RELEASE Updating to v0.8 release (#288)

* Updating to v0.8 release * Only run wheels on macos-12 * Build wheels into consoidated folder-s --------- Signed-off-by: Adam Li <adam2392@gmail.com>
neurodata · Jun 24, 2024 · 7ea563c · 7ea563c
1 parent 580e087
commit 7ea563c
Show file tree

Hide file tree

Showing 10 changed files with 109 additions and 170 deletions.
diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
@@ -1,4 +1,4 @@
-name: Build Wheels
+name: Build_Wheels
 
 on:
   pull_request:
@@ -19,17 +19,6 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  create_artifacts_folder:
-    name: Create Artifacts Folder
-    runs-on: ubuntu-latest
-    outputs:
-      artifacts_folder: ${{ steps.set_folder.outputs.folder_name }}
-
-    steps:
-      - name: Set Artifacts Folder
-        id: set_folder
-        run: echo "folder_name=artifacts/${{ github.run_id }}" >> $GITHUB_ENV
-
   build_wheels:
     name: Build wheels on ${{ matrix.os[1] }} - ${{ matrix.os[2] }} with Python ${{ matrix.python[0] }}
     runs-on: ${{ matrix.os[0] }}
@@ -40,12 +29,18 @@ jobs:
       matrix:
         os:  # see scipy wheels.yml GH actions
           - [ubuntu-22.04, manylinux, x86_64]
-          - [macos-11, macosx, x86_64]
+          - [macos-12, macosx, x86_64]
           # - [macos-12, macosx_*, arm64]
           - [windows-2019, win, AMD64]
 
-        python: [["cp39", "3.9"], ["cp310", "3.10"], ["cp311", "3.11"], ["cp312", "3.12"]]
         # python[0] is used to specify the python versions made by cibuildwheel
+        python:
+          [
+            ["cp39", "3.9"],
+            ["cp310", "3.10"],
+            ["cp311", "3.11"],
+            ["cp312", "3.12"],
+          ]
 
     env:
       IS_32_BIT: ${{ matrix.os[2] == 'x86' }}
@@ -99,8 +94,14 @@ jobs:
       # Ensure that a wheel builder finishes even if another fails
       fail-fast: false
       matrix:
-        python: [["cp39", "3.9"], ["cp310", "3.10"], ["cp311", "3.11"], ["cp312", "3.12"]]
         # python[0] is used to specify the python versions made by cibuildwheel
+        python:
+          [
+            ["cp39", "3.9"],
+            ["cp310", "3.10"],
+            ["cp311", "3.11"],
+            ["cp312", "3.12"],
+          ]
 
     steps:
       - name: Checkout code
@@ -141,21 +142,40 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.10"  # update once build dependencies are available
+          python-version: "3.10"
 
       - name: Build source distribution
         run: |
           pip install spin build
           spin setup-submodule
           pip install .[build]
-          python -m build
+          python -m build --sdist
 
-      - name: Store artifacts
-        uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v4
         with:
-          path: dist/*.tar.gz
+          name: ${{ matrix.python[0] }}-${{ matrix.os[1] }}
+          path: dist
+
+  merge-wheels:
+    name: Merge all wheels into one directory
+    needs: [build_wheels, build-wheels-m1, build_sdist]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          path: all
+
+      - name: List all files
+        run: |
+          ls all/**
+
+      - name: Merge files
+        run: |
+          mkdir dist
+          mv all/**/*.whl ./dist
+          mv all/**/*.tar.gz ./dist
 
       - uses: actions/upload-artifact@v4
         with:
           path: dist
-          name: ${{ matrix.python[0] }}-${{ matrix.os[1] }}
+          name: dist
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -143,7 +143,7 @@ jobs:
   build_and_test_slow:
     name: Slow Meson build ${{ matrix.os }} - py${{ matrix.python-version }}
     timeout-minutes: 20
-    # needs: [build_and_test]
+    needs: [build_and_test]
     strategy:
       fail-fast: false
       matrix:

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -7,160 +7,43 @@ concurrency:
 on:
   release:
     types: [published]
-  push:
-    branches:
-      - main
-  pull_request:
-    branches:
-      - main
+  workflow_run:
+    workflows: [Build_Wheels]
+    branches: [main]
+    types: [completed]  # This ensures it triggers only after the workflow completes
 
 permissions:
   contents: read
 
-env:
-  INSTALLDIR: "build-install"
-  CCACHE_DIR: "${{ github.workspace }}/.ccache"
-
 jobs:
-  # release is ran when a release is made on Github
-  # Build the source distribution under Linux
-  build_sdist:
-    name: Source distribution
+  check_wheels:
     runs-on: ubuntu-latest
-
-    steps:
-      - name: Checkout scikit-tree
-        uses: actions/checkout@v4
-
-      - name: Setup Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.10"  # update once build dependencies are available
-
-      - name: Build source distribution
-        run: |
-          pip install spin build
-          spin setup-submodule
-          pip install .[build]
-          python -m build
-
-      - name: Store artifacts
-        uses: actions/upload-artifact@v4
-        with:
-          path: dist/*.tar.gz
-
-  build_wheels:
-    name: Build wheels on ${{ matrix.os[1] }} - ${{ matrix.os[2] }} with Python ${{ matrix.python[0] }}
-    runs-on: ${{ matrix.os[0] }}
-
-    strategy:
-      # Ensure that a wheel builder finishes even if another fails
-      fail-fast: false
-      matrix:
-        os:  # see scipy wheels.yml GH actions
-          - [ubuntu-22.04, manylinux, x86_64]
-          - [macos-11, macosx, x86_64]
-          # - [macos-12, macosx_*, arm64]
-          - [windows-2019, win, AMD64]
-
-        python: [["cp39", "3.9"], ["cp310", "3.10"], ["cp311", "3.11"], ["cp312", "3.12"]]
-        # python[0] is used to specify the python versions made by cibuildwheel
-
-    env:
-      IS_32_BIT: ${{ matrix.os[2] == 'x86' }}
-
     steps:
-      - name: Checkout scikit-tree
-        uses: actions/checkout@v4
-
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.10"
-
-      - name: Setup submodule
+      - name: Get run ID of "Build_Wheels" workflow
+        id: get-run-id
         run: |
-          python -m pip install --upgrade pip spin
-          python -m spin setup-submodule
-
-      - name: win_amd64 - install rtools
-        run: |
-          choco install rtools -y --no-progress --force --version=4.0.0.20220206
-          echo "c:\rtools40\ucrt64\bin;" >> $env:GITHUB_PATH
-        if: ${{ runner.os == 'Windows' && env.IS_32_BIT == 'false' }}
-
-      - name: Build wheels
-        uses: pypa/cibuildwheel@v2.19.1
-        # Build all wheels here, apart from macosx_arm64, linux_aarch64
-        # cibuildwheel is currently unable to pass configuration flags to
-        # CIBW_BUILD_FRONTEND https://github.com/pypa/cibuildwheel/issues/1227
-        # (pip/build). Cross compilation with meson requires an initial
-        # configuration step to create a build directory. The subsequent wheel
-        # build then needs to use that directory. This can be done with pip
-        # using a command like:
-        # pip wheel --config-settings builddir=build .
-        # if: >-
-        #   ( ! contains(matrix.os[2], 'arm64' ) )
+          OTHER_REPO="${{ github.repository }}"
+          WF_NAME="Build_Wheels"
+          RUN_ID=`gh run --repo ${OTHER_REPO} list --workflow ${WF_NAME} --json databaseId --jq .[0].databaseId`
+          echo "Detected latest run id of ${RUN_ID} for workflow ${WF_NAME}"
+          echo "run-id=${RUN_ID}" >> "$GITHUB_OUTPUT"
         env:
-          CIBW_BUILD: ${{ matrix.python[0] }}-${{ matrix.os[1] }}*
-          CIBW_ARCHS: ${{ matrix.os[2] }}
-          CIBW_ENVIRONMENT_PASS_LINUX: RUNNER_OS
+          GH_TOKEN: ${{ github.token }}
 
-      - name: Move wheels to dist
-        run: |
-          mkdir -p dist
-          mv ./wheelhouse/* dist/
-
-      - uses: actions/upload-artifact@v4
+      - name: Download artifact from "Build_Wheels" workflow
+        uses: actions/download-artifact@v4
         with:
-          path: ./dist/
-          name: ${{ matrix.python[0] }}-${{ matrix.os[1] }}
-
-  build-wheels-m1:
-    name: Build wheels on Arm M1 with Python ${{ matrix.python[0] }}
-    runs-on: macos-latest
+          name: dist  # Match name used in build_wheels.yml upload artifact step
+          github-token: ${{ github.token }}
+          repository: ${{ github.repository }}
+          run-id: ${{ steps.get-run-id.outputs.run-id }}
 
-    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"], ["cp312", "3.12"]]
-        # python[0] is used to specify the python versions made by cibuildwheel
-
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v4
-
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.10"  # Replace with the desired Python version
-
-      - name: Install cibuildwheel dependencies
-        run: |
-          pip install cibuildwheel
-          pip install spin
-          spin setup-submodule
-          pip install .[build]
-
-      - name: Build wheels
-        uses: pypa/cibuildwheel@v2.19.1
-        env:
-          CIBW_BUILD: ${{ matrix.python[0] }}-macosx_arm64
-          CIBW_ARCHS_MACOS: arm64
-
-      - name: Move wheels to dist
-        run: |
-          mkdir -p dist
-          mv ./wheelhouse/* dist/
-
-      - uses: actions/upload-artifact@v4
-        with:
-          path: ./dist/
-          name: ${{ matrix.python[0] }}-arm
+      - name: Show downloaded files
+        run: ls -la
 
   # PyPI on release
   pypi:
-    needs: [build_sdist, build_wheels, build-wheels-m1]
+    needs: [check_wheels]
     runs-on: ubuntu-latest
     if: github.event_name == 'release'
     permissions:

diff --git a/doc/_static/versions.json b/doc/_static/versions.json
@@ -1,14 +1,19 @@
 [
     {
-        "name": "0.8 (devel)",
+        "name": "0.9 (devel)",
         "version": "dev",
         "url": "https://docs.neurodata.io/scikit-tree/dev/"
     },
     {
-        "name": "0.7",
-        "version": "stable",
+        "name": "0.8",
+        "version": "dev",
         "url": "https://docs.neurodata.io/scikit-tree/stable/"
     },
+    {
+        "name": "0.7",
+        "version": "0.7",
+        "url": "https://docs.neurodata.io/scikit-tree/v0.7/"
+    },
     {
         "name": "0.6",
         "version": "0.6",

diff --git a/doc/whats_new/v0.8.rst b/doc/whats_new/v0.8.rst
@@ -3,12 +3,15 @@
 .. include:: _contributors.rst
 .. currentmodule:: sktree
 
-.. _current:
+.. _v0_9:
 
 Version 0.8
 ===========
 
-**In Development**
+This development fixes a major bug with (CO)MIGHT, where low sample sizes produce biased tree
+posteriors, which is fixed by stratifying the sampling of the dataset to ensure that each class
+is represented in the bootstrap sample. Additionally, the release includes a number of bug fixes
+and improvements to the codebase.
 
 Changelog
 ---------

diff --git a/doc/whats_new/v0.9.rst b/doc/whats_new/v0.9.rst
@@ -0,0 +1,25 @@
+:orphan:
+
+.. include:: _contributors.rst
+.. currentmodule:: sktree
+
+.. _current:
+
+Version 0.9
+===========
+
+**In Development**
+
+Changelog
+---------
+
+- 
+
+Code and Documentation Contributors
+-----------------------------------
+
+Thanks to everyone who has contributed to the maintenance and improvement of
+the project since version inception, including:
+
+* `Adam Li`_
+
diff --git a/meson.build b/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: '0.8.0dev0',
+  version: '0.8.0',
   license: 'BSD-3',
   meson_version: '>= 1.1.0',
   default_options: [

diff --git a/pyproject.toml b/pyproject.toml
@@ -17,7 +17,7 @@ requires = [
 
 [project]
 name = "scikit-tree"
-version = "0.8.0dev0"
+version = "0.8.0"
 description = "Modern decision trees in Python"
 maintainers = [
   {name = "Neurodata", email = "adam.li@columbia.edu"}

diff --git a/sktree/__init__.py b/sktree/__init__.py
@@ -4,7 +4,7 @@
 import os
 import sys
 
-__version__ = "0.8.0dev0"
+__version__ = "0.8.0"
 logger = logging.getLogger(__name__)