Miniscope-io

Linting and code formatting :)

Added `black` and `ruff` for linting and formatting,
reformatted the package.

See the [Contributing](https://miniscope-io.readthedocs.io/en/latest/meta/contributing.html) documentation for
details and usage.

StreamDaq enhancements and testing

- https://github.com/Aharoni-Lab/miniscope-io/pull/26

Testing:

- [t-sasatani](https://github.com/t-sasatani) - add end-to-end test for {class}`~miniscope_io.stream_daq.streamDaq`
- Add a mock class for {class}`~miniscope_io.devices.opalkelly.okDev`
- replace `tmpdir` fixture and `tempfile` module with `tmp_path`

New:

- [t-sasatani](https://github.com/t-sasatani) - allow use of okDev on Windows
- {meth}`~miniscope_io.stream_daq.StreamDaq.capture` can export video :)
- More specific exceptions:
- {class}`~miniscope_io.exceptions.StreamError`
- {class}`~miniscope_io.exceptions.StreamReadError`
- {class}`~miniscope_io.exceptions.DeviceError`
- {class}`~miniscope_io.exceptions.DeviceOpenError`
- {class}`~miniscope_io.exceptions.DeviceConfigurationError`
- {func}`~miniscope_io.utils.hash_video` - hash decoded video frames, rather than encoded video file


Fixed:

- Removed `print` statements in {class}`~miniscope_io.devices.opalkelly.okDev`
- {meth}`~miniscope_io.stream_daq.StreamDaq.capture`
- Don't require `config`
- Replace logging with {func}`~miniscope_io.logging.init_logger`
- Use of {attr}`~miniscope_io.stream_daq.StreamDaq.terminate` to control inner loops


Models:

- added `fs` and `show_video` to {class}`~miniscope_io.models.stream.StreamDaqConfig`

CI:

- [t-sasatani](https://github.com/t-sasatani) - restore windows and mac tests (oops)
- caching dependency installs
- not using pytest-emoji, it was always annoying

- https://github.com/Aharoni-Lab/miniscope-io/pull/21
- https://github.com/Aharoni-Lab/miniscope-io/pull/15

New features:

- **Support for Various Image Formats**: `streamDaq` now supports multiple image formats, including different image sizes, frame rates (FPS), and bit-depths. These configurations can be provided via a YAML file. Examples of these configurations can be found in `miniscope_io.data.config`.
- **Pydantic Model for Configuration**: Added a Pydantic model to validate the configuration of `streamDaq`.
- **Bitstream Loader**: Added a bitstream loader to automatically configure the Opal Kelly FPGA when running `streamDaq`.
- **Updated Command Line Script**: The command line script for running `streamDaq` has been updated. Use `streamDaq -c path/to/config/yaml/file.yml` to run the process with your YAML configuration file.
- **Logger Module**: Added a logger module that can be configured using environmental variables or a `.env` file.

Note: Version 0.1.7 was skipped accidentally and does not exist.

- https://github.com/Aharoni-Lab/miniscope-io/pull/14

New features:

- Added support for the wireless FPGA and UART daqs - work in progress unifying the API, but
initial version of code is present in `stream_daq.py`
- Vendored opalkelly device drivers - see `devices` and `vendor`

- https://github.com/Aharoni-Lab/miniscope-io/pull/9
- https://github.com/Aharoni-Lab/miniscope-io/pull/10

Bugfixes:
- Handle absolute paths correctly on windows, which can't deal with {meth}`pathlib.Path.resolve()`, apparently

New features:
- Added {meth}`~miniscope_io.io.SDCard.to_video` to export videos
- Added notebook demonstrating {meth}`~miniscope_io.io.SDCard.to_video`
- Added {mod}`miniscope_io.utils` module with {func}`~.utils.hash_file` function for hashing files (used in testing)

Code structure:
- (Minor) moved {meth}`~miniscope_io.io.SDCard.skip` to general methods block (no change)

Tests:
- Run tests on macos and windows