water_column_sonar_processing 25.4.5
Processing tool for water column sonar data.
Requires Python: >=3.12
Keywords: ocean, sonar, water column

# Water Column Sonar Processing
Processing tool for converting Level_0 water column sonar data to Level_1 and Level_2 derived data sets as well as generating geospatial information.

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# Setting up the Python Environment
> Python 3.12.9

# Installing Dependencies
```
source .venv/bin/activate

uv pip install --upgrade pip

uv pip install -r pyproject.toml --all-extras

uv run pre-commit install
```

# Pytest
```
uv run pytest tests -W ignore::DeprecationWarning
```
or
> pytest --cache-clear --cov=src tests/ --cov-report=xml

# Instructions
Following this tutorial:
https://packaging.python.org/en/latest/tutorials/packaging-projects/

# Pre Commit Hook
see here for installation: https://pre-commit.com/
https://dev.to/rafaelherik/using-trufflehog-and-pre-commit-hook-to-prevent-secret-exposure-edo
```
uv run pre-commit install --allow-missing-config
# or
uv run pre-commit install
```

# Black
https://ljvmiranda921.github.io/notebook/2018/06/21/precommits-using-black-and-flake8/
```
Settings > Black
Execution mode: Package
Python Interpreter: .../.venv/bin/python
Use Black Formatter: X On Code reformat, X On Save
```

# Linting
Ruff
https://plugins.jetbrains.com/plugin/20574-ruff

# Colab Test
https://colab.research.google.com/drive/1KiLMueXiz9WVB9o4RuzYeGjNZ6PsZU7a#scrollTo=AayVyvpBdfIZ

# Test Coverage
TODO

# Tag a Release
Step 1 --> increment the semantic version in the zarr_manager.py "metadata" & the "pyproject.toml"
```commandline
git tag -a v25.4.5 -m "Releasing v25.4.5"
git push origin --tags
```

# To Publish To PROD
```commandline
uv build --no-sources
uv publish
```

# TODO:
add https://pypi.org/project/setuptools-scm/
for extracting the version

# Security scanning
> bandit -r water_column_sonar_processing/

# Data Debugging
Experimental Plotting in Xarray (hvPlot):
https://colab.research.google.com/drive/18vrI9LAip4xRGEX6EvnuVFp35RAiVYwU#scrollTo=q9_j9p2yXsLV

HB0707 Zoomable Cruise:
https://hb0707.s3.us-east-1.amazonaws.com/index.html


# UV Debugging
```
uv lock --check
uv lock
uv sync --extra dev
#uv run pytest tests
```

# Fixing S3FS Problems
```commandline
To enable/disa asyncio for the debugger, follow the steps:
Open PyCharm
Use Shift + Shift (Search Everywhere)
In the popup type: Registry and press Enter
Find "Registry" in the list of results and click on it.
In the new popup find python.debug.asyncio.repl line and check the respective checkbox
Press Close.
Restart the IDE.
The asyncio support will be enabled in the debugger.
```