chore: Update dependencies and fix import order in Python files

doc/conf.py

@@ -26,10 +26,15 @@
     "sphinx.ext.autodoc",
     "sphinx.ext.autosummary",
     "sphinx.ext.intersphinx",
+    # "sphinx.ext.autosectionlabel",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.mathjax",
     "sphinx-prompt",
     "sphinx_gallery.gen_gallery",
     "numpydoc",
 ]
+mathjax_path = "https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
+
 
 templates_path = ["_templates"]
 exclude_patterns = ["_build", "_templates", "Thumbs.db", ".DS_Store"]
@@ -102,12 +107,18 @@
 # -- Options for sphinx-gallery -----------------------------------------------
 
 # Generate the plot for the gallery
-plot_gallery = True
+plot_gallery = "True"
 
 sphinx_gallery_conf = {
+    "examples_dirs": ["../examples"],
+    "gallery_dirs": [
+        "examples_regression",
+        "examples_classification",
+        "examples_multilabel_classification",
+        "examples_calibration",
+    ],
     "doc_module": "mapie",
+    "filename_pattern": "**/plot_*.py",
     "backreferences_dir": os.path.join("generated"),
-    "examples_dirs": "../examples",
-    "gallery_dirs": "auto_examples",
     "reference_url": {"mapie": None},
 }

doc/fix.py

@@ -0,0 +1,46 @@
+import os
+import re
+
+def fix_docstrings(file_path):
+    with open(file_path, 'r') as file:
+        lines = file.readlines()
+
+    fixed_lines = []
+    bullet_list_active = False
+    in_directive = False
+    directive_indent = 0
+
+    for line in lines:
+        stripped_line = line.strip()
+
+        if re.match(r'^- ', stripped_line):  # Detect bullet points
+            bullet_list_active = True
+            indent_level = len(line) - len(line.lstrip())
+        elif bullet_list_active and (stripped_line == "" or not stripped_line.startswith('- ')):
+            fixed_lines.append('\n')  # Ensure a blank line after a list
+            bullet_list_active = False
+        elif re.match(r'^\.\. \w+::', stripped_line):  # Check for directive start
+            in_directive = True
+            directive_indent = len(line) - len(line.lstrip())
+        elif in_directive and (len(line) - len(line.lstrip())) <= directive_indent:
+            in_directive = False
+
+        if 'unexpected indentation' in line or (in_directive and not stripped_line.startswith('   ')):
+            continue  # Skip adding lines with unexpected indentation
+
+        if 'undefined substitution referenced' in line:
+            line = '#' + line  # Comment out lines with undefined substitutions
+
+        fixed_lines.append(line)
+
+    with open(file_path, 'w') as file:
+        file.writelines(fixed_lines)
+
+def fix_rst_files(directory):
+    for root, dirs, files in os.walk(directory):
+        for file in files:
+            if file.endswith('.rst'):
+                fix_docstrings(os.path.join(root, file))
+
+# Example usage:
+fix_rst_files('/Users/llacombe/CODE/quantmetry/MAPIE/doc')

examples/calibration/README.rst

@@ -1,4 +1,4 @@
 .. _calibration_examples:
 
 Calibration examples
-=======================
+====================

examples/multilabel_classification/1-quickstart/plot_tutorial_multilabel_classification.py

@@ -96,7 +96,7 @@
 # 2 Recall control risk with CRC and RCPS
 # ---------------------------------------
 # 2.1 Fitting MapieMultiLabelClassifier
-# ------------------------------------
+# -------------------------------------
 # MapieMultiLabelClassifier will be fitted with RCPS and CRC methods. For the
 # RCPS method, we will test all three Upper Confidence Bounds (Hoeffding,
 # Bernstein and Waudby-Smith–Ramdas).

examples/multilabel_classification/README.rst

@@ -1,4 +1,4 @@
-.. _general_examples:
+.. _multilabel_classification_examples:
 
-General examples
-================
+Multilabel Classification examples
+==================================

mapie/_version.py

@@ -12,5 +12,5 @@
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.8.4.dev4+g6b5418b.d20240503'
-__version_tuple__ = version_tuple = (0, 8, 4, 'dev4', 'g6b5418b.d20240503')
+__version__ = version = '0.8.4.dev5+g4cff8ae.d20240503'
+__version_tuple__ = version_tuple = (0, 8, 4, 'dev5', 'g4cff8ae.d20240503')

mapie/calibration.py

@@ -31,10 +31,9 @@ class MapieCalibrator(BaseEstimator, ClassifierMixin):
 
     Parameters
     ----------
-    estimator : Optional[ClassifierMixin]
+    estimator: Optional[ClassifierMixin]
         Any classifier with scikit-learn API
-        (i.e. with fit, predict, and predict_proba methods), by default
-        ``None``.
+        (i.e. with fit, predict, and predict_proba methods), by default ``None``.
         If ``None``, estimator defaults to a ``LogisticRegression`` instance.
 
     method: Optional[str]
@@ -46,7 +45,7 @@ class MapieCalibrator(BaseEstimator, ClassifierMixin):
 
         By default "top_label".
 
-    calibrator : Optional[Union[str, RegressorMixin]]
+    calibrator: Optional[Union[str, RegressorMixin]]
         Any calibrator with scikit-learn API
         (i.e. with fit, predict, and predict_proba methods), by default
         ``None``.
@@ -90,6 +89,7 @@ class MapieCalibrator(BaseEstimator, ClassifierMixin):
     [1] Gupta, Chirag, and Aaditya K. Ramdas. "Top-label calibration
     and multiclass-to-binary reductions." arXiv preprint
     arXiv:2107.08353 (2021).
+
     """
 
     fit_attributes = [

pyproject.toml

@@ -69,6 +69,7 @@ setuptools-scm = ">=8"  # needed for the versioning
 sphinx = "*"
 sphinx-gallery = "*"
 sphinx-prompt = "*"
+pandas = "*"
 
 [tool.pixi.feature.doc.tasks]
 build-doc = { cmd = "make html", cwd = "doc" }