PaperFarm 0.2.0b1__tar.gz

paperfarm-0.2.0b1/.github/ISSUE_TEMPLATE/bug_report.yml

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+name: Bug Report
+description: Report a bug or unexpected behavior
+labels: ["bug"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for reporting! Please run `open-researcher doctor` and paste the output below.
+
+  - type: textarea
+    id: description
+    attributes:
+      label: Bug description
+      description: What happened? What did you expect to happen?
+    validations:
+      required: true
+
+  - type: textarea
+    id: reproduce
+    attributes:
+      label: Steps to reproduce
+      description: Minimal steps to trigger the bug.
+      placeholder: |
+        1. `open-researcher init`
+        2. `open-researcher run --agent claude-code`
+        3. See error...
+    validations:
+      required: true
+
+  - type: textarea
+    id: doctor
+    attributes:
+      label: Doctor output
+      description: Paste the output of `open-researcher doctor`
+      render: text
+    validations:
+      required: true
+
+  - type: input
+    id: os
+    attributes:
+      label: OS
+      placeholder: "macOS 15.2 / Ubuntu 24.04 / Windows 11"
+    validations:
+      required: true
+
+  - type: input
+    id: python
+    attributes:
+      label: Python version
+      placeholder: "3.12.1"
+    validations:
+      required: true
+
+  - type: input
+    id: agent
+    attributes:
+      label: Agent used
+      placeholder: "claude-code / codex / aider / opencode"
+
+  - type: textarea
+    id: logs
+    attributes:
+      label: Relevant logs
+      description: Paste from `.research/run.log` or terminal output.
+      render: text

paperfarm-0.2.0b1/.github/ISSUE_TEMPLATE/feature_request.yml

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+name: Feature Request
+description: Suggest a new feature or improvement
+labels: ["enhancement"]
+body:
+  - type: textarea
+    id: problem
+    attributes:
+      label: Problem or use case
+      description: What are you trying to do that isn't possible or convenient today?
+    validations:
+      required: true
+
+  - type: textarea
+    id: solution
+    attributes:
+      label: Proposed solution
+      description: How would you like this to work?
+    validations:
+      required: true
+
+  - type: dropdown
+    id: area
+    attributes:
+      label: Area
+      options:
+        - CLI commands
+        - TUI dashboard
+        - Agent adapters
+        - Parallel workers / GPU
+        - Config / templates
+        - Documentation
+        - Other
+    validations:
+      required: true
+
+  - type: textarea
+    id: alternatives
+    attributes:
+      label: Alternatives considered
+      description: Any workarounds or alternative approaches you've tried?

paperfarm-0.2.0b1/.github/dependabot.yml

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+version: 2
+updates:
+  # Python dependencies
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+      day: "monday"
+    open-pull-requests-limit: 5
+    labels:
+      - "dependencies"
+    commit-message:
+      prefix: "deps"
+
+  # GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+      day: "monday"
+    open-pull-requests-limit: 5
+    labels:
+      - "dependencies"
+      - "ci"
+    commit-message:
+      prefix: "ci"

paperfarm-0.2.0b1/.github/pull_request_template.md

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+## Summary
+
+<!-- What does this PR do? 1-2 sentences. -->
+
+## Changes
+
+<!-- Bulleted list of key changes. -->
+
+-
+
+## Test plan
+
+<!-- How was this tested? -->
+
+- [ ] `make test` passes
+- [ ] `make lint` passes
+- [ ] New tests added for new functionality
+
+## Related issues
+
+<!-- Link any related issues: Fixes #123, Closes #456 -->

paperfarm-0.2.0b1/.github/workflows/cancel-on-merge.yml

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+name: Cancel PR workflows on merge
+
+on:
+  pull_request_target:
+    types: [closed]
+
+permissions:
+  actions: write
+
+jobs:
+  cancel:
+    if: github.event.pull_request.merged == true
+    runs-on: ubuntu-latest
+    timeout-minutes: 5
+    steps:
+      - name: Cancel in-progress and queued CI runs for merged PR
+        uses: actions/github-script@v7
+        with:
+          script: |
+            const branch = context.payload.pull_request.head.ref;
+            const headRepo = context.payload.pull_request.head.repo.full_name;
+
+            for (const status of ['in_progress', 'queued']) {
+              const { data: runs } = await github.rest.actions.listWorkflowRunsForRepo({
+                owner: context.repo.owner,
+                repo: context.repo.repo,
+                branch,
+                status,
+              });
+              for (const run of runs.workflow_runs) {
+                // Skip our own run
+                if (run.id === context.runId) continue;
+                // Only cancel runs from the same head repo (avoid fork name collisions)
+                if (run.head_repository?.full_name !== headRepo) continue;
+                // Only cancel PR-triggered runs
+                if (run.event !== 'pull_request') continue;
+
+                console.log(`Cancelling ${status} run ${run.id} (${run.name})`);
+                await github.rest.actions.cancelWorkflowRun({
+                  owner: context.repo.owner,
+                  repo: context.repo.repo,
+                  run_id: run.id,
+                });
+              }
+            }

paperfarm-0.2.0b1/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pull-requests: read
+
+concurrency:
+  group: ci-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  COVERAGE_MIN: "75"
+  UV_CACHE_DIR: /tmp/.uv-cache
+
+jobs:
+  # ── Path-based change detection ───────────────────────────────────
+  # Inverted logic: '**' matches every file, then '!' excludes docs/images.
+  # If ANY changed file is NOT a doc, 'code' is true → run CI.
+  # If ALL changed files are docs/images, 'code' is false → skip CI.
+  # On push/workflow_dispatch the filter always evaluates to true.
+  changes:
+    runs-on: ubuntu-latest
+    outputs:
+      should_run: ${{ steps.decide.outputs.should_run }}
+    steps:
+      - uses: actions/checkout@v6
+      - uses: dorny/paths-filter@v3
+        id: filter
+        with:
+          filters: |
+            code:
+              - '**'
+              - '!docs/**'
+              - '!plans/**'
+              - '!docs/**/*.md'
+              - '!CHANGELOG.md'
+              - '!CONTRIBUTING.md'
+              - '!**/*.png'
+              - '!**/*.jpg'
+              - '!**/*.svg'
+              - '!LICENSE'
+              - '!.gitignore'
+      - id: decide
+        run: |
+          # On push/workflow_dispatch always run; on PR skip if only docs changed
+          if [[ "${{ github.event_name }}" != "pull_request" ]]; then
+            echo "should_run=true" >> "$GITHUB_OUTPUT"
+          elif [[ "${{ steps.filter.outputs.code }}" == "true" ]]; then
+            echo "should_run=true" >> "$GITHUB_OUTPUT"
+          else
+            echo "should_run=false" >> "$GITHUB_OUTPUT"
+          fi
+
+  # ── Lint ──────────────────────────────────────────────────────────
+  lint:
+    needs: changes
+    if: needs.changes.outputs.should_run == 'true'
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: astral-sh/setup-uv@v7
+        with:
+          enable-cache: true
+          cache-dependency-glob: "pyproject.toml"
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.11"
+
+      - name: Install dependencies
+        run: uv pip install --system -e ".[dev]"
+
+      - name: Lint
+        run: make lint
+
+  # ── Test matrix ───────────────────────────────────────────────────
+  test:
+    needs: [lint, changes]
+    if: needs.changes.outputs.should_run == 'true'
+    runs-on: ubuntu-latest
+    timeout-minutes: 20
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: astral-sh/setup-uv@v7
+        with:
+          enable-cache: true
+          cache-dependency-glob: "pyproject.toml"
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: uv pip install --system -e ".[dev]"
+
+      - name: Test
+        run: pytest tests/ -q
+
+  # ── Coverage ──────────────────────────────────────────────────────
+  coverage:
+    needs: [lint, changes]
+    if: needs.changes.outputs.should_run == 'true'
+    runs-on: ubuntu-latest
+    timeout-minutes: 20
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: astral-sh/setup-uv@v7
+        with:
+          enable-cache: true
+          cache-dependency-glob: "pyproject.toml"
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.11"
+
+      - name: Install dependencies
+        run: uv pip install --system -e ".[dev]"
+
+      - name: Coverage
+        run: |
+          pytest tests/ \
+            --cov=paperfarm \
+            --cov-report=term-missing \
+            --cov-report=xml \
+            --cov-fail-under=${COVERAGE_MIN}
+
+      - name: Upload coverage artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-xml
+          path: coverage.xml
+
+      - name: Upload to Codecov
+        if: always()
+        uses: codecov/codecov-action@v5
+        with:
+          files: coverage.xml
+          fail_ci_if_error: false
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+  # ── Security: pip-audit ───────────────────────────────────────────
+  security-audit:
+    needs: changes
+    if: needs.changes.outputs.should_run == 'true'
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: astral-sh/setup-uv@v7
+        with:
+          enable-cache: true
+          cache-dependency-glob: "pyproject.toml"
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.11"
+
+      - name: Install dependencies from frozen lockfile
+        run: |
+          uv sync --frozen
+          uv pip install --system pip-audit
+
+      - name: Audit dependencies for known vulnerabilities
+        run: |
+          uv export --frozen --no-hashes -o /tmp/requirements-audit.txt
+          pip-audit -r /tmp/requirements-audit.txt
+
+  # ── Package smoke test ────────────────────────────────────────────
+  package-smoke:
+    needs: [lint, changes]
+    if: needs.changes.outputs.should_run == 'true'
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: astral-sh/setup-uv@v7
+        with:
+          enable-cache: true
+          cache-dependency-glob: "pyproject.toml"
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.11"
+
+      - name: Build and install wheel
+        run: |
+          uv pip install --system build
+          python -m build
+          uv pip install --system dist/*.whl
+
+      - name: Smoke CLI entrypoint
+        run: paperfarm --help > /dev/null
+

paperfarm-0.2.0b1/.github/workflows/codeql.yml

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+name: CodeQL
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  schedule:
+    - cron: "0 6 * * 1" # Every Monday at 06:00 UTC
+
+permissions:
+  contents: read
+  security-events: write
+
+concurrency:
+  group: codeql-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  analyze:
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v4
+        with:
+          languages: python
+          queries: +security-extended
+
+      - name: Perform CodeQL analysis
+        uses: github/codeql-action/analyze@v4
+        with:
+          category: "/language:python"

paperfarm-0.2.0b1/.github/workflows/publish.yml

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+name: Publish to PyPI
+
+on:
+  push:
+    tags: ["v*"]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.11"
+
+      - name: Install build tools
+        run: pip install build
+
+      - name: Build sdist and wheel
+        run: python -m build
+
+      - name: Upload dist artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish-pypi:
+    needs: build
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    environment: pypi
+    permissions:
+      id-token: write
+
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

paperfarm-0.2.0b1/.gitignore

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+__pycache__/
+*.py[cod]
+*$py.class
+*.egg-info/
+dist/
+build/
+.eggs/
+*.egg
+.venv/
+.venv-pf/
+venv/
+env/
+.pytest_cache/
+.ruff_cache/
+.mypy_cache/
+htmlcov/
+.coverage
+coverage.xml
+*.log
+.DS_Store
+
+# Research runtime data (created by `open-researcher init`)
+.research/
+/events.jsonl
+
+# Demo workspace
+_demo_workspace/
+
+# Editor/IDE
+.idea/
+.vscode/
+*.swp
+*.swo
+*~
+
+# OS
+Thumbs.db
+
+# Analysis reports (generated, not source)
+analysis/
+.worktrees/