Stoch file plotting tool

[lispandfound]

Adds a plot-stoch tool to plot the contents of a stoch file for workflow validation. I've also added a simple regression test and a wiki entry describing how to use it.

[sungeunbae]

==================================== ERRORS ====================================
_____________________ ERROR collecting tests/test_plots.py _____________________
ImportError while importing test module '/home/jenkins/workspace/visualisation/tests/test_plots.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/local/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_plots.py:7: in <module>
    from visualisation.sources import (
visualisation/sources/plot_stoch.py:12: in <module>
    from source_modelling import stoch
E   ImportError: cannot import name 'stoch' from 'source_modelling' (/home/jenkins/workspace/visualisation/.venv/lib/python3.13/site-packages/source_modelling/__init__.py)

[lispandfound]

==================================== ERRORS ====================================
_____________________ ERROR collecting tests/test_plots.py _____________________
ImportError while importing test module '/home/jenkins/workspace/visualisation/tests/test_plots.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/local/lib/python3.13/importlib/__init__.py:88: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_plots.py:7: in <module>
    from visualisation.sources import (
visualisation/sources/plot_stoch.py:12: in <module>
    from source_modelling import stoch
E   ImportError: cannot import name 'stoch' from 'source_modelling' (/home/jenkins/workspace/visualisation/.venv/lib/python3.13/site-packages/source_modelling/__init__.py)

Yeah that's because it requires the stoch module in source modelling. Since that PR has merged now it should work.

[Copilot]

Pull Request Overview

This pull request adds a new tool, plot-stoch, for plotting the contents of stoch files to aid in workflow validation, along with a corresponding regression test and wiki documentation update.

• Added a new wiki section documenting the plot-stoch tool usage.
• Introduced the plot_stoch.py module with functions to generate stoch plots.
• Added a regression test to validate plot-stoch tool functionality.

Reviewed Changes

Copilot reviewed 5 out of 6 changed files in this pull request and generated 2 comments.

File	Description
wiki/Sources.md	Added documentation for plotting stoch files in the wiki.
visualisation/sources/plot_stoch.py	Introduced plot_stoch tool implementation and CLI command.
tests/test_plots.py	Added regression test for the plot-stoch tool.
pyproject.toml	Registered the plot-stoch tool with the CLI entry point.

Files not reviewed (1)

• tests/stoch/realisation.stoch: Language not supported

[Copilot]

Pull Request Overview

This PR introduces a new command-line tool, plot-stoch, to visualize stoch files, updating the documentation, implementation, and regression tests accordingly.

• Added a new plotting tool in visualisation/sources/plot_stoch.py for stoch files.
• Updated documentation in wiki/Sources.md and registered the new tool in pyproject.toml.
• Added regression test coverage for the new tool in tests/test_plots.py.

Reviewed Changes

Copilot reviewed 5 out of 6 changed files in this pull request and generated 2 comments.

File	Description
wiki/Sources.md	Added documentation for plotting stoch files.
visualisation/sources/plot_stoch.py	Introduced the plot_stoch tool implementation and CLI interface.
tests/test_plots.py	Added regression tests for the plot_stoch tool.
pyproject.toml	Registered the new plot-stoch command.

Files not reviewed (1)

• tests/stoch/realisation.stoch: Language not supported

Comments suppressed due to low confidence (1)

visualisation/sources/plot_stoch.py:65

• The parameter 'width' is re-assigned in this function, shadowing its original value. Consider renaming the computed width (e.g., to 'plot_width') to avoid confusion with the CLI parameter.

width = dy * slip.shape[0]