Fix pandas warning

.github/workflows/python_tests.yml

@@ -12,7 +12,7 @@ jobs:
       fail-fast: false
       matrix:
         platform: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: [3.7, 3.8, 3.9]
+        python-version: [3.7, 3.8, 3.9, 3.10.8]
 
     runs-on: ${{ matrix.platform }}
 
@@ -39,21 +39,21 @@ jobs:
         pytest --cov --cov-report=xml --cov-config=setup.cfg --verbose
 
     - name: Build docs
-      if: ${{ matrix.platform == 'ubuntu-latest' && matrix.python-version == 3.8 }}
+      if: ${{ matrix.platform == 'ubuntu-latest' && matrix.python-version == 3.9 }}
       run: |
         pip install --upgrade sphinx sphinx_bootstrap_theme numpydoc sphinx-copybutton sphinx-panels
         make -C docs clean
         make -C docs html
 
     - name: Upload doc build artifacts
-      if: ${{ matrix.platform == 'ubuntu-latest' && matrix.python-version == 3.8 }}
+      if: ${{ matrix.platform == 'ubuntu-latest' && matrix.python-version == 3.9 }}
       uses: actions/upload-artifact@v1
       with:
         name: docs-artifact
         path: docs/build/html
 
     - name: Upload coverage report
-      if: ${{ matrix.platform == 'ubuntu-latest' && matrix.python-version == 3.8 }}
+      if: ${{ matrix.platform == 'ubuntu-latest' && matrix.python-version == 3.9 }}
       uses: codecov/codecov-action@v1
       with:
         token: c6ed6ca6-a040-4f23-9ebf-8c474c998097

README.rst

@@ -92,7 +92,7 @@ In addition, some functions require :
 * `Scikit-learn <https://scikit-learn.org/>`_
 * `Mpmath <http://mpmath.org/>`_
 
-Pingouin is a Python 3 package and is currently tested for Python 3.7-3.9. It does not support Python 2.
+Pingouin is a Python 3 package and is currently tested for Python 3.7-3.10. It does not support Python 2.
 
 User installation
 -----------------

docs/index.rst

@@ -63,7 +63,7 @@ the :code:`ttest` function of Pingouin returns the T-value, the p-value, the deg
 Installation
 ============
 
-Pingouin is a Python 3 package and is currently tested for Python 3.7-3.9. It does not support Python 2.
+Pingouin is a Python 3 package and is currently tested for Python 3.7-3.10. It does not support Python 2.
 
 The main dependencies of Pingouin are :
 

pingouin/distribution.py

@@ -494,7 +494,11 @@ def _check_multilevel_rm(data, func="epsilon"):
             # We end up with a one-way design. It is similar to applying
             # a paired T-test to gain scores instead of using repeated measures
             # on two time points. Here we have computed the gain scores.
-            data = data.groupby(level=1, axis=1, observed=True).diff(axis=1).dropna(axis=1)
+            data = (
+                data.groupby(level=1, axis=1, observed=True, group_keys=False)
+                .diff(axis=1)
+                .dropna(axis=1)
+            )
             data = data.droplevel(level=0, axis=1)
         else:
             # Both factors have more than 2 levels -- differ from R / JASP

pingouin/parametric.py

@@ -545,7 +545,7 @@ def rm_anova(
     # Groupby
     # I think that observed=True is actually not needed here since we have already used
     # `observed=True` in pivot_table.
-    grp_with = data.groupby(within, observed=True)[dv]
+    grp_with = data.groupby(within, observed=True, group_keys=False)[dv]
     rm = list(data[within].unique())
     n_rm = len(rm)
     n_obs = int(grp_with.count().max())
@@ -989,12 +989,12 @@ def anova(data=None, dv=None, between=None, ss_type=2, detailed=False, effsize="
     N = data[dv].size
 
     # Calculate sums of squares
-    grp = data.groupby(between, observed=True)[dv]
+    grp = data.groupby(between, observed=True, group_keys=False)[dv]
     # Between effect
     ssbetween = ((grp.mean() - data[dv].mean()) ** 2 * grp.count()).sum()
     # Within effect (= error between)
     #  = (grp.var(ddof=0) * grp.count()).sum()
-    sserror = grp.apply(lambda x: (x - x.mean()) ** 2).sum()
+    sserror = grp.transform(lambda x: (x - x.mean()) ** 2).sum()
     # In 1-way ANOVA, sstotal = ssbetween + sserror
     # sstotal = ssbetween + sserror
 
@@ -1062,7 +1062,7 @@ def anova2(data=None, dv=None, between=None, ss_type=2, effsize="np2"):
 
     # Reset index (avoid duplicate axis error)
     data = data.reset_index(drop=True)
-    grp_both = data.groupby(between, observed=True)[dv]
+    grp_both = data.groupby(between, observed=True, group_keys=False)[dv]
 
     if grp_both.count().nunique() == 1:
         # BALANCED DESIGN
@@ -1338,7 +1338,7 @@ def welch_anova(data=None, dv=None, between=None):
     ddof1 = r - 1
 
     # Compute weights and ajusted means
-    grp = data.groupby(between, observed=True)[dv]
+    grp = data.groupby(between, observed=True, group_keys=False)[dv]
     weights = grp.count() / grp.var()
     adj_grandmean = (weights * grp.mean()).sum() / weights.sum()
 
@@ -1512,7 +1512,7 @@ def mixed_anova(
     ss_betw = aov_betw.at[0, "SS"]
     ss_with = aov_with.at[0, "SS"]
     # Extract residuals and interactions
-    grp = data.groupby([between, within], observed=True)[dv]
+    grp = data.groupby([between, within], observed=True, group_keys=False)[dv]
     # ssresall = residuals within + residuals between
     ss_resall = grp.apply(lambda x: (x - x.mean()) ** 2).sum()
     # Interaction

pingouin/plotting.py

@@ -732,7 +732,6 @@ def plot_shift(
 
     .. plot::
 
-        >>> import numpy as np
         >>> import pingouin as pg
         >>> import matplotlib.pyplot as plt
         >>> data = pg.read_dataset("pairwise_corr")

pingouin/tests/test_parametric.py

@@ -591,7 +591,7 @@ def test_mixed_anova(self):
 
         # With overlapping subject IDs in the between-subject groups
         df_overlap = df.copy()
-        df_overlap["Subject"] = df_overlap.groupby(["Group"])["Subject"].apply(
+        df_overlap["Subject"] = df_overlap.groupby(["Group"], group_keys=False)["Subject"].apply(
             lambda x: x - x.min()
         )
         with pytest.raises(ValueError):

setup.cfg

@@ -5,13 +5,16 @@ test=pytest
 addopts =
   --showlocals
   --durations=10
+  --maxfail=2
   --cov
 # --doctest-modules --doctest-continue-on-failure | do not work with travis
 doctest_optionflags= NORMALIZE_WHITESPACE IGNORE_EXCEPTION_DETAIL
 markers =
     slow: mark a test as slow.
 filterwarnings =
     ignore::UserWarning
+    ignore::RuntimeWarning
+    ignore::FutureWarning
 
 [flake8]
 # W605 : bug when math equation in numpydoc

setup.py

@@ -44,6 +44,7 @@ def read(fname):
     "Programming Language :: Python :: 3.7",
     "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
     "Topic :: Scientific/Engineering :: Mathematics",
     "Operating System :: POSIX",
     "Operating System :: Unix",