Coast/Land Mask + Tidy Up

[claudio525]

• Added function for getting a coast/land mask
• Updated pyproject.toml, removed requirements.txt
• Tidied up workflow actions to use the meta-ci-action
• Updated srf.py example to use source-modelling instead of qcore srf.py (no longer exists)
• Addressed ruff/type checking issues.

[Copilot]

Pull request overview

This PR migrates dependency management into pyproject.toml, introduces a coastline/inland-water masking helper for more accurate gridding/plotting, and consolidates CI into the shared meta-ci-action workflows while updating examples and lint/type-check configuration.

Changes:

• Moved runtime/test/dev dependencies into pyproject.toml (and removed requirements.txt).
• Added coastline + inland-water masking logic to improve land/water handling in gridded outputs and plotting.
• Replaced multiple bespoke GitHub Actions workflows with shared ucgmsim/meta-ci-action workflows; updated examples to match current upstream dependencies.

Reviewed changes

Copilot reviewed 15 out of 17 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
requirements.txt	Removed in favor of pyproject.toml dependency declaration.
pyproject.toml	Defines core + optional dependencies and adds deptry/ruff/ty configuration.
pygmt_helper/plotting.py	Adds coast/water mask helper and adjusts plotting/gridding behavior and typing.
pygmt_helper/plots.py	API cleanup for plotting helpers; updates options for roads/topo and disagg return typing.
pygmt_helper/examples/srf.py	Updates SRF example to use source-modelling SRF reader instead of removed qcore SRF API.
pygmt_helper/examples/polygons.py	Formatting/cleanup of polygon example.
pygmt_helper/examples/fault_traces.py	Updates example to match plotting API changes (no explicit NZMapData wiring).
pygmt_helper/examples/event_stations.py	Minor cleanup/formatting change.
.github/workflows/ruff.yml	Removed (superseded by consolidated CI workflow).
.github/workflows/pytest.yml	Removed (superseded by consolidated CI workflow).
.github/workflows/numpydoc.yml	Removed (superseded by consolidated CI workflow).
.github/workflows/deptry.yml	Removed (superseded by consolidated CI workflow).
.github/workflows/git-extension.yml	Updated to validate git dependency formatting against pyproject.toml.
.github/workflows/claude-review.yml	Adds shared Claude review workflow wiring.
.github/workflows/ci.yml	Adds consolidated CI workflow via ucgmsim/meta-ci-action.
.github/dependabot.yml	Enables dependabot updates for uv ecosystem configuration.

Suppressed comments (1)

pygmt_helper/plotting.py:328

• Coastline is drawn twice: once in the land background plot (with both fill and pen) and again later in the dedicated coastline plot. This duplicates strokes and can cause thicker/darker coastlines depending on pen settings. Consider removing the pen from the land-fill pass so the coastline is only stroked once on top.

    # Plot background land
    fig.plot(
        data=map_data.coastline_df,
        pen=f"{plot_kwargs['coastline_pen_width']}p,{plot_kwargs['coastline_pen_color']}",
        fill=plot_kwargs["land_color"],
    )

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[lispandfound]

Use dependency groups rather than the per-ignore rules below to avoid transient dependencies on packages we don't use

Suggested change

	dependencies = [
	"numpy",
	"pandas",
	"geopandas>1.0",
	"pyarrow",
	"pygmt>=0.16.0",
	"pyproj",
	"xarray",
	"scipy",
	"shapely>=2",
	"qcore-utils",
	"pooch",
	"tqdm",
	"netcdf4",
	dependencies = [
	"numpy",
	"pandas[parquet]",
	"geopandas>1.0",
	"pygmt>=0.16.0",
	"pyproj",
	"xarray[io]",
	"scipy",
	"shapely>=2",
	"qcore-utils",
	"pooch",
	"tqdm",

[lispandfound]

The io group for xarray pulls in all io packages required for various formats, and similar for pandas with parquet.

[lispandfound]

Can drop these

Suggested change