raphaelvallat · raphaelvallat · Feb 25, 2024 · Feb 16, 2024 · Feb 22, 2024
diff --git a/.github/workflows/python_tests.yml b/.github/workflows/python_tests.yml
@@ -30,13 +30,11 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -r requirements.txt
-        pip install -r requirements-test.txt
-        pip install .
+        pip install .[test]
 
     - name: Test with pytest
       run: |
-        pytest --cov --cov-report=xml --cov-config=setup.cfg --verbose
+        pytest --cov --cov-report=xml --verbose
 
     - name: Build docs
       if: ${{ matrix.platform == 'ubuntu-latest' && matrix.python-version == 3.9 }}

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,36 +1,6 @@
 # Add README, LICENSE and requirements :
 include README.rst
 include LICENSE
-include requirements.txt
 
 # Add datasets .csv files
-include pingouin/datasets/ancova.csv
-include pingouin/datasets/anova.csv
-include pingouin/datasets/anova2.csv
-include pingouin/datasets/anova2_unbalanced.csv
-include pingouin/datasets/anova3.csv
-include pingouin/datasets/anova3_unbalanced.csv
-include pingouin/datasets/blandaltman.csv
-include pingouin/datasets/chi2_independence.csv
-include pingouin/datasets/chi2_mcnemar.csv
-include pingouin/datasets/circular.csv
-include pingouin/datasets/cochran.csv
-include pingouin/datasets/cronbach_alpha.csv
-include pingouin/datasets/cronbach_wide_missing.csv
-include pingouin/datasets/datasets.csv
-include pingouin/datasets/icc.csv
-include pingouin/datasets/mediation.csv
-include pingouin/datasets/mixed_anova.csv
-include pingouin/datasets/mixed_anova_unbalanced.csv
-include pingouin/datasets/multivariate.csv
-include pingouin/datasets/pairwise_corr.csv
-include pingouin/datasets/pairwise_tests.csv
-include pingouin/datasets/pairwise_tests_missing.csv
-include pingouin/datasets/partial_corr.csv
-include pingouin/datasets/penguins.csv
-include pingouin/datasets/rm_anova.csv
-include pingouin/datasets/rm_anova2.csv
-include pingouin/datasets/rm_anova_wide.csv
-include pingouin/datasets/rm_corr.csv
-include pingouin/datasets/rm_missing.csv
-include pingouin/datasets/tips.csv
+recursive-include src/pingouin/datasets *.csv
diff --git a/README.rst b/README.rst
@@ -114,6 +114,19 @@ New releases are frequent so always make sure that you have the latest version:
 
   pip install --upgrade pingouin
 
+Development
+-----------
+
+To build and install from source, clone this repository or download the source archive and decompress the files
+
+.. code-block:: shell
+
+  cd pingouin
+  python -m build            # optional, build a wheel and sdist
+  pip install .              # install the package
+  pip install --editable .   # or editable install
+  pytest                     # test the package
+
 Quick start
 ============
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,4 +1,121 @@
+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "pingouin"
+description = "Pingouin: statistical package for Python"
+authors = [
+    {name = "Raphael Vallat", email = "raphaelvallat9@gmail.com"},
+]
+dependencies = [
+    "matplotlib",
+    "numpy",
+    "pandas>=1.5",
+    "pandas_flavor",
+    "scikit-learn>=1.2",
+    "scipy",
+    "seaborn",
+    "statsmodels",
+    "tabulate",
+]
+requires-python = ">=3.8"
+readme = "README.rst"
+license = {text = "GPL-3.0"}
+maintainers = [
+    {name = "Raphael Vallat", email = "raphaelvallat9@gmail.com"},
+]
+dynamic = ["version"]
+classifiers = [
+    "Intended Audience :: Science/Research",
+    "Operating System :: MacOS",
+    "Operating System :: POSIX",
+    "Operating System :: Unix",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Topic :: Scientific/Engineering :: Mathematics",
+]
+
+[project.optional-dependencies]
+test = [
+    "pytest>=6",
+    "pytest-cov",
+    "codecov",
+    "openpyxl",
+    "mpmath",
+    # Ensure coverage is new enough for `source_pkgs`.
+    "coverage[toml]>=5.3",
+]
+
+[project.urls]
+Homepage = "https://pingouin-stats.org/index.html"
+Downloads = "https://github.com/raphaelvallat/pingouin/"
+
+[tool.setuptools]
+py-modules = ["pingouin"]
+include-package-data = true
+
+[tool.setuptools.package-data]
+pingouin = [
+    "datasets/*.csv",
+]
+
+[tool.setuptools.packages.find]
+namespaces = false
+where = ["src"]
+
+[tool.setuptools.dynamic]
+version = {attr = "pingouin.__version__"}
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+addopts = "--showlocals --durations=10 --maxfail=2 --cov"
+doctest_optionflags= ["NORMALIZE_WHITESPACE", "IGNORE_EXCEPTION_DETAIL"]
+filterwarnings = [
+    "ignore::UserWarning",
+    "ignore::RuntimeWarning",
+    "ignore::FutureWarning",
+]
+markers = ["slow"]
+
+[tool.coverage.run]
+branch = true
+omit = [
+    "*/setup.py",
+    "*/examples/*",
+    "*/tests/*",
+    "*/datasets/*",
+]
+source_pkgs = ["pingouin"]
+
+[tool.coverage.paths]
+source = ["src"]
+
+[tool.coverage.report]
+show_missing = true
+# sort = "Cover"
+
 [tool.black]
 line-length = 100
 target-version = ['py311']
-include = '\.pyi?$'
+include = '\.pyi?$'
+
+[tool.flake8]
+# W605 : bug when math equation in numpydoc
+# W503, W504 : line-break with math operator
+# E203: E203 whitespace before ':', not compatible with Black
+# DXXX: Docstring related
+max-line-length = 100
+ignore = ["N806", "N803", "W503", "W504", "W605", "D100", "D200", "D205", "D301", "D400", "D401", "E203"]
+exclude = [
+    ".git",
+    "__pycache__",
+    "docs",
+    "build",
+    "__init__.py",
+    "examples",
+    "setup.py",
+]
+statistics = true
diff --git a/requirements-test.txt b/requirements-test.txt
diff --git a/requirements.txt b/requirements.txt
diff --git a/setup.cfg b/setup.cfg
diff --git a/setup.py b/setup.py
diff --git a/pingouin/__init__.py → src/pingouin/__init__.py b/pingouin/__init__.py → src/pingouin/__init__.py
diff --git a/pingouin/bayesian.py → src/pingouin/bayesian.py b/pingouin/bayesian.py → src/pingouin/bayesian.py
diff --git a/pingouin/circular.py → src/pingouin/circular.py b/pingouin/circular.py → src/pingouin/circular.py
diff --git a/pingouin/config.py → src/pingouin/config.py b/pingouin/config.py → src/pingouin/config.py
diff --git a/pingouin/contingency.py → src/pingouin/contingency.py b/pingouin/contingency.py → src/pingouin/contingency.py
diff --git a/pingouin/correlation.py → src/pingouin/correlation.py b/pingouin/correlation.py → src/pingouin/correlation.py
diff --git a/pingouin/datasets/__init__.py → src/pingouin/datasets/__init__.py b/pingouin/datasets/__init__.py → src/pingouin/datasets/__init__.py
diff --git a/pingouin/datasets/ancova.csv → src/pingouin/datasets/ancova.csv b/pingouin/datasets/ancova.csv → src/pingouin/datasets/ancova.csv
diff --git a/pingouin/datasets/anova.csv → src/pingouin/datasets/anova.csv b/pingouin/datasets/anova.csv → src/pingouin/datasets/anova.csv
diff --git a/pingouin/datasets/anova2.csv → src/pingouin/datasets/anova2.csv b/pingouin/datasets/anova2.csv → src/pingouin/datasets/anova2.csv
diff --git a/pingouin/datasets/anova2_unbalanced.csv → src/pingouin/datasets/anova2_unbalanced.csv b/pingouin/datasets/anova2_unbalanced.csv → src/pingouin/datasets/anova2_unbalanced.csv
diff --git a/pingouin/datasets/anova3.csv → src/pingouin/datasets/anova3.csv b/pingouin/datasets/anova3.csv → src/pingouin/datasets/anova3.csv
diff --git a/pingouin/datasets/anova3_unbalanced.csv → src/pingouin/datasets/anova3_unbalanced.csv b/pingouin/datasets/anova3_unbalanced.csv → src/pingouin/datasets/anova3_unbalanced.csv
diff --git a/pingouin/datasets/blandaltman.csv → src/pingouin/datasets/blandaltman.csv b/pingouin/datasets/blandaltman.csv → src/pingouin/datasets/blandaltman.csv
diff --git a/pingouin/datasets/chi2_independence.csv → src/pingouin/datasets/chi2_independence.csv b/pingouin/datasets/chi2_independence.csv → src/pingouin/datasets/chi2_independence.csv
diff --git a/pingouin/datasets/chi2_mcnemar.csv → src/pingouin/datasets/chi2_mcnemar.csv b/pingouin/datasets/chi2_mcnemar.csv → src/pingouin/datasets/chi2_mcnemar.csv
diff --git a/pingouin/datasets/circular.csv → src/pingouin/datasets/circular.csv b/pingouin/datasets/circular.csv → src/pingouin/datasets/circular.csv
diff --git a/pingouin/datasets/cochran.csv → src/pingouin/datasets/cochran.csv b/pingouin/datasets/cochran.csv → src/pingouin/datasets/cochran.csv
diff --git a/pingouin/datasets/cronbach_alpha.csv → src/pingouin/datasets/cronbach_alpha.csv b/pingouin/datasets/cronbach_alpha.csv → src/pingouin/datasets/cronbach_alpha.csv
diff --git a/pingouin/datasets/cronbach_wide_missing.csv → ...ngouin/datasets/cronbach_wide_missing.csv b/pingouin/datasets/cronbach_wide_missing.csv → ...ngouin/datasets/cronbach_wide_missing.csv
diff --git a/pingouin/datasets/datasets.csv → src/pingouin/datasets/datasets.csv b/pingouin/datasets/datasets.csv → src/pingouin/datasets/datasets.csv
diff --git a/pingouin/datasets/icc.csv → src/pingouin/datasets/icc.csv b/pingouin/datasets/icc.csv → src/pingouin/datasets/icc.csv
diff --git a/pingouin/datasets/mediation.csv → src/pingouin/datasets/mediation.csv b/pingouin/datasets/mediation.csv → src/pingouin/datasets/mediation.csv
diff --git a/pingouin/datasets/mixed_anova.csv → src/pingouin/datasets/mixed_anova.csv b/pingouin/datasets/mixed_anova.csv → src/pingouin/datasets/mixed_anova.csv
diff --git a/pingouin/datasets/mixed_anova_unbalanced.csv → ...gouin/datasets/mixed_anova_unbalanced.csv b/pingouin/datasets/mixed_anova_unbalanced.csv → ...gouin/datasets/mixed_anova_unbalanced.csv
diff --git a/pingouin/datasets/multivariate.csv → src/pingouin/datasets/multivariate.csv b/pingouin/datasets/multivariate.csv → src/pingouin/datasets/multivariate.csv
diff --git a/pingouin/datasets/pairwise_corr.csv → src/pingouin/datasets/pairwise_corr.csv b/pingouin/datasets/pairwise_corr.csv → src/pingouin/datasets/pairwise_corr.csv
diff --git a/pingouin/datasets/pairwise_tests.csv → src/pingouin/datasets/pairwise_tests.csv b/pingouin/datasets/pairwise_tests.csv → src/pingouin/datasets/pairwise_tests.csv
diff --git a/pingouin/datasets/pairwise_tests_missing.csv → ...gouin/datasets/pairwise_tests_missing.csv b/pingouin/datasets/pairwise_tests_missing.csv → ...gouin/datasets/pairwise_tests_missing.csv
diff --git a/pingouin/datasets/partial_corr.csv → src/pingouin/datasets/partial_corr.csv b/pingouin/datasets/partial_corr.csv → src/pingouin/datasets/partial_corr.csv
diff --git a/pingouin/datasets/penguins.csv → src/pingouin/datasets/penguins.csv b/pingouin/datasets/penguins.csv → src/pingouin/datasets/penguins.csv
diff --git a/pingouin/datasets/rm_anova.csv → src/pingouin/datasets/rm_anova.csv b/pingouin/datasets/rm_anova.csv → src/pingouin/datasets/rm_anova.csv
diff --git a/pingouin/datasets/rm_anova2.csv → src/pingouin/datasets/rm_anova2.csv b/pingouin/datasets/rm_anova2.csv → src/pingouin/datasets/rm_anova2.csv
diff --git a/pingouin/datasets/rm_anova_wide.csv → src/pingouin/datasets/rm_anova_wide.csv b/pingouin/datasets/rm_anova_wide.csv → src/pingouin/datasets/rm_anova_wide.csv
diff --git a/pingouin/datasets/rm_corr.csv → src/pingouin/datasets/rm_corr.csv b/pingouin/datasets/rm_corr.csv → src/pingouin/datasets/rm_corr.csv
diff --git a/pingouin/datasets/rm_missing.csv → src/pingouin/datasets/rm_missing.csv b/pingouin/datasets/rm_missing.csv → src/pingouin/datasets/rm_missing.csv
diff --git a/pingouin/datasets/tips.csv → src/pingouin/datasets/tips.csv b/pingouin/datasets/tips.csv → src/pingouin/datasets/tips.csv
diff --git a/pingouin/distribution.py → src/pingouin/distribution.py b/pingouin/distribution.py → src/pingouin/distribution.py
diff --git a/pingouin/effsize.py → src/pingouin/effsize.py b/pingouin/effsize.py → src/pingouin/effsize.py
diff --git a/pingouin/equivalence.py → src/pingouin/equivalence.py b/pingouin/equivalence.py → src/pingouin/equivalence.py
diff --git a/pingouin/multicomp.py → src/pingouin/multicomp.py b/pingouin/multicomp.py → src/pingouin/multicomp.py
diff --git a/pingouin/multivariate.py → src/pingouin/multivariate.py b/pingouin/multivariate.py → src/pingouin/multivariate.py
diff --git a/pingouin/nonparametric.py → src/pingouin/nonparametric.py b/pingouin/nonparametric.py → src/pingouin/nonparametric.py
diff --git a/pingouin/pairwise.py → src/pingouin/pairwise.py b/pingouin/pairwise.py → src/pingouin/pairwise.py
diff --git a/pingouin/parametric.py → src/pingouin/parametric.py b/pingouin/parametric.py → src/pingouin/parametric.py
diff --git a/pingouin/plotting.py → src/pingouin/plotting.py b/pingouin/plotting.py → src/pingouin/plotting.py
diff --git a/pingouin/power.py → src/pingouin/power.py b/pingouin/power.py → src/pingouin/power.py
diff --git a/pingouin/regression.py → src/pingouin/regression.py b/pingouin/regression.py → src/pingouin/regression.py
diff --git a/pingouin/reliability.py → src/pingouin/reliability.py b/pingouin/reliability.py → src/pingouin/reliability.py
diff --git a/pingouin/utils.py → src/pingouin/utils.py b/pingouin/utils.py → src/pingouin/utils.py
diff --git a/pingouin/tests/__init__.py → tests/__init__.py b/pingouin/tests/__init__.py → tests/__init__.py
diff --git a/pingouin/tests/test_bayesian.py → tests/test_bayesian.py b/pingouin/tests/test_bayesian.py → tests/test_bayesian.py
diff --git a/pingouin/tests/test_circular.py → tests/test_circular.py b/pingouin/tests/test_circular.py → tests/test_circular.py
diff --git a/pingouin/tests/test_config.py → tests/test_config.py b/pingouin/tests/test_config.py → tests/test_config.py
diff --git a/pingouin/tests/test_contingency.py → tests/test_contingency.py b/pingouin/tests/test_contingency.py → tests/test_contingency.py
diff --git a/pingouin/tests/test_correlation.R → tests/test_correlation.R b/pingouin/tests/test_correlation.R → tests/test_correlation.R
diff --git a/pingouin/tests/test_correlation.py → tests/test_correlation.py b/pingouin/tests/test_correlation.py → tests/test_correlation.py
diff --git a/pingouin/tests/test_distribution.py → tests/test_distribution.py b/pingouin/tests/test_distribution.py → tests/test_distribution.py
diff --git a/pingouin/tests/test_effsize.py → tests/test_effsize.py b/pingouin/tests/test_effsize.py → tests/test_effsize.py
diff --git a/pingouin/tests/test_equivalence.py → tests/test_equivalence.py b/pingouin/tests/test_equivalence.py → tests/test_equivalence.py
diff --git a/pingouin/tests/test_multicomp.py → tests/test_multicomp.py b/pingouin/tests/test_multicomp.py → tests/test_multicomp.py
diff --git a/pingouin/tests/test_multivariate.py → tests/test_multivariate.py b/pingouin/tests/test_multivariate.py → tests/test_multivariate.py
diff --git a/pingouin/tests/test_nonparametric.py → tests/test_nonparametric.py b/pingouin/tests/test_nonparametric.py → tests/test_nonparametric.py
diff --git a/pingouin/tests/test_pairwise.py → tests/test_pairwise.py b/pingouin/tests/test_pairwise.py → tests/test_pairwise.py
diff --git a/pingouin/tests/test_pandas.py → tests/test_pandas.py b/pingouin/tests/test_pandas.py → tests/test_pandas.py
diff --git a/pingouin/tests/test_parametric.py → tests/test_parametric.py b/pingouin/tests/test_parametric.py → tests/test_parametric.py
diff --git a/pingouin/tests/test_plotting.py → tests/test_plotting.py b/pingouin/tests/test_plotting.py → tests/test_plotting.py
diff --git a/pingouin/tests/test_power.py → tests/test_power.py b/pingouin/tests/test_power.py → tests/test_power.py
diff --git a/pingouin/tests/test_regression.py → tests/test_regression.py b/pingouin/tests/test_regression.py → tests/test_regression.py
diff --git a/pingouin/tests/test_reliability.py → tests/test_reliability.py b/pingouin/tests/test_reliability.py → tests/test_reliability.py
diff --git a/pingouin/tests/test_utils.py → tests/test_utils.py b/pingouin/tests/test_utils.py → tests/test_utils.py