Add pyproject.toml and make various fixes (#10)

* Add pyproject.toml and make various fixes

Signed-off-by: 1597463007 <squid-shape-fifty@duck.com>

* Fix flake8 error

Signed-off-by: 1597463007 <squid-shape-fifty@duck.com>

* Fix mypy error

Signed-off-by: 1597463007 <squid-shape-fifty@duck.com>

---------

Signed-off-by: 1597463007 <squid-shape-fifty@duck.com>

.github/workflows/linter.yml

@@ -0,0 +1,39 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python Linter And Unittest
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.8"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 pyproject-flake8 mypy
+          pip install -r requirements.txt
+      - name: Lint with flake8
+        run: |
+          pflake8 .
+      - name: Lint with MyPy
+        run: |
+          mypy .
+      - name: Run python unittest
+        run: |
+          python -m unittest discover -v tests

.github/workflows/scorecard.yml

@@ -0,0 +1,58 @@
+name: Scorecard supply-chain security
+on:
+  # For Branch-Protection check. Only the default branch is supported. See
+  # https://github.com/ossf/scorecard/blob/main/docs/checks.md#branch-protection
+  branch_protection_rule:
+  # To guarantee Maintained check is occasionally updated. See
+  # https://github.com/ossf/scorecard/blob/main/docs/checks.md#maintained
+  schedule:
+    - cron: '26 18 * * 0'
+  push:
+    branches: [ "main" ]
+
+# Declare default permissions as read only.
+permissions: read-all
+
+jobs:
+  analysis:
+    name: Scorecard analysis
+    runs-on: ubuntu-latest
+    permissions:
+      # Needed to upload the results to code-scanning dashboard.
+      security-events: write
+      # Needed to publish results and get a badge (see publish_results below).
+      id-token: write
+      # Uncomment the permissions below if installing in a private repository.
+      # contents: read
+      # actions: read
+
+    steps:
+      - name: Harden Runner
+        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
+        with:
+          egress-policy: audit
+
+      - name: "Checkout code"
+        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
+        with:
+          persist-credentials: false
+
+      - name: "Run analysis"
+        uses: ossf/scorecard-action@62b2cac7ed8198b15735ed49ab1e5cf35480ba46 # v2.4.0
+        with:
+          results_file: results.sarif
+          results_format: sarif
+          # (Optional) "write" PAT token. Uncomment the `repo_token` line below if:
+          # - you want to enable the Branch-Protection check on a *public* repository, or
+          # - you are installing Scorecard on a *private* repository
+          # To create the PAT, follow the steps in https://github.com/ossf/scorecard-action#authentication-with-pat.
+          # repo_token: ${{ secrets.SCORECARD_TOKEN }}
+
+          # Public repositories:
+          #   - Publish results to OpenSSF REST API for easy access by consumers
+          #   - Allows the repository to include the Scorecard badge.
+          #   - See https://github.com/ossf/scorecard-action#publishing-results.
+          # For private repositories:
+          #   - `publish_results` will always be set to `false`, regardless
+          #     of the value entered here.
+          publish_results: true

.gitignore

@@ -0,0 +1,17 @@
+__pychace__/
+*.py[cod]
+*$py.class
+
+build/
+dist/
+sdist/
+wheels/
+eggs/
+.eggs/
+.idea/
+.vscode/
+*.egg-info/
+*.egg
+.mypy_cache/
+
+venv*/

Makefile

@@ -12,7 +12,7 @@ _doc: requirements.txt
 	rm -fr docsvenv build; mkdir build
 	python3.8 -m venv docsvenv
 	. docsvenv/bin/activate; \
-	pip install -r docs/requirements.txt; \
-	pip install -r requirements.txt; \
-	cd docs; make clean && make html
+		pip install -r docs/requirements.txt; \
+		pip install -r requirements.txt; \
+		cd docs; make clean && make html
 	zip -r build/pargraph_docs.zip docs/build/html/*

docs/source/api/index.rst → docs/source/api.rst

@@ -11,17 +11,15 @@ Graph Generation
 .. autoclass:: pargraph.Result
    :members:
 
-   .. automethod:: __init__
-
-.. autoclass:: pargraph.graph.decorators.Graphable
+.. autoclass:: pargraph.graph.decorators.Graphable()
    :members:
+   :special-members: __call__
 
-    .. automethod:: __call__
+.. autoclass:: pargraph.graph.objects.Graph()
+   :members:
 
 Graph Engine
 ------------
 
 .. autoclass:: pargraph.GraphEngine
    :members:
-
-   .. automethod:: __init__

docs/source/conf.py

@@ -47,3 +47,6 @@
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ["_static"]
 html_css_files = ["style.css"]
+
+# Autodoc settings
+autodoc_member_order = "bysource"

docs/source/index.rst

@@ -9,7 +9,7 @@ Welcome to Pargraph's documentation!
 .. toctree::
    :maxdepth: 2
 
-   api/index
+   api
 
 Indices and tables
 ==================

pargraph/about.py

@@ -1 +1 @@
-__version__ = "0.7.1"
+__version__ = "0.8.0"

pargraph/engine/engine.py

@@ -3,20 +3,19 @@
 import logging
 from collections import defaultdict, deque
 from concurrent.futures import FIRST_COMPLETED, Future, wait
-from typing import Any, Dict, Iterable, List, Optional, Set
+from typing import Any, DefaultDict, Dict, Hashable, Iterable, Optional, Set
 
 from loky import get_reusable_executor
 
 try:
     from pargraph.utility.graphlib_graphblas import TopologicalSorter
 except ImportError:
-    from graphlib import TopologicalSorter
+    from graphlib import TopologicalSorter  # type: ignore[assignment,no-redef]
 
 
 class Backend(metaclass=abc.ABCMeta):
     @abc.abstractmethod
-    def submit(self, fn, /, *args, **kwargs) -> Future:
-        ...
+    def submit(self, fn, /, *args, **kwargs) -> Future: ...
 
 
 class GraphEngine:
@@ -58,8 +57,8 @@ def get(self, dsk: Dict, keys: Any, **kwargs) -> Any:
         graph = TopologicalSorter(graphlib_graph)
         graph.prepare()
 
-        results = {}
-        future_to_key = {}
+        results: Dict[Hashable, Any] = {}
+        future_to_key: Dict[Future[Any], Hashable] = {}
 
         # perform automatic reference counting to free results that are no longer needed
         def dereference_key(key):
@@ -139,7 +138,7 @@ def _pack_results(cls, results: Dict, keys: Any) -> Any:
         return results[keys]
 
     @classmethod
-    def _flatten_iter(cls, seq: Iterable, container=list) -> List:
+    def _flatten_iter(cls, seq: Iterable, container=list) -> Iterable:
         for el in seq:
             # recursively flatten specific container types
             if isinstance(el, container):
@@ -149,7 +148,7 @@ def _flatten_iter(cls, seq: Iterable, container=list) -> List:
 
     @staticmethod
     def _is_submittable_function_computation(computation: Any) -> bool:
-        return isinstance(computation, tuple) and computation and callable(computation[0])
+        return isinstance(computation, tuple) and len(computation) > 0 and callable(computation[0])
 
     def _submit_function_computation(self, computation: Any, results: Dict, **kwargs) -> Optional[Future]:
         func, *args = computation
@@ -214,7 +213,7 @@ def flatten(value: Any) -> Set[Any]:
 
     @staticmethod
     def _create_ref_count_graph(graph: Dict) -> Dict:
-        ref_count_graph = defaultdict(int)
+        ref_count_graph: DefaultDict[str, int] = defaultdict(int)
         for value in graph.values():
             for sub_value in value:
                 ref_count_graph[sub_value] += 1

pargraph/graph/annotation.py

@@ -21,6 +21,11 @@ def my_function() -> Annotated[str, Result("my_output")]:
     """
 
     def __init__(self, name: str):
+        """
+        Initialize Result annotation
+
+        :param name: result name
+        """
         self.name = name
 
     def get_name(self) -> str:
@@ -32,7 +37,7 @@ def get_name(self) -> str:
         return self.name
 
 
-def _get_output_names(function: Callable) -> Union[str, Tuple[str]]:
+def _get_output_names(function: Callable) -> Union[str, Tuple[str, ...]]:
     annotation = inspect.signature(function).return_annotation
     origin = get_origin(annotation)