Refactor and add comprehensive testing for hashing

.github/workflows/run-tests.yml

@@ -0,0 +1,38 @@
+name: Run Tests
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  workflow_dispatch:  # Allows manual triggering
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install -e ".[test]"
+
+    - name: Run tests
+      run: |
+        pytest -v --cov=src --cov-report=term-missing --cov-report=xml
+
+    - name: Upload coverage reports to Codecov
+      uses: codecov/codecov-action@v5
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+

.gitignore

@@ -1,5 +1,5 @@
 # Ignore example dataset storage generated in tutorial
-pod_data/
+**/pod_data/
 
 # Autogenerated version file
 _version.py

README.md

@@ -1,2 +1,31 @@
 # orcabridge
 Prototype of Orcapod as implemented in Python with functions
+
+## Continuous Integration
+
+This project uses GitHub Actions for continuous integration:
+
+- **Run Tests**: A workflow that runs tests on Ubuntu with multiple Python versions.
+
+### Running Tests Locally
+
+To run tests locally:
+
+```bash
+# Install the package with test dependencies
+pip install -e ".[test]"
+
+# Run tests with coverage
+pytest -v --cov=src --cov-report=term-missing
+```
+
+### Development Setup
+
+For development, you can install all optional dependencies:
+
+```bash
+# Install all development dependencies 
+pip install -e ".[test,dev]"
+# or
+pip install -r requirements-dev.txt
+```

pyproject.toml

@@ -4,10 +4,17 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "orcabridge"
-description = "Prototype Oracapod Pipeline implementation in Python"
-dynamic = ["version", "dependencies"]
+description = "Function-based Oracapod Pipeline implementation in Python"
+dynamic = ["version"]
+dependencies = [
+    "numpy",
+    "xxhash",
+    "networkx",
+    "matplotlib",
+    "typing_extensions",
+]
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 license = { text = "MIT License" }
 classifiers = [
     "Programming Language :: Python :: 3",
@@ -18,14 +25,12 @@ classifiers = [
 [project.urls]
 Homepage = "https://github.com/walkerlab/orcabridge"
 
+[project.optional-dependencies]
+test = ["pytest>=7.4.0", "pytest-cov>=4.1.0"]
+dev = ["black>=23.0.0", "flake8>=6.0.0", "isort>=5.12.0", "orcabridge[test]"]
+
 [tool.setuptools.packages.find]
 where = ["src"]
 
 [tool.setuptools_scm]
 version_file = "src/orcabridge/_version.py"
-
-[tool.setuptools.dynamic]
-dependencies = { file = ["requirements.txt"] }
-
-[tool.black]
-line-length = 80

pytest.ini

@@ -0,0 +1,6 @@
+[pytest]
+testpaths = tests
+python_files = test_*.py
+python_classes = Test*
+python_functions = test_*
+addopts = -v --cov=src --cov-report=term-missing --cov-report=html --cov-report=xml

src/orcabridge/__init__.py

@@ -1,15 +1,20 @@
 from .tracker import Tracker
-
-DEFAULT_TRACKER = Tracker()
-DEFAULT_TRACKER.activate()
-
-# make modules and subpackages available
 from . import hashing
 from . import pod
 from . import mapper
 from . import stream
 from . import source
 from . import store
+from .mapper import MapTags, MapPackets, Join, tag, packet
+from .pod import FunctionPod, function_pod
+from .source import GlobSource
+from .store import DirDataStore, SafeDirDataStore
+
+
+
+DEFAULT_TRACKER = Tracker()
+DEFAULT_TRACKER.activate()
+
 
 __all__ = [
     "hashing",
@@ -30,9 +35,6 @@
     "DirDataStore",
     "SafeDirDataStore",
     "DEFAULT_TRACKER",
+    "SyncStreamFromLists",
 ]
 
-from .mapper import MapTags, MapPackets, Join, tag, packet
-from .pod import FunctionPod, function_pod
-from .source import GlobSource
-from .store import DirDataStore, SafeDirDataStore