Modernize Python package structure

Author: danieleongari

.github/workflows/docbuild.yml

@@ -30,9 +30,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install -r requirements.txt
-        python -m pip install -r requirements-dev.txt
-        python -m pip install .
+        python -m pip install ".[docs]"
     - name: Build docs
       working-directory: docs
       run: make html

.github/workflows/pythonpackage.yml

@@ -63,9 +63,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install -r requirements-test.txt
-        python -m pip install "numpy<2" "${{ matrix.sklearn-spec }}"
-        python -m pip install --no-deps .
+        python -m pip install ".[test]" "numpy<2" "${{ matrix.sklearn-spec }}"
         python -m pip check
     - name: Show resolved versions
       run: |

MANIFEST.in

@@ -31,14 +31,16 @@ and test increasing the number of trees in the model to reach convergence.
 
 Before installing the module you will need `numpy`, `scipy` and `scikit-learn`.
 
-To install `forest-confidence-interval` execute:
+To install `forest-confidence-interval`, run:
+
 ```
-pip install forestci
+python -m pip install forestci
 ```
-If would like to install the development version of the software use:
+
+To install the development version from GitHub, use:
 
 ```shell
-pip install git+git://github.com/scikit-learn-contrib/forest-confidence-interval.git
+python -m pip install git+https://github.com/scikit-learn-contrib/forest-confidence-interval.git
 ```
 
 Usage:
@@ -84,12 +86,25 @@ E-mail [Ariel Rokem](mailto:arokem@gmail.com), [Kivan Polimis](mailto:kivan.poli
 
 ## Testing
 
-Tests live in the top-level `tests/` directory. To test against the
-scikit-learn version already installed in your current environment, install
-only the test runner and the local package without resolving its dependencies:
+The project uses a `pyproject.toml` build configuration and a `src/` package
+layout. Runtime, test, documentation, and development dependencies are declared
+as project dependency groups, while tests live in the top-level `tests/`
+directory.
+
+For a complete development environment, install the editable package and its
+development dependencies:
+
+```shell
+python -m pip install -e ".[dev]"
+python -m pytest
+```
+
+To test only against the scikit-learn version already installed in the current
+environment, install the test runner and then install `forestci` without
+resolving dependencies:
 
 ```shell
-python -m pip install -r requirements-test.txt
+python -m pip install pytest==9.0.3
 python -m pip install --no-deps -e .
 python -m pytest
 ```

README.md

@@ -15,7 +15,6 @@
 import sys
 import os
 
-import sphinx_gallery
 import sphinx_rtd_theme
 
 # If extensions (or modules to document with autodoc) are in another directory,
@@ -36,6 +35,7 @@
     'sphinx.ext.autosummary',
     'sphinx.ext.doctest',
     'sphinx.ext.intersphinx',
+    'sphinx.ext.imgmath',
     'sphinx.ext.viewcode',
     'numpydoc',
     'sphinx_gallery.gen_gallery',
@@ -47,14 +47,6 @@
 # see https://github.com/numpy/numpydoc/issues/69
 numpydoc_show_class_members = False
 
-# pngmath / imgmath compatibility layer for different sphinx versions
-import sphinx
-from distutils.version import LooseVersion
-if LooseVersion(sphinx.__version__) < LooseVersion('1.4'):
-    extensions.append('sphinx.ext.pngmath')
-else:
-    extensions.append('sphinx.ext.imgmath')
-
 # autodoc_default_flags = ['members', 'inherited-members']
 
 # autodoc_default_options = True
@@ -150,9 +142,6 @@
 # documentation.
 #html_theme_options = {}
 
-# Add any paths that contain custom themes here, relative to this directory.
-html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
-
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
 #html_title = None
@@ -229,10 +218,10 @@
 intersphinx_mapping = {
     'python': ('https://docs.python.org/{.major}'.format(
         sys.version_info), None),
-    'numpy': ('https://docs.scipy.org/doc/numpy/', None),
-    'scipy': ('https://docs.scipy.org/doc/scipy/reference', None),
-    'matplotlib': ('https://matplotlib.org/', None),
-    'sklearn': ('http://scikit-learn.org/stable', None)
+    'numpy': ('https://numpy.org/doc/stable/', None),
+    'scipy': ('https://docs.scipy.org/doc/scipy/', None),
+    'matplotlib': ('https://matplotlib.org/stable/', None),
+    'sklearn': ('https://scikit-learn.org/stable/', None)
 }
 
 # sphinx-gallery configuration

docs/conf.py

@@ -3,21 +3,17 @@
 Installation Guide
 ==================
 
-Before installing the `forestci` module, you will need `numpy`, `scipy`
-and `scikit-learn`
+To install `forestci` and its dependencies:
 
 .. code-block:: bash
 
-   pip install numpy scipy scikit-learn
+   python -m pip install forestci
 
-Then, to install `forestci`:
+If you wish to install from the source code (available `here <https://github.com/scikit-learn-contrib/forest-confidence-interval>`_),
+change your working directory to the top-level directory and install the
+package in editable mode. Development dependencies are declared in
+``pyproject.toml``:
 
 .. code-block:: bash
 
-   pip install forestci
-
-If you wish to install from the source code (available `here <https://github.com/scikit-learn-contrib/forest-confidence-interval>`_ ), change your working directory to the top-level directory of the source code, and issue:
-
-.. code-block:: bash
-
-   python setup.py install
+   python -m pip install -e ".[dev]"

docs/installation_guide.rst

@@ -0,0 +1,86 @@
+[build-system]
+requires = ["setuptools>=77"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "forestci"
+dynamic = ["version"]
+description = "Confidence intervals for scikit-learn forest algorithms"
+readme = "README.md"
+license = "MIT"
+license-files = ["LICENSE"]
+authors = [
+    { name = "Ariel Rokem", email = "arokem@uw.edu" },
+    { name = "Bryna Hazelton" },
+    { name = "Kivan Polimis" },
+]
+maintainers = [
+    { name = "Ariel Rokem", email = "arokem@uw.edu" },
+]
+requires-python = ">=3.10"
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Environment :: Console",
+    "Intended Audience :: Science/Research",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering",
+]
+dependencies = [
+    "numpy>=1.20",
+    "scikit-learn>=1.0,<2.0",
+    "scipy",
+]
+
+[project.optional-dependencies]
+test = [
+    "pytest==9.0.3",
+]
+docs = [
+    "matplotlib",
+    "numpydoc",
+    "pandas",
+    "pillow",
+    "sphinx",
+    "sphinx-autoapi",
+    "sphinx-gallery",
+    "sphinx-rtd-theme",
+]
+dev = [
+    "flake8",
+    "matplotlib",
+    "numpydoc",
+    "pandas",
+    "pillow",
+    "pytest==9.0.3",
+    "sphinx",
+    "sphinx-autoapi",
+    "sphinx-gallery",
+    "sphinx-rtd-theme",
+]
+
+[project.urls]
+Documentation = "https://contrib.scikit-learn.org/forest-confidence-interval/"
+Source = "https://github.com/scikit-learn-contrib/forest-confidence-interval"
+Issues = "https://github.com/scikit-learn-contrib/forest-confidence-interval/issues"
+
+[tool.setuptools]
+package-dir = { "" = "src" }
+
+[tool.setuptools.dynamic]
+version = { attr = "forestci.version.__version__" }
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.pytest.ini_options]
+addopts = "--doctest-modules"
+testpaths = [
+    "src/forestci",
+    "tests",
+]