Feat/first commit

.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: astral-sh/setup-uv@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: uv sync --group dev
+
+      - name: Run tests
+        run: uv run pytest
+
+  ruff:
+    runs-on: ubuntu-latest
+    if: github.event_name == 'pull_request'
+    permissions:
+      contents: read
+      pull-requests: write
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: benny123tw/action-ruff@v1.1.0
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          reporter: github-pr-review
+          filter_mode: diff_context

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.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
+.python-version
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# 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
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/
+
+# VSCode
+.vscode/
+
+# Custom
+tmpdev/
+
+# setuptools-scm generated version file
+src/sosci/__about__.py

.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pycqa/isort
+    rev: 6.0.1
+    hooks:
+      - id: isort
+
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.12.5
+    hooks:
+      - id: ruff
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-yaml
+        args: [--unsafe]
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: check-added-large-files
+      - id: check-toml
+      - id: check-merge-conflict
+      - id: debug-statements
+
+# Replace commitsar with conventional commit checker
+  - repo: https://github.com/compilerla/conventional-pre-commit
+    rev: v2.1.1
+    hooks:
+      - id: conventional-pre-commit
+        stages: [commit-msg]
+        args: [] # default: [feat, fix, ci, chore, docs, style, refactor, perf, test, build, revert]

README.md

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+# sosci
+
+**S**imons **O**bservatory **S**oftware and **C**omputing **I**nfrastructure — a daemon that watches a local directory for file changes and automatically syncs them to one or more remote destinations using Globus.
+
+## Features
+
+- **Polling-based file watcher** — monitors a source directory for created, modified, and deleted files using watchdog's polling observer, compatible with any filesystem (including network mounts).
+- **File stability detection** — waits for files to stop growing before triggering a transfer, avoiding partial uploads.
+- **Multi-destination sync** — supports syncing to multiple Globus endpoints, each with its own authentication credentials.
+- **Crash recovery via snapshots** — saves a `DirectorySnapshot` on shutdown. On restart, diffs the snapshot against the current filesystem to detect changes that occurred while the daemon was down.
+- **Globus transfers** — uses the Globus SDK for reliable, encrypted, checksum-verified file transfers with automatic retry.
+- **Rsync backend** — an alternative rsync-based transfer for local or SSH-accessible destinations.
+- **Clean shutdown** — handles SIGTERM and SIGINT (Ctrl+C) to ensure all threads stop gracefully and snapshots are saved.
+
+## Architecture
+
+```
+┌──────────────────────────────────────────────────────┐
+│                    Main Thread                        │
+│  - Parses config                                     │
+│  - Wires watcher → transfer manager                  │
+│  - Blocks until SIGTERM / SIGINT                     │
+│  - Orchestrates clean shutdown                       │
+└──────────────────────────────────────────────────────┘
+         │                           │
+         ▼                           ▼
+┌─────────────────────┐   ┌─────────────────────────┐
+│   Watcher Thread     │   │  Transfer Manager Thread │
+│  (PollingObserver)   │   │                          │
+│                      │   │  - Receives file lists   │
+│  - Polls source dir  │──▶│    via callback          │
+│  - Detects changes   │   │  - Transfers to each     │
+│  - Checks stability  │   │    Globus destination    │
+│  - Calls on_cycle_   │   │  - Handles deletes       │
+│    done callback     │   │                          │
+└─────────────────────┘   └─────────────────────────┘
+```
+
+**Data flow:** Source directory → Watcher detects stable files → `on_cycle_done` callback → TransferManager syncs to all configured Globus destinations.
+
+## Configuration
+
+sosci is configured via a JSON file:
+
+```json
+{
+  "source": {
+    "path": "/data/experiment",
+    "endpoint": "source-endpoint-uuid",
+    "globus_root_path": "/root/path/on/source",
+    "base_path": "/data/experiment"
+  },
+  "destination": [
+    {
+      "path": "/data/backup",
+      "endpoint": "dest-endpoint-uuid",
+      "globus_root_path": "/root/path/on/dest",
+      "client_id": "globus-native-app-client-id",
+      "refresh_token_file": "~/.globus/tokens.json"
+    }
+  ],
+  "poll_interval": 30,
+  "check_interval": 60,
+  "max_retries": 3,
+  "snapshot_path": "~/.sosci/sosci_snapshot.pkl"
+}
+```
+
+| Field | Description |
+|-------|-------------|
+| `source` | Source directory and Globus endpoint configuration |
+| `destination` | List of destination configurations, each with its own Globus credentials |
+| `poll_interval` | Seconds between filesystem polls (default: 30) |
+| `check_interval` | Seconds between modified-file checks during transfer (default: 60) |
+| `max_retries` | Max checks for modified files before giving up (default: 3) |
+| `snapshot_path` | Where to persist the directory snapshot for crash recovery (default: `~/.sosci/sosci_snapshot.pkl`) |
+
+## Testing
+
+Run the test suite with:
+
+```bash
+uv run pytest
+```
+
+## Usage
+
+```bash
+sosci --config config.json
+```
+
+Stop with Ctrl+C or `kill <pid>` — the daemon will save a snapshot and shut down cleanly.
+
+[!NOTE]
+README was edited with Claude AI.