research-os 1.1.0__tar.gz

research_os-1.1.0/.github/ISSUE_TEMPLATE/bug_report.md

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+name: Bug Report
+description: Create a report to help us improve Research OS
+title: "[BUG] "
+labels: ["bug"]
+assignees: []
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for taking the time to fill out this bug report!
+  - type: textarea
+    id: what-happened
+    attributes:
+      label: What happened?
+      description: Also tell us, what did you expect to happen?
+      placeholder: Tell us what you see!
+    validations:
+      required: true
+  - type: textarea
+    id: steps
+    attributes:
+      label: Steps to reproduce
+      description: Steps to reproduce the behavior.
+      placeholder: |
+        1. Run `ros init`
+        2. ...
+    validations:
+      required: true

research_os-1.1.0/.github/ISSUE_TEMPLATE/feature_request.md

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+name: Feature Request
+description: Suggest an idea for this project
+title: "[FEATURE] "
+labels: ["enhancement"]
+assignees: []
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for your interest in improving Research OS!
+  - type: textarea
+    id: feature-description
+    attributes:
+      label: Describe the feature
+      description: A clear and concise description of what you want to happen.
+    validations:
+      required: true
+  - type: textarea
+    id: use-cases
+    attributes:
+      label: Use Cases
+      description: In what situations would this feature be useful?

research_os-1.1.0/.github/workflows/publish.yml

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+name: Publish to PyPI
+
+# Trusted Publishing (OIDC) — no API tokens stored.
+# Configured on PyPI with:
+#   Owner: VibhavSetlur
+#   Repository: Research-OS
+#   Workflow filename: publish.yml
+#   Environment: pypi
+
+on:
+  push:
+    tags:
+      - "v*"
+  workflow_dispatch:
+
+jobs:
+  build:
+    name: Build sdist and wheel
+    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 backend
+        run: python -m pip install --upgrade pip build
+
+      - name: Build sdist and wheel
+        run: python -m build --sdist --wheel
+
+      - name: Upload distribution artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish:
+    name: Publish to PyPI
+    needs: build
+    # Only publish on tag pushes; workflow_dispatch builds but does not publish.
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/research-os
+    permissions:
+      id-token: write  # required for Trusted Publishing (OIDC)
+    steps:
+      - name: Download distribution artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Publish to PyPI via Trusted Publishing
+        uses: pypa/gh-action-pypi-publish@release/v1

research_os-1.1.0/.github/workflows/test.yml

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+name: tests
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  workflow_dispatch:
+
+# Cancel an in-progress run for the same ref when a new commit lands.
+concurrency:
+  group: tests-${{ github.ref }}
+  cancel-in-progress: true
+
+# Pip resilience for transient network blips.
+env:
+  PIP_DISABLE_PIP_VERSION_CHECK: "1"
+  PIP_NO_INPUT: "1"
+  PIP_RETRIES: "5"
+  PIP_TIMEOUT: "60"
+
+jobs:
+  # ── Fast feedback: lint + preflight + unit tests on one Python ─────────
+  fast:
+    name: Lint + preflight + unit (3.11)
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+          cache: pip
+          cache-dependency-path: pyproject.toml
+
+      - name: Install package + ci extras
+        run: |
+          python -m pip install --upgrade pip
+          pip install --prefer-binary -e ".[ci,dev]"
+
+      - name: Lint (ruff)
+        run: ruff check src/ tests/ scripts/
+
+      - name: Preflight smoke check
+        run: python scripts/preflight.py
+
+      - name: Unit tests
+        run: pytest tests/unit -v
+
+  # ── Full matrix: integration + tools tests on every supported Python ───
+  full:
+    name: Integration + tools (Python ${{ matrix.python-version }})
+    needs: fast
+    runs-on: ubuntu-latest
+    timeout-minutes: 20
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+          cache-dependency-path: pyproject.toml
+
+      - name: Install package + ci extras
+        run: |
+          python -m pip install --upgrade pip
+          pip install --prefer-binary -e ".[ci,dev]"
+
+      - name: Integration tests
+        run: pytest tests/integration -v
+
+      - name: Tools tests
+        env:
+          # The scratch + tasks tests spawn real subprocesses; they need a
+          # writable HOME. Default GitHub-hosted runners are fine, but be
+          # explicit.
+          HOME: ${{ runner.temp }}
+        run: pytest tests/tools -v
+
+  # ── Build sdist + wheel to confirm packaging is healthy (full extras) ──
+  build:
+    name: Build sdist + wheel
+    needs: fast
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - name: Build
+        run: |
+          python -m pip install --upgrade pip build
+          python -m build
+      - name: Confirm wheel imports cleanly + ships protocols
+        run: |
+          python -m venv /tmp/wheel-check
+          /tmp/wheel-check/bin/pip install --prefer-binary dist/*.whl
+          /tmp/wheel-check/bin/python -c "import research_os; print('OK', research_os.__version__)"
+          /tmp/wheel-check/bin/python -c "
+          import zipfile, sys
+          import glob
+          whl = glob.glob('dist/*.whl')[0]
+          with zipfile.ZipFile(whl) as z:
+              yamls = [n for n in z.namelist() if n.endswith('.yaml')]
+              print(f'YAMLs in wheel: {len(yamls)}')
+              assert len(yamls) >= 30, 'protocols missing from wheel'
+          "
+      - name: Upload artefacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+          retention-days: 7

research_os-1.1.0/.gitignore

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+# Research OS — Git Ignore Rules
+TODO.md
+
+# Python
+__pycache__/
+*.pyc
+*.pyo
+*.pyd
+*.egg-info/
+dist/
+build/
+.pytest_cache/
+.benchmarks/
+.mypy_cache/
+.ruff_cache/
+
+# IDE configs
+/.cursor/
+/.cursorrules
+/.clinerules
+/AGENTS.md
+
+# OS state (auto-created during pipeline runs)
+.os_state/
+
+# Virtual environments
+.venv/
+venv/
+env/
+environment/venv/
+
+# User data (keep directories, ignore contents)
+!inputs/data/raw/.gitkeep
+!inputs/context/.gitkeep
+!inputs/context/README.md
+!inputs/papers/.gitkeep
+!inputs/papers/README.md
+
+# Researcher config (contains API keys)
+inputs/researcher_config.yaml
+
+# Large files (never commit)
+*.h5
+*.hdf5
+*.feather
+*.parquet
+*.sav
+*.dta
+*.sas7bdat
+*.zip
+*.tar.gz
+*.rar
+
+# OS files
+.DS_Store
+Thumbs.db
+desktop.ini
+
+# AI assistant caches
+.aider*
+
+.antigravitycli/
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+
+# Jupyter
+.ipynb_checkpoints/
+
+# Environment files (user-specific)
+.env
+.env.local
+
+# Task logs
+*.log
+
+# Temporary scratch folder
+scratch/
+/workspace/

research_os-1.1.0/.pre-commit-config.yaml

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+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+-   repo: https://github.com/psf/black
+    rev: 23.3.0
+    hooks:
+    -   id: black
+        language_version: python3.10