General formatting

.gitignore

@@ -160,3 +160,4 @@ cython_debug/
 #  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/
+projects/

.pre-commit-config.yaml

@@ -0,0 +1,14 @@
+repos:
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.6.8
+  hooks:
+    # Run the linter.
+    - id: ruff
+      args: [--select, "E1,E4,F,I,W", --extend-ignore, "W5,W6,F841,W291", --fix, --line-length, "92"]
+      types:
+        - python
+    # Run the formatter.
+    - id: ruff-format
+      types:
+        - python

README.md

@@ -19,33 +19,42 @@ environment and separate from `bnd`.
    # Miniconda
    $ curl https://repo.anaconda.com/miniconda/Miniconda3-latest-Windows-x86_64.exe -o miniconda.exe; Start-Process -FilePath ".\miniconda.exe" -ArgumentList "/S" -Wait; del miniconda.exe
    ```
+3. Clone repo and navigate to folder:
+   ```shell
+   git clone git@github.com:BeNeuroLab/beneuro_pose_estimation.git
+   cd ./beneuro_pose_estimation
+   ```
+4. Creating the conda environment
+
+```shell
+conda create -y -n bnp -c conda-forge -c nvidia -c sleap/label/dev -c sleap -c anaconda sleap=1.4.1
+
+# Activate the Conda environment
+conda activate bnp
+
+# Remove opencv pypi version to avoid conflicts
+pip uninstall -y opencv-python-headless
+
+# Install the required version of OpenCV
+pip install "opencv-contrib-python<4.7.0"
+
+# Install sleap_anipose and the required version of anipose
+pip install sleap_anipose
+pip install "anipose<1.1"
+
+# Upgrade apptools to the latest version
+pip install --upgrade apptools
+
+# Install package in editable form
+pip install -e .\  # Windows
+```
 
-3. Creating the conda environment
-
-    This seems to be working:
-      ```shell
-      # Create the environment called bnp and install sleap
-      $ conda create -y -n bnp -c conda-forge -c nvidia -c sleap -c anaconda sleap
-      $ conda activate bnp
-
-      # Remove opencv pypi version because it conflicts with sleap-anipose and anipose
-      $ pip uninstall -y opencv-python-headless 
-
-      # Install required version
-      $ pip install "opencv-contrib-python<4.7.0" 
-
-      # Install sleap anipose and anipose version 1.0 because we cannot use 1.1
-      $ pip install sleap_anipose
-      $ pip install "anipose<1.1" 
-      $ pip install --upgrade apptools
-      ```
-
-   The key package versions are:
-      ```text
-      # Name                    Version                   Build  Channel
-      anipose                   1.0.1                    pypi_0    pypi
-      aniposelib                0.5.1                    pypi_0    pypi
-      sleap-anipose             0.1.8                    pypi_0    pypi
-      opencv-contrib-python     4.6.0.66                 pypi_0    pypi
-      opencv-python             4.10.0.84                pypi_0    pypi
-      ```
+The key package versions are:
+```text
+# Name                    Version                   Build  Channel
+anipose                   1.0.1                    pypi_0    pypi
+aniposelib                0.5.1                    pypi_0    pypi
+sleap-anipose             0.1.8                    pypi_0    pypi
+opencv-contrib-python     4.6.0.66                 pypi_0    pypi
+opencv-python             4.10.0.84                pypi_0    pypi
+```

beneuro_pose_estimation/__init__.py

@@ -1,27 +1,39 @@
-"""
-Initialize macro variables and functions
-"""
 import logging
-from pathlib import Path
-
-from rich.logging import RichHandler
-
-def set_logging(file_path = None, overwrite = True):
-    frmt = '%(asctime)s - %(levelname)s - %(message)s'
-
-    if file_path is not None:
-        file_path = Path(file_path)
-        if overwrite is True and file_path.exists() is True:
-            file_path.unlink()
-        logging.basicConfig(
-            filename=file_path,
-            level=logging.INFO,
-            format=frmt,
-            datefmt='%Y-%m-%d %H:%M:%S'
-        )
-    else:
-        logging.basicConfig(
-            handlers=[RichHandler(level="NOTSET")],
-            level=logging.INFO,
-            format=frmt, datefmt='%Y-%m-%d %H:%M:%S'
-        )
+import warnings
+
+
+# Create a logger for the package
+def set_logging(
+    file_name: str,
+) -> logging.Logger:
+    """
+    Set project-wide logging
+
+    Parameters
+    ----------
+    file_name: str
+        Name of the module being logged
+
+    Returns
+    -------
+    logger: logging.Logger
+        logger object
+    """
+    logging.basicConfig(
+        level=logging.INFO,
+        format="%(asctime)s - %(name)s - %(levelname)s - %(message)s",
+        datefmt="%Y-%m-%d %H:%M:%S",
+    )
+    logging.captureWarnings(True)
+
+    logger = logging.getLogger(file_name)
+
+    def custom_warning_handler(
+        message, category, filename, lineno, file=None, line=None
+    ):
+        logger.warning(f"{category.__name__}: {message}")
+
+    # Set the custom handler
+    warnings.showwarning = custom_warning_handler
+
+    return logger