[Bug, Update]: tf.keras.Sequential error, uv, ruff, python 3.10, 3.11, 3.12, 3.13

.github/workflows/deploy-docs.yml

@@ -15,22 +15,21 @@ jobs:
 
     steps:
       - name: "Checkout"
-        uses: actions/checkout@v3
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
       - name: "Set up Python"
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v6
         with:
-          python-version: '3.10'
+          python-version-file: pyproject.toml
+
+      - name: "Set up uv"
+        uses: astral-sh/setup-uv@v6
 
       - name: "Install Dependencies"
         run: |
-          python -m pip install --upgrade pip
-          pip install mkdocs mkdocs-material numkdoc mike
-          pip install -r requirements.txt
-          pip install torch
-          pip install -e .
+          uv pip install --system -r pyproject.toml --group dev .
 
       - name: "Setup Docs Deploy"
         run: |
@@ -39,5 +38,5 @@ jobs:
 
       - name: "Deploy Github Pages"
         run: |
-          mike deploy --push --update-aliases ${{ github.event.release.tag_name }} latest
-          mike set-default --push latest
+          uv run mike deploy --push --update-aliases ${{ github.event.release.tag_name }} latest
+          uv run mike set-default --push latest

.github/workflows/python-lints.yml

@@ -1,26 +1,23 @@
-name: pylint
+name: ruff
 
 on:
   pull_request:
   workflow_dispatch:
 
 jobs:
   checks:
-    runs-on: ubuntu-22.04
-    strategy:
-      max-parallel: 4
-      matrix:
-        python-version: [3.7.14, 3.8, 3.9, "3.10"]
+    runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v1
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install tox
-    - name: Check lint
-      run: tox -e py$(echo ${{ matrix.python-version }} | tr -d .)-lint
+      - uses: actions/checkout@v6
+      - name: Set up Python 3.13
+        uses: actions/setup-python@v6
+        with:
+          python-version: 3.13
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v6
+      - name: Install dependencies
+        run: |
+          uv pip install --system tox tox-uv
+      - name: Check lint
+        run: tox -e py313-lint

.github/workflows/python-publish.yml

@@ -9,19 +9,20 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: '3.x'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel twine
-    - name: Build and publish
-      env:
-        TWINE_USERNAME: __token__
-        TWINE_PASSWORD: ${{ secrets.XPLIQUE_TOKEN }}
-      run: |
-        python setup.py sdist bdist_wheel
-        twine upload dist/*
+      - uses: actions/checkout@v6
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: '3.x'
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v6
+      - name: Install dependencies
+        run: |
+          uv pip install --system build twine
+      - name: Build and publish
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.XPLIQUE_TOKEN }}
+        run: |
+          uv run python -m build
+          uv run twine upload dist/*

.github/workflows/python-tests.yml

@@ -6,29 +6,47 @@ on:
 
 jobs:
   checks:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     strategy:
       max-parallel: 4
       matrix:
         include:
-            - python-version: 3.7.14
-              tf-version: 2.2
-            - python-version: 3.8.12
-              tf-version: 2.5
-            - python-version: 3.9
-              tf-version: 2.8
-            - python-version: "3.10"
-              tf-version: 2.11
+          # Matches tox.ini (non-torch envs only)
+          - python-version: "3.10"
+            toxenv: py310-tf218
+          - python-version: "3.10"
+            toxenv: py310-tf219
+          - python-version: "3.10"
+            toxenv: py310-tf220
+
+          - python-version: "3.11"
+            toxenv: py311-tf218
+          - python-version: "3.11"
+            toxenv: py311-tf219
+          - python-version: "3.11"
+            toxenv: py311-tf220
+
+          - python-version: "3.12"
+            toxenv: py312-tf218
+          - python-version: "3.12"
+            toxenv: py312-tf219
+          - python-version: "3.12"
+            toxenv: py312-tf220
+
+          - python-version: "3.13"
+            toxenv: py313-tf220
 
     steps:
-    - uses: actions/checkout@v1
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install tox
-    - name: Test with tox (Python ${{ matrix.python-version }} - TF ${{ matrix.tf-version }})
-      run: tox -e py$(echo ${{ matrix.python-version }}-tf${{ matrix.tf-version }} | tr -d .)
+      - uses: actions/checkout@v6
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v6
+      - name: Create virtualenv and install tox
+        run: |
+          uv venv
+          . .venv/bin/activate
+          uv pip install --upgrade pip
+          uv pip install tox tox-uv
+      - name: Test with tox (${{ matrix.toxenv }})
+        run: |
+          . .venv/bin/activate
+          tox -e ${{ matrix.toxenv }}

.github/workflows/python-torch.yml

@@ -1,47 +1,69 @@
-name: tests for torch
+name: tests torch
 
 on:
   pull_request:
   workflow_dispatch:
 
 jobs:
+  discover-tox-envs:
+    runs-on: ubuntu-latest
+    outputs:
+      matrix: ${{ steps.build-matrix.outputs.matrix }}
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Set up Python (from pyproject)
+        uses: actions/setup-python@v6
+        with:
+          python-version-file: pyproject.toml
+
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v6
+
+      - name: Install tox tooling
+        run: |
+          uv pip install --system tox tox-uv pytest
+
+      - name: Build matrix from tox.ini
+        id: build-matrix
+        run: |
+          python - <<'PY'
+          import json
+          import os
+          import subprocess
+
+          envs = subprocess.check_output(["tox", "-l"], text=True).splitlines()
+          envs = [e.strip() for e in envs if e.strip().startswith("py")]
+          envs = [e for e in envs if "-torch" in e]
+
+          matrix = {"toxenv": envs}
+          with open(os.environ["GITHUB_OUTPUT"], "a", encoding="utf-8") as f:
+              f.write(f"matrix={json.dumps(matrix)}\n")
+          PY
+
   checks:
+    needs: discover-tox-envs
     runs-on: ubuntu-latest
+    # The 'fail-fast' strategy option determines whether to cancel all in-progress jobs
+    # if any matrix job fails. When set to 'false', failed jobs do not cancel other
+    # running jobs, allowing all matrix combinations to complete independently.
+    # This is useful for testing across multiple configurations to see all failures.
     strategy:
-      max-parallel: 4
+      fail-fast: false
       matrix:
-        include:
-            - python-version: 3.8
-              tf-version: 2.5
-              torch-version: 1.11
-            - python-version: 3.8
-              tf-version: 2.8
-              torch-version: 1.11
-            - python-version: 3.8
-              tf-version: 2.11
-              torch-version: 1.11
-            - python-version: 3.9
-              tf-version: 2.8
-              torch-version: 1.13
-            - python-version: 3.9
-              tf-version: 2.11
-              torch-version: 1.13
-            - python-version: "3.10"
-              tf-version: 2.8
-              torch-version: 2.0.0
-            - python-version: "3.10"
-              tf-version: 2.11
-              torch-version: 2.0.0
+        toxenv: ${{ fromJson(needs.discover-tox-envs.outputs.matrix).toxenv }}
 
     steps:
-    - uses: actions/checkout@v1
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install tox
-    - name: Test with tox (Python ${{ matrix.python-version }} - TF ${{ matrix.tf-version }} - PyTorch ${{ matrix.torch-version }})
-      run: tox -e py$(echo ${{ matrix.python-version }}-tf${{ matrix.tf-version }}-torch${{matrix.torch-version}} | tr -d .)
+      - uses: actions/checkout@v6
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v6
+      - name: Create virtualenv and install tox
+        run: |
+          uv venv
+          . .venv/bin/activate
+          uv pip install --upgrade pip
+          uv pip install tox tox-uv
+      - name: Test with tox (${{ matrix.toxenv }})
+        run: |
+          . .venv/bin/activate
+          tox -e ${{ matrix.toxenv }}

.gitignore

@@ -31,6 +31,7 @@ pip-delete-this-directory.txt
 # Unit test / coverage reports
 htmlcov/
 .tox/
+tox.out
 .nox/
 .coverage
 .coverage.*

.pre-commit-config.yaml

@@ -1,10 +1,18 @@
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
+    rev: v6.0.0
     hooks:
     -   id: trailing-whitespace
     -   id: check-added-large-files
     -   id: check-ast
     -   id: check-docstring-first
     -   id: check-merge-conflict
     -   id: end-of-file-fixer
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.2
+    hooks:
+    -   id: ruff-check
+        args: [".", "--fix"]
+
+    -   id: ruff-format
+        args: ["."]