foldmatch 0.1.0__tar.gz

foldmatch-0.1.0/.dockerignore

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+# Only list files that could be under version control or could be created in CI/CD.
+
+# Note: Patterns are absolute, like `.prettierignore` but unlike `.gitignore`.
+
+# Gitignored files
+**/.*
+**/[~#$]*
+**/*[~#$]
+
+# Gitignored directories
+node_modules/
+
+# Directories
+/dist/
+/tests/
+/assets/
+/examples/
+
+# Files in the root directory
+/*.md
+/*.txt
+/CITATION.cff
+/compose.yaml
+/justfile
+/mkdocs.yaml
+/uv.lock
+
+# Keep README.md (needed for build)
+!/README.md
+
+# Keep .dockerignore and .gitignore
+!/.dockerignore
+!/.gitignore
+
+# Keep legal files
+!/LICENSE.*
+!/NOTICE.txt

foldmatch-0.1.0/.github/workflows/_workflow-docker.yaml

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+# Docker build and push workflow
+
+name: Run CI/CD Docker Workflow
+
+on:
+  workflow_call:
+
+jobs:
+  run-workflow:
+    if: github.event_name == 'release'
+    name: "Run automated docker workflow"
+    uses: rcsb/devops-cicd-github-actions/.github/workflows/workflow-docker.yaml@master
+    with:
+      dockerfile_location: "Dockerfile"  # The location of the Dockerfile relative to the root of the repository. Defaults to "Dockerfile".
+      repo_project: "rcsb"  # REQUIRED. The name of the project or organization in the remote Docker image repository.
+      docker_image_name: "foldmatch"  # REQUIRED. The name of the Docker image to create.
+      docker_build_context: "."  # The path location of the docker build context, relative to the project root. Defaults to the project root.

foldmatch-0.1.0/.github/workflows/publish.yaml

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+name: CI Pipeline
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+  release:
+    types: [published]
+
+jobs:
+
+  hatch-test:
+    name: Test on Python ${{ matrix.python-version }}
+    runs-on: ["self-hosted", "buildchain"]
+    timeout-minutes: 20
+    strategy:
+      matrix:
+        python-version: ["3.12"]
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Install build dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y build-essential pkg-config libzstd-dev
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Hatch and HaggingFace
+        run: pip install hatch huggingface_hub[cli]
+
+      - name: Run tests
+        run: hatch test
+
+  hatch-build:
+    name: Build to PyPI
+    needs:
+      - hatch-test
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release'
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.12"
+
+      - name: Install Hatch
+        run: pip install hatch
+
+      - name: Build distribution
+        run: hatch build
+
+      - name: Store the distribution packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+  push-image:
+    needs:
+      - hatch-build
+    name: Push image to harbor
+    uses: ./.github/workflows/_workflow-docker.yaml
+
+  publish-to-pypi:
+    name: >-
+      Publish Python 🐍 distribution 📦 to PyPI
+    if: github.event_name == 'release'
+    needs:
+      - push-image
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/foldmatch
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

foldmatch-0.1.0/.gitignore

@@ -0,0 +1,7 @@
+/.idea
+/rcsb-embedding-model.iml
+/dist/
+/.pypi.rc
+__pycache__
+/tests/resources/tmp
+/.claude

foldmatch-0.1.0/Dockerfile

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+# Build stage
+FROM python:3.12-slim AS builder
+
+WORKDIR /app
+
+# Copy only necessary files for installation
+COPY pyproject.toml README.md LICENSE.md ./
+COPY src/ ./src/
+
+# Install build dependencies, build, strip, and cleanup in one layer
+# hadolint ignore=DL3008
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends gcc g++ binutils && \
+    pip install --no-cache-dir -e . && \
+    # Strip binaries immediately to reduce size before copying
+    find /usr/local/lib/python3.12 -name "*.so" -exec strip --strip-unneeded {} \; 2>/dev/null || true && \
+    find /usr/local/lib/python3.12 -type f -executable -exec strip --strip-unneeded {} \; 2>/dev/null || true && \
+    # Remove unnecessary files in builder stage
+    find /usr/local/lib/python3.12 -type d -name "tests" -exec rm -rf {} + 2>/dev/null || true && \
+    find /usr/local/lib/python3.12 -type d -name "test" -exec rm -rf {} + 2>/dev/null || true && \
+    find /usr/local/lib/python3.12 -type d -name "__pycache__" -exec rm -rf {} + 2>/dev/null || true && \
+    find /usr/local/lib/python3.12 -name "*.pyc" -delete && \
+    find /usr/local/lib/python3.12 -name "*.pyo" -delete && \
+    # Remove build dependencies immediately
+    apt-get purge -y gcc g++ binutils && \
+    apt-get autoremove -y && \
+    rm -rf /var/lib/apt/lists/*
+
+# Runtime stage
+FROM python:3.12-slim
+
+WORKDIR /app
+
+# Copy the cleaned packages from builder
+COPY --from=builder /usr/local/lib/python3.12/site-packages /usr/local/lib/python3.12/site-packages
+COPY --from=builder /usr/local/bin /usr/local/bin
+COPY --from=builder /app /app
+
+# Final cleanup for runtime image
+# hadolint ignore=SC2015
+RUN find /usr/share/locale -mindepth 1 -maxdepth 1 ! -name 'en*' -exec rm -rf {} + 2>/dev/null || true && \
+    find /usr/share/i18n/locales -mindepth 1 -maxdepth 1 ! -name 'en_*' -exec rm -rf {} + 2>/dev/null || true && \
+    rm -rf /usr/share/doc/* /usr/share/man/* /usr/share/info/* 2>/dev/null || true
+
+ENTRYPOINT ["fm-inference"]

foldmatch-0.1.0/LICENSE.md

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+# Cambrian Non-Commercial License Agreement
+
+This project is licensed under the EvolutionaryScale Cambrian Non-Commercial License Agreement.
+See: https://www.evolutionaryscale.ai/policies/cambrian-non-commercial-license-agreement