fix(ci): resolve all GitHub Actions workflow failures

- Replace cache-dependency-glob "uv.lock" with "**/pyproject.toml" since
  uv.lock is gitignored (build.yml, test.yml, release.yml)
- Pin numba>=0.59.0 and llvmlite>=0.43.0 in scientific/ml/singlecell/performance
  extras to fix Python 3.12 compatibility (llvmlite 0.36.0 only supports <3.10)
- Replace uv add --dev with uv pip install for CI-only deps (build, twine, sphinx)
- Rewrite fat-filesystem-test to use astral-sh/setup-uv@v3 instead of building
  uv from Rust source (container lacked cargo)
- Remove broken "uv add --dev --group test" line (no package specified)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: docxology

.github/workflows/build.yml

@@ -37,15 +37,14 @@ jobs:
       with:
         version: "latest"
         enable-cache: true
-        cache-dependency-glob: "uv.lock"
+        cache-dependency-glob: "**/pyproject.toml"
 
     - name: Set up Python ${{ matrix.python-version }}
       run: uv python install ${{ matrix.python-version }}
 
     - name: Install build dependencies
       run: |
-        uv add --dev build twine
-        uv add --dev --group test  # For build validation tests
+        uv pip install build twine
 
     - name: Build package
       run: |

.github/workflows/release.yml

@@ -68,13 +68,13 @@ jobs:
       with:
         version: "latest"
         enable-cache: true
-        cache-dependency-glob: "uv.lock"
+        cache-dependency-glob: "**/pyproject.toml"
 
     - name: Set up Python 3.12
       run: uv python install 3.12
 
     - name: Install build dependencies
-      run: uv add --dev build twine
+      run: uv pip install build twine
 
     - name: Build distribution packages
       run: bash scripts/package/build.sh --check
@@ -115,7 +115,7 @@ jobs:
 
     - name: Install documentation dependencies
       run: |
-        uv add --dev sphinx sphinx-autodoc-typehints myst-parser nbsphinx
+        uv pip install sphinx sphinx-autodoc-typehints myst-parser nbsphinx
 
     - name: Build documentation
       run: bash scripts/package/uv_docs.sh build

.github/workflows/test.yml

@@ -54,7 +54,7 @@ jobs:
       with:
         version: "latest"
         enable-cache: true
-        cache-dependency-glob: "uv.lock"
+        cache-dependency-glob: "**/pyproject.toml"
 
     - name: Set up Python ${{ matrix.python-version }}
       run: uv python install ${{ matrix.python-version }}
@@ -187,7 +187,7 @@ jobs:
       with:
         version: "latest"
         enable-cache: true
-        cache-dependency-glob: "uv.lock"
+        cache-dependency-glob: "**/pyproject.toml"
 
     - name: Set up Python 3.12
       run: uv python install 3.12
@@ -218,37 +218,29 @@ jobs:
 
   fat-filesystem-test:
     runs-on: ubuntu-latest
-    container:
-      image: ubuntu:latest
-      options: --tmpfs /tmp:rw,noexec,nosuid,size=100m
     steps:
     - name: Checkout code
       uses: actions/checkout@v4
 
     - name: Install uv
-      uses: actions/checkout@v4
+      uses: astral-sh/setup-uv@v3
       with:
-        repository: astral-sh/uv
-        path: uv-install
+        version: "latest"
 
-    - name: Set up uv
-      run: |
-        cd uv-install
-        cargo build --release
-        sudo cp target/release/uv /usr/local/bin/
+    - name: Set up Python 3.12
+      run: uv python install 3.12
 
     - name: Create FAT-like filesystem simulation
       run: |
-        # Simulate FAT filesystem limitations
-        sudo mkdir -p /tmp/fat_test
-        sudo mount -t tmpfs -o size=1g,nr_inodes=1000 tmpfs /tmp/fat_test
-        cd /tmp/fat_test
-        git clone ${{ github.server_url }}/${{ github.repository }} .
+        # Simulate FAT filesystem limitations using tmpfs
+        sudo mkdir -p /mnt/fat_test
+        sudo mount -t tmpfs -o size=1g,nr_inodes=1000 tmpfs /mnt/fat_test
+        sudo cp -a . /mnt/fat_test/
 
     - name: Test on simulated FAT filesystem
       run: |
-        cd /tmp/fat_test
-        bash scripts/package/setup.sh
+        cd /mnt/fat_test
+        bash scripts/package/setup.sh --skip-tests
         bash scripts/package/test.sh --mode fast
 
   summary:

pyproject.toml

@@ -36,6 +36,8 @@ scientific = [
     "scikit-learn>=1.3.0",
     "seaborn>=0.13.0",
     "networkx>=3.2",
+    "numba>=0.59.0",  # JIT compilation, must be >=0.59 for Python 3.12
+    "llvmlite>=0.43.0",  # Required by numba, must be >=0.43 for Python 3.12
     "umap-learn>=0.5.4",
     "scanpy>=1.9.6",  # Single-cell analysis
     "anndata>=0.10.0",  # Annotated data structures
@@ -45,6 +47,7 @@ scientific = [
 ml = [
     "scipy>=1.11.0",
     "scikit-learn>=1.3.0",
+    "numba>=0.59.0",  # Required by umap-learn, must be >=0.59 for Python 3.12
     "umap-learn>=0.5.4",
     "optuna>=3.4.0",  # Hyperparameter optimization
     "joblib>=1.3.0",  # Parallel processing
@@ -66,6 +69,7 @@ singlecell = [
     "anndata>=0.10.0",
     "scipy>=1.11.0",
     "scikit-learn>=1.3.0",
+    "numba>=0.59.0",  # Required by umap-learn, must be >=0.59 for Python 3.12
     "umap-learn>=0.5.4",
     "seaborn>=0.13.0",
     "leidenalg>=0.10.0",  # Leiden clustering
@@ -128,7 +132,7 @@ scraping = [
 
 # Performance and parallel computing
 performance = [
-    "numba>=0.56.0",  # JIT compilation
+    "numba>=0.59.0",  # JIT compilation, must be >=0.59 for Python 3.12
     "dask>=2022.8.0",  # Parallel computing
     "ray>=2.0.0",  # Distributed computing
     "joblib>=1.2.0",  # Parallel processing