From fee630655344a4ed4b1385baf0996cdb3a355184 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sat, 8 Mar 2025 14:17:02 +0100 Subject: [PATCH 1/8] first attempt at minimal env for core functionality --- README.md | 9 +- pixi.lock | 824 +++++++++++++++-------- pyfixest/estimation/decomposition.py | 27 +- pyfixest/estimation/feols_compressed_.py | 10 +- pyfixest/estimation/ritest.py | 10 +- pyfixest/report/summarize.py | 16 +- pyproject.toml | 25 +- scripts/run_notebooks.py | 9 +- 8 files changed, 629 insertions(+), 301 deletions(-) diff --git a/README.md b/README.md index a1e7cd8e7..128a2f4b8 100644 --- a/README.md +++ b/README.md @@ -57,7 +57,14 @@ You can install the release version from `PyPI` by running python -m pip install pyfixest ``` -or the development version from github by running +The above will install a bare-bone version of pyfixest that will allow you to fit models but lacks post-processing functionality and +estimation extensions. We recommend to install all dependencies by running + +```py +python -m pip install pyfixest[full] +``` + +You can install the development version from github by running ```py python -m pip install git+https://github.com/py-econometrics/pyfixest diff --git a/pixi.lock b/pixi.lock index 02acb2ab3..dc9041fcc 100644 --- a/pixi.lock +++ b/pixi.lock @@ -37,19 +37,11 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/tomli-2.2.1-pyhd8ed1ab_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2025a-h78e105d_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/zipp-3.21.0-pyhd8ed1ab_1.conda - - pypi: https://files.pythonhosted.org/packages/ed/20/bc79bc575ba2e2a7f70e8a1155618bb1301eaa5132a8271373a6903f73f8/babel-2.16.0-py3-none-any.whl - - pypi: https://files.pythonhosted.org/packages/b1/92/dfd892312d822f36c55366118b95d914e5f16de11044a27cf10a7d71bbbf/commonmark-0.9.1-py2.py3-none-any.whl - pypi: https://files.pythonhosted.org/packages/ba/99/6794142b90b853a9155316c8f470d2e4821fe6f086b03e372aca848227dd/contourpy-1.3.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl - 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_bootstrapped = Parallel(n_jobs=self.nthreads)( - delayed(self._bootstrap)(rng=rng) for _ in tqdm(range(B)) - ) + if joblib_available: + _bootstrapped = Parallel(n_jobs=self.nthreads)( + delayed(self._bootstrap)(rng=rng) for _ in tqdm(range(B)) + ) + else: + _bootstrapped = [self._bootstrap(rng=rng) for _ in tqdm(range(B))] self._bootstrapped = { key: np.concatenate([d[key] for d in _bootstrapped]) diff --git a/pyfixest/estimation/feols_compressed_.py b/pyfixest/estimation/feols_compressed_.py index be453386d..f29219783 100644 --- a/pyfixest/estimation/feols_compressed_.py +++ b/pyfixest/estimation/feols_compressed_.py @@ -6,7 +6,15 @@ import narwhals as nw import numpy as np import pandas as pd -from tqdm import tqdm + +try: + from tqdm import tqdm +except ImportError: + + def tqdm(iterable, *args, **kwargs): + "Define a dummy tqdm function." + return iterable + from pyfixest.estimation.feols_ import Feols, PredictionErrorOptions, PredictionType from pyfixest.estimation.FormulaParser import FixestFormula diff --git a/pyfixest/estimation/ritest.py b/pyfixest/estimation/ritest.py index d1d1365e6..4891711ac 100644 --- a/pyfixest/estimation/ritest.py +++ b/pyfixest/estimation/ritest.py @@ -26,7 +26,15 @@ _HAS_LETS_PLOT = False from scipy.stats import norm -from tqdm import tqdm + +try: + from tqdm import tqdm +except ImportError: + + def tqdm(iterable, *args, **kwargs): + """Define a dummy tqdm function.""" + return iterable + from pyfixest.estimation.demean_ import demean diff --git a/pyfixest/report/summarize.py b/pyfixest/report/summarize.py index 354b98768..669bda63b 100644 --- a/pyfixest/report/summarize.py +++ b/pyfixest/report/summarize.py @@ -6,8 +6,6 @@ import numpy as np import pandas as pd -from great_tables import GT -from tabulate import tabulate from pyfixest.estimation.feiv_ import Feiv from pyfixest.estimation.feols_ import Feols @@ -156,6 +154,8 @@ def etable( pf.etable([fit1, fit2]) ``` """ + # check if etable installed else error + if signif_code is None: signif_code = [0.001, 0.01, 0.05] assert isinstance(signif_code, list) and len(signif_code) == 3, ( @@ -683,6 +683,11 @@ def _tabulate_etable_md(df, n_coef, n_fixef, n_models, n_model_stats): ------- - formatted_table (str): The formatted table as a string. """ + try: + from tabulate import tabulate + except ImportError: + raise ImportError("The tabulate package is required but it is not installed.") + # Format the DataFrame for tabulate table = tabulate( df, @@ -1064,6 +1069,13 @@ def make_table( rowname_col = dfs.columns[0] groupname_col = None + try: + from great_tables import GT + except ImportError: + raise ImportError( + "The great_tables package is for running pf.etable() in 'gt' mode." + ) + # Generate the table with GT gt = GT(dfs, auto_align=False) diff --git a/pyproject.toml b/pyproject.toml index b75876ac5..aad240c1b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -15,19 +15,23 @@ dependencies = [ "formulaic>=1.1.0", "pandas>=1.1.0", "numba>=0.58.0", - "seaborn>=0.13.2", - "tabulate>=0.9.0", - "tqdm>=4.0.0", - "great-tables>=0.10.0", "numpy>=1.19.0", "narwhals>=1.13.3", - "joblib>=1.4.2,<2", + "seaborn>=0.13.2", ] [tool.pixi.feature.dev.dependencies] rpy2 = ">=3.5.11,<4" [project.optional-dependencies] + +full = [ + "joblib>=1.4.2,<2", + "tabulate>=0.9.0", + "tqdm>=4.0.0", + "great-tables>=0.10.0", +] + dev = [ "pytest>=7.2.0", "pytest-cov>=4.1.0", @@ -84,11 +88,12 @@ pyfixest = { path = ".", editable = true } [tool.pixi.environments] default = { solve-group = "default" } -dev = { features = ["dev"], solve-group = "default" } -docs = { features = ["docs"], solve-group = "default" } -build = { features = ["build"], solve-group = "default" } -jax = { features = ["jax"], solve-group = "default" } -plots = { features = ["plots"], solve-group = "default" } +full = {features = ["full"], solve-group = "default"} +dev = { features = ["dev"], solve-group = "full" } +docs = { features = ["docs"], solve-group = "full" } +build = { features = ["build"], solve-group = "full" } +jax = { features = ["jax"], solve-group = "full" } +plots = { features = ["plots"], solve-group = "full" } [tool.pixi.feature.dev.tasks] tests = "pytest -n 4 --cov-report=term tests" diff --git a/scripts/run_notebooks.py b/scripts/run_notebooks.py index 5fde39732..83a277f1e 100644 --- a/scripts/run_notebooks.py +++ b/scripts/run_notebooks.py @@ -8,7 +8,14 @@ import papermill from joblib import Parallel, delayed -from tqdm import tqdm + +try: + from tqdm import tqdm +except ImportError: + + def tqdm(iterable, *args, **kwargs): + return iterable + KERNEL_NAME: str = "python3" DOCS = Path("docs") From 2fcd4f2616a63955127f95f2e1b9ce73389093d9 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Sun, 9 Mar 2025 10:30:29 +0100 Subject: [PATCH 2/8] default env has richer dependency set --- README.md | 6 +- pixi.lock | 425 ++++++++++++++++++++++++++++++++++++++----------- pyproject.toml | 16 +- 3 files changed, 338 insertions(+), 109 deletions(-) diff --git a/README.md b/README.md index 128a2f4b8..bd1bf6cd1 100644 --- a/README.md +++ b/README.md @@ -56,12 +56,10 @@ You can install the release version from `PyPI` by running # inside an active virtual environment python -m pip install pyfixest ``` - -The above will install a bare-bone version of pyfixest that will allow you to fit models but lacks post-processing functionality and -estimation extensions. We recommend to install all dependencies by running +To install a version with only core functionality and a reduced dependency set, you can run ```py -python -m pip install pyfixest[full] +python -m pip install pyfixest[minimal] ``` You can install the development version from github by running diff --git a/pixi.lock b/pixi.lock index dc9041fcc..85893096c 100644 --- a/pixi.lock +++ b/pixi.lock @@ -222,15 +222,24 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda - conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2025a-h78e105d_0.conda + - pypi: https://files.pythonhosted.org/packages/b7/b8/3fe70c75fe32afc4bb507f75563d39bc5642255d1d94f1f23604725780bf/babel-2.17.0-py3-none-any.whl + - pypi: https://files.pythonhosted.org/packages/b1/92/dfd892312d822f36c55366118b95d914e5f16de11044a27cf10a7d71bbbf/commonmark-0.9.1-py2.py3-none-any.whl - 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pypi: . name: pyfixest version: 0.28.0 - sha256: b1f042ae4fa0df24dc6c6a18e17e452104b33992f01d445a2cf6a6e43f74b66c + sha256: e826860fd8bdc3ae7dda69ff9438a33f10e72f85f7a256409b8f068b4fe97246 requires_dist: - scipy>=1.6 - formulaic>=1.1.0 @@ -9343,7 +9319,7 @@ packages: - numba>=0.58.0 - numpy>=1.19.0 - narwhals>=1.13.3 - - seaborn>=0.13.2 + - matplotlib>=3.4 - joblib>=1.4.2,<2 ; extra == 'core' - tabulate>=0.9.0 ; extra == 'core' - tqdm>=4.0.0 ; extra == 'core' @@ -9361,6 +9337,7 @@ packages: - pyarrow>=14.0 ; extra == 'dev' - jax>=0.4.15 ; extra == 'dev' - jaxlib>=0.4.15 ; extra == 'dev' + - seaborn>=0.13.2 ; extra == 'dev' - lets-plot>=4.0.0 ; extra == 'plots' - quartodoc>=0.7.2 ; extra == 'docs' - jupyterlab>=4.0.12 ; extra == 'docs' diff --git a/pyfixest/estimation/ritest.py b/pyfixest/estimation/ritest.py index 4891711ac..8b3f79edc 100644 --- a/pyfixest/estimation/ritest.py +++ b/pyfixest/estimation/ritest.py @@ -5,7 +5,7 @@ import numba as nb import numpy as np import pandas as pd -import seaborn as sns +from scipy.stats import gaussian_kde # Make lets-plot an optional dependency try: @@ -27,17 +27,17 @@ from scipy.stats import norm +from pyfixest.estimation.demean_ import demean + try: from tqdm import tqdm except ImportError: def tqdm(iterable, *args, **kwargs): - """Define a dummy tqdm function.""" + "Define a dummy tqdm function." return iterable -from pyfixest.estimation.demean_ import demean - # Only setup lets-plot if it's available if _HAS_LETS_PLOT: LetsPlot.setup_html() @@ -390,10 +390,23 @@ def _plot_ritest_pvalue( x_lab = "Test statistic" y_lab = "Density" + def _plot_matplotlib(values: np.ndarray, sample_stat: np.ndarray) -> None: + kde = gaussian_kde(values) + x_range = np.linspace(min(values), max(values), 1000) + y_range = kde(x_range) + + plt.figure(figsize=(10, 6)) + plt.fill_between(x_range, y_range, color="blue", alpha=0.5) + plt.axvline(x=sample_stat, color="red", linestyle="--") + plt.title(title) + plt.xlabel(x_lab) + plt.ylabel(y_lab) + plt.show() + if plot_backend == "lets_plot": if not _HAS_LETS_PLOT: print("lets-plot is not installed. Falling back to matplotlib.") - plot_backend = "matplotlib" + return _plot_matplotlib(df["ri_stats"].to_numpy(), sample_stat) else: plot = ( ggplot(df, aes(x="ri_stats")) @@ -405,16 +418,10 @@ def _plot_ritest_pvalue( + ylab(y_lab) ) - return plot.show() + return plot.show() elif plot_backend == "matplotlib": - plt.figure(figsize=(10, 6)) - sns.kdeplot(data=df, x="ri_stats", fill=True, color="blue", alpha=0.5) - plt.axvline(x=sample_stat, color="red", linestyle="--") - plt.title(title) - plt.xlabel(x_lab) - plt.ylabel(y_lab) - plt.show() + return _plot_matplotlib(df["ri_stats"].to_numpy(), sample_stat) else: raise ValueError(f"Unsupported plot backend: {plot_backend}") diff --git a/pyproject.toml b/pyproject.toml index ff782a47d..9089c7355 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -17,7 +17,7 @@ dependencies = [ "numba>=0.58.0", "numpy>=1.19.0", "narwhals>=1.13.3", - "seaborn>=0.13.2", + "matplotlib>=3.4", ] [tool.pixi.feature.dev.dependencies] @@ -46,6 +46,7 @@ dev = [ "pyarrow>=14.0", "jax>=0.4.15", "jaxlib>=0.4.15", + "seaborn>=0.13.2", ] plots = [ From e6db76d8cd27cd4338d68eb9aa034e0309725d12 Mon Sep 17 00:00:00 2001 From: Alexander Fischer Date: Mon, 17 Mar 2025 21:44:08 +0100 Subject: [PATCH 7/8] add tests for minimal env --- .github/workflows/ci-tests.yaml | 1 + pixi.lock | 5014 ++++++++++--------------------- pyproject.toml | 19 +- 3 files changed, 1529 insertions(+), 3505 deletions(-) diff --git a/.github/workflows/ci-tests.yaml b/.github/workflows/ci-tests.yaml index 011e196b7..3b1338b21 100644 --- a/.github/workflows/ci-tests.yaml +++ b/.github/workflows/ci-tests.yaml @@ -99,6 +99,7 @@ jobs: - name: Run tests against r run: | pixi run tests-against-r + pixi run tests-fixest-minimal - name: Upload coverage to Codecov (partial) uses: codecov/codecov-action@v4 diff --git a/pixi.lock b/pixi.lock index eb7a88b8e..e5d94aef6 100644 --- a/pixi.lock +++ b/pixi.lock @@ -1112,155 +1112,36 @@ environments: linux-64: - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2 - - conda: https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2 - - conda: https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.43-h4bf12b8_2.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/bwidget-1.10.1-ha770c72_0.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/c-ares-1.34.4-hb9d3cd8_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.12.14-hbcca054_0.conda - 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Progress bars are disabled. Note that tqdm is included in the pyfixest default environment." + ) def tqdm(iterable, *args, **kwargs): "Define a dummy tqdm function." @@ -22,6 +26,9 @@ def tqdm(iterable, *args, **kwargs): joblib_available = True except ImportError: joblib_available = False + warnings.warn( + "The joblib package is not installed. Parallel processing is disabled. Note that joblib is included in the pyfixest default environment." + ) @dataclass diff --git a/pyfixest/estimation/feols_compressed_.py b/pyfixest/estimation/feols_compressed_.py index f29219783..fc5f2b5f0 100644 --- a/pyfixest/estimation/feols_compressed_.py +++ b/pyfixest/estimation/feols_compressed_.py @@ -1,4 +1,5 @@ import logging +import warnings from collections.abc import Mapping from dataclasses import dataclass from typing import Any, Literal, Optional, Union @@ -10,6 +11,9 @@ try: from tqdm import tqdm except ImportError: + warnings.warn( + "The tqdm package is not installed. Progress bars are disabled. Note that tqdm is included in the pyfixest default environment." + ) def tqdm(iterable, *args, **kwargs): "Define a dummy tqdm function." diff --git a/pyfixest/estimation/ritest.py b/pyfixest/estimation/ritest.py index 8b3f79edc..56cfc897a 100644 --- a/pyfixest/estimation/ritest.py +++ b/pyfixest/estimation/ritest.py @@ -25,6 +25,8 @@ except ImportError: _HAS_LETS_PLOT = False +import warnings + from scipy.stats import norm from pyfixest.estimation.demean_ import demean @@ -32,6 +34,9 @@ try: from tqdm import tqdm except ImportError: + warnings.warn( + "The tqdm package is not installed. Progress bars are disabled. Note that tqdm is included in the pyfixest default environment." + ) def tqdm(iterable, *args, **kwargs): "Define a dummy tqdm function." diff --git a/scripts/run_notebooks.py b/scripts/run_notebooks.py index 83a277f1e..a6a903b6e 100644 --- a/scripts/run_notebooks.py +++ b/scripts/run_notebooks.py @@ -4,6 +4,7 @@ """ import logging +import warnings from pathlib import Path import papermill @@ -12,8 +13,12 @@ try: from tqdm import tqdm except ImportError: + warnings.warn( + "The tqdm package is not installed. Progress bars are disabled. Note that tqdm is included in the pyfixest default environment." + ) def tqdm(iterable, *args, **kwargs): + "Define a dummy tqdm function." return iterable