "min", False),
-)
-
-
R[write to console]: NOTE: 3 observations removed because of NA values (LHS: 1, RHS: 1, Fixed-effects: 1).
-
-R[write to console]: NOTE: 3 observations removed because of NA values (LHS: 1, RHS: 1, Fixed-effects: 1).
-
-R[write to console]: NOTE: 3 observations removed because of NA values (LHS: 1, RHS: 1, Fixed-effects: 1).
-
-
-
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fit_iid._vcov - stats.vcov(fit_r_iid)
-
-
array([[ 1.20791284e-08, -6.55604931e-10],
-       [-6.55604931e-10,  1.69958097e-09]])
-
-
-
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fit_hetero._vcov - stats.vcov(fit_r_hetero)
-
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array([[ 2.18101847e-08, -7.38711972e-10],
-       [-7.38711972e-10,  3.07587753e-09]])
-
-
-
-
fit_crv._vcov - stats.vcov(fit_r_crv)
-
-
array([[ 1.58300904e-08, -1.20806815e-10],
-       [-1.20806815e-10,  3.17512746e-09]])
-
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pf.etable([fit_iid, fit_hetero, fit_crv], digits=6)
-
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- - - ------ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Y
(1)(2)(3)
coef
X1-0.006591
-(0.040758)		-0.006591
-(0.039145)		-0.006591
-(0.034745)
X2-0.014924
-(0.010994)		-0.014924
-(0.010501)		-0.014924
-(0.010303)
fe
f1xxx
f2xxx
modelstats
Observations997997997
S.E. typeiidheteroby: f1
R2---
Significance levels: * p < 0.05, ** p < 0.01, *** p < 0.001. Format of coefficient cell: Coefficient (Std. Error)
- - -
- -
-
-
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pd.DataFrame(fixest.etable(fit_r_iid, fit_r_hetero, fit_r_crv, digits=6)).T
-
-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
0123
0Dependent Var.:YYY
1
2X1-0.006591 (0.040758)-0.006591 (0.039145)-0.006591 (0.034745)
3X2-0.014924 (0.010994)-0.014924 (0.010501)-0.014924 (0.010302)
4Fixed-Effects:------------------------------------------------------------
5f1YesYesYes
6f2YesYesYes
7___________________________________________________________________________
8S.E. typeIIDHeteroskedasti.-rob.by: f1
9Observations997997997
10Squared Cor.0.076870.076870.07687
11Pseudo R20.028660.028660.02866
12BIC2,934.72,934.72,934.7
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Contributing

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Overview

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Thanks for showing interest in contributing to pyfixest! We appreciate all contributions and constructive feedback, whether that be reporting bugs, requesting new features, or suggesting improvements to documentation.

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If you’d like to get involved, but are not yet sure how, please feel free to send us an email. Some familiarity with either Python or econometrics will help, but you really don’t need to be a numpy core developer or have published in Econometrica =) We’d be more than happy to invest time to help you get started!

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Reporting bugs

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We use GitHub issues to track bugs. You can report a bug by opening a new issue or contribute to an existing issue if related to the bug you are reporting.

-

Before creating a bug report, please check that your bug has not already been reported, and that your bug exists on the latest version of pyfixest. If you find a closed issue that seems to report the same bug you’re experiencing, open a new issue and include a link to the original issue in your issue description.

-

Please include as many details as possible in your bug report. The information helps the maintainers resolve the issue faster.

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Suggesting enhancements

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We use GitHub issues to track bugs and suggested enhancements. You can suggest an enhancement by opening a new feature request. Before creating an enhancement suggestion, please check that a similar issue does not already exist.

-

Please describe the behavior you want and why, and provide examples of how pyfixest would be used if your feature were added.

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-
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Contributing to the codebase

-
-

Setting up your local environment

-

Start by forking the pyfixest GitHub repository, then clone your forked repository using git:

-
git clone https://github.com/<username>/pyfixest.git
-cd pyfixest
-

In order to work on pyfixest, you will need Python and R installed. If working on documentation, you will need Quarto installed. Note that you only need a local R installation if you want to run unit tests locally.

-

For suggestions on how to install R and Python, see the sections below.

-
-
-

Package Management via pixi

-

PyFixest is using pixi.

-

Please follow the installation instructions from the pixi documentation.

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Afterwards, you can initiate the project environment and install all dependencies by running

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cd path-to-pyfixest
-pixi install
-

If you type

-
pixi shell
-

you will see that you have activated a custom pixi environment for pyfixest.

-
-
-

Code Style

-

We use ruff and pre-commit to ensure a consistent code style.

-

To install the required hooks, run

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pixi run lint
-

and you’re ready to go!

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-
-

Pixi tasks

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There are several command line targets that assist with development included as pixi tasks.

-

To avtivate relevant pixi environments, you can type

-
pixi shell                      # open the base environment
-pixi shell --environment dev    # open the dev environment
-

For development, it is recommended to activate the dev environment (as it includes all development dependencies).

-
# 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
-

To rebuild the documentation locally, you can run

-
# Build documentation and website
-pixi run docs-build
-# render the docs
-pixi run docs-render
-# preview the docs
-pixi run docs-preview
-

Note that you need to have quarto installed in order to build the documentation locally.

-

To run the linter, you can run

-
pixi run lint
-

To build the package for PyPi, you can run

-
pixi run build-pip
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To re-create the csv files in tests/data that contain results from R packages for testing, you can run

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`pixi run update-tests-data`
-
-
-
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Installing Python, R and Quarto

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-

Installing Python

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The minimal Python version to develop pyfixest is 3.9. You can installed it on Mac/Linux via Hombrew:

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brew install python@3.11 # specify the version of python you prefer
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On Windows via Winget:

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winget install -e --id Python.Python.3.11
-
-
-

Installing R

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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.

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On Mac/Linux:

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brew install r
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Depending on your local set up, you may need to install additional libraries, for example:

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sudo apt install gcc-11 cmake
-

On Windows using Winget:

-
winget install -e --id RProject.R
-
-
-

Installing Quarto

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Documentation for pyfixest is written, compiled, and published using Quarto.

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To install Quarto, run:

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On MacOS via Homebrew:

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brew install --cask quarto
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On Linux (Ubuntu using gdebi):

-
sudo curl -o quarto-linux-amd64.deb -L <https://github.com/quarto-dev/quarto-cli/releases/download/v${QUARTO_VERSION}/quarto-${QUARTO_VERSION}-linux-amd64.deb>
-sudo gdebi quarto-linux-amd64.deb
-

On Windows:

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scoop bucket add extras
-scoop install extras/quarto
- - -
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- - - - - diff --git a/docs/difference-in-differences.html b/docs/difference-in-differences.html deleted file mode 100644 index 8ca682d6..00000000 --- a/docs/difference-in-differences.html +++ /dev/null @@ -1,1871 +0,0 @@ - - - - - - - - - -Difference-in-Differences Estimation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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- - - - -
- -
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Difference-in-Differences Estimation

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- - - -
- - - - -
- - - -
- - -

PyFixest supports event study designs via the canonical two-way fixed effects design, the 2-Step imputation estimator, and local projections.

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See also NBER SI methods lectures on Linear Panel Event Studies.

-
-
from importlib import resources
-
-import pandas as pd
-
-import pyfixest as pf
-from pyfixest.did.estimation import did2s, lpdid
-from pyfixest.did.visualize import panelview
-from pyfixest.report.utils import rename_event_study_coefs
-from pyfixest.utils.dgps import get_sharkfin
-
-%load_ext watermark
-%watermark --iversions
-
- -
- - -
-
- -
- - -
-
-
pandas  : 2.2.2
-pyfixest: 0.24.2
-
-
-
-
-
# one-shot adoption data - parallel trends is true
-df_one_cohort = get_sharkfin()
-df_one_cohort.head()
-
-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
unityeartreatYever_treated
00001.6293070
10100.8259020
20200.2089880
3030-0.2447390
40400.8046650
- -
-
-
-
-
# multi-cohort adoption data
-df_multi_cohort = pd.read_csv(
-    resources.files("pyfixest.did.data").joinpath("df_het.csv")
-)
-df_multi_cohort.head()
-
-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
unitstategroupunit_fegyearyear_fetreatrel_yearrel_year_binnederrortete_dynamicdep_var
0133Group 27.043016201019900.066159False-20.0-6-0.08646600.07.022709
1133Group 27.04301620101991-0.030980False-19.0-60.76659300.07.778628
2133Group 27.04301620101992-0.119607False-18.0-61.51296800.08.436377
3133Group 27.043016201019930.126321False-17.0-60.02187000.07.191207
4133Group 27.04301620101994-0.106921False-16.0-6-0.01760300.06.918492
- -
-
-
-
-

Examining Treatment Timing

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Before any DiD estimation, we need to examine the treatment timing, since it is crucial to our choice of estimator.

-
-
panelview(
-    df_one_cohort,
-    unit="unit",
-    time="year",
-    treat="treat",
-    collapse_to_cohort=True,
-    sort_by_timing=True,
-    ylab="Cohort",
-    xlab="Year",
-    title="Treatment Assignment Cohorts",
-)
-
-
-
-

-
-
-
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-
-
panelview(
-    df_multi_cohort,
-    unit="unit",
-    time="year",
-    treat="treat",
-    collapse_to_cohort=True,
-    sort_by_timing=True,
-    ylab="Cohort",
-    xlab="Year",
-    title="Treatment Assignment Cohorts",
-)
-
-
-
-

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-
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We immediately see that we have staggered adoption of treatment in the second case, which implies that a naive application of 2WFE might yield biased estimates under substantial effect heterogeneity.

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We can also plot treatment assignment in a disaggregated fashion, which gives us a sense of cohort sizes.

-
-
panelview(
-    df_multi_cohort,
-    unit="unit",
-    time="year",
-    treat="treat",
-    sort_by_timing=True,
-    ylab="Unit",
-    xlab="Year",
-    title="Treatment Assignment (all units)",
-)
-
-
-
-

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One-shot adoption: Static and Dynamic Specifications

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-
fit_static_twfe = pf.feols(
-    "Y ~ treat | unit + year",
-    df_one_cohort,
-    vcov={"CRV1": "unit"},
-)
-fit_static_twfe.summary()
-
-
###
-
-Estimation:  OLS
-Dep. var.: Y, Fixed effects: unit+year
-Inference:  CRV1
-Observations:  30000
-
-| Coefficient   |   Estimate |   Std. Error |   t value |   Pr(>|t|) |   2.5% |   97.5% |
-|:--------------|-----------:|-------------:|----------:|-----------:|-------:|--------:|
-| treat         |      0.206 |        0.052 |     3.929 |      0.000 |  0.103 |   0.308 |
----
-RMSE: 0.701 R2: 0.905 R2 Within: 0.003
-
-
-

Since this is a single-cohort dataset, this estimate is consistent for the ATT under parallel trends. We can estimate heterogeneous effects by time by interacting time with the treated group:

-
-
fit_dynamic_twfe = pf.feols(
-    "Y ~ i(year, ever_treated,  ref = 14) | unit + year",
-    df_one_cohort,
-    vcov={"CRV1": "unit"},
-)
-
-
-
fit_dynamic_twfe.iplot(
-    coord_flip=False,
-    title="Event Study",
-    figsize=[1200, 400],
-    yintercept=0,
-    xintercept=13.5,
-    labels=rename_event_study_coefs(fit_dynamic_twfe._coefnames),
-)
-
-
- -
-
-

Event study plots like this are very informative, as they allow us to visually inspect the parallel trends assumption and also the dynamic effects of the treatment.

-

Based on a cursory glance, one would conclude that parallel trends does not hold because one of the pre-treatment coefficient has a confidence interval that does not include zero. However, we know that parallel trends is true because the treatment is randomly assigned in the underlying DGP.

-
-

Pointwise vs Simultaneous Inference in Event Studies

-

This is an example of a false positive in testing for pre-trends produced by pointwise inference (where each element of the coefficient vector is tested separately).

-

As an alternative, we can use simultaneous confidence bands of the form \([a, b] = ([a_k, b_k])_{k=1}^K\) such that

-

\[ -P(\beta \in [a, b]) = P(\beta_k \in [a_k, b_k] \forall k) \rightarrow 1 - \alpha -\]

-

These bands can be constructed by using a carefully chosen critical value \(c\) that accounts for the covariance between coefficients using the multiplier bootstrap. In pointwise inference, the critical value is \(c = z_{1 - \alpha/2} = 1.96\) for \(\alpha = 0.05\); the corresponding critical value for simultaneous inference is typically larger. These are also known as sup-t bands in the literature (see lec 3 of the NBER SI methods lectures linked above).

-

This is implemented in the confint(joint=True) method in the feols class. If we pass the joint='both' argument to iplot, we get the simultaneous confidence bands (for all event study coefficients) in addition to the pointwise confidence intervals. Note that simultaneous inference for all event study coefficients may be overly conservative, especially when the number of coefficients is large; one may instead choose to perform joint inference for all pre-treatment coefficients and all post-treatment coefficients separately.

-
-
fit_dynamic_twfe.iplot(
-    coord_flip=False,
-    title="Event Study",
-    figsize=[1200, 400],
-    yintercept=0,
-    xintercept=13.5,
-    joint="both",
-    labels=rename_event_study_coefs(fit_dynamic_twfe._coefnames),
-)
-
-
- -
-
-

The joint confidence bands are wider than the pointwise confidence intervals, and they include zero for all pre-treatment coefficients. This is consistent with the parallel trends assumption.

-
-
-
-

Event Study under Staggered Adoption via feols(), did2s() and lpdid()

-

We can estimate a simple two-way fixed effects DiD regression via feols():

-
-
fit_twfe = pf.feols(
-    "dep_var ~ i(rel_year, ref=-1.0) | state + year",
-    df_multi_cohort,
-    vcov={"CRV1": "state"},
-)
-
-

To do the same via Gardners 2-stage estimator, we employ the the did2s() function:

-
-
fit_did2s = did2s(
-    df_multi_cohort,
-    yname="dep_var",
-    first_stage="~ 0 | state + year",
-    second_stage="~i(rel_year,ref=-1.0)",
-    treatment="treat",
-    cluster="state",
-)
-
-

Last, we can estimate the ATT for each time period via local projections by using the lpdid() function:

-
-
fit_lpdid = lpdid(
-    data=df_multi_cohort,
-    yname="dep_var",
-    gname="g",
-    tname="year",
-    idname="unit",
-    vcov={"CRV1": "state"},
-    pre_window=-20,
-    post_window=20,
-    att=False,
-)
-
-

Let’s look at some results:

-
-
figsize = [1200, 400]
-
-
-
fit_twfe.iplot(
-    coord_flip=False,
-    title="TWFE-Estimator",
-    figsize=figsize,
-    xintercept=18.5,
-    yintercept=0,
-    labels=rename_event_study_coefs(fit_twfe._coefnames),  # rename coefficients
-).show()
-
-
- -
-
-
-
fit_did2s.iplot(
-    coord_flip=False,
-    title="DID2s-Estimator",
-    figsize=figsize,
-    xintercept=18.5,
-    yintercept=0,
-    labels=rename_event_study_coefs(fit_twfe._coefnames),
-).show()
-
-
- -
-
-
-
fit_lpdid.iplot(
-    coord_flip=False,
-    title="Local-Projections-Estimator",
-    figsize=figsize,
-    yintercept=0,
-    xintercept=18.5,
-).show()
-
-
- -
-
-

What if we are not interested in the ATT per treatment period, but in a pooled effects?

-
-
fit_twfe = pf.feols(
-    "dep_var ~ i(treat) | unit + year",
-    df_multi_cohort,
-    vcov={"CRV1": "state"},
-)
-
-fit_did2s = did2s(
-    df_multi_cohort,
-    yname="dep_var",
-    first_stage="~ 0 | unit + year",
-    second_stage="~i(treat)",
-    treatment="treat",
-    cluster="state",
-)
-
-fit_lpdid = lpdid(
-    data=df_multi_cohort,
-    yname="dep_var",
-    gname="g",
-    tname="year",
-    idname="unit",
-    vcov={"CRV1": "state"},
-    pre_window=-20,
-    post_window=20,
-    att=True,
-)
-pd.concat(
-    [
-        fit_twfe.tidy().assign(estimator="TWFE"),
-        fit_did2s.tidy().assign(estimator="DID2s"),
-        fit_lpdid.tidy().assign(estimator="LPDID").drop("N", axis=1),
-    ],
-    axis=0,
-)
-
-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
EstimateStd. Errort valuePr(>|t|)2.5%97.5%estimator
C(treat)[T.True]1.9825400.019331102.5561800.01.9434392.021642TWFE
C(treat)[T.True]2.2304820.02470990.2714370.02.1820542.278910DID2s
treat_diff2.5067460.07135735.1296480.02.3624132.651080LPDID
- -
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z;%piF0|9hYIMidKb^OGMAEms>(Lfavpe2bt9J6pE4K^6Ned$d}c3qs4!HG;B5>W*A z#Pv~95a>_2WZU*0#RAJ7n*%M&Q+?`Jfm!Q2`$w@L)~OMuMa4yHMo@TpB@!{k6lm8K_X@ z2Y(I@{q$&=4~RG4LY#;k#yg5b4`gBwF@0x~;0=@>a0TZ24`dZMkV{1hlf*x)>-BAA rv(4qb?%76wczu8HU$+)0i}abPS)V7i^n~MhJVjpi diff --git a/docs/marginaleffects.html b/docs/marginaleffects.html deleted file mode 100644 index 1edb1677..00000000 --- a/docs/marginaleffects.html +++ /dev/null @@ -1,937 +0,0 @@ - - - - - - - - - -Marginal Effects and Hypothesis Tests via marginaleffects - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Marginal Effects and Hypothesis Tests via marginaleffects

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We can compute marginal effects and linear and non-linear hypothesis tests via the excellent marginaleffects package.

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from marginaleffects import hypotheses
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-import pyfixest as pf
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-data = pf.get_data()
-fit = pf.feols("Y ~ X1 + X2", data=data)
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-fit.tidy()
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EstimateStd. Errort valuePr(>|t|)2.5%97.5%
Coefficient
Intercept0.8887790.1084228.1973748.881784e-160.6760161.101542
X1-0.9929360.082117-12.0916500.000000e+00-1.154079-0.831792
X2-0.1763420.021766-8.1017431.554312e-15-0.219055-0.133630
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Suppose we were interested in testing the hypothesis that \(X_{1} = X_{2}\). Given the relatively large differences in coefficients and small standard errors, we will likely reject the null that the two parameters are equal.

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We can run the formal test via the hypotheses function from the marginaleffects package.

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hypotheses(fit, "X1 - X2 = 0")
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-shape: (1, 8) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
termestimatestd_errorstatisticp_values_valueconf_lowconf_high
strf64f64f64f64f64f64f64
"X1-X2=0"-0.8165930.085179-9.5867970.0inf-0.983541-0.649646
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And indeed, we reject the null of equality of coefficients: we get a p-value of zero and a confidence interval that does not contain 0.

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Ratio Estimates

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We can also test run-linear hypotheses, in which case marginaleffects will automatically compute correct standard errors based on the estimated covariance matrix and the Delta method. This is for example useful for computing inferential statistics for the “relative uplift” in an AB test.

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For the moment, let’s assume that \(X1\) is a randomly assigned treatment variable. As before, \(Y\) is our variable / KPI of interest.

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Under randomization, the model intercept measures the “baseline”, i.e. the population average of \(Y\) in the absence of treatment. To compute a relative uplift, we might compute

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(fit.coef().xs("X1") / fit.coef().xs("Intercept") - 1) * 100
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-211.71906665561212
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So we have a really big negative treatment effect of around minus 212%! To conduct correct inference on this ratio statistic, we need to use the delta method.

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The Multivariate Delta Method

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In a nutshell, the delta method provides a way to approximate the asympotic distribution of any non-linear transformation \(g()\) or one or more random variables.

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In the case of the ratio statistics, this non-linear transformation can be denoted as \(g(\theta_{1}, \theta_{2}) = \theta_{1} / \theta_{2}\).

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Here’s the Delta Method theorem:

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First, we define \(\theta = (\theta_{1}, \theta_{2})'\) and \(\mu = (\mu_{1}, \mu_{2})'\).

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By the law of large numbers, we know that

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\[ -\sqrt{N} (\theta - \mu) \rightarrow_{d} N(0_{2}, \Sigma_{2,2}) \text{ if } N \rightarrow \infty. -\]

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By the Delta Method, we can then approximate the limit distribution of \(g(\theta)\) as

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\[ -\sqrt{N} (g(\theta) - g(\mu)) \rightarrow_{d} N(0_{1}, g'(\theta) \times \Sigma \times g(\theta)) \text{ if } N \rightarrow \infty. -\].

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Here’s a long derivation of how to use the the delta method for inference of ratio statistics.. The key steps from the formula above is to derive the expression for the asymptotic variance $ g’() g()$.

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But hey - we’re lucky, because marginaleffects will do all this work for us: we don’t have to derive analytic gradients ourselves =)

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Using the Delta Method via marginaleffects:

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We can employ the Delta Method via marginaleffects via the hypotheses function:

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hypotheses(fit, "(X1 / Intercept - 1) * 100 = 0")
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strf64f64f64f64f64f64f64
"(X1/Intercept-…-211.7190678.478682-24.9707510.0inf-228.336979-195.101155
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As before, we get an estimate of around -212%. Additionally, we obtain a 95% CI via the Delta Method of [-228%, -195%].

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Besides hypopotheses testing, you can do a range of other cool things with the marginaleffects package. For example (and likely unsurprisingly), you can easily compute all sorts of marginal effects for your regression models. For all the details, we highly recommend to take a look at the marginaleffects zoo book!.

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PyFixest 0.22.0

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Changes

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  • Fix bug in wildboottest method @s3alfisc (#506)
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  • docs: add sanskriti2005 as a contributor for infra @allcontributors (#503)
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  • Infra: added the release-drafter for automation of release notes @sanskriti2005 (#502)
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  • Fix broken link in contributing.md @s3alfisc (#499)
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  • docs: add leostimpfle as a contributor for bug @allcontributors (#495)
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  • Update justfile @leostimpfle (#494)
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  • docs: add baggiponte as a contributor for doc @allcontributors (#490)
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  • Bump tornado from 6.4 to 6.4.1 @dependabot (#487)
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  • Feols: speed up the creation of interacted fixed effects via fe1^fe2 syntax @leostimpfle (#475)
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  • rename resampling iterations to ‘reps’ in all methods @s3alfisc (#474)
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Infrastructure

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PyFixest 0.21.0

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import pyfixest as pf
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-fit = pf.feols("Y ~ X1", data = data)
-fit.ritest(resampvar="X1=0", reps = 1000)
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PyFixest 0.20.0

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PyFixest 0.19.0

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  • Fixes multiple smaller and larger performance regressions. The NYC-Taxi example regression now takes approximately 22 seconds to run (… if my laptopt is connected to a power charger)!
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%load_ext autoreload
-%autoreload 2
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-import duckdb
-import time
-import numpy as np
-import pyfixest as pf
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-# %%
-nyc = duckdb.sql(
-    '''
-    FROM 'C:/Users/alexa/Documents/nyc-taxi/**/*.parquet'
-    SELECT
-        tip_amount, trip_distance, passenger_count,
-        vendor_id, payment_type, dropoff_at,
-        dayofweek(dropoff_at) AS dofw
-    WHERE year = 2012 AND month <= 3
-    '''
-    ).df()
-
-# convert dowf, vendor_id, payment_type to categorical
-tic = time.time()
-nyc["dofw"] = nyc["dofw"].astype(int)
-nyc["vendor_id"] = nyc["vendor_id"].astype("category")
-nyc["payment_type"] = nyc["payment_type"].astype("category")
-print(f"""
-    I am convering columns of type 'objects' to 'categories' and 'int'data types outside
-    of the regression, hence I am cheating a bit. This saves {np.round(time.time() - tic)} seconds.
-    """
-)
-#    I am convering columns of type 'objects' to 'categories' and 'int'data types outside
-#    of the regression, hence I am cheating a bit. This saves 7.0 seconds.
-
-run = True
-if run:
-
-    # mock regression for JIT compilation
-    fit = pf.feols(
-        fml = "tip_amount ~ trip_distance + passenger_count | vendor_id + payment_type + dofw",
-        data = nyc.iloc[1:10_000],
-        copy_data = False,
-        store_data = False
-        )
-
-    import time
-    tic = time.time()
-    fit = pf.feols(
-        fml = "tip_amount ~ trip_distance + passenger_count | vendor_id + payment_type + dofw",
-        data = nyc,
-        copy_data = False, # saves a few seconds
-        store_data = False # saves a few second
-        )
-    passed = time.time() - tic
-    print(f"Passed time is {np.round(passed)}.")
-    # Passed time is 22.
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import pyfixest as pf
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-data = pf.get_data(N = 10000, model = "Fepois")
-df_weighted = data[["Y", "X1", "f1"]].groupby(["Y", "X1", "f1"]).size().reset_index().rename(columns={0: "count"})
-df_weighted["id"] = list(range(df_weighted.shape[0]))
-
-print("Dimension of the aggregated df:", df_weighted.shape)
-print(df_weighted.head())
-
-fit = pf.feols(
-    "Y ~ X1 | f1",
-    data = data
-)
-fit_weighted = pf.feols(
-    "Y ~ X1 | f1",
-    data = df_weighted,
-    weights = "count",
-    weights_type = "fweights"
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-pf.etable([fit, fit_weighted], coef_fmt = "b(se) \n (t) \n (p)")
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Dimension of the aggregated df: (1278, 5)
-     Y   X1   f1  count  id
-0  0.0  0.0  0.0     17   0
-1  0.0  0.0  1.0     11   1
-2  0.0  0.0  2.0     10   2
-3  0.0  0.0  3.0     17   3
-4  0.0  0.0  4.0     14   4
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f1xx
stats
Observations99979997
S.E. typeby: f1by: f1
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PyFixest 0.18.0

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-data = pf.get_data()
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-fit1.coef()[0:8]
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Via the ref syntax, via can set the reference level:

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  • Restructures the codebase and reorganizes how users can interact with the pyfixest API. It is now recommended to use pyfixest in the following way:

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    import numpy as np
-import pyfixest as pf
-data = pf.get_data()
-data["D"] = data["X1"] > 0
-fit = pf.feols("Y ~ D + f1", data = data)
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    Intercept0.7788490.1702614.5744370.0000050.4447371.112961
    D-1.4026170.152224-9.2141400.000000-1.701335-1.103899
    f10.0047740.0080580.5925080.553645-0.0110380.020587
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    C:\Users\alexa\Documents\pyfixest\pyfixest\estimation\feols_.py:1364: UserWarning: The initial model was not clustered. CRV1 inference is computed and stored in the model object.
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PyFixest 0.16.0

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PyFixest 0.15.

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PyFixest 0.14.0

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from pyfixest.did.estimation import did2s, lpdid, event_study
-
-
-
-

PyFixest 0.13.5

-
    -
  • Fixes a bug that lead to incorrect results when the dependent variable and all covariates (excluding the fixed effects) where integers.
    • -
-
-
-

PyFixest 0.13.4

-
    -
  • Fixes a bug in etable() with IV’s that occurred because feols() does not report R2 statistics for IVs.
    • -
-
-
-

PyFixest 0.13.2

-
    -
  • Fixes a bug in etable() and a warning in fixest_model_matrix that arose with higher pandas versions. Thanks to @aeturrell for reporting!
    • -
-
-
-

PyFixest 0.13.0

-
-

New Features

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    -
  • Introduces a new pyfixest.did module which contains routines for Difference-in-Differences estimation.
    • -
  • Introduces support for basic versions of the local projections DiD estimator following Dube et al (2023)
    • -
  • Adds a new vignette for Difference-in-Differences estimation.
    • -
  • Reports R2 values in etable().
    • -
-
-
-
-

PyFixest 0.12.0

-
-

Enhancements:

-
    -
  • Good performance improvements for singleton fixed effects detection. Thanks to @styfenschaer for the PR! See #229.
    • -
  • Uses the r2u project for installing R and R packages on github actions, with great performance improvements.
    • -
  • Allows to pass polars data frames to feols(), fepois() and predict(). #232. Thanks to @vincentarelbundock for the suggestion!
    • -
-
-
-

Bug Fixes:

-
    -
  • Missing variables in features were not always handled correctly in predict() with newdata not None in the presence of missing data, which would lead to an error. See #246 for details.
    • -
  • Categorical variables were not always handled correctly in predict() with newdata not None, because the number of fixed effects levels in newdata might be smaller than in data. In consequence, some levels were not found, which lead to an error. See #245 for details. Thanks to @jiafengkevinchen for the pointer!
    • -
  • Multicollinearity checks for over-identified IV was not implemented correctly, which lead to a dimension error. See #236 for details. Thanks to @jiafengkevinchen for the pointer!
    • -
  • The number of degrees of freedom k was computed incorrectly if columns were dropped from the design matrix X in the presence of multicollinearity. See #235 for details. Thanks to @jiafengkevinchen for the pointer!
    • -
  • If all variables were dropped due to multicollinearity, an unclear and imprecise error message was produced. See #228 for details. Thanks to @manferdinig for the pointer!
    • -
  • If selection fixef_rm = 'singleton', feols() and fepois() would fail, which has been fixed. #192
    • -
-
-
-

Dependency Requirements

-
    -
  • For now, sets formulaic versions to be 0.6.6 or lower as version 1.0.0 seems to have introduced a problem with the i() operator, See #244 for details.
    • -
  • Drops dependency on pyhdfe.
    • -
-
-
-
-

PyFixest 0.11.1

-
    -
  • Fixes some bugs around the computation of R-squared values (see issue #103).
    • -
  • Reports R-squared values again when calling .summary().
    • -
-
-
-

PyFixest 0.11.0

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    -
  • Significant speedups for CRV1 inference.
    • -
-
-
-

PyFixest 0.10.12

-

Fixes a small bug with the separation check for poisson regression #138.

-
-
-

PyFixest 0.10.11

-

Fixes bugs with i(var1, var2) syntax introduced with PyFixest 0.10.10.

-
-
-

PyFixest 0.10.10

-

Fixes a bug with variable interactions via i(var) syntax. See issue #221.

-
-
-

PyFixest 0.10.9

-

Makes etable() prettier and more informative.

-
-
-

PyFixest 0.10.8

-
-

Breaking changes

-

Reference levels for the i() formula syntax can no longer be set within the formula, but need to be added via the i_ref1 function argument to either feols() and fepois().

-
-
-

New feature

-

A dids2() function is added, which implements the 2-stage difference-in-differences procedure à la Gardner and follows the syntax of @kylebutts did2s R package.

-
from pyfixest.did.did import did2s
-from pyfixest.estimation import feols
-from pyfixest.visualize import iplot
-import pandas as pd
-import numpy as np
-
-df_het = pd.read_csv("https://raw.githubusercontent.com/py-econometrics/pyfixest/master/pyfixest/did/data/df_het.csv")
-
-fit = did2s(
-    df_het,
-    yname = "dep_var",
-    first_stage = "~ 0 | state + year",
-    second_stage = "~i(rel_year)",
-    treatment = "treat",
-    cluster = "state",
-    i_ref1 = [-1.0, np.inf],
-)
-
-fit_twfe = feols(
-    "dep_var ~ i(rel_year) | state + year",
-    df_het,
-    i_ref1 = [-1.0, np.inf]
-)
-
-iplot([fit, fit_twfe], coord_flip=False, figsize = (900, 400), title = "TWFE vs DID2S")
-

-
-
-
-

PyFixest 0.10.7

-
    -
  • Adds basic support for event study estimation via two-way fixed effects and Gardner’s two-stage “Did2s” approach. This is a beta version and experimental. Further updates (i.e. proper event studies vs “only” ATTs) and a more flexible did2s front end will follow in future releases.
    • -
-
%load_ext autoreload
-%autoreload 2
-
-from pyfixest.did.did import event_study
-import pyfixest as pf
-import pandas as pd
-df_het = pd.read_csv("pyfixest/did/data/df_het.csv")
-
-fit_twfe = event_study(
-    data = df_het,
-    yname = "dep_var",
-    idname= "state",
-    tname = "year",
-    gname = "g",
-    estimator = "twfe"
-)
-
-fit_did2s = event_study(
-    data = df_het,
-    yname = "dep_var",
-    idname= "state",
-    tname = "year",
-    gname = "g",
-    estimator = "did2s"
-)
-
-pf.etable([fit_twfe, fit_did2s])
-# | Coefficient   | est1             | est2             |
-# |:--------------|:-----------------|:-----------------|
-# | ATT           | 2.135*** (0.044) | 2.152*** (0.048) |
-# Significance levels: * p < 0.05, ** p < 0.01, *** p < 0.001
-
-
-

PyFixest 0.10.6

-
    -
  • Adds an etable() function that outputs markdown, latex or a pd.DataFrame.
    • -
-
-
-

PyFixest 0.10.5

-
    -
  • Fixes a big in IV estimation that would trigger an error. See here for details. Thanks to @aeturrell for reporting!
    • -
-
-
-

PyFixest 0.10.4

-
    -
  • Implements a custom function to drop singleton fixed effects.
    • -
  • Additional small performance improvements.
    • -
-
-
-

PyFixest 0.10.3

-
    -
  • Allows for white space in the multiway clustering formula.
    • -
  • Adds documentation for multiway clustering.
    • -
-
-
-

PyFixest 0.10.2

-
    -
  • Adds support for two-way clustering.
    • -
  • Adds support for CRV3 inference for Poisson regression.
    • -
-
-
-

PyFixest 0.10.1

-
    -
  • Adapts the internal fixed effects demeaning criteron to match `PyHDFE’s default.
    • -
  • Adds Styfen as coauthor.
    • -
-
-
-

PyFixest 0.10

-
    -
  • Multiple performance improvements.
    • -
  • Most importantly, implements a custom demeaning algorithm in numba - thanks to Styfen Schaer (@styfenschaer), which leads to performance improvements of 5x or more:
    • -
-
%load_ext autoreload
-%autoreload 2
-
-import numpy as np
-import time
-import pyhdfe
-from pyfixest.demean import demean
-
-np.random.seed(1238)
-N = 10_000_000
-x = np.random.normal(0, 1, 10*N).reshape((N,10))
-f1 = np.random.choice(list(range(1000)), N).reshape((N,1))
-f2 = np.random.choice(list(range(1000)), N).reshape((N,1))
-
-flist = np.concatenate((f1, f2), axis = 1)
-weights = np.ones(N)
-
-algorithm = pyhdfe.create(flist)
-
-start_time = time.time()
-res_pyhdfe = algorithm.residualize(x)
-end_time = time.time()
-print(end_time - start_time)
-# 26.04527711868286
-
-
-start_time = time.time()
-res_pyfixest, success = demean(x, flist, weights, tol = 1e-10)
-# Calculate the execution time
-end_time = time.time()
-print(end_time - start_time)
-#4.334428071975708
-
-np.allclose(res_pyhdfe , res_pyfixest)
-# True
-
-
-

PyFixest 0.9.11

-
    -
  • Bump required formulaic version to 0.6.5.
    • -
  • Stop copying the data frame in fixef().
    • -
-
-
-

PyFixest 0.9.10

-
    -
  • Fixes a big in the wildboottest method (see #158).
    • -
  • Allows to run a wild bootstrap after fixed effect estimation.
    • -
-
-
-

PyFixest 0.9.9

-
    -
  • Adds support for wildboottest for Python 3.11.
    • -
-
-
-

PyFixest 0.9.8

-
    -
  • Fixes a couple more bugs in the predict() and fixef() methods.
    • -
  • The predict() argument data is renamed to newdata.
    • -
-
-
-

PyFixest 0.9.7

-

Fixes a bug in predict() produced when multicollinear variables are dropped.

-
-
-

PyFixest 0.9.6

-

Improved Collinearity handling. See #145

-
-
-

PyFixest 0.9.5

-
    -
  • Moves plotting from matplotlib to lets-plot.
    • -
  • Fixes a few minor bugs in plotting and the fixef() method.
    • -
-
-
-

PyFixest 0.9.1

-
-

Breaking API changes

-

It is no longer required to initiate an object of type Fixest prior to running [Feols(/reference/Feols.qmd) or fepois. Instead, you can now simply use feols() and fepois() as functions, just as in fixest. Both function can be found in an estimation module and need to obtain a pd.DataFrame as a function argument:

-
from pyfixest.estimation import fixest, fepois
-from pyfixest.utils import get_data
-
-data = get_data()
-fit = feols("Y ~ X1 | f1", data = data, vcov = "iid")
-

Calling feols() will return an instance of class [Feols(/reference/Feols.qmd), while calling fepois() will return an instance of class Fepois. Multiple estimation syntax will return an instance of class FixestMulti.

-

Post processing works as before via .summary(), .tidy() and other methods.

-
-
-

New Features

-

A summary function allows to compare multiple models:

-
from pyfixest.summarize import summary
-fit2 = feols("Y ~ X1 + X2| f1", data = data, vcov = "iid")
-summary([fit, fit2])
-

Visualization is possible via custom methods (.iplot() & .coefplot()), but a new module allows to visualize a list of [Feols(/reference/Feols.qmd) and/or Fepois instances:

-
from pyfixest.visualize import coefplot, iplot
-coefplot([fit, fit2])
-

The documentation has been improved (though there is still room for progress), and the code has been cleaned up a bit (also lots of room for improvements).

- - -
-
- -
- -
- - - - - diff --git a/docs/pyfixest.html b/docs/pyfixest.html deleted file mode 100644 index c7bc3dd6..00000000 --- a/docs/pyfixest.html +++ /dev/null @@ -1,795 +0,0 @@ - - - - - - - - - -pyfixest - - - - - - - - - - - - - - - - - - - - - - - - - - -
-
- -
- -
- - - - -
- - - - -

-
-

PyFixest: Fast High-Dimensional Fixed Effects Regression in Python

-

License PyPI -Version PyPI - Python Version Downloads Downloads image Ruff Pixi Badge All Contributors

-

PyFixest is a Python implementation of the formidable fixest package for fast high-dimensional fixed effects regression.

-

The package aims to mimic fixest syntax and functionality as closely as Python allows: if you know fixest well, the goal is that you won’t have to read the docs to get started! In particular, this means that all of fixest's defaults are mirrored by PyFixest - currently with only one small exception.

-

Nevertheless, for a quick introduction, you can take a look at the quickstart or the regression chapter of Arthur Turrell’s book on Coding for Economists.

-
-

Features

-
    -
  • OLS, WLS and IV Regression
    • -
  • Poisson Regression following the pplmhdfe algorithm
    • -
  • Multiple Estimation Syntax
    • -
  • Several Robust and Cluster Robust Variance-Covariance Estimators
    • -
  • Wild Cluster Bootstrap Inference (via wildboottest)
    • -
  • Difference-in-Differences Estimators: -
    • -
  • Multiple Hypothesis Corrections following the Procedure by Romano and Wolf and Simultaneous Confidence Intervals using a Multiplier Bootstrap
    • -
  • The Causal Cluster Variance Estimator (CCV) following Abadie et al.
    • -
  • Publication-ready tables with Great Tables or LaTex booktabs
    • -
-
-
-

Installation

-

You can install the release version from PyPi by running

-
pip install -U pyfixest
-

or the development version from github by running

-
pip install git+https://github.com/py-econometrics/pyfixest.git
-
-
-

Benchmarks

-

All benchmarks follow the fixest benchmarks. All non-pyfixest timings are taken from the fixest benchmarks.

-

-
-
-

Quickstart

-
import pyfixest as pf
-
-data = pf.get_data()
-pf.feols("Y ~ X1 | f1 + f2", data=data).summary()
-
###
-
-Estimation:  OLS
-Dep. var.: Y, Fixed effects: f1+f2
-Inference:  CRV1
-Observations:  997
-
-| Coefficient   |   Estimate |   Std. Error |   t value |   Pr(>|t|) |   2.5% |   97.5% |
-|:--------------|-----------:|-------------:|----------:|-----------:|-------:|--------:|
-| X1            |     -0.919 |        0.065 |   -14.057 |      0.000 | -1.053 |  -0.786 |
----
-RMSE: 1.441   R2: 0.609   R2 Within: 0.2
-
-

Multiple Estimation

-

You can estimate multiple models at once by using multiple estimation syntax:

-
# OLS Estimation: estimate multiple models at once
-fit = pf.feols("Y + Y2 ~X1 | csw0(f1, f2)", data = data, vcov = {'CRV1':'group_id'})
-# Print the results
-fit.etable()
-
                           est1               est2               est3               est4               est5               est6
-------------  -----------------  -----------------  -----------------  -----------------  -----------------  -----------------
-depvar                        Y                 Y2                  Y                 Y2                  Y                 Y2
-------------------------------------------------------------------------------------------------------------------------------
-Intercept      0.919*** (0.121)   1.064*** (0.232)
-X1            -1.000*** (0.117)  -1.322*** (0.211)  -0.949*** (0.087)  -1.266*** (0.212)  -0.919*** (0.069)  -1.228*** (0.194)
-------------------------------------------------------------------------------------------------------------------------------
-f2                            -                  -                  -                  -                  x                  x
-f1                            -                  -                  x                  x                  x                  x
-------------------------------------------------------------------------------------------------------------------------------
-R2                        0.123              0.037              0.437              0.115              0.609              0.168
-S.E. type          by: group_id       by: group_id       by: group_id       by: group_id       by: group_id       by: group_id
-Observations                998                999                997                998                997                998
-------------------------------------------------------------------------------------------------------------------------------
-Significance levels: * p < 0.05, ** p < 0.01, *** p < 0.001
-Format of coefficient cell:
-Coefficient (Std. Error)
-
-
-

Adjust Standard Errors “on-the-fly”

-

Standard Errors can be adjusted after estimation, “on-the-fly”:

-
fit1 = fit.fetch_model(0)
-fit1.vcov("hetero").summary()
-
Model:  Y~X1
-###
-
-Estimation:  OLS
-Dep. var.: Y
-Inference:  hetero
-Observations:  998
-
-| Coefficient   |   Estimate |   Std. Error |   t value |   Pr(>|t|) |   2.5% |   97.5% |
-|:--------------|-----------:|-------------:|----------:|-----------:|-------:|--------:|
-| Intercept     |      0.919 |        0.112 |     8.223 |      0.000 |  0.699 |   1.138 |
-| X1            |     -1.000 |        0.082 |   -12.134 |      0.000 | -1.162 |  -0.838 |
----
-RMSE: 2.158   R2: 0.123
-
-
-

Poisson Regression via fepois()

-

You can estimate Poisson Regressions via the fepois() function:

-
poisson_data = pf.get_data(model = "Fepois")
-pf.fepois("Y ~ X1 + X2 | f1 + f2", data = poisson_data).summary()
-
###
-
-Estimation:  Poisson
-Dep. var.: Y, Fixed effects: f1+f2
-Inference:  CRV1
-Observations:  997
-
-| Coefficient   |   Estimate |   Std. Error |   t value |   Pr(>|t|) |   2.5% |   97.5% |
-|:--------------|-----------:|-------------:|----------:|-----------:|-------:|--------:|
-| X1            |     -0.007 |        0.035 |    -0.190 |      0.850 | -0.075 |   0.062 |
-| X2            |     -0.015 |        0.010 |    -1.449 |      0.147 | -0.035 |   0.005 |
----
-Deviance: 1068.169
-
-
-

IV Estimation via three-part formulas

-

Last, PyFixest also supports IV estimation via three part formula syntax:

-
fit_iv = pf.feols("Y ~ 1 | f1 | X1 ~ Z1", data = data)
-fit_iv.summary()
-
###
-
-Estimation:  IV
-Dep. var.: Y, Fixed effects: f1
-Inference:  CRV1
-Observations:  997
-
-| Coefficient   |   Estimate |   Std. Error |   t value |   Pr(>|t|) |   2.5% |   97.5% |
-|:--------------|-----------:|-------------:|----------:|-----------:|-------:|--------:|
-| X1            |     -1.025 |        0.115 |    -8.930 |      0.000 | -1.259 |  -0.790 |
----
-
-
-
-

Call for Contributions

-

Thanks for showing interest in contributing to pyfixest! We appreciate all contributions and constructive feedback, whether that be reporting bugs, requesting new features, or suggesting improvements to documentation.

-

If you’d like to get involved, but are not yet sure how, please feel free to send us an email. Some familiarity with either Python or econometrics will help, but you really don’t need to be a numpy core developer or have published in Econometrica =) We’d be more than happy to invest time to help you get started!

-
-
-

Contributors ✨

-

Thanks goes to these wonderful people:

- - - - - - - - - - - - - - - -
-styfenschaer
styfenschaer
💻 -		 -Niall Keleher
Niall Keleher
🚇 💻 -		 -Wenzhi Ding
Wenzhi Ding
💻 -		 -Apoorva Lal
Apoorva Lal
💻 🐛 -		 -Juan Orduz
Juan Orduz
🚇 💻 -		 -Alexander Fischer
Alexander Fischer
💻 🚇 -		 -aeturrell
aeturrell
✅ 📖 📣 -
- - - -

This project follows the all-contributors specification. Contributions of any kind welcome!

- - -
-
- -
- -
- - - - - From 24e30470790ecc178915b3ce8aeb65e3b515b22c Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Fri, 27 Sep 2024 21:07:21 +0200 Subject: [PATCH 101/102] Update contributing.md --- docs/contributing.qmd | 74 ++++++++++++++++++------------------------- 1 file changed, 30 insertions(+), 44 deletions(-) diff --git a/docs/contributing.qmd b/docs/contributing.qmd index 2dea6938..5c9ae52a 100644 --- a/docs/contributing.qmd +++ b/docs/contributing.qmd @@ -30,66 +30,68 @@ Please describe the behavior you want and why, and provide examples of how pyfix ### Setting up your local environment -Start by forking the pyfixest GitHub repository, then clone your forked repository -using `git`: +Would you like to contribute to pyfixest, or run some of the unit tests locally? Awesome! +Here's how you can get started: + +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 on `pyfixest`, you will need Python and R installed. If working -on documentation, you will need Quarto installed. Note that you only need -a local R installation if you want to run unit tests locally. - -For suggestions on how to install R and Python, see the sections below. +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. +For guidance on installing R and Python, check out the sections below. ### Package Management via `pixi` + `PyFixest` is using [pixi](https://pixi.sh/latest/). -Please follow the [installation instructions](https://pixi.sh/latest/#installation) from the `pixi` documentation. +Just follow the [installation instructions](https://pixi.sh/latest/#installation) from the `pixi` documentation +to set up `pixi`. -Afterwards, you can initiate the project environment and install all dependencies by running +Once `pixi` is installed, initialize the project environment and install all dependencies with: ```{.bash .code-copy} cd path-to-pyfixest pixi install ``` -If you type +After installation, activate your custom `pixi` environment for `pyfixest` by typing: + ```{.bash .code-copy} pixi shell ``` -you will see that you have activated a custom `pixi` environment for `pyfixest`. +You'll now be in the `pixi` environment and ready to go! -### Code Style +### `Pixi` tasks -We use `ruff` and `pre-commit` to ensure a consistent code style. +To help with development, we've included several handy pixi tasks. -To install the required hooks, run +To avtivate relevant pixi environments, you can type ```{.bash .code-copy} -pixi run lint +pixi shell # open the base environment +pixi shell --environment dev # open the dev environment ``` -and you're ready to go! - -### `Pixi` tasks +For most development tasks, it’s best to activate the development environment since it includes all the necessary dependencies for development. -There are several command line targets that assist with development included -as `pixi` tasks. +For example, we use `ruff` and `pre-commit` to ensure code consistency across the project. -To avtivate relevant pixi environments, you can type +To install the required hooks, simply run ```{.bash .code-copy} -pixi shell # open the base environment -pixi shell --environment dev # open the dev environment +pixi run lint ``` -For development, it is recommended to activate the dev environment (as it includes all development dependencies). +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} # install all R development dependencies @@ -98,9 +100,11 @@ pixi run install-r pixi run tests # run all tests excluding very computationally demanding tests pixi run tests-regular +# rerun failed tests +pixi run tests-rerun ``` -To rebuild the documentation locally, you can run +Building the documentation is also straightforward. We’ve got tasks to build, render, and preview the docs: ```{.bash .code-copy} # Build documentation and website @@ -111,25 +115,7 @@ pixi run docs-render pixi run docs-preview ``` -Note that you need to have `quarto` installed in order to build the documentation locally. - -To run the linter, you can run - -```{.bash .code-copy} -pixi run lint -``` - -To build the package for PyPi, you can run - -```{.bash .code-copy} -pixi run build-pip -``` - -To re-create the csv files in `tests/data` that contain results from R packages for testing, you can run - -```{.bash .code-copy} -`pixi run update-tests-data` -``` +Keep in mind that you’ll need quarto installed to build the documentation locally. ## Installing Python, R and Quarto From 452010bbb869724debe600202605a03c84e7acb6 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Fri, 27 Sep 2024 21:12:45 +0200 Subject: [PATCH 102/102] support mac --- pixi.lock | 5375 ++++++++++++++++++++++++++++++++++++++++++++++-- pyproject.toml | 2 +- 2 files changed, 5257 insertions(+), 120 deletions(-) diff --git a/pixi.lock b/pixi.lock index be0da573..59f92755 100644 --- a/pixi.lock +++ b/pixi.lock @@ -72,6 +72,120 @@ environments: - 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