[Chore] update project metadata + CI

Author: nx10

.github/workflows/docs.yaml

@@ -1,7 +1,15 @@
 name: Build and publish docs
 
 permissions:
-  contents: write
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  # Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+  # However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+  group: pages
+  cancel-in-progress: false
 
 on:
   workflow_run:
@@ -10,25 +18,38 @@ on:
     - completed
     branches:
     - main
+  workflow_dispatch:
+
 
 jobs:
   build-and-publish-docs:
     if: ${{ github.event.workflow_run.conclusion == 'success' }}
     runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
     steps:
     - uses: actions/checkout@v4
-    - uses: actions/setup-python@v5
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
+      with:
+        enable-cache: true
+    - name: Set up Python
+      uses: actions/setup-python@v5
       with:
         python-version-file: pyproject.toml
-    - name: Install dependencies
-      run: |
-        python -m pip install poetry
-        poetry install --with docs
+    - name: Install the project
+      run: uv sync --only-group docs
     - name: Build docs
       run: |
         APP_MODULE_NAME=$(ls src -U | head -1)  # Get the first module name in the src directory
-        poetry run pdoc src/"$APP_MODULE_NAME" -o docs_build -t docs/pdoc-theme --docformat google
-        touch docs_build/.nojekyll
-    - uses: JamesIves/github-pages-deploy-action@v4
+        uv run pdoc src/"$APP_MODULE_NAME" -o docs_build -t docs/pdoc-theme --docformat google
+    - name: Setup Pages
+      uses: actions/configure-pages@v5
+    - name: Upload artifact
+      uses: actions/upload-pages-artifact@v4
       with:
-        folder: docs_build
+        path: ./docs_build
+    - name: Deploy to GitHub Pages
+      id: deployment
+      uses: actions/deploy-pages@v4

.github/workflows/publish-pypi.yaml

@@ -15,16 +15,16 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
-    - name: Install poetry
-      run: pipx install poetry
-    - uses: actions/setup-python@v5
+
+    - name: Setup uv
+      uses: astral-sh/setup-uv@v6
       with:
-        python-version-file: pyproject.toml
-        cache: poetry
+        enable-cache: true
+
     - name: Install dependencies and build
       run: |
-        poetry install
-        poetry build
+        uv sync --frozen --no-dev --no-install-project
+        uv build
 
     - name: Publish to PyPi
       id: pypi_publish

.github/workflows/test.yaml

@@ -11,27 +11,25 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - name: Install poetry
-      run: pipx install poetry
-    - uses: actions/setup-python@v5
+
+    - name: Setup uv
+      uses: astral-sh/setup-uv@v6
       with:
-        python-version-file: pyproject.toml
-        cache: poetry
-    - name: Install dependencies
-      run: |
-        poetry install
+        enable-cache: true
+
     - name: Run tests
       id: run-tests
       run: >
-        poetry run pytest \
+        uv run --frozen pytest \
           --junitxml=pytest.xml \
           --cov-report=term-missing:skip-covered \
           --cov-report=xml:coverage.xml \
           --cov=src tests \
           --log-level=DEBUG \
           --verbose
+
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         verbose: true
@@ -40,30 +38,26 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - name: Install poetry
-      run: pipx install poetry
-    - uses: actions/setup-python@v5
+
+    - name: Setup uv
+      uses: astral-sh/setup-uv@v6
       with:
-        python-version-file: pyproject.toml
-        cache: poetry
-    - name: Install dependencies
-      run: |
-        poetry install
+        enable-cache: true
+
     - name: Ruff format
-      run: poetry run ruff format --check
+      run: uv run ruff format --check
+
     - name: Ruff check
-      run: poetry run ruff check
+      run: uv run ruff check
 
   mypy:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - name: Install poetry
-      run: pipx install poetry
-    - uses: actions/setup-python@v5
+
+    - name: Setup uv
+      uses: astral-sh/setup-uv@v6
       with:
-        python-version: '3.11'
-        cache: poetry
-    - run: |
-        poetry install
-        poetry run mypy .
+        enable-cache: true
+
+    - run: uv run mypy .

.pre-commit-config.yaml

@@ -1,38 +1,33 @@
 fail_fast: false
 
 repos:
-- repo: https://github.com/python-poetry/poetry
-  rev: 2.1.1
-  hooks:
-  - id: poetry-check
-
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.9.6
+  rev: v0.12.10
   hooks:
   - id: ruff
   - id: ruff-format
 
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.15.0
+  rev: v1.17.1
   hooks:
   - id: mypy
     args: [--ignore-missing-imports]
 - repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
-  rev: v2.14.0
+  rev: v2.15.0
   hooks:
   - id: pretty-format-yaml
     args:
     - --autofix
     - --indent=2
   - id: pretty-format-toml
-    exclude: ^poetry.lock$
+    exclude: ^uv.lock$
     args:
     - --autofix
     - --indent=2
     - --no-sort
 
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v5.0.0
+  rev: v6.0.0
   hooks:
   - id: check-case-conflict
   - id: end-of-file-fixer
@@ -42,6 +37,7 @@ repos:
     - --autofix
     - --indent=4
     - --no-sort-keys
+    exclude_types: [jupyter]
   - id: check-merge-conflict
   - id: check-yaml
   - id: check-json

README.md

@@ -1,11 +1,11 @@
 # Singularity/Apptainer Runner for Styx compiled wrappers
 
-[![Build](https://github.com/childmindresearch/styxsingularity/actions/workflows/test.yaml/badge.svg?branch=main)](https://github.com/childmindresearch/styxsingularity/actions/workflows/test.yaml?query=branch%3Amain)
-[![codecov](https://codecov.io/gh/childmindresearch/styxsingularity/branch/main/graph/badge.svg?token=22HWWFWPW5)](https://codecov.io/gh/childmindresearch/styxsingularity)
+[![Build](https://github.com/styx-api/styxsingularity/actions/workflows/test.yaml/badge.svg?branch=main)](https://github.com/styx-api/styxsingularity/actions/workflows/test.yaml?query=branch%3Amain)
+[![codecov](https://codecov.io/gh/styx-api/styxsingularity/branch/main/graph/badge.svg?token=22HWWFWPW5)](https://codecov.io/gh/styx-api/styxsingularity)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 ![stability-stable](https://img.shields.io/badge/stability-stable-green.svg)
-[![MIT License](https://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/childmindresearch/styxsingularity/blob/main/LICENSE)
-[![pages](https://img.shields.io/badge/api-docs-blue)](https://childmindresearch.github.io/styxsingularity)
+[![MIT License](https://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/styx-api/styxsingularity/blob/main/LICENSE)
+[![pages](https://img.shields.io/badge/api-docs-blue)](https://styx-api.github.io/styxsingularity)
 
 `styxsingularity` is a Python package that provides Singularity/Apptainer integration for Styx compiled wrappers. It allows you to run Styx functions within Singularity containers, offering improved isolation and reproducibility for your workflows.
 
@@ -63,28 +63,28 @@ runner = SingularityRunner(
 
 ## Contributing
 
-Contributions to `styxsingularity` are welcome! Please refer to the [GitHub repository](https://github.com/childmindresearch/styxsingularity) for information on how to contribute, report issues, or submit pull requests.
+Contributions to `styxsingularity` are welcome! Please refer to the [GitHub repository](https://github.com/styx-api/styxsingularity) for information on how to contribute, report issues, or submit pull requests.
 
 ## License
 
 `styxsingularity` is released under the MIT License. See the LICENSE file for details.
 
 ## Documentation
 
-For detailed API documentation, please visit our [API Docs](https://childmindresearch.github.io/styxsingularity).
+For detailed API documentation, please visit our [API Docs](https://styx-api.github.io/styxsingularity).
 
 ## Support
 
-If you encounter any issues or have questions, please open an issue on the [GitHub repository](https://github.com/childmindresearch/styxsingularity).
+If you encounter any issues or have questions, please open an issue on the [GitHub repository](https://github.com/styx-api/styxsingularity).
 
 ## Requirements
 
 - Python 3.10+
 - Singularity or Apptainer installed and running on your system
 
-## Comparison with [`styxdocker`](https://github.com/childmindresearch/styxdocker)
+## Comparison with [`styxdocker`](https://github.com/styx-api/styxdocker)
 
-While [`styxdocker`](https://github.com/childmindresearch/styxdocker) and [`styxsingularity`](https://github.com/childmindresearch/styxsingularity) serve similar purposes, they have some key differences:
+While [`styxdocker`](https://github.com/styx-api/styxdocker) and [`styxsingularity`](https://github.com/styx-api/styxsingularity) serve similar purposes, they have some key differences:
 
 - Container Technology: `styxdocker` uses Docker, while `styxsingularity` uses Singularity/Apptainer.
 - Platform Support: `styxdocker` works on Windows, Linux, and macOS, whereas `styxsingularity` is not supported on Windows.