Add `visualize sos` CLI command and heatmap `--vmin`/`--vmax` by Hackshaven · Pull Request #228 · zyra-project/zyra

Hackshaven · 2026-06-18T06:30:37Z

Summary

Wires the existing PlotManager Science On a Sphere (SOS) renderer to the CLI and adds fixed color scaling — closing the gap the issue identified between "frames render" and "production-quality SOS animation." The library already did full-globe / PlateCarree / 2:1 / edge-to-edge rendering via PlotManager; it just wasn't reachable from the CLI or zyra run YAML.

Addresses NOAA-GSL/zyra#284.

Changes

New command

zyra visualize sos (alias render sos), backed by PlotManager (src/zyra/visualization/cli_sos.py). Renders gridded data as SOS frames (full-globe, PlateCarree, 2:1, edge-to-edge). Supports single (--input/--output) and batch (--inputs/--output-dir) modes with a fixed --vmin/--vmax color range for flicker-free sequences. Defaults to 4096×2048; NaN/inf masked transparent.
```
zyra visualize sos --inputs ./nc/*.nc --output-dir ./frames \
  --var <VAR> --cmap YlOrBr --width 4096 --height 2048 --vmin 0 --vmax 50
```

Heatmap (the "additionally" option in the issue)

Added --vmin/--vmax to visualize heatmap so frame sequences share a fixed color scale instead of self-scaling per frame.

Supporting changes

Shared load_data_array helper (.nc/.nc4/.npy) in cli_utils.py, validating --var before the heavy xarray import.
PlotManager.sos_plot_data now returns the saved output path.
pipeline_runner expands list/tuple arg values into multi-token flags so nargs options (inputs, extent) work from zyra run YAML/JSON.
Registered sos in both the CLI (cli_register.py) and API manifest (__init__.py) registration paths; regenerated both wizard capability manifests (only the new sos entries and heatmap --vmin/--vmax differ).

Tests & samples

tests/visualization/test_sos.py: single + batch render, 2:1 edge-to-edge assertion, and identical color scaling across frames. Render tests are gated behind DATAVIZHUB_RUN_CARTOPY_TESTS=1 (repo convention); lightweight CLI/helper tests always run.
Pipeline-runner list-expansion test in tests/misc/test_pipeline_runner.py.
Sample pipeline samples/pipelines/sos_fv3chem_frames.yaml (FV3-Chem SOS frames → MP4), dry-run verified.

Notes

OpenAPI snapshot not regenerated: the update script is gated on changes to api/{routers,server,models,schemas}, none of which were touched. The CLI command list is a runtime discovery endpoint, not baked into the OpenAPI schema, so the hash is unaffected.
Pre-existing (not introduced here): test_cli_heatmap_smoke invokes python -m zyra.visualization.cli heatmap without the visualize prefix the compat wrapper now requires. It fails on the untouched baseline and is normally skipped in CI — left as-is, out of scope.

🤖 Generated with Claude Code

Generated by Claude Code

Wire the existing PlotManager Science On a Sphere renderer to the CLI so gridded data can be rendered as SOS frames (full-globe, PlateCarree, 2:1, edge-to-edge) directly from `zyra visualize sos` and from `zyra run` YAML. - Add `zyra visualize sos` (alias `render sos`) backed by PlotManager, with single (--input/--output) and batch (--inputs/--output-dir) modes and a fixed --vmin/--vmax color range for flicker-free frame sequences. - Add --vmin/--vmax to `visualize heatmap` so frame sequences can share a fixed color scale instead of self-scaling per frame. - Add a shared `load_data_array` helper (.nc/.nc4/.npy) in cli_utils. - PlotManager.sos_plot_data now returns the saved output path. - pipeline_runner: expand list/tuple arg values to multi-token flags so nargs options (e.g. inputs, extent) work from YAML/JSON pipelines. - Register sos in both the CLI and API manifest registration paths and regenerate the wizard capabilities manifests. - Add tests (single + batch render, 2:1 edge-to-edge, consistent color scaling across frames) and a sample FV3-Chem SOS pipeline. Signed-off-by: Claude <noreply@anthropic.com>

github-actions · 2026-06-18T06:31:03Z

🔁 Relay created/updated upstream PR: NOAA-GSL/zyra#287

Copilot

Pull request overview

Adds a new visualization entry point for Science On a Sphere (SOS) frame rendering and introduces fixed color scaling (--vmin/--vmax) to avoid per-frame autoscaling “flicker” in sequences. It also improves zyra run pipeline argument handling to support argparse nargs options from YAML/JSON.

Changes:

Added zyra visualize sos (and render sos alias) wired to PlotManager, supporting single and batch frame rendering with optional fixed --vmin/--vmax.
Added --vmin/--vmax to visualize heatmap CLI plumbing.
Updated pipeline runner argv building to expand list/tuple args into multi-token flags; updated wizard capability manifests and added tests/samples.

Reviewed changes

Copilot reviewed 13 out of 13 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
`src/zyra/visualization/cli_sos.py`	New SOS CLI handler + parser registration.
`src/zyra/visualization/cli_utils.py`	Adds `load_data_array` helper for `.nc/.nc4/.npy` inputs.
`src/zyra/visualization/plot_manager.py`	`sos_plot_data` now returns the saved output path (or `None`).
`src/zyra/visualization/cli_register.py`	Registers `sos` subcommand; adds `--vmin/--vmax` to heatmap parser.
`src/zyra/visualization/__init__.py`	Mirrors CLI registration changes for the alternate registration path.
`src/zyra/visualization/cli_heatmap.py`	Passes through `vmin/vmax` to `HeatmapManager.render`.
`src/zyra/pipeline_runner.py`	Expands list/tuple stage args into multi-token argv entries.
`tests/visualization/test_sos.py`	New SOS CLI + helper tests; includes Cartopy-gated render assertions.
`tests/visualization/test_cli_commands.py`	Includes `visualize sos --help` in subcommand help smoke test.
`tests/misc/test_pipeline_runner.py`	Adds regression test for list expansion in `_build_argv_for_stage`.
`src/zyra/wizard/zyra_capabilities/visualize.json`	Updates wizard capabilities for SOS + heatmap `--vmin/--vmax`.
`src/zyra/wizard/zyra_capabilities.json`	Updates aggregated wizard capabilities for SOS + heatmap `--vmin/--vmax`.
`samples/pipelines/sos_fv3chem_frames.yaml`	Adds sample pipeline rendering SOS frames and composing them into MP4.

+        elif isinstance(v, (list, tuple)):
+            # Expand to a multi-valued flag (argparse nargs), e.g.
+            # ``inputs: [a, b]`` -> ``--inputs a b`` and
+            # ``extent: [-180, 180, -90, 90]`` -> ``--extent -180 180 -90 90``.
+            argv.append(to_flag(k))
+            argv.extend(str(item) for item in v)


+        outputs: list[str] = []
+        for src in ns.inputs:
+            dest = outdir_p / f"{Path(str(src)).stem}.png"
+            out = _render_one(ns, src, str(dest))
+            if out:
+                logging.info(out)
+                outputs.append(out)
+        try:
+            print(json.dumps({"outputs": outputs}))
+        except Exception:
+            pass
+        return 0


+    out = _render_one(ns, ns.input, ns.output)
+    if out:
+        logging.info(out)
+    return 0


+    frame_a = np.full((32, 64), 25.0)
+    frame_b = np.full((32, 64), 25.0)
+
+    out_a = tmp_path / "a.png"
+    out_b = tmp_path / "b.png"
+
+    for arr, out in ((frame_a, out_a), (frame_b, out_b)):
+        pm = PlotManager(image_extent=[-180, 180, -90, 90])
+        pm.sos_plot_data(
+            arr,
+            custom_cmap="YlOrBr",
+            output_path=str(out),
+            width=256,
+            height=128,
+            vmin=0.0,
+            vmax=50.0,
+        )
+
+    from PIL import Image
+
+    a = np.asarray(Image.open(out_a).convert("RGB"))
+    b = np.asarray(Image.open(out_b).convert("RGB"))
+    assert a.shape == b.shape
+    # Identical inputs + identical fixed scale -> pixel-identical output.
+    assert np.array_equal(a, b)


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github-actions · 2026-06-22T01:05:08Z

🔁 Relay created/updated upstream PR: NOAA-GSL/zyra#287

github-actions · 2026-06-22T01:07:14Z

🔁 Relay created/updated upstream PR: NOAA-GSL/zyra#287

…e test - cli_sos: exit non-zero when a frame fails to render (single and batch modes) instead of silently returning 0, so `zyra run` pipelines see failures. - test_sos: rewrite the fixed-scale test to use two frames with different ranges sharing a mid-value, comparing the center pixel block; add a "teeth" assertion that self-scaling differs. Add failure-exit regression tests. Signed-off-by: Eric Hackathorn <62408375+Hackshaven@users.noreply.github.com>

github-actions · 2026-06-22T01:08:37Z

🔁 Relay created/updated upstream PR: NOAA-GSL/zyra#287

Skip empty list/tuple stage args rather than emitting a bare `--flag`, which is a hard parse error for argparse nargs='+' options. Signed-off-by: Eric Hackathorn <62408375+Hackshaven@users.noreply.github.com>

github-actions · 2026-06-22T01:11:14Z

🔁 Relay created/updated upstream PR: NOAA-GSL/zyra#287

Signed-off-by: Eric Hackathorn <62408375+Hackshaven@users.noreply.github.com>

github-actions · 2026-06-22T01:12:17Z

🔁 Relay created/updated upstream PR: NOAA-GSL/zyra#287

Hackshaven mentioned this pull request Jun 18, 2026

Codex Relay: zyra-project/zyra PR #228 — Add visualize sos CLI command and heatmap --vmin/--vmax NOAA-GSL/zyra#287

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Hackshaven requested a review from Copilot June 18, 2026 06:33

Copilot started reviewing on behalf of Hackshaven June 18, 2026 06:33 View session

Copilot AI reviewed Jun 18, 2026

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Hackshaven force-pushed the claude/github-issue-access-w3t2pd branch from a7a29f5 to 53fc45b Compare June 22, 2026 01:06

Address review: omit empty list args in pipeline argv builder

f9c6c5d

Skip empty list/tuple stage args rather than emitting a bare `--flag`, which is a hard parse error for argparse nargs='+' options. Signed-off-by: Eric Hackathorn <62408375+Hackshaven@users.noreply.github.com>

Address review: add empty-list argv regression test

34da338

Signed-off-by: Eric Hackathorn <62408375+Hackshaven@users.noreply.github.com>

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Hackshaven commented Jun 18, 2026

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