Fix CI and cleanup repo

.github/workflows/publish.yml

@@ -1,33 +1,95 @@
-name: Publish Python package
+name: Build and publish the package to internal PDBe PyPi registry, DockerHub and GitLab Container Registry
+permissions:
+  contents: read
 
 on:
-  release:
-    types: [published]
-  workflow_dispatch:
+  pull_request:
+    branches:
+      - main
+  push:
+    branches:
+      - main
+    tags:
+      - "*"
 
-permissions:
-  contents: read
-  id-token: write
+env:
+  BASE_PYTHON_VERSION: &base_python_version "3.12"
 
 jobs:
-  publish:
+  build:
+    name: Lint and Test (Python ${{ matrix.python-version }})
     runs-on: ubuntu-latest
-    environment: pypi
+    strategy:
+      matrix:
+        python-version: [*base_python_version, "3.13", "3.14"]
 
     steps:
-      - name: Check out repository
-        uses: actions/checkout@v4
-
-      - name: Set up Python
-        uses: actions/setup-python@v5
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
         with:
-          python-version: "3.11"
-
-      - name: Set up UV
-        uses: astral-sh/setup-uv@v5
+            python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          uv sync --locked --group test
+      - name: Run pre-commit checks
+        uses: pre-commit/action@v3.0.1
+        if: matrix.python-version == env.BASE_PYTHON_VERSION
+      - name: Run Tests
+        run: |
+          uv run make test
 
-      - name: Build distributions
-        run: uv build
+  publish:
+    name: Publish
+    if: startsWith(github.ref, 'refs/tags/v')
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/project/pdbe-shape-retrieval
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
 
-      - name: Publish to PyPI
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+        with:
+            python-version: "${{ env.BASE_PYTHON_VERSION }}"
+      - name: Create distribution
+        run: |
+          uv build
+      - name: Publish to internal PyPi
+        run: |
+          pip install twine
+          TWINE_PASSWORD=${{ secrets.TWINE_PASSWORD }} TWINE_USERNAME=${{ secrets.TWINE_USERNAME }} python -m twine upload --repository-url ${{ secrets.PIP_INDEX_URL }} dist/*
+      - name: Publish to public PyPi
         uses: pypa/gh-action-pypi-publish@release/v1
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      - name: Login to DockerHub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+      - name: Extract Docker tag from GitHub ref
+        run: echo "DOCKER_TAG=${GITHUB_REF_NAME#v}" >> $GITHUB_ENV
+      - name: Build and push
+        uses: docker/build-push-action@v6
+        with:
+          push: true
+          platforms: linux/amd64,linux/arm64/v8
+          tags: |
+            ${{ secrets.DOCKER_USERNAME }}/pdbe-shape-retrieval:${{ env.DOCKER_TAG }}
+            ${{ secrets.DOCKER_USERNAME }}/pdbe-shape-retrieval:latest
+      - name: Login to GitLab Container Registry
+        run: echo ${{ secrets.REGISTRY_PASSWORD }} | docker login -u ${{ secrets.REGISTRY_USERNAME }} --password-stdin ${{ vars.REGISTRY_URL }}
+      - name: Build and tag Docker image
+        run: docker build -t ${{ vars.REGISTRY_URL }}/${{ secrets.REGISTRY_USERNAME }}/packages/pdbe-shape-retrieval:latest -t ${{ vars.REGISTRY_URL }}/${{ secrets.REGISTRY_USERNAME }}/packages/pdbe-shape-retrieval:${{ env.DOCKER_TAG }} .
+      - name: Push Docker image to GitLab Container Registry
+        run: |
+          docker push ${{ vars.REGISTRY_URL }}/${{ secrets.REGISTRY_USERNAME }}/packages/pdbe-shape-retrieval:latest
+          docker push ${{ vars.REGISTRY_URL }}/${{ secrets.REGISTRY_USERNAME }}/packages/pdbe-shape-retrieval:${{ env.DOCKER_TAG }}

.gitignore

@@ -2,8 +2,6 @@
 **/.vscode/
 .idea/
 Pipfile
-# Vagrant
-.vagrant/
 
 # Mac/OSX
 .DS_Store
@@ -40,16 +38,6 @@ wheels/
 *.egg
 MANIFEST
 
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
 # Unit test / coverage reports
 htmlcov/
 .tox/
@@ -59,72 +47,13 @@ htmlcov/
 .cache
 nosetests.xml
 coverage.xml
+report.xml
 *.cover
 .hypothesis/
 .pytest_cache/
 
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-db.sqlite3
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-target/
-
 # Jupyter Notebook
 .ipynb_checkpoints
 
-# IPython
-profile_default/
-ipython_config.py
-
-# pyenv
-.python-version
-
-# celery beat schedule file
-celerybeat-schedule
-
-# SageMath parsed files
-*.sage.py
-
 # Environments
-.env
 .venv
-env/
-venv/
-ENV/
-env.bak/
-venv.bak/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-.dmypy.json
-dmypy.json
-.envrc
-
-
-TODO

.pre-commit-config.yaml

@@ -1,6 +1,12 @@
+default_install_hook_types:
+  - pre-commit
+  - post-checkout
+  - post-merge
+  - post-rewrite
+
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.1.0
+    rev: v6.0.0
     hooks:
       - id: check-yaml
       - id: check-added-large-files
@@ -12,23 +18,13 @@ repos:
       - id: fix-byte-order-marker
       - id: end-of-file-fixer
       - id: check-ast
-      - id: no-commit-to-branch
-  - repo: https://gitlab.com/pycqa/flake8
-    rev: 4.0.1
+  - repo: https://github.com/astral-sh/uv-pre-commit
+    rev: 0.11.28
     hooks:
-      - id: flake8
-        additional_dependencies: [flake8-bugbear==21.4.3]
-  - repo: https://github.com/asottile/blacken-docs
-    rev: v1.12.0
+      - id: uv-lock
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.20
     hooks:
-      - id: blacken-docs
-        additional_dependencies: [black==20.8b1]
-  - repo: https://github.com/pycqa/isort
-    rev: 5.10.1
-    hooks:
-      - id: isort
-        name: isort (python)
-  - repo: https://github.com/psf/black
-    rev: 21.12b0
-    hooks:
-      - id: black
+      - id: ruff-check
+        args: [ --fix ]
+      - id: ruff-format

.python-version

@@ -0,0 +1 @@
+3.12

Dockerfile

@@ -1,23 +1,43 @@
-FROM python:3.11-slim
+# Inspired from https://github.com/astral-sh/uv-docker-example/blob/5748835918ec293d547bbe0e42df34e140aca1eb/multistage.Dockerfile
+FROM ghcr.io/astral-sh/uv:python3.12-bookworm-slim AS builder
 
-ENV PYTHONUNBUFFERED=1 \
-    PIP_NO_CACHE_DIR=1 \
-    MAP2ZERNIKE_SETUP_DIR=/usr/local/bin \
-    OBJ2GRID_PATH=/usr/local/bin/obj2grid \
-    PATH="/usr/local/bin:${PATH}"
+ENV UV_COMPILE_BYTECODE=1 UV_LINK_MODE=copy
+
+# Omit development dependencies
+ENV UV_NO_DEV=1
+
+ENV UV_PYTHON_DOWNLOADS=0
+
+ARG PIP_INDEX_URL
+ENV UV_DEFAULT_INDEX=$PIP_INDEX_URL
+ENV UV_EXTRA_INDEX_URL=https://pypi.org/simple
 
 WORKDIR /app
+COPY pyproject.toml uv.lock /app/
+RUN uv sync --locked --no-install-project --no-dev
+
+COPY shape_retrieval /app/shape_retrieval
+RUN uv tool install shape_retrieval
+
+FROM python:3.12-slim-bookworm
+LABEL maintainer="Sreenath Sasidharan Nair <sreenath@ebi.ac.uk>"
 
-RUN apt-get update \
-    && apt-get install -y --no-install-recommends libgl1 libglib2.0-0 libgomp1 \
-    && rm -rf /var/lib/apt/lists/*
+RUN groupadd --system --gid 101 nonroot \
+    && useradd --system --gid 101 --uid 101 --create-home nonroot
 
-RUN python -m pip install --upgrade pip uv
+COPY --from=builder --chown=nonroot:nonroot /app /app
 
-COPY . /app
+ENV PATH="/app/.venv/bin:$PATH"
 
-RUN install -m 0755 /app/bin/map2zernike /usr/local/bin/map2zernike \
-    && install -m 0755 /app/bin/obj2grid /usr/local/bin/obj2grid \
-    && uv pip install --system .
+ENV PYTHONDONTWRITEBYTECODE=1
+ENV PYTHONUNBUFFERED=1
+
+# Disable core dumps
+RUN echo -e "* soft core 0\n* hard core 0" >> /etc/security/limits.conf
+
+USER nonroot
+
+# Set the working directory to /app
+WORKDIR /app
 
-ENTRYPOINT ["shape_retrieval"]
+CMD ["shape_retrieval"]

LICENSE

@@ -10,4 +10,3 @@ software distributed under the License is distributed on an
 either express or implied. See the License for the specific
 language governing permissions and limitations under the
 License.
-