# Changelog

## 0.6 - Becoming `mio`

### 0.6.0 - 24-12-10

#### Breaking Changes

- `miniscope-io` is now known as `mio`! Big thanks to [`@heuer`](https://github.com/Aharoni-Lab/mio/issues/77)
  for graciously giving us the name. This gives us a nice, short name that is uniform
  across pypi, the repository, and the cli.
- The {meth}`mio.models.config.LogConfig.level_file` and {meth}`mio.models.config.LogConfig.level_stdout`
  fields are no longer automatically populated from the `level` field. 
  This was because of the way the multi-source config system propagates values between
  sources with different priorities. Now downstream consumers should check if these values
  are `None` and use the `level` field if so. 

#### Config

Two big changes to config:

- [`#72`](https://github.com/Aharoni-Lab/mio/pull/72) - `@sneakers-the-rat` - Global config, user config
  from multiple sources: see the [config](../guide/config.md) documentation for more
- [`#76`](https://github.com/Aharoni-Lab/mio/pull/76) - `@sneakers-the-rat` - Convert `formats` to `yaml`.
  We finally got rid of the godforsaken self-inflicted wound of having instantiated models
  serve as config, and instead are using `yaml` everywhere for static config. This includes
  every yaml-able config having a header that indicates which model the config corresponds to,
  a (locally) unique id, which can be used anywhere a path can be, and a version stamp in anticipation
  of being able to handle model migrations.

#### CI

- [`#75`](https://github.com/Aharoni-Lab/mio/pull/75) - `@sneakers-the-rat` - Test docs builds on PRs
  to avoid broken links and references

## 0.5

### 0.5.0 - 24-11-11
Enhancements and bugfixes to `StreamDaq`; adding `device_update` module; CI/CD updates.

#### Features / bugfixes
- **Over-the-air device config:** modules and commands for updating and rebooting; *e.g.,* `mio update --key LED --value 10`, `mio device --reboot`.
- **Continuous run:** updated error handling to continuously capture even when the data stream is interrupted.
- **UNIX timestamp:** added UNIX timestamp to metadata file export.
- **More Opal Kelly bitfiles:** added FPGA configuration images and organized them based on Manchester encoding conventions, frequency, etc.
#### CI/CD
- Switched to `pdm` from `poetry`; now `pdm install --with all` for contributing.
- Added workflow for readthedocs preview link in PRs.
- Added snake_case enforcement (Lint).

Related PRs: [#45](https://github.com/Aharoni-Lab/mio/pull/45), [#48](https://github.com/Aharoni-Lab/mio/pull/48), [#49](https://github.com/Aharoni-Lab/mio/pull/49), [#50](https://github.com/Aharoni-Lab/miniscope-io/pull/50), [#53](https://github.com/Aharoni-Lab/miniscope-io/pull/53), 
Contributors: [@t-sasatani](https://github.com/t-sasatani), [@sneakers-the-rat](https://github.com/sneakers-the-rat), [@MarcelMB](https://github.com/MarcelMB), [@phildong](https://github.com/phildong)

## 0.4

### 0.4.1 - 24-09-01

#### Added Features
- Support dummy words at the beginning of buffer to make data detection in `StreamDaq` more robust. The length of this word can be set via the device config YAML file.
- `models.stream.ADCScaling` class for converting ADC raw values into voltage. The scaling factors can be set via the device config YAML file.

Related PRs: [#41](https://github.com/Aharoni-Lab/miniscope-io/pull/41), [#44](https://github.com/Aharoni-Lab/miniscope-io/pull/44)
Related Issues: [#36](https://github.com/Aharoni-Lab/miniscope-io/issues/36)
Contributors: [@t-sasatani](https://github.com/t-sasatani), [@sneakers-the-rat](https://github.com/sneakers-the-rat), [@MarcelMB](https://github.com/MarcelMB).

### 0.4.0 - 24-08-27

Enhancements and bugfixes to `StreamDaq`. Mostly around handling metadata.

Contributors: [@t-sasatani](https://github.com/t-sasatani), [@sneakers-the-rat](https://github.com/sneakers-the-rat), [@MarcelMB](https://github.com/MarcelMB).
Related PRs: [#35](https://github.com/Aharoni-Lab/miniscope-io/pull/35), [#38](https://github.com/Aharoni-Lab/miniscope-io/pull/38), [#33](https://github.com/Aharoni-Lab/miniscope-io/pull/33)
Related Issues: [#34](https://github.com/Aharoni-Lab/miniscope-io/issues/34), [#36](https://github.com/Aharoni-Lab/miniscope-io/issues/36), [#38](https://github.com/Aharoni-Lab/miniscope-io/issues/38), [#40](https://github.com/Aharoni-Lab/miniscope-io/issues/40)

**Features:**
- **Metadata handling**: CSV export and real-time plotting of metadata. The plotting feature is experimental and is still very unstable. Also improved metadata error handling.
- **CLI enhancement**: Generate video and metadata csv files with same stem names.

**Models/Formats:**
- **Runtime config**: `StreamDevRuntime` now configures queue and buffer sizes used in `StreamDaq`.

**CI / Bugfix:**
- **Fix termination**: Now buffer size doesn't affect output video. Very good for tests.
- **Device docs section**: For adding documentation about specific devices.
- **CLI docs on RTD**: Mock binaries so CLI docs show up on RTD.
- **Dependency**: Update some packages for Windows compatibility.

## 0.3

### 0.3.0 - 24-07-04

Enhancements to `StreamDaq` and improved CI processes.

Contributors: [@sneakers-the-rat](https://github.com/sneakers-the-rat),  [@t-sasatani](https://github.com/t-sasatani).
Related PRs and Issues: [#29](https://github.com/Aharoni-Lab/miniscope-io/pull/29), [#31](https://github.com/Aharoni-Lab/miniscope-io/pull/31), [#27](https://github.com/Aharoni-Lab/miniscope-io/issues/27)

**Features:**
- **Performance enhancements**: Refactoring of streamDaq to eliminate delays in the default configuration.
- **New CLI**: Introduced a `click`-based CLI offering greater flexibility and scalability.
- **Test coverage**: Integrated Coveralls to display test coverage statistics.
- **BufferFormatter class**: Added for flexible bit/byte operations and decoding incoming buffers.

**Models/Formats:**
- **Configuration changes**: Isolated device config and user config. device config is now stored in `StreamDevConfig` (renamed from `StreamDaqConfig`). User configs are segregated to the CLI.

**CI:**
- **Python 3.12 compatibility**: Added tests for Python 3.12.
- **StreamDaq tests**: Fixed issues with video hash assert tests in `streamDaq`.
- **Global test timeout**: added global timeout for all tests.

## 0.2

### 0.2.1 - 24-06-21

Linting and code formatting :)

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

See the [Contributing](./contributing.md) documentation for 
details and usage.

### 0.2.0 - 24-06-21

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}`~mio.stream_daq.streamDaq`
- Add a mock class for {class}`~mio.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}`~mio.stream_daq.StreamDaq.capture` can export video :)
- More specific exceptions:
  - {class}`~mio.exceptions.StreamError`
  - {class}`~mio.exceptions.StreamReadError`
  - {class}`~mio.exceptions.DeviceError`
  - {class}`~mio.exceptions.DeviceOpenError`
  - {class}`~mio.exceptions.DeviceConfigurationError`
- {func}`~mio.utils.hash_video` - hash decoded video frames, rather than encoded video file


Fixed:

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


Models:

- added `fs` and `show_video` to {class}`~mio.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

## 0.1

### 0.1.8 - 24-06-16

- 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 `mio.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.

### 0.1.6 - 24-04-09

- 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`

### 0.1.5 - 23-09-03

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

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

Tests:
- Run tests on macos and windows

### 0.1.4 - 23-09-03

https://github.com/Aharoni-Lab/miniscope-io/pull/8

New features:

- Data models! Hold a collection of frames and get their headers
- Plots! Mimic the plots from ye olde notebook
- Update to pydantic v2
- Version field in formats
- Format for miniscope firmware with battery voltage level

Reverted:

- grab_frames notebook is restored to using the example data and having the evaluated output present



### 0.1.1 - 23-07-13

#### Additions

- Added {class}`~mio.exceptions.EndOfRecordingException` when attempting to read past last frame
- Added {attr}`~mio.io.SDCard.frame_count` property inferred from the number of buffers and buffers per frame
- Return `self` when entering {class}`~.SDCard` context
- Optionally return {class}`~mio.sd.DataHeader`s from frame when reading

#### Bugfixes

- Index the position of the 0th frame in {attr}`~.SDCard.positions`
- reset internal frame counter to 0 when exiting context