Updated GitHub Workflows

.github/release-drafter-config.yml

@@ -0,0 +1,37 @@
+name-template: 'v$RESOLVED_VERSION'
+tag-template: 'v$RESOLVED_VERSION'
+categories:
+  - title: '🚀 Features'
+    labels:
+      - 'feature'
+      - 'enhancement'
+  - title: '🐛 Bug Fixes'
+    labels:
+      - 'fix'
+      - 'bugfix'
+      - 'bug'
+  - title: '🧰 Maintenance'
+    labels:
+      - 'dependencies'
+  - title: '📚️ Documentation'
+    labels:
+      - 'documentation'
+change-template: '- $TITLE @$AUTHOR (#$NUMBER)'
+change-title-escapes: '\<*_&' # You can add # and @ to disable mentions, and add ` to disable code blocks.
+version-resolver:
+  major:
+    labels:
+      - 'major'
+  minor:
+    labels:
+      - 'minor'
+  patch:
+    labels:
+      - 'patch'
+  default: patch
+template: |
+  ## Changes
+
+  $CHANGES
+
+  $CONTRIBUTORS

.github/scripts/get_example_dataset.py

@@ -7,7 +7,7 @@
 
 DATASET_PATH = "angelolab/ark_example"
 
-valid_configs = datasets.get_dataset_config_names(DATASET_PATH)
+valid_configs = datasets.get_dataset_config_names(DATASET_PATH, trust_remote_code=True)
 
 def load_dataset(cache_dir: Path, name: str):
     _ = datasets.load_dataset(
@@ -25,4 +25,4 @@ def load_dataset(cache_dir: Path, name: str):
 
 # Download all available datasets
 for dataset_config in valid_configs:
-    load_dataset(cache_dir=cache_dir, name=dataset_config)
+    load_dataset(cache_dir=cache_dir, name=dataset_config)

.github/workflows/build.yml

@@ -21,6 +21,7 @@ jobs:
         uses: actions/checkout@v4
         with:
           fetch-depth: 0
+
 
       - name: Set up QEMU (For Linux ARM)
         if: runner.os == 'Linux'
@@ -29,7 +30,7 @@ jobs:
           platforms: arm64
 
       - name: Build Wheels
-        uses: pypa/cibuildwheel@v2.16.5
+        uses: pypa/cibuildwheel@v2.18.0
         with:
           package-dir: .
           output-dir: wheelhouse
@@ -38,7 +39,7 @@ jobs:
       - name: Store Wheel Artifacts
         uses: actions/upload-artifact@v4
         with:
-          name: dist-${{ matrix.os }}
+          name: dist-wheels-${{ matrix.os }}
           path: wheelhouse/*.whl
 
   build_sdist:
@@ -47,6 +48,8 @@ jobs:
     steps:
       - name: Checkout ${{ github.repository }}
         uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
 
       - name: Build sdist
         run: pipx run build --sdist

.github/workflows/ci.yml

@@ -19,7 +19,7 @@ permissions:
 jobs:
   get_dataset:
     env:
-      cache-name: dataset
+      cache-name: dataset-cache
 
     name: Get / Update Example Dataset
     runs-on: ubuntu-latest
@@ -31,7 +31,6 @@ jobs:
 
       - name: Restore Example Dataset Cache
         uses: actions/cache@v4
-        id: dataset-cache
         with:
           path: ./data/cache/
           key: huggingface-${{ env.cache-name }}

.github/workflows/release-drafter.yml

@@ -23,10 +23,10 @@ jobs:
       pull-requests: write # for release-drafter/release-drafter to add label to PR
     steps:
       # Drafts your next Release notes as Pull Requests are merged into "master"
-      - uses: release-drafter/release-drafter@v5.22.0
+      - uses: release-drafter/release-drafter@v6
         # Specify config name to use, relative to .github/. Default: release-drafter.yml
         with:
-          config-name: release-drafter.yml
+          config-name: release-drafter-config.yml
         #   disable-autolabeler: true
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/release.yml

@@ -0,0 +1,121 @@
+name: Build Wheels and upload to PyPI
+
+on:
+  pull_request:
+    branches: ["releases/**"]
+    types: [labeled, opened, synchronize, reopened]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read # to fetch code (actions/checkout)
+
+jobs:
+  test:
+    name: Test
+    permissions:
+      contents: read
+    secrets: inherit
+    uses: ./.github/workflows/test.yml
+
+  build:
+    name: Build distribution 📦
+    uses: ./.github/workflows/build.yml
+    secrets: inherit
+
+  publish-to-testpypi:
+    # Test PyPI publish, requires wheels and source dist to pass
+    name: >-
+      Publish Python 🐍 distribution 📦 to TestPyPI
+    needs: [test, build]
+    runs-on: ubuntu-latest
+
+    environment:
+        name: testpypi
+        url: https://test.pypi.org/p/ark-analysis
+
+    permissions:
+      id-token: write # Necessary for trusted publishing
+
+    steps:
+      - name: Download Built Distributions 📦
+        uses: actions/download-artifact@v4
+        with:
+          pattern: dist-*
+          merge-multiple: true
+          path: dist
+
+      - name: Publish distributions 📦 to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1.9
+        with:
+          repository-url: https://test.pypi.org/legacy/
+
+
+  publish-to-pypi:
+    # PyPI publish requires test, wheels, source dist, and testpypi to pass
+    name: >-
+      Publish Python 🐍 Distributions 📦 to PyPI
+    needs: [test, build, publish-to-testpypi]
+    runs-on: ubuntu-latest
+
+    environment:
+      name: pypi
+      url: https://pypi.org/p/ark-analysis
+
+    permissions:
+        id-token: write
+
+    # Publish when a GitHub Release is created, use the following rule:
+    if: github.event_name == 'release' && github.event.action == 'published'
+    steps:
+      - name: Download Built Distributions 📦
+        uses: actions/download-artifact@v4
+        with:
+          pattern: dist-*
+          merge-multiple: true
+          path: dist/
+
+      - name: Publish Distributions 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1.9
+
+
+  github-release-upload-dists:
+    name: >-
+      Sign the Python 🐍 distribution 📦 with Sigstore
+      and upload them to the GitHub Release
+    needs: [test, build, publish-to-testpypi, publish-to-pypi]
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write  # IMPORTANT: mandatory for making GitHub Releases
+      id-token: write  # IMPORTANT: mandatory for sigstore
+
+    steps:
+      - name: Download Built Distributions 📦
+        uses: actions/download-artifact@v4
+        with:
+          pattern: dist-*
+          merge-multiple: true
+          path: dist/
+
+      - name: Sign the dists with Sigstore
+        uses: sigstore/[email protected]
+        with:
+          inputs: >-
+            ./dist/*.tar.gz
+            ./dist/*.whl
+      - name: Upload artifact signatures to GitHub Release
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        # Upload to GitHub Release using the `gh` CLI.
+        # `dist/` contains the built packages, and the
+        # sigstore-produced signatures and certificates.
+        run: >-
+          gh release upload
+          '${{ github.ref_name }}' dist/**
+          --repo '${{ github.repository }}'

.github/workflows/test.yml

@@ -22,6 +22,7 @@ jobs:
         os: [ubuntu-latest, macos-13, windows-latest]
     env:
       GITHUB_WORKSPACE: ${{ github.workspace }}
+      cache-name: dataset-cache
 
     steps:
       - name: Checkout ${{ github.repository }}
@@ -31,11 +32,9 @@ jobs:
 
       - name: Download Example Dataset Cache
         uses: actions/cache/restore@v4
-        env:
-          cache-name: dataset
         with:
           path: ./data/cache/
-          key: huggingface-${{env.cache-name}}
+          key: huggingface-${{ env.cache-name }}
           enableCrossOsArchive: true
           fail-on-cache-miss: true
 

pyproject.toml

@@ -3,7 +3,8 @@ requires = [
     "setuptools",
     "Cython>=3",
     "numpy>=1.20,<1.24",
-    "setuptools_scm[toml]>=6",
+    "setuptools_scm>=8",
+    "build",
 ]
 build-backend = "setuptools.build_meta"
 
@@ -44,6 +45,7 @@ dependencies = [
     "xmltodict>=0.13.0,<1",
     "zstandard>=0.19.0,<1",
     "zarr",
+    "python-dateutil>=2.9.0",
     "ark-analysis[colors]",
 ]
 name = "ark-analysis"
@@ -65,6 +67,11 @@ dynamic = ["version"]
 urls = { repository = "https://github.com/angelolab/ark-analysis" }
 
 [project.optional-dependencies]
+dev = [
+    "ark-analysis[test]",
+    "build>=1.2.1",
+    "setuptools_scm[rich]>=8",
+]
 colors = [
     "palettable",
     "cmasher",

setup.py

@@ -5,6 +5,7 @@
 from Cython.Build import cythonize
 from Cython.Compiler.Options import get_directive_defaults
 from setuptools import Extension, setup
+import setuptools_scm
 
 _compiler_directives = get_directive_defaults()