Release v0.1.3

---------

Signed-off-by: Adam Li <adam2392@gmail.com>

.github/workflows/build_wheels.yml

@@ -6,6 +6,7 @@ on:
       - "**.py"
       - "**.pxd"
       - "**.pyx"
+      - "**"
   push:
     branches: [main]
   workflow_dispatch:
@@ -77,29 +78,82 @@ jobs:
 
       - uses: actions/upload-artifact@v3
         with: 
-          path: ./wheelhouse/*.whl
+          path: ./wheelhouse/
           name: ${{ matrix.python[0] }}-${{ matrix.os[1] }}
 
-  # TODO: let's figure out how to build these wheels?
-  # build_wheels_macos:
-  #   name: Build wheels on macos-11
-  #   runs-on: macos-11
-  #   steps:
-  #     - uses: actions/checkout@v3
-
-  #     - uses: actions/setup-python@v4.6.1
-  #       with:
-  #         python-version: 3.9
-
-  #     - name: macosx_arm64 - setup builddir
-  #       run: |
-  #         python -m pip wheel --config-settings builddir=build .
-
-  #     - name: Build wheels
-  #       uses: pypa/cibuildwheel@v2.13.1
-  #       env:
-  #         CIBW_ARCHS_MACOS: arm64
-
-  #     - uses: actions/upload-artifact@v3
-  #       with:
-  #         path: ./wheelhouse/*.whl
+  build-wheels-m1:
+    name: Build wheels on Arm M1 with Python ${{ matrix.python[0] }}
+    runs-on: macos-latest
+
+    strategy:
+      # Ensure that a wheel builder finishes even if another fails
+      fail-fast: false
+      matrix:
+        python: [["cp39", "3.9"], ["cp310", "3.10"], ["cp311", "3.11"]]
+        # python[0] is used to specify the python versions made by cibuildwheel
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4.6.1
+        with:
+          python-version: 3.9  # Replace with the desired Python version
+
+      - name: Install cibuildwheel dependencies
+        run: |
+          python -m pip install cibuildwheel
+          python -m pip install -r build_requirements.txt
+          python -m pip install spin
+          python spin setup-submodule
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v2.13.1
+        env:
+          CIBW_BUILD: ${{ matrix.python[0] }}-macosx_arm64
+          CIBW_ARCHS_MACOS: arm64
+
+      - uses: actions/upload-artifact@v3
+        with: 
+          path: ./wheelhouse
+          name: ${{ matrix.python[0] }}-arm
+
+  # Build the source distribution under Linux
+  build_sdist:
+    name: Source distribution
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout scikit-tree
+        uses: actions/checkout@v3
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'  # update once build dependencies are available
+
+      - name: Build source distribution
+        run: |
+          python -m pip install -r build_requirements.txt
+          python -m pip install spin
+          python spin setup-submodule
+          python spin sdist
+        # run: bash build_tools/github/build_source.sh
+        # env:
+          # SKLEARN_BUILD_PARALLEL: 3
+
+      # - name: Test source distribution
+      #   run: bash build_tools/github/test_source.sh
+      #   env:
+      #     SKLEARN_SKIP_NETWORK_TESTS: 1
+
+      - name: Store artifacts
+        uses: actions/upload-artifact@v3
+        with:
+          path: dist/*.tar.gz
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: dist
+          name: ${{ matrix.python[0] }}-${{ matrix.os[1] }}

.github/workflows/main.yml

@@ -31,7 +31,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-22.04, macos-latest]
-        python-version: [3.8, 3.9, "3.10"]
+        python-version: [3.9, "3.10", "3.11"]
         poetry-version: [1.3.0]
     runs-on: ${{ matrix.os }}
     defaults:
@@ -171,7 +171,9 @@ jobs:
       - name: pip-packages
         run: |
           pip install -r build_requirements.txt
+          pip install -r test_requirements.txt
           pip install spin
+          pip install numpy==1.22.4
 
       - name: openblas-libs
         # shell: bash

.github/workflows/style.yml

@@ -32,10 +32,10 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v3
-      - name: Setup Python 3.9
+      - name: Setup Python 3.10
         uses: actions/setup-python@v4.6.1
         with:
-          python-version: "3.9"
+          python-version: "3.10"
           architecture: "x64"
 
       - name: Install packages for Ubuntu

.gitmodules

@@ -1,4 +1,4 @@
 [submodule "sktree/_lib/sklearn"]
 	path = sktree/_lib/sklearn_fork
 	url = https://github.com/neurodata/scikit-learn
-	branch = submodulev2
+	branch = v1.3

.spin/cmds.py

@@ -160,3 +160,9 @@ def build(ctx, meson_args, jobs=None, clean=False, forcesubmodule=False, verbose
 
     # run build as normal
     ctx.invoke(meson.build, meson_args=meson_args, jobs=jobs, clean=clean, verbose=verbose)
+
+
+@click.command()
+def sdist():
+    """📦 Build a source distribution in `dist/`"""
+    util.run(["python", "-m", "build", ".", "--sdist"])

DEVELOPING.md

@@ -57,3 +57,23 @@ In order for any code to be added to the repository, we require unit tests to pa
 The general design of scikit-tree follows that of the tree-models inside scikit-learn, where tree-based models are inherently Cythonized, or written with C++. Then the actual forest (e.g. RandomForest, or ExtraForest) is just a Python API wrapper that creates an ensemble of the trees.
 
 In order to develop new tree models, generally Cython and C++ code will need to be written in order to optimize the tree building process, otherwise fitting a single forest model would take very long.
+
+# Making a Release
+
+Scikit-tree is in-line with scikit-learn and thus relies on each new version released there. Moreover, scikit-tree relies on compiled code, so releases are a bit more complex than the typical Python package.
+
+1. Download wheels from GH Actions and put all wheels into a ``dist/`` folder
+
+https://github.com/neurodata/scikit-tree/actions/workflows/build_wheels.yml will have all the wheels for common OSes built for each Python version.
+
+2. Upload wheels to test PyPi
+
+    twine upload --repository-url https://test.pypi.org/legacy/ dist/*
+
+Verify that installations work as expected on your machine.
+
+3. Upload wheels
+
+    twine upload dist/*
+
+4. Update version number on ``meson.build`` and ``_version.py`` to the relevant version.

build_requirements.txt

@@ -9,3 +9,4 @@ rich-click
 doit
 pydevtool
 spin
+build

meson.build

@@ -4,7 +4,7 @@ project(
   # Note that the git commit hash cannot be added dynamically here
   # That only happens when importing from a git repository.
   # See `sktree/__init__.py`
-  version: '0.0.0.dev0',
+  version: '0.1.3',
   license: 'BSD-3',
   meson_version: '>= 0.64.0',
   default_options: [
@@ -45,7 +45,8 @@ if not cython.found()
   error('MESON_BUILD_FAILED: Cython3 not found. Please install it.')
 endif
 
-run_command('git', 'submodule', 'update', '--init', check: true)
+# r = run_command('git', 'submodule', 'update', '--init', check: false)
+r = run_command('mv', 'sktree/_lib/sklearn_fork/sklearn', 'sktree/_lib/sklearn', check: false)
 
 # Setup Python:
 # https://mesonbuild.com/Python-module.html
@@ -62,8 +63,8 @@ py3 = py3_mod.find_installation(
 # print some debugging output
 message(py3.full_path())
 message(py3.get_install_dir())
-if py3.language_version().version_compare('<3.8')
-    error('At least Python 3.8 is required.')
+if py3.language_version().version_compare('<3.9')
+    error('At least Python 3.9 is required.')
 endif
 py3_dep = py3.dependency()
 

pyproject.toml

@@ -1,3 +1,41 @@
+[project]
+name = "sktree"
+#
+# 0.0.0 is standard placeholder for poetry-dynamic-versioning
+# any changes to this should not be checked in
+#
+version = "0.1.3"
+description = "Modern decision trees in Python"
+maintainers = [
+    {name="Neurodata", email="adam.li@columbia.edu"}
+]
+documentation = "https://scikit-tree.neurodata.io"
+repository = "https://github.com/neurodata/scikit-tree"
+readme = "README.md"
+requires-python = ">=3.9"
+classifiers = [
+    'Development Status :: 4 - Beta',
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Developers",
+    "License :: OSI Approved :: BSD License",
+    "Programming Language :: C",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    'Programming Language :: Python :: 3.9',
+    'Programming Language :: Python :: 3.10',
+    'Programming Language :: Python :: 3.11',
+    "Topic :: Scientific/Engineering",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX :: Linux",
+    "Operating System :: POSIX",
+    "Operating System :: Unix",
+    "Operating System :: MacOS",
+]
+keywords = ['tree', 'oblique trees', 'manifold-learning', 'scikit-learn']
+include = [
+    { path = "meson.build", format = "sdist" },
+]
+
 [tool.poetry]
 name = "sktree"
 #
@@ -13,8 +51,6 @@ repository = "https://github.com/neurodata/scikit-tree"
 readme = "README.md"
 classifiers = [
     'Development Status :: 4 - Beta',
-    'License :: OSI Approved :: BSD-3 License',
-    'Programming Language :: Python :: 3.8',
     'Programming Language :: Python :: 3.9',
     'Programming Language :: Python :: 3.10',
     'Programming Language :: Python :: 3.11',
@@ -216,6 +252,7 @@ Build = [
     # "spin.cmds.meson.build", 
     ".spin/cmds.py:build",
     ".spin/cmds.py:setup_submodule",
+    ".spin/cmds.py:sdist",
     "spin.cmds.meson.test",
 ]
 Environments = [

sktree/__init__.py

@@ -3,7 +3,7 @@
 import os
 import sys
 
-__version__ = "0.0.0dev0"
+__version__ = "0.1.3"
 logger = logging.getLogger(__name__)