FedGWAS 0.3.1__tar.gz

fedgwas-0.3.1/.flwr/.gitignore

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+.credentials

fedgwas-0.3.1/.github/workflows/deploy-docs.yml

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+name: Deploy documentation
+
+on:
+  push:
+    tags:
+      - '*'
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: github-pages
+  cancel-in-progress: false
+
+jobs:
+  build:
+    name: Build Docusaurus site
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: 20
+          cache: npm
+          cache-dependency-path: website/package-lock.json
+
+      - name: Install dependencies
+        working-directory: website
+        run: npm ci
+
+      - name: Build documentation
+        working-directory: website
+        run: npm run build
+
+      - name: Configure GitHub Pages
+        uses: actions/configure-pages@v5
+
+      - name: Upload Pages artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: website/build
+
+  deploy:
+    name: Deploy to GitHub Pages
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    steps:
+      - name: Deploy
+        id: deployment
+        uses: actions/deploy-pages@v4

fedgwas-0.3.1/.github/workflows/publish-pypi.yml

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+name: Publish Python package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install build tools
+        run: python -m pip install --upgrade build twine
+
+      - name: Build distributions
+        run: python -m build
+
+      - name: Check distributions
+        run: python -m twine check dist/*
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+  publish:
+    name: Publish to PyPI
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/project/FedGWAS/
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Download distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+      - name: Publish distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

fedgwas-0.3.1/.gitignore

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+.venv
+dist/
+sdist/
+**/__pycache__/
+.pytest_cache/
+*.pyc
+.mypy_cache/
+website/.docusaurus/
+
+# Data
+user_data/
+
+# Logs
+logs
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+dev-debug.log
+
+# Dependency directories
+website/node_modules/
+website/build/
+
+# Environment variables
+.env
+
+# Editor directories and files
+.idea
+.vscode
+*.suo
+*.ntvs*
+*.njsproj
+*.sln
+*.sw?
+
+# OS specific
+.DS_Store
+**/.DS_Store
+
+# Legacy/archived directories
+archived/
+bin/
+centers/
+data/
+
+# Unused / local-only pipeline paths
+pipeline/exerpiements.md
+pipeline/experiments.md
+pipeline/simulation/
+pipeline/visualization_archived/
+pipeline/server/strategy.py
+pipeline/server/strategy_new.py
+pipeline/server/aggregator_qc.py
+pipeline/utils/bloom_filter.py
+
+# Redundant/outdated documentation
+Readme_pipeline.md
+EXPERIMENT_RUNNER_README.md
+prd/
+.pre-commit-config.yaml
+!cluster_deployment/docs/
+!cluster_deployment/docs/**
+
+# Docker (local workflow only; cluster deployment is under cluster_deployment/)
+docker/
+.dockerignore
+
+# Performance manuscript drafts (local only; configs stay in repo)
+experiments/performance/README.md
+experiments/performance/appendix_sections.md
+experiments/performance/appendix_table.md
+experiments/performance/appendix_table.tex
+experiments/performance/manuscript_sections.md
+
+# Local notes, reports, and archives (not shipped)
+ISSUES_REPORT.md
+ISSUES_REPORT_UPDATED.md
+plan.md
+experiments.docx
+InfoSummit_kinship.pdf
+mkdocs.yml
+pipeline.pdf
+pipeline.zip
+plink.zip
+results/
+
+# Experiment run outputs and synthetic data artifacts
+experiments/**/results/
+experiments/**/results_*/
+experiments/*/*/results/
+experiments/**/data/**/*.bed
+experiments/**/data/**/*.bim
+experiments/**/data/**/*.fam
+experiments/**/data/**/*.log
+experiments/**/data/**/*.kin0
+experiments/**/data/**/*.assoc*
+experiments/**/data/**/*.genome
+experiments/**/data/**/*.hwe
+experiments/**/data/**/*.imiss
+experiments/**/data/**/*.lmiss
+experiments/**/data/**/*.frq
+experiments/**/intermediate/
+**/__pycache__/
+
+# Task / cluster bundles
+fedgwas-cluster.tar.gz
+cluster_deployment/wheels/
+
+# Log files
+*.log
+**/*.log
+
+# PLINK output files
+*.bed
+*.bim
+*.fam
+*.kin0
+*.assoc*
+*.genome
+*.hwe
+*.imiss
+*.lmiss
+*.frq
+
+# Large data files (duplicate patterns for safety)
+*.bed
+*.bim
+*.fam
+
+# claude
+.claude/
+.venv/
+claude.md
+.windsurfrules
+README-task-manager.md
+.env.example
+/scripts/
+.cursor/*
+.test_scenario_a.py