Switch to uv min/max dependency resolution.

Rather than our custom script. This matches what we do in TabPFN.

Author: oscarkey

.github/workflows/pull_request.yml

@@ -35,23 +35,23 @@ jobs:
         include:
           - os: ubuntu-latest
             python-version: "3.9"
-            dependency-set: minimum
+            dependency-set: lowest-direct
           - os: macos-15-intel # We need x86 as ARM is  python>= 3.11 only.
             # https://github.com/actions/setup-python/issues/855
             python-version: "3.9"
-            dependency-set: minimum
+            dependency-set: lowest-direct
           - os: windows-latest
             python-version: "3.9"
-            dependency-set: minimum
+            dependency-set: lowest-direct
           - os: ubuntu-latest
             python-version: "3.13"
-            dependency-set: maximum
+            dependency-set: highest
           - os: macos-latest
             python-version: "3.13"
-            dependency-set: maximum
+            dependency-set: highest
           - os: windows-latest
             python-version: "3.13"
-            dependency-set: maximum
+            dependency-set: highest
     runs-on: ${{ matrix.os }}
 
     env:
@@ -71,23 +71,8 @@ jobs:
         with:
           enable-cache: true
 
-      - name: Generate requirements file
-        run: python scripts/generate_dependencies.py ${{ matrix.dependency-set }}
-
       - name: Install dependencies
-        run: |
-          uv pip install --system ".[all]"
-          # onnx is required for onnx export tests
-          # we don't install all dev dependencies here for speed
-          uv pip install --system -r requirements.txt
-          uv pip install --system pytest psutil
-          # licensecheck is required for license checking
-          uv pip install --system licensecheck
-          # onnx is not supported on python 3.13 yet https://github.com/onnx/onnx/issues/6339
-          if [[ "${{ matrix.python-version }}" != "3.13" ]]; then
-            uv pip install --system onnx
-          fi
-        shell: bash
+        run: uv sync --all-extras --group ci --resolution ${{ matrix.dependency-set }}
 
       - name: Restore model cache
         id: restore-model-cache
@@ -105,12 +90,13 @@ jobs:
         env:
           HF_TOKEN: ${{ secrets.HF_TOKEN }}
           TABPFN_TOKEN: ${{ secrets.TABPFN_TOKEN }}
-        run: python scripts/download_all_models.py
+        run: uv run --no-sync python scripts/download_all_models.py
 
       - name: Check for forbidden licenses
         if: runner.os == 'MacOS' && matrix.python-version == '3.9'
+        shell: bash
         run: |
-          licensecheck \
+          uv run --no-sync licensecheck \
             --requirements-paths pyproject.toml \
             --only-licenses APACHE MIT BSD ISC PYTHON UNLICENSE UNKNOWN \
             --ignore-packages certifi "tabpfn*" \
@@ -122,13 +108,13 @@ jobs:
         env:
           TABPFN_EXCLUDE_DEVICES: mps
         run: |
-          FAST_TEST_MODE=1 pytest tests/
+          FAST_TEST_MODE=1 uv run --no-sync pytest tests/
 
       - name: Run Tests (Windows)
         if: runner.os == 'Windows'
         run: |
           $env:FAST_TEST_MODE = 1
-          pytest tests/
+          uv run --no-sync pytest tests/
 
       - name: Save model cache
         if: github.ref == 'refs/heads/main'

pyproject.toml

@@ -81,30 +81,25 @@ unsupervised = []
 
 # Meta-package that installs all extensions
 all = [
-    "shap>=0.41.0",
-    "shapiq>=0.4.0",
-    "seaborn>=0.12.2",
-
-    "llvmlite>=0.30.0",
-    "hyperopt>=0.2.7",
-    # https://discuss.python.org/t/pkg-resources-removal-how-to-go-from-there/106079
-    "setuptools>=67.0.0,<82",
-    "autogluon.tabular==1.4.0",
-
-    "scikit-survival>=0.25.0; python_version >= '3.10'",
+    "tabpfn-extensions[interpretability,post_hoc_ensembles,hpo,survival]",
 ]
 
 [dependency-groups]
+# The minimum subset of the dev dependencies required to run the tests on the CI.
+# The idea is to be as close to the deployment environment as possible.
+ci = [
+    "pytest>=8.0.0",
+    "licensecheck>=2025.1.0",
+]
 dev = [
+    {include-group = "ci"},
     "pre-commit>=3.0.0",
     "ruff==0.8.6", # This must be the same version as in .pre-commit-config.yaml
     "mypy>=1.0.0",
-    "pytest>=8.0.0",
     "pytest-xdist>=3.6.0",
     "pytest-mock>=3.15.1",
     "build>=1.3.0",
     "twine>=6.2.0",
-    "licensecheck>=2025.1.0",
 ]
 
 [tool.pytest.ini_options]