Restore Pipeline.show_graph, fix graph rendering, add tests by eywalker · Pull Request #114 · nauticalab/orcapod-python

eywalker · 2026-03-26T23:23:34Z

Summary

Remove redundant VizGraphNode class — actual pipeline nodes already carry .label and .node_type
Replace all kernel_type references in GraphRenderer with node_type so render_graph works directly with pipeline._node_graph
Add Pipeline.show_graph() convenience method
Add comprehensive test coverage for graph rendering (26 tests)
Centralize @pytest.mark.postgres skip logic in root conftest.py with --postgres CLI opt-in flag
Update CI postgres workflow to pass --postgres

Fixes PLT-1180

Test plan

All 26 new graph rendering tests pass
Full test suite passes (2847 passed, 49 skipped, 0 errors)
PostgreSQL tests properly skipped without --postgres flag
CI postgres workflow passes with --postgres flag

🤖 Generated with Claude Code

…add show_graph Remove the redundant VizGraphNode class — actual pipeline nodes already carry .label and .node_type. Rename all kernel_type references in GraphRenderer to node_type so render_graph works directly with pipeline._node_graph. Add Pipeline.show_graph() convenience method. Update tutorial notebook. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

… via --postgres Add test_graph_rendering.py covering GraphRenderer, render_graph, render_graph_dark_theme, StyleRuleSets, and Pipeline.show_graph. Centralize @pytest.mark.postgres skip logic in root conftest.py with a --postgres CLI flag (opt-in). Update CI postgres workflow to pass the flag. Remove duplicated skip hooks from subdirectory conftests. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

codecov · 2026-03-26T23:24:48Z

Codecov Report

❌ Patch coverage is 96.29630% with 1 line in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
src/orcapod/pipeline/graph.py	96.29%	1 Missing ⚠️

📢 Thoughts on this report? Let us know!

Avoids blocking PRs on untestable rendering paths (matplotlib display, graphviz file output) while still catching meaningful coverage gaps. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Copilot

Pull request overview

This PR restores and modernizes pipeline graph visualization by removing an unnecessary visualization node wrapper, switching the renderer to use the pipeline’s real node metadata (node_type/label), adding a Pipeline.show_graph() convenience API, and expanding automated coverage around graph rendering. It also centralizes PostgreSQL test opt-in behavior behind a --postgres flag and updates CI accordingly.

Changes:

Add Pipeline.show_graph() and update GraphRenderer to style/label nodes based on GraphNode.node_type.
Add a new tests/test_pipeline/test_graph_rendering.py suite covering graph rendering utilities and the new pipeline API.
Centralize @pytest.mark.postgres opt-in skipping in tests/conftest.py and pass --postgres in the PostgreSQL CI workflow.

Reviewed changes

Copilot reviewed 7 out of 8 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
`src/orcapod/pipeline/graph.py`	Removes legacy viz wrapper, adds `Pipeline.show_graph()`, and refactors `GraphRenderer` to use `node_type`/`label`.
`tests/test_pipeline/test_graph_rendering.py`	Adds broad unit test coverage for graph rendering utilities and `Pipeline.show_graph()`.
`tests/conftest.py`	Introduces `--postgres` opt-in flag and default skipping of `@pytest.mark.postgres` tests.
`tests/test_databases/conftest.py`	Updates documentation to reflect centralized postgres skip behavior.
`tests/test_core/sources/conftest.py`	Removes duplicated postgres skip logic (now handled in root conftest) while keeping the psycopg stub behavior.
`.github/workflows/run-postgres-tests.yml`	Runs postgres workflow tests with `--postgres` enabled.

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

Copilot · 2026-03-26T23:28:25Z

+        if node.node_type in rules:
+            default_attrs.update(rules[node.node_type])



_get_node_attributes() now keys style rules strictly by node.node_type, but DARK_THEME_RULES still uses the key "pod" for function nodes. Since FunctionNode.node_type == "function", dark-theme styling will never apply to function nodes. Rename the dark-theme key to "function" (and optionally keep "pod" as a backwards-compatible alias) so function nodes get themed correctly.

Suggested change

if node.node_type in rules:

default_attrs.update(rules[node.node_type])

# Determine which style rule key to use.

# Primary key is the node's node_type; fall back to "pod" for

# backward compatibility with themes that still use that key

# for function nodes.

style_key = node.node_type

if (

style_key == "function"

and style_key not in rules

and "pod" in rules

):

style_key = "pod"

if style_key in rules:

default_attrs.update(rules[style_key])

Fixed in 727f221. Renamed "pod" → "function" in DARK_THEME_RULES. No backward-compat alias needed (pre-v0.1.0 greenfield).

Copilot · 2026-03-26T23:28:26Z

                "shape": "box",
                "fontcolor": pod_main_fcolor,
                "style": "filled,rounded",
-                "type_font_color": kernel_type_fcolor,
+                "type_font_color": node_type_fcolor,
            },


In StyleRuleSets.create_custom_rules(), the returned dict uses type_font_color keys (e.g. in the function rule). GraphRenderer expects typefontcolor in node_attrs (and the built-in rule sets also use typefontcolor), so these overrides won't affect the HTML label and may emit an unrecognized DOT attribute. Use typefontcolor consistently in the custom rules output.

Fixed in 727f221. create_custom_rules now uses typefontcolor consistently, matching the built-in rule sets.

Copilot · 2026-03-26T23:28:26Z

        **style_overrides,
    ) -> str:
-        # Get final styles (defaults + overrides)
        styles = self._merge_styles(**style_overrides)

        import graphviz


Within generate_dot(), the global fontsize logic later in the function checks styles.get("font_size") but then reads styles["fontsize"]. This means passing fontsize=... won't take effect, and passing font_size=... can raise KeyError. Use a single key consistently (e.g. fontsize) and access it via .get(...) to avoid runtime errors.

Fixed in 727f221. generate_dot now checks styles.get("fontsize") consistently, matching render_graph.

Codecov expects bare numbers, not percentage strings. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Add tests that run the non-raw_output render_graph paths including graphviz DOT compilation, output_path file writing, and show=True with mocked matplotlib. Brings patch coverage for rendering code well above 80%. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

The secrets context is not available in job-level `if` expressions, causing workflow validation to fail. Move the event-type check to the job level and gate individual steps on the env var instead. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

…, fontsize - Rename DARK_THEME_RULES "pod" key to "function" to match node_type - Use "typefontcolor" consistently in style rules dicts (was "type_font_color" in create_custom_rules) - Fix font_size/fontsize key mismatch in generate_dot Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

eywalker and others added 2 commits March 26, 2026 23:03

Copilot AI review requested due to automatic review settings March 26, 2026 23:23

Copilot started reviewing on behalf of eywalker March 26, 2026 23:23 View session

eywalker requested a review from brian-arnold March 26, 2026 23:24

ci: add codecov.yml with 80% patch / 70% project coverage targets

d82189a

Avoids blocking PRs on untestable rendering paths (matplotlib display, graphviz file output) while still catching meaningful coverage gaps. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Copilot AI reviewed Mar 26, 2026

View reviewed changes

eywalker and others added 4 commits March 26, 2026 23:29

fix(ci): remove percent signs from codecov.yml targets

b7f949d

Codecov expects bare numbers, not percentage strings. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

brian-arnold merged commit b1edaaf into dev Mar 27, 2026
8 checks passed

eywalker deleted the eywalker/plt-1180-restore-pipelineshow_graph-method-with-tests branch May 18, 2026 21:15

Navigation Menu

Uh oh!

Restore Pipeline.show_graph, fix graph rendering, add tests - #114

Restore Pipeline.show_graph, fix graph rendering, add tests#114
brian-arnold merged 7 commits into
devfrom
eywalker/plt-1180-restore-pipelineshow_graph-method-with-tests

eywalker commented Mar 26, 2026 •

edited

Loading

Uh oh!

codecov Bot commented Mar 26, 2026 •

edited

Loading

Uh oh!

Copilot AI left a comment

Uh oh!

Copilot AI Mar 26, 2026

Uh oh!

eywalker Mar 27, 2026

Uh oh!

Copilot AI Mar 26, 2026

Uh oh!

eywalker Mar 27, 2026

Uh oh!

Copilot AI Mar 26, 2026

Uh oh!

eywalker Mar 27, 2026

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

		if node.node_type in rules:
		default_attrs.update(rules[node.node_type])

-        if node.node_type in rules:
-            default_attrs.update(rules[node.node_type])
+        # Determine which style rule key to use.
+        # Primary key is the node's node_type; fall back to "pod" for
+        # backward compatibility with themes that still use that key
+        # for function nodes.
+        style_key = node.node_type
+        if (
+            style_key == "function"
+            and style_key not in rules
+            and "pod" in rules
+        ):
+            style_key = "pod"
+        if style_key in rules:
+            default_attrs.update(rules[style_key])

Uh oh!

Conversation

eywalker commented Mar 26, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Summary

Test plan

Uh oh!

codecov Bot commented Mar 26, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Codecov Report

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull request overview

Reviewed changes

Uh oh!

Copilot AI Mar 26, 2026

Choose a reason for hiding this comment

Uh oh!

eywalker Mar 27, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Mar 26, 2026

Choose a reason for hiding this comment

Uh oh!

eywalker Mar 27, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Mar 26, 2026

Choose a reason for hiding this comment

Uh oh!

eywalker Mar 27, 2026

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

eywalker commented Mar 26, 2026 •

edited

Loading

codecov Bot commented Mar 26, 2026 •

edited

Loading