Merge pull request #68 from biomarkersParkinson/typechecking

Introduce type checking with pytype

.github/workflows/python-package.yml

@@ -5,7 +5,7 @@ name: Python package
 
 on:
   push:
-    branches: [ main, improve-docs ]
+    branches: [ main ]
   pull_request:
     branches: [ main ]
 

.github/workflows/pytype-checking.yml

@@ -0,0 +1,27 @@
+name: Pytype Type Check
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.9'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install poetry
+        poetry install
+
+    - name: Run pytype
+      run: poetry run pytype .

README.md

@@ -4,7 +4,7 @@
 | Badges | |
 |:----:|----|
 | **Packages and Releases** | [![Latest release](https://img.shields.io/github/release/biomarkersparkinson/tsdf.svg)](https://github.com/biomarkersparkinson/tsdf/releases/latest) [![PyPI](https://img.shields.io/pypi/v/tsdf.svg)](https://pypi.python.org/pypi/tsdf/)  [![Static Badge](https://img.shields.io/badge/RSD-tsdf-lib)](https://research-software-directory.org/software/tsdf) |
-| **Build Status** | [![](https://img.shields.io/badge/python-3.9+-blue.svg)](https://www.python.org/downloads/) ![Python package](https://github.com/biomarkersparkinson/tsdf/workflows/Python%20package/badge.svg) |
+| **Build Status** | [![](https://img.shields.io/badge/python-3.9+-blue.svg)](https://www.python.org/downloads/) ![Python package](https://github.com/biomarkersparkinson/tsdf/workflows/Python%20package/badge.svg) [![pytype Type Check](https://github.com/biomarkersParkinson/tsdf/actions/workflows/pytype-checking.yml/badge.svg)](https://github.com/biomarkersParkinson/tsdf/actions/workflows/pytype-checking.yml) |
 | **DOI** | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7867899.svg)](https://doi.org/10.5281/zenodo.7867899) |
 | **License** |  [![GitHub license](https://img.shields.io/github/license/biomarkersParkinson/tsdf)](https://github.com/biomarkersparkinson/tsdf/blob/main/LICENSE) |
 | **Fairness** |  [![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu) [![OpenSSF Best Practices](https://bestpractices.coreinfrastructure.org/projects/8083/badge)](https://www.bestpractices.dev/projects/8083) |

pyproject.toml

@@ -30,6 +30,7 @@ coverage = "^7.0.0"
 matplotlib = "^3.6.3"
 mkdocs = "^1.4.2"
 mkdocs-jupyter = "^0.22.0"
+pytype = "^2024.2.27"
 
 [tool.poetry.scripts]
 validate-tsdf = "tsdf.validator:main"

pytype.cfg

@@ -0,0 +1,12 @@
+[pytype]
+# Path to source files
+inputs = .
+# Path to exclude from analysis
+exclude = 
+    **/node_modules
+    **/venv
+    **/.venv
+    **/build
+    **/dist
+# Python version (matches the project's runtime environment)
+python_version = 3.9

src/tsdf/read_tsdf.py

@@ -6,6 +6,7 @@
 
 import json
 import os
+from pathlib import Path
 from typing import Dict, List
 from tsdf import file_utils 
 from tsdf.constants import METADATA_NAMING_PATTERN
@@ -71,7 +72,7 @@ def load_metadatas_from_dir(
     return metadatas
 
 
-def load_metadata_from_path(path: str) -> Dict[str, TSDFMetadata]:
+def load_metadata_from_path(path: Path) -> Dict[str, TSDFMetadata]:
     """
     Loads a TSDF metadata file, returns a dictionary
 

src/tsdf/write_binary.py

@@ -5,16 +5,16 @@
 """
 
 import os
-from typing import Any, Dict
+from typing import Any, Dict, List
 import numpy as np
 import pandas as pd
-from tsdf import numpy_utils 
+from tsdf import numpy_utils
 
 from tsdf.tsdfmetadata import TSDFMetadata
 
 
 def write_dataframe_to_binaries(
-    file_dir: str, df: pd.DataFrame, metadatas: [TSDFMetadata]
+    file_dir: str, df: pd.DataFrame, metadatas: List[TSDFMetadata]
 ) -> None:
     """
     Save binary file based on the provided pandas DataFrame.