Release v0.6.0

.github/workflows/coverage.yml

@@ -31,8 +31,8 @@ jobs:
           pytest --cov --cov-report=xml --verbose
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
-          file: ./coverage.xml
+          files: ./coverage.xml
           fail_ci_if_error: true

.github/workflows/deploy_doc.yml

@@ -0,0 +1,48 @@
+name: Deploy Documentation to GitHub Pages
+
+on:
+  push:
+    branches: [main]
+  workflow_dispatch:
+
+# Cancel any in-progress job or run
+# https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#concurrency
+concurrency:
+  group: ${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  deploy-to-gh-pages:
+    runs-on: ubuntu-latest
+    environment:
+      name: documentation-github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    permissions:
+      pages: write
+      id-token: write
+    env:
+      FORCE_COLOR: true
+      UV_SYSTEM_PYTHON: 1
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+    - name: Setup Python
+      uses: actions/setup-python@v6
+      with:
+        python-version-file: "pyproject.toml"
+    - name: Set up uv
+      uses: astral-sh/setup-uv@v7
+    - name: Install dependencies
+      run: |
+        uv pip install --group=docs --editable .
+    - name: Build documentation
+      run: |
+        make -C docs clean
+        make -C docs html
+    - name: Upload artifact
+      uses: actions/upload-pages-artifact@v3
+      with:
+        path: 'docs/build/html'
+    - id: deployment
+      name: Deploy to GitHub Pages
+      uses: actions/deploy-pages@v4

.github/workflows/doc.yml

@@ -1,4 +1,4 @@
-name: Documentation
+name: Build documentation and upload as artifact to GitHub Actions
 on:
   push:
     branches: [main]

README.rst

@@ -11,7 +11,7 @@
 .. image:: https://img.shields.io/github/license/raphaelvallat/pingouin.svg
   :target: https://github.com/raphaelvallat/pingouin/blob/master/LICENSE
 
-.. image:: https://github.com/raphaelvallat/pingouin/actions/workflows/python_tests.yml/badge.svg
+.. image:: https://github.com/raphaelvallat/pingouin/actions/workflows/pytest.yml/badge.svg
   :target: https://github.com/raphaelvallat/pingouin/actions
 
 .. image:: https://codecov.io/gh/raphaelvallat/pingouin/branch/master/graph/badge.svg

docs/changelog.rst

@@ -3,6 +3,49 @@
 What's new
 ##########
 
+v0.6.0 (February 2026)
+----------------------
+
+This is a major release with several bugfixes and breaking changes, as well as critical updates to the build infrastructure, dependencies and test suite (see `PR489 <https://github.com/raphaelvallat/pingouin/pull/489>`_)
+
+Some of the key highlights are described below:
+
+**Bugfixes**
+
+- Disable one-sided Bayes Factor for T-tests, which were ill-defined (`PR487 <https://github.com/raphaelvallat/pingouin/pull/487>`_)
+- Update RBC calculation for Wilcoxon signed-rank test to be dependent on the alternative (`PR457 <https://github.com/raphaelvallat/pingouin/pull/457>`_)
+- Sphericity fix with very low eigenvalues (`PR482 <https://github.com/raphaelvallat/pingouin/pull/482>`_)
+- Fix divide-by-zero in internal ``_correl_pvalue`` when ``r == 1`` (`PR474 <https://github.com/raphaelvallat/pingouin/pull/474>`_
+- Fix boxplot z-order in :py:func:`pingouin.plot_paired` (`PR442 <https://github.com/raphaelvallat/pingouin/pull/442>`_)
+
+**API breaking changes**
+
+- Column names update (`PR443 <https://github.com/raphaelvallat/pingouin/pull/443>`_): removed characters that restrict column access to the bracket format (df["p_val"]) rather than dot method (df.p_val). This includes:
+
+    - Replaced dashes with underscores in column names (e.g., p-val --> p_val)
+    - Replaced parentheses with underscores in column names (e.g., mean(A) --> mean_A)
+    - Removed percent signs and brackets in column names (e.g., CI95% --> CI95, CI[97.5%] --> CI97.5)
+
+**Dependency requirements**
+
+This is the first version to be fully compatible with pandas 3.x and numpy 2.x (`PR480 <https://github.com/raphaelvallat/pingouin/pull/480>`_).
+
+This version requires Python >= 3.10 (tested on Python 3.10-3.14) and:
+
+* `NumPy <https://numpy.org/>`_ >= 1.22.4
+* `SciPy <https://www.scipy.org/>`_ >= 1.8.0
+* `Pandas <https://pandas.pydata.org/>`_ >= 2.1.1
+* `Statsmodels <https://www.statsmodels.org/>`_ >= 0.14.1
+* `Scikit-learn <https://scikit-learn.org/>`_ >= 1.2.2
+
+**Build infrastructure**
+
+- Replaced `black <https://black.readthedocs.io/>`_ and `flake8 <https://flake8.pycqa.org/>`_ with `Ruff <https://github.com/astral-sh/ruff>`_ for unified linting and formatting (`PR446 <https://github.com/raphaelvallat/pingouin/pull/446>`_)
+- Adopted `uv <https://docs.astral.sh/uv/>`_ for faster dependency management in CI
+- Extended CI matrix to Ubuntu, macOS and Windows across Python 3.10, 3.12 and 3.14, plus a separate matrix testing minimum through latest dependency versions (`PR489 <https://github.com/raphaelvallat/pingouin/pull/489>`_)
+
+The full changelog can be found on GitHub: https://github.com/raphaelvallat/pingouin/releases/tag/v0.6.0
+
 v0.5.5 (September 2024)
 -----------------------
 

docs/conf.py

@@ -177,6 +177,21 @@ def linkcode_resolve(domain, info):
     )
 
 
+# -- 404 page  ------------------------------------------------
+
+# Remove default url prefix on 404 pages
+# https://sphinx-notfound-page.readthedocs.io/en/latest/configuration.html#confval-notfound_urls_prefix
+notfound_urls_prefix = None
+
+notfound_context = {
+    "title": "Page Not Found (404)",
+    "body": """
+        <h1>Page Not Found</h1>
+        <p>Sorry, we couldn't find that page.</p>
+        <p>Try using the search box or go to the homepage.</p>
+        """,
+}
+
 # -- Intersphinx ------------------------------------------------
 
 intersphinx_mapping = {

docs/index.rst

@@ -9,7 +9,7 @@
 .. image:: https://img.shields.io/github/license/raphaelvallat/pingouin.svg
   :target: https://github.com/raphaelvallat/pingouin/blob/master/LICENSE
 
-.. image:: https://github.com/raphaelvallat/pingouin/actions/workflows/python_tests.yml/badge.svg
+.. image:: https://github.com/raphaelvallat/pingouin/actions/workflows/pytest.yml/badge.svg
   :target: https://github.com/raphaelvallat/pingouin/actions
 
 .. image:: https://codecov.io/gh/raphaelvallat/pingouin/branch/master/graph/badge.svg

notebooks/02_BayesianTTests.ipynb

@@ -23,6 +23,7 @@
    "outputs": [],
    "source": [
     "import numpy as np\n",
+    "\n",
     "np.random.seed(123)\n",
     "nx, ny = 30, 30\n",
     "drug = np.random.normal(loc=1, size=nx)\n",
@@ -68,8 +69,8 @@
        "      <th>p_val</th>\n",
        "      <th>CI95</th>\n",
        "      <th>cohen_d</th>\n",
-       "      <th>BF10</th>\n",
        "      <th>power</th>\n",
+       "      <th>BF10</th>\n",
        "    </tr>\n",
        "  </thead>\n",
        "  <tbody>\n",
@@ -81,19 +82,19 @@
        "      <td>0.0054</td>\n",
        "      <td>[0.28, 1.53]</td>\n",
        "      <td>0.746384</td>\n",
-       "      <td>7.71</td>\n",
        "      <td>0.811273</td>\n",
+       "      <td>7.71</td>\n",
        "    </tr>\n",
        "  </tbody>\n",
        "</table>\n",
        "</div>"
       ],
       "text/plain": [
-       "               T  dof alternative   p_val          CI95   cohen_d  BF10  \\\n",
-       "T_test  2.890732   58   two-sided  0.0054  [0.28, 1.53]  0.746384  7.71   \n",
+       "               T  dof alternative   p_val          CI95   cohen_d     power  \\\n",
+       "T_test  2.890732   58   two-sided  0.0054  [0.28, 1.53]  0.746384  0.811273   \n",
        "\n",
-       "           power  \n",
-       "T_test  0.811273  "
+       "        BF10  \n",
+       "T_test  7.71  "
       ]
      },
      "execution_count": 2,
@@ -103,6 +104,7 @@
    ],
    "source": [
     "from pingouin import ttest\n",
+    "\n",
     "ttest(drug, placebo)"
    ]
   },
@@ -129,7 +131,7 @@
     }
    ],
    "source": [
-    "print('BF01 = %.2f' % (1 / 7.71))"
+    "print(\"BF01 = %.2f\" % (1 / 7.71))"
    ]
   },
   {