removed pdf docs and cleaned example

[starry-phoenix]

• removed option to generate pdfs

Summary by Sourcery

Remove legacy salinity-specific example configuration and outputs while adding a quickstart notebook-based example and simplifying docs build options.

New Features:

• Add a Jupyter quickstart example demonstrating model configuration, execution, analysis, and visualisation without Hydra.

Enhancements:

• Simplify example configuration by inlining salinity and related parameters in the quickstart notebook instead of separate config fragments.
• Remove obsolete example outputs and Hydra artefacts from version control to keep the repository clean.

Build:

• Drop the Sphinx latexpdf docs build target, limiting docs builds to HTML and related commands.

[sourcery-ai]

Reviewer's Guide

Removes PDF/LaTeX documentation build support and obsolete salinity/Hydra example artifacts, and adds a self-contained Jupyter quickstart notebook demonstrating a simple SPyice model run without Hydra-based configuration files.

Sequence diagram for the new Hydra-free SPyice quickstart notebook workflow

sequenceDiagram
    actor User
    participant JupyterNotebook
    participant OmegaConf
    participant ConfigSort
    participant Utils_create_output_directory as create_output_directory
    participant PreProcess
    participant SeaIceModel
    participant Analysis
    participant VisualiseModel
    participant FileSystem

    User->>JupyterNotebook: Open quickstart_example.ipynb
    User->>JupyterNotebook: Run import cell
    JupyterNotebook->>OmegaConf: create(constants_dict)
    OmegaConf-->>JupyterNotebook: config_raw (OmegaConf)

    JupyterNotebook->>ConfigSort: getconfig_dataclass(config_raw, config_type_jupyter)
    ConfigSort-->>JupyterNotebook: config (dataclass)

    JupyterNotebook->>Utils_create_output_directory: create_output_directory(wo_hydra_dir, S_IC, dz, dt, iter_max, example)
    Utils_create_output_directory->>FileSystem: mkdir output paths
    FileSystem-->>Utils_create_output_directory: output_dir paths created
    Utils_create_output_directory-->>JupyterNotebook: out_dir_final

    User->>JupyterNotebook: Run preprocessing cell
    JupyterNotebook->>PreProcess: get_variables(config_raw, out_dir_final)
    PreProcess->>FileSystem: write preprocessing outputs
    PreProcess-->>JupyterNotebook: preprocess_data, userinput_data

    User->>JupyterNotebook: Set model options on userinput_data

    User->>JupyterNotebook: Run model cell
    JupyterNotebook->>SeaIceModel: get_results(preprocess_data, userinput_data)
    SeaIceModel->>FileSystem: write simulation outputs
    SeaIceModel-->>JupyterNotebook: results_data

    JupyterNotebook->>Analysis: get_error_results(t_k_diff, t_stefan_diff, residual, temperature_mushy, phi_mushy, salinity_mushy, output_dir)
    Analysis->>FileSystem: export residuals and error summaries
    Analysis-->>JupyterNotebook: analysis_data

    User->>JupyterNotebook: Create visualization object
    JupyterNotebook->>VisualiseModel: __init__(userinput_data, results_data, analysis_data)
    VisualiseModel-->>JupyterNotebook: model_visualization_object

    User->>JupyterNotebook: Call plot_error_temp, plot_depth_over_time, plot_temperature_heatmap, plot_salinity_heatmap
    JupyterNotebook->>VisualiseModel: plotting methods
    VisualiseModel->>FileSystem: optionally save figures, CSV
    VisualiseModel-->>JupyterNotebook: rendered plots in notebook

Loading

Flow diagram for updated documentation build scripts (HTML only, no PDF)

flowchart LR
    subgraph DocsScripts["Docs build scripts in pyproject.toml"]
      Clean["clean: make clean --directory=docs"]
      Html["html: make html --directory=docs"]
      Serve["serve: python -m http.server --directory=docs/build/html/"]
      Build["build: make clean --directory=docs && make html --directory=docs"]
    end

    User["Developer running docs commands"] --> Clean
    User --> Html
    User --> Serve
    User --> Build

    %% Previously there was a latexpdf target to build PDFs; it is now removed
    %% so the flow now only supports HTML documentation generation.

Loading

File-Level Changes

Change	Details	Files
Removed PDF/LaTeX Sphinx docs build support from the project configuration.	Removed the docs latexpdf build target from the Hatch docs environment scripts so only HTML-related tasks remain	pyproject.toml
Simplified example configuration by dropping the salinity initial-condition preset from Hydra config and removing corresponding example salinity configs and outputs.	Removed S_IC from the example Hydra defaults list so salinity IC is no longer a selectable default in that example config Removed S_IC from the Hydra help/choice list for example runs Deleted example salinity configuration files and associated sample output artifacts and Hydra run metadata	example/conf/config.yaml example/conf/S_IC/S34.yaml example/conf/salinity/no.yaml example/conf/salinity/yes.yaml example/output/with_hydra/Temperature_S34_Dirichlet_0.01_47.0_500_const_dens-mushfix/Temperature0.01.csv example/outputs/2024-08-26/234047_real_47.0_1000/.hydra/config.yaml example/outputs/2024-08-26/234047_real_47.0_1000/.hydra/hydra.yaml example/outputs/2024-08-26/234047_real_47.0_1000/.hydra/overrides.yaml example/outputs/2024-08-26/234047_real_47.0_1000/main_config.log
Added a new self-contained Jupyter quickstart notebook illustrating building, running, and visualizing a simple SPyice sea-ice model without Hydra.	Introduced a notebook that constructs an OmegaConf config in-code for constants, dt, S_IC, iter_max, and dz and converts it to the internal dataclass via ConfigSort.getconfig_dataclass with config_type='jupyter' Demonstrated creation of an output directory using create_output_directory and running preprocessing with PreProcess.get_variables Showed how to set model options (e.g., is_diffusiononly_equation), run SeaIceModel.get_results, perform error analysis via Analysis.get_error_results, and create a VisualiseModel for plotting error, depth-over-time, and temperature/salinity heatmaps	example/quickstart_example.ipynb

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[sourcery-ai]

Hey - I've left some high level feedback:

• The quickstart_example.ipynb is checked in with execution counts, outputs, and large embedded images; consider clearing outputs and resetting execution counts before committing to keep diffs small and avoid bloating the repo.
• The notebook hardcodes documentation links to http://[::1]:8000; it would be more robust to point to a stable public URL or a relative docs path so that users running the notebook elsewhere don't get broken links.
• In quickstart_example.ipynb you import both create_output_directory and ConfigSort from spyice.utils in separate statements; you can simplify by importing them together from the same module in one line to keep the imports tidy.

Prompt for AI Agents

Please address the comments from this code review:

## Overall Comments
- The quickstart_example.ipynb is checked in with execution counts, outputs, and large embedded images; consider clearing outputs and resetting execution counts before committing to keep diffs small and avoid bloating the repo.
- The notebook hardcodes documentation links to http://[::1]:8000; it would be more robust to point to a stable public URL or a relative docs path so that users running the notebook elsewhere don't get broken links.
- In quickstart_example.ipynb you import both `create_output_directory` and `ConfigSort` from `spyice.utils` in separate statements; you can simplify by importing them together from the same module in one line to keep the imports tidy.

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