Merge in from Gorkowski Dev

Gorkowski commented 1 month ago

Fixes #473

Summary by Sourcery

Introduce new coagulation strategies and surface tension factories, enhance existing classes with improved methods and flexibility, fix bugs in mean free path calculations, and update documentation and tests to reflect these changes.

New Features:

Introduce a new CoagulationStrategy module with various strategies for calculating coagulation rates, including DiscreteSimple, DiscreteGeneral, ContinuousGeneralPDF, and ParticleResolved strategies.
Add a SurfaceFactory class to create surface tension strategy builders for calculating surface tension and the Kelvin effect for species in particulate phases.
Implement a VaporPressureFactory class to create vapor pressure strategy builders for calculating vapor pressure of gas species.
Add new functions for converting mass concentrations to mole and volume fractions in the convert_mass_concentration module.

Bug Fixes:

Fix issues in the mean_free_path calculation by updating the method to use the correct dynamic viscosity and gas constant values.
Correct the handling of temperature unit conversions in the convert_units function to ensure accurate conversions between Celsius, Fahrenheit, and Kelvin.

Enhancements:

Refactor the GasSpecies class to support both single and array inputs for gas properties, improving flexibility and usability.
Improve the Stream and StreamAveraged classes by adding methods for data manipulation, such as __getitem__, __setitem__, and get_std.
Enhance the CoulombEnhancement class by adding detailed docstrings and improving the calculation methods for potential ratio and enhancement limits.
Refactor the vapor_pressure_builders module to use a base BuilderABC class for better code organization and error handling.

Build:

Update the setup-python action in GitHub workflows to cache pip dependencies, improving build efficiency.

CI:

Add caching for pip dependencies in GitHub Actions workflows to speed up the continuous integration process.

Documentation:

Update the documentation to include new notebooks on light scattering and equilibria, providing users with more examples and guides.
Revise the mean_free_path notebook to reflect changes in the calculation method and improve clarity.

Tests:

Add new tests for the CoagulationStrategy module to ensure the correctness of different coagulation strategies.
Introduce tests for the SurfaceFactory class to verify the creation of surface tension strategies.
Enhance existing tests for the convert_mass_concentration module to cover new functionalities and edge cases.

Chores:

Update the version number to 0.0.17.dev0 to reflect ongoing development changes.
Clean up and organize imports across multiple modules for better readability and maintainability.

sourcery-ai[bot] commented 1 month ago

Reviewer's Guide by Sourcery

This pull request implements significant changes across multiple modules in the particula project, including updates to gas species handling, coagulation strategies, and various utility functions. The changes involve refactoring existing code, adding new functionality, and improving type hinting and error handling.

Class diagram for GasSpecies

classDiagram
    class GasSpecies {
        - name: Union[str, NDArray[np.str_]]
        - molar_mass: Union[float, NDArray[np.float64]]
        - pure_vapor_pressure_strategy: Union[VaporPressureStrategy, list[VaporPressureStrategy]]
        - condensable: Union[bool, NDArray[np.bool_]]
        - concentration: Union[float, NDArray[np.float64]]
        + get_molar_mass() Union[float, NDArray[np.float64]]
        + get_condensable() Union[bool, NDArray[np.bool_]]
        + get_concentration() Union[float, NDArray[np.float64]]
        + get_pure_vapor_pressure(temperature: Union[float, NDArray[np.float64]]) Union[float, NDArray[np.float64]]
        + get_partial_pressure(temperature: Union[float, NDArray[np.float64]]) Union[float, NDArray[np.float64]]
        + get_saturation_ratio(temperature: Union[float, NDArray[np.float64]]) Union[float, NDArray[np.float64]]
        + get_saturation_concentration(temperature: Union[float, NDArray[np.float64]]) Union[float, NDArray[np.float64]]
        + add_concentration(added_concentration: Union[float, NDArray[np.float64]])
    }

Class diagram for Stream and StreamAveraged

classDiagram
    class Stream {
        - header: List[str]
        - data: NDArray[np.float64]
        - time: NDArray[np.float64]
        - files: List[str]
        + validate_inputs()
        + __getitem__(index: Union[int, str]) NDArray[np.float64]
        + __setitem__(index: Union[int, str], value: NDArray[np.float64])
        + __len__() int
        + datetime64() NDArray[np.float64]
        + header_dict() dict[int, str]
        + header_float() NDArray[np.float64]
    }
    class StreamAveraged {
        - average_interval: float
        - start_time: float
        - stop_time: float
        - standard_deviation: NDArray[np.float64]
        + validate_averaging_params()
        + get_std(index: Union[int, str]) NDArray[np.float64]
    }
    StreamAveraged --|> Stream

File-Level Changes

Change	Details	Files
Refactored and enhanced gas species handling	Updated GasSpecies class with new methods and properties Implemented new vapor pressure strategies and factories Added new gas properties calculations Improved type hinting and error handling in gas-related modules	`particula/next/gas/species.py` `particula/next/gas/vapor_pressure_strategies.py` `particula/next/gas/vapor_pressure_factories.py` `particula/next/gas/properties/mean_free_path.py` `particula/next/gas/properties/thermal_conductivity.py`
Implemented new coagulation strategies and related functionality	Added abstract CoagulationStrategy class and concrete implementations Implemented particle-resolved coagulation method Added new utility functions for coagulation calculations	`particula/next/dynamics/coagulation/strategy.py` `particula/next/particles/properties/friction_factor_module.py` `particula/next/particles/properties/knudsen_number_module.py`
Updated and refactored utility functions and modules	Improved input handling and unit conversion functions Updated time management utilities Refactored and enhanced statistical functions	`particula/util/input_handling.py` `particula/util/time_manage.py` `particula/util/stats.py` `particula/util/reduced_quantity.py`
Updated data handling and processing modules	Refactored Stream and Lake classes Updated data loading and processing functions Improved error handling and logging in data-related modules	`particula/data/stream.py` `particula/data/lake.py` `particula/data/loader.py` `particula/data/process/size_distribution.py`
Updated documentation and examples	Updated README and version number Added new example notebooks Updated existing documentation in various modules	`README.md` `particula/__init__.py` `docs/How-To-Guides/Light_Scattering/index.md` `docs/How-To-Guides/Equilibria/index.md`

Tips and commands

#### Interacting with Sourcery - **Trigger a new review:** Comment `@sourcery-ai review` on the pull request. - **Continue discussions:** Reply directly to Sourcery's review comments. - **Generate a GitHub issue from a review comment:** Ask Sourcery to create an issue from a review comment by replying to it. #### Customizing Your Experience Access your [dashboard](https://app.sourcery.ai) to: - Enable or disable review features such as the Sourcery-generated pull request summary, the reviewer's guide, and others. - Change the review language. - Add, remove or edit custom review instructions. - Adjust other review settings. #### Getting Help - [Contact our support team](mailto:support@sourcery.ai) for questions or feedback. - Visit our [documentation](https://docs.sourcery.ai) for detailed guides and information. - Keep in touch with the Sourcery team by following us on [X/Twitter](https://x.com/SourceryAI), [LinkedIn](https://www.linkedin.com/company/sourcery-ai/) or [GitHub](https://github.com/sourcery-ai).

github-actions[bot] commented 1 month ago

PR Preview Action v1.4.8 :---: :rocket: Deployed preview to https://uncscode.github.io/particula/pr-preview/pr-474/ on branch gh-pages at 2024-10-04 12:29 UTC

Gorkowski commented 1 month ago

I'm just wanted to create some issues for most of the soucery comments so we don't forget

I'm good with it now

uncscode / particula