python/ Convert examples into sphinx galleries.

python/.gitignore

@@ -77,6 +77,8 @@ instance/
 doc/_build/
 doc/jupyter_execute/
 doc/source/reference/generated/
+doc/source/auto_examples
+doc/source/sg_execution_times.rst
 
 # PyBuilder
 .pybuilder/

python/Makefile

@@ -1,6 +1,6 @@
 # This file should be almost identical to
 # https://github.com/multi-objective/mooplot/blob/main/python/Makefile
-.PHONY : install build test doc clean docdeps pre-commit
+.PHONY : install build test docs fastdocs clean docdeps pre-commit
 
 install: build
 	python3 -m pip install -e . --disable-pip-version-check
@@ -21,12 +21,15 @@ docdeps:
 show:
 	$(MAKE) -C doc show
 
-doc:
+docs:
 	$(MAKE) -C doc clean html
 
+fastdocs:
+	$(MAKE) -C doc clean html-noplot
+
 clean:
 	$(MAKE) -C doc clean
 	$(MAKE) -C src/moocore/libmoocore/ clean
 	find . -name '__pycache__' | xargs $(RM) -r
-	$(RM) -rf .pytest_cache .tox build src/*.egg-info/ doc/source/reference/generated
+	$(RM) -rf .pytest_cache .tox build src/*.egg-info/ doc/source/reference/generated doc/source/auto_examples
 	$(RM) -f .coverage coverage.xml c_coverage.xml dist/*

python/doc/Makefile

@@ -24,6 +24,10 @@ help:
 show:
 	@python3 -c "import webbrowser; webbrowser.open_new_tab('file://$(root_dir)/$(BUILDDIR)/html/index.html')"
 
+html-noplot:
+	@$(SPHINXBUILD) -D plot_gallery=0 -b html $(ALLSPHINXOPTS) "$(SOURCEDIR)" "$(BUILDDIR)/html"
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile

python/doc/source/conf.py

@@ -12,11 +12,20 @@
 import sphinx
 import moocore
 
+# Set plotly renderer to capture _repr_html_ for sphinx-gallery
+try:
+    import plotly.io
+except ImportError:
+    pass
+else:
+    plotly.io.renderers.default = "sphinx_gallery"
+
 project = "moocore"
 _full_version = moocore.__version__
 release = _full_version  # _full_version.split("+", 1)[0]
 version = _full_version  # ".".join(release.split(".")[:2])
 year = date.today().year
+# Can we get this from pyproject.toml ?
 author = "Manuel López-Ibáñez and Fergus Rooney"
 copyright = f"2024-{year}, {author}"
 html_site_root = f"https://multi-objective.github.io/{project}/python/"
@@ -40,9 +49,10 @@
     "sphinx.ext.autosummary",  # Create neat summary tables for modules/classes/methods etc
     "sphinx_copybutton",  # A small sphinx extension to add a "copy" button to code blocks.
     "sphinx.ext.mathjax",
-    "myst_nb",
-    "sphinx.ext.autosectionlabel",
+    # "sphinx.ext.autosectionlabel", DO NOT USE: causes duplicated labels.
     "sphinxcontrib.bibtex",
+    "sphinx_gallery.gen_gallery",
+    "matplotlib.sphinxext.plot_directive",
 ]
 
 # -----------------------------------------------------------------------------
@@ -122,6 +132,13 @@ def setup(app):
     # Add light/dark mode and documentation version switcher:
     # "navbar_end": ["theme-switcher", "version-switcher", "navbar-icon-links"],
     "navbar_end": ["theme-switcher", "navbar-icon-links"],
+    "icon_links": [
+        {
+            "name": "PyPI",
+            "url": f"https://pypi.org/project/{project}",
+            "icon": "fa-solid fa-box",
+        },
+    ],
     # "icon_links": [
     #     {
     #         # Label for this link
@@ -155,7 +172,7 @@ def setup(app):
 templates_path = ["_templates"]
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-# This pattern also affects html_static_path and html_extra_path .
+# This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = [
     "_build",
     "Thumbs.db",
@@ -164,6 +181,10 @@ def setup(app):
     "_templates",
     "modules.rst",
     "source",
+    # Exclude .py and .ipynb files in auto_examples generated by sphinx-gallery.
+    # This is to prevent sphinx from complaining about duplicate source files.
+    "auto_examples/*.ipynb",
+    "auto_examples/*.py",
 ]
 suppress_warnings = ["mystnb.unknown_mime_type"]
 
@@ -190,3 +211,40 @@ def setup(app):
     "sympy": ("https://docs.sympy.org/latest/", None),
     "mooplot": ("https://multi-objective.github.io/mooplot/python/", None),
 }
+
+# From https://github.com/scikit-learn/scikit-learn/blob/main/doc/conf.py
+sphinx_gallery_conf = {
+    "examples_dirs": "../../examples",
+    "gallery_dirs": "auto_examples",
+    # Directory where function/class granular galleries are stored.
+    "backreferences_dir": "reference/generated/backreferences",
+    # Modules for which function/class level galleries are created.
+    "doc_module": (project),
+    # Regexes to match objects to exclude from implicit backreferences.
+    # The default option is an empty set, i.e. exclude nothing.
+    # To exclude everything, use: '.*'
+    "exclude_implicit_doc": {r"pyplot\.show"},
+    "show_memory": False,
+    # "reference_url": {"mooplot": None},
+    # "subsection_order": SubSectionTitleOrder("../examples"),
+    # "within_subsection_order": SKExampleTitleSortKey,
+    # "binder": {
+    #     "org": "scikit-learn",
+    #     "repo": "scikit-learn",
+    #     "binderhub_url": "https://mybinder.org",
+    #     "branch": binder_branch,
+    #     "dependencies": "./binder/requirements.txt",
+    #     "use_jupyter_lab": True,
+    # },
+    # avoid generating too many cross links
+    "inspect_global_variables": False,
+    "remove_config_comments": True,
+    "matplotlib_animations": True,
+    # "plot_gallery": "True",
+    # "recommender": {"enable": True, "n_examples": 5, "min_df": 12},
+    # "reset_modules": ("matplotlib", "seaborn"),
+}
+# if with_jupyterlite:
+#     sphinx_gallery_conf["jupyterlite"] = {
+#         "notebook_modification_function": notebook_modification_function
+#     }

python/doc/source/index.rst

@@ -9,7 +9,7 @@ moocore: Core Algorithms for Multi-Objective Optimization
    :hidden:
 
    API reference <reference/index>
-   Examples <examples/index>
+   Examples <auto_examples/index>
 
 **Version**: |version|
 
@@ -53,7 +53,7 @@ performance measures, performance assessment
         :img-top: _static/index_getting_started.svg
         :class-card: intro-card
         :shadow: md
-        :link: examples
+        :link: auto_examples
         :link-type: ref
 
         Detailed examples and tutorials.

python/examples/README.rst

@@ -0,0 +1,8 @@
+.. _auto_examples:
+
+Examples
+========
+
+These are longer and more detailed examples than those accompanying the
+documentation of each function.  These examples may require additional packages
+to run.

python/examples/plot_hv_approx.py

@@ -0,0 +1,60 @@
+r"""Comparing methods for approximating the hypervolume
+===================================================
+
+This example shows how to approximate the hypervolume metric of the ``CPFs.txt`` dataset using both HypE, :func:`moocore.whv_hype()`, and DZ2019, :func:`moocore.hv_approx()` for several
+values of the number of samples between :math:`10^1` and :math:`10^5`. We repeat each
+calculation 10 times to account for stochasticity.
+"""
+
+import numpy as np
+import moocore
+
+ref = 2.1
+x = moocore.get_dataset("CPFs.txt")[:, :-1]
+x = moocore.filter_dominated(x)
+x = moocore.normalise(x, to_range=[1, 2])
+true_hv = moocore.hypervolume(x, ref=ref)
+rng1 = np.random.default_rng(42)
+rng2 = np.random.default_rng(42)
+
+hype = {}
+dz = {}
+for i in range(1, 6):
+    hype[i] = []
+    dz[i] = []
+    for r in range(15):
+        res = moocore.whv_hype(x, ref=ref, ideal=0, nsamples=10**i, seed=rng1)
+        hype[i].append(res)
+        res = moocore.hv_approx(x, ref=ref, nsamples=10**i, seed=rng2)
+        dz[i].append(res)
+print(
+    f"True HV    : {true_hv:.5f}",
+    f"Mean HYPE  : {np.mean(hype[5]):.5f} [{np.min(hype[5]):.5f}, {np.max(hype[5]):.5f}]",
+    f"Mean DZ2019: {np.mean(dz[5]):.5f} [{np.min(dz[5]):.5f}, {np.max(dz[5]):.5f}]",
+    sep="\n",
+)
+
+
+# %%
+# Next, we plot the results.
+
+import pandas as pd
+
+hype = pd.DataFrame(hype)
+dz = pd.DataFrame(dz)
+hype["Method"] = "HypE"
+dz["Method"] = "DZ2019"
+df = (
+    pd.concat([hype, dz])
+    .reset_index(names="rep")
+    .melt(id_vars=["rep", "Method"], var_name="samples")
+)
+df["samples"] = 10 ** df["samples"]
+df["value"] = np.abs(df["value"] - true_hv) / true_hv
+
+import matplotlib.pyplot as plt
+import seaborn as sns
+
+ax = sns.lineplot(x="samples", y="value", hue="Method", data=df, marker="o")
+ax.set(xscale="log", yscale="log", ylabel="Relative error")
+plt.show()

python/examples/plot_metrics.py

@@ -0,0 +1,41 @@
+"""Computing Multi-Objective Quality Metrics
+=========================================
+
+TODO: Expand this
+
+"""
+
+import numpy as np
+import moocore
+
+# %%
+# First, read the datasets.
+#
+
+spherical = moocore.get_dataset("spherical-250-10-3d.txt")
+uniform = moocore.get_dataset("uniform-250-10-3d.txt")
+
+ref = 1.1
+ref_set = moocore.filter_dominated(
+    np.vstack((spherical[:, :-1], uniform[:, :-1]))
+)
+
+
+def apply_within_sets(x, fun, **kwargs):
+    """Apply ``fun`` for each dataset in ``x``."""
+    _, uniq_index = np.unique(x[:, -1], return_index=True)
+    x_split = np.vsplit(x[:, :-1], uniq_index[1:])
+    return [fun(g, **kwargs) for g in x_split]
+
+
+uniform_igd_plus = apply_within_sets(uniform, moocore.igd_plus, ref=ref_set)
+spherical_igd_plus = apply_within_sets(
+    spherical, moocore.igd_plus, ref=ref_set
+)
+
+print(f"""
+            Uniform       Spherical
+            -------       ---------
+Mean IGD+:  {np.mean(uniform_igd_plus):.5f}       {np.mean(spherical_igd_plus):.5f}
+
+""")

python/pyproject.toml

@@ -36,6 +36,7 @@ dependencies = [
   "cffi>=1.15.1",
   "numpy>=1.22.3",
 ]
+
 urls.Documentation = "https://multi-objective.github.io/moocore/python/"
 urls.Homepage = "https://multi-objective.github.io/moocore/python/"
 urls.Source = "https://github.com/multi-objective/moocore/"
@@ -114,6 +115,13 @@ lint.ignore = [
   "D213", # multi-line-summary-second-line
 ]
 
+lint.per-file-ignores."*examples*/*.py" = [
+  "D205", # 1 blank line required between summary line and description
+  "D400", # First line should end with a period
+  "D415", #  First line should end with a period, question mark, or exclamation point
+  "E402", # Module level import not at top of file
+]
+
 [tool.pytest.ini_options]
 doctest_optionflags = "NUMBER"
 addopts = [

python/requirements_dev.txt

@@ -1,9 +1,9 @@
+setuptools>=70.1,<74 # Sync with .pre-commit-config.yaml
+cffi >= 1.15.1
 numpy >= 1.22.3
 
 pre-commit >= 3.3.2
-ruff >= 0.1.4 # Sync with .pre-commit-config.yaml
-setuptools >= 65.5.1
-cffi >= 1.15.1
+ruff >= 0.1.4
 
 tox >= 4.6.2 # Sync with tox.ini
 pytest >= 7  # Sync with tox.ini
@@ -16,7 +16,7 @@ pydata_sphinx_theme
 jupyter
 ipykernel
 kaleido
-myst-nb
+sphinx-gallery
 sphinxcontrib-napoleon
 sphinxcontrib-bibtex
 sphinx-autodoc-typehints

python/src/moocore/_moocore.py

@@ -486,6 +486,9 @@ def hv_approx(
     >>> moocore.hv_approx(x, ref = reference, maximise = True, seed = 42)
     1.0563125590974458
 
+    .. minigallery:: moocore.hv_approx
+       :add-heading:
+
     """
     # Convert to numpy.array in case the user provides a list.  We use
     # np.asarray to convert it to floating-point, otherwise if a user inputs