style: address linting and typing issues

.github/workflows/ci.yml

@@ -2,43 +2,44 @@ name: CI
 
 on:
   push:
-    branches: [ main ]
+    branches: '*'
   pull_request:
-    branches: [ main ]
+    branches: '*'
 
 jobs:
   build:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
-
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: '3.11'
-
-    - name: Install Poetry
-      run: |
-        curl -sSL https://install.python-poetry.org | python3 -
-        poetry install
-
-    - name: Lint with Ruff
-      run: |
-        poetry run ruff check crategen/
-
-    - name: Type check with Mypy
-      run: |
-        poetry run mypy crategen/
-
-    - name: Run security checks with Bandit
-      run: |
-        poetry run bandit -r crategen/
-
-    - name: Install test dependencies
-      run: |
-        poetry add pytest pytest-cov pytest-mock
-
-    # - name: Run tests
-    #   run: |
-    #     poetry run pytest --cov=crategen
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+
+      - name: Install Poetry
+        run: |
+          curl -sSL https://install.python-poetry.org | python3 -
+          poetry install
+
+      - name: Lint with Ruff
+        run: |
+          poetry run ruff check crategen/
+        if: ${{ success() }}
+
+      - name: Type check with Mypy
+        run: |
+          poetry run mypy crategen/
+
+      - name: Run security checks with Bandit
+        run: |
+          poetry run bandit -r crategen/
+
+      - name: Install test dependencies
+        run: |
+          poetry add pytest pytest-cov pytest-mock
+
+      # - name: Run tests
+      #   run: |
+      #     poetry run pytest --cov=crategen

crategen/cli.py

@@ -1,30 +1,38 @@
-import click
+"""CLI module for converting TES and WES data to WRROC."""
+
 import json
+
+import click
+
 from crategen.converter_manager import ConverterManager
 
+
 @click.command()
-@click.option('--input', prompt='Input file', help='Path to the input JSON file.')
-@click.option('--output', prompt='Output file', help='Path to the output JSON file.')
-@click.option('--conversion-type', prompt='Conversion type', type=click.Choice(['tes-to-wrroc', 'wes-to-wrroc']), help='Type of conversion to perform.')
-def cli(input, output, conversion_type):
-    """
-    Command Line Interface for converting TES/WES to WRROC.
-    """
+@click.option("--input", prompt="Input file", help="Path to the input JSON file.")
+@click.option("--output", prompt="Output file", help="Path to the output JSON file.")
+@click.option(
+    "--conversion-type",
+    prompt="Conversion type",
+    type=click.Choice(["tes-to-wrroc", "wes-to-wrroc"]),
+    help="Type of conversion to perform.",
+)
+def cli(input: str, output: str, conversion_type: str) -> None:
+    """Command Line Interface for converting TES/WES to WRROC."""
     manager = ConverterManager()
 
     # Load input data from JSON file
-    with open(input, 'r') as input_file:
+    with open(input) as input_file:
         data = json.load(input_file)
 
     # Perform the conversion based on the specified type
-    if conversion_type == 'tes-to-wrroc':
+    if conversion_type == "tes-to-wrroc":
         result = manager.convert_tes_to_wrroc(data)
-    elif conversion_type == 'wes-to-wrroc':
+    elif conversion_type == "wes-to-wrroc":
         result = manager.convert_wes_to_wrroc(data)
-    
+
     # Save the result to the output JSON file
-    with open(output, 'w') as output_file:
+    with open(output, "w") as output_file:
         json.dump(result, output_file, indent=4)
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     cli()

crategen/converter_manager.py

@@ -1,13 +1,23 @@
+"""Manager for handling TES and WES to WRROC conversions."""
+
+from typing import Any, Dict
+
 from .converters.tes_converter import TESConverter
 from .converters.wes_converter import WESConverter
 
+
 class ConverterManager:
-    def __init__(self):
+    """Manages conversion between TES/WES and WRROC formats."""
+
+    def __init__(self) -> None:
+        """Initializes the converters for TES and WES."""
         self.tes_converter = TESConverter()
         self.wes_converter = WESConverter()
 
-    def convert_tes_to_wrroc(self, tes_data):
+    def convert_tes_to_wrroc(self, tes_data: Dict[str, Any]) -> Dict[str, Any]:
+        """Converts TES data to WRROC format."""
         return self.tes_converter.convert_to_wrroc(tes_data)
 
-    def convert_wes_to_wrroc(self, wes_data):
+    def convert_wes_to_wrroc(self, wes_data: Dict[str, Any]) -> Dict[str, Any]:
+        """Converts WES data to WRROC format."""
         return self.wes_converter.convert_to_wrroc(wes_data)

crategen/converters/abstract_converter.py

@@ -1,10 +1,16 @@
+"""Abstract base class for converters between TES/WES and WRROC formats."""
+
 from abc import ABC, abstractmethod
+from typing import Any, Dict
+
 
 class AbstractConverter(ABC):
+    """Abstract converter for TES/WES to WRROC and vice versa."""
+
     @abstractmethod
-    def convert_to_wrroc(self, data):
-        """Convert data to WRROC format"""
+    def convert_to_wrroc(self, data: Dict[str, Any]) -> Dict[str, Any]:
+        """Convert data to WRROC format."""
 
     @abstractmethod
-    def convert_from_wrroc(self, wrroc_data):
-        """Convert WRROC data to the original format"""
+    def convert_from_wrroc(self, wrroc_data: Dict[str, Any]) -> Dict[str, Any]:
+        """Convert WRROC data to the original format."""

crategen/converters/tes_converter.py

@@ -1,20 +1,32 @@
+"""Module for converting TES data to WRROC format and vice versa."""
+
+from typing import Any, Dict
+
 from .abstract_converter import AbstractConverter
 from .utils import convert_to_iso8601
 
+
 class TESConverter(AbstractConverter):
+    """Converter for TES data to WRROC and vice versa."""
+
+    def convert_to_wrroc(self, tes_data: Dict[str, Any]) -> Dict[str, Any]:
+        """Convert TES data to WRROC format.
 
-    def convert_to_wrroc(self, tes_data):
-        # Validate and extract data with defaults
+        Args:
+            tes_data (Dict[str, Any]): The TES data to be converted.
+
+        Returns:
+            Dict[str, Any]: The converted WRROC data.
+        """
         id = tes_data.get("id", "")
         name = tes_data.get("name", "")
         description = tes_data.get("description", "")
         executors = tes_data.get("executors", [{}])
         inputs = tes_data.get("inputs", [])
         outputs = tes_data.get("outputs", [])
         creation_time = tes_data.get("creation_time", "")
-        end_time = tes_data.get("logs", [{}])[0].get("end_time", "")  # Corrected to fetch from logs
+        end_time = tes_data.get("logs", [{}])[0].get("end_time", "")
 
-        # Convert to WRROC
         wrroc_data = {
             "@id": id,
             "name": name,
@@ -27,8 +39,15 @@ def convert_to_wrroc(self, tes_data):
         }
         return wrroc_data
 
-    def convert_from_wrroc(self, wrroc_data):
-        # Validate and extract data with defaults
+    def convert_from_wrroc(self, wrroc_data: Dict[str, Any]) -> Dict[str, Any]:
+        """Convert WRROC data to TES format.
+
+        Args:
+            wrroc_data (Dict[str, Any]): The WRROC data to be converted.
+
+        Returns:
+            Dict[str, Any]: The converted TES data.
+        """
         id = wrroc_data.get("@id", "")
         name = wrroc_data.get("name", "")
         description = wrroc_data.get("description", "")
@@ -38,7 +57,6 @@ def convert_from_wrroc(self, wrroc_data):
         start_time = wrroc_data.get("startTime", "")
         end_time = wrroc_data.get("endTime", "")
 
-        # Convert from WRROC to TES
         tes_data = {
             "id": id,
             "name": name,
@@ -47,6 +65,6 @@ def convert_from_wrroc(self, wrroc_data):
             "inputs": [{"url": obj.get("@id", ""), "path": obj.get("name", "")} for obj in object_data],
             "outputs": [{"url": res.get("@id", ""), "path": res.get("name", "")} for res in result_data],
             "creation_time": start_time,
-            "logs": [{"end_time": end_time}],  # Added to logs
+            "logs": [{"end_time": end_time}],
         }
         return tes_data

crategen/converters/utils.py

@@ -1,29 +1,31 @@
+"""Utility functions for handling data conversion."""
+
 import datetime
+from typing import Optional
+
+
+def convert_to_iso8601(timestamp: Optional[str]) -> Optional[str]:
+    """Convert a given timestamp to ISO 8601 format.
 
-def convert_to_iso8601(timestamp):
-    """
-    Convert a given timestamp to ISO 8601 format.
     Handles multiple formats including RFC 3339, ISO 8601 with and without fractional seconds.
 
     Args:
-        timestamp (str): The timestamp to be converted.
+        timestamp (Optional[str]): The timestamp to be converted.
 
     Returns:
-        str: The converted timestamp in ISO 8601 format, or None if the input format is incorrect.
+        Optional[str]: The converted timestamp in ISO 8601 format, or None if the input format is incorrect.
     """
     if timestamp:
-        # List of supported formats
         formats = [
-            "%Y-%m-%dT%H:%M:%S.%fZ",    # RFC 3339 with fractional seconds
-            "%Y-%m-%dT%H:%M:%SZ",       # RFC 3339 without fractional seconds
-            "%Y-%m-%dT%H:%M:%S%z",      # ISO 8601 with timezone
-            "%Y-%m-%dT%H:%M:%S.%f%z",   # ISO 8601 with fractional seconds and timezone
+            "%Y-%m-%dT%H:%M:%S.%fZ",    
+            "%Y-%m-%dT%H:%M:%SZ",       
+            "%Y-%m-%dT%H:%M:%S%z",      
+            "%Y-%m-%dT%H:%M:%S.%f%z",
         ]
         for fmt in formats:
             try:
                 return datetime.datetime.strptime(timestamp, fmt).isoformat() + "Z"
             except ValueError:
                 continue
-        # Handle incorrect format or other issues
         return None
     return None

crategen/converters/wes_converter.py

@@ -1,18 +1,30 @@
+"""Module for converting WES data to WRROC format and vice versa."""
+
+from typing import Any, Dict
+
 from .abstract_converter import AbstractConverter
 from .utils import convert_to_iso8601
 
+
 class WESConverter(AbstractConverter):
+    """Converter for WES data to WRROC and vice versa."""
+
+    def convert_to_wrroc(self, wes_data: Dict[str, Any]) -> Dict[str, Any]:
+        """Convert WES data to WRROC format.
 
-    def convert_to_wrroc(self, wes_data):
-        # Validate and extract data with defaults
+        Args:
+            wes_data (Dict[str, Any]): The WES data to be converted.
+
+        Returns:
+            Dict[str, Any]: The converted WRROC data.
+        """
         run_id = wes_data.get("run_id", "")
         name = wes_data.get("run_log", {}).get("name", "")
         state = wes_data.get("state", "")
         start_time = wes_data.get("run_log", {}).get("start_time", "")
         end_time = wes_data.get("run_log", {}).get("end_time", "")
         outputs = wes_data.get("outputs", {})
 
-        # Convert to WRROC
         wrroc_data = {
             "@id": run_id,
             "name": name,
@@ -23,16 +35,22 @@ def convert_to_wrroc(self, wes_data):
         }
         return wrroc_data
 
-    def convert_from_wrroc(self, wrroc_data):
-        # Validate and extract data with defaults
+    def convert_from_wrroc(self, wrroc_data: Dict[str, Any]) -> Dict[str, Any]:
+        """Convert WRROC data to WES format.
+
+        Args:
+            wrroc_data (Dict[str, Any]): The WRROC data to be converted.
+
+        Returns:
+            Dict[str, Any]: The converted WES data.
+        """
         run_id = wrroc_data.get("@id", "")
         name = wrroc_data.get("name", "")
         start_time = wrroc_data.get("startTime", "")
         end_time = wrroc_data.get("endTime", "")
         state = wrroc_data.get("status", "")
         result_data = wrroc_data.get("result", [])
-
-        # Convert from WRROC to WES
+
         wes_data = {
             "run_id": run_id,
             "run_log": {

lefthook.yml

@@ -0,0 +1,10 @@
+pre-push:
+  commands:
+    ruff:
+      files: git diff --name-only --diff-filter=d $(git merge-base origin/main HEAD)..HEAD
+      run: poetry run ruff check {files}
+      glob: '*.py'
+    mypy:
+      files: git diff --name-only --diff-filter=d $(git merge-base origin/main HEAD)..HEAD
+      run: poetry run mypy {files}
+      glob: '*.py'

pyproject.toml

@@ -84,9 +84,15 @@ select = [
   "SIM", # flake8-simplify
   "UP", # pyupgrade
 ]
+ignore = ["E501"]
+fixable = ["ALL"]
 
 [tool.ruff.lint.pydocstyle]
 convention = "google"
 
 [tool.typos.default.extend-words]
 mke = 'mke'
+
+[tool.mypy]
+python_version = "3.11"
+strict = true