feat: add synthesis pathway visualization utility by redrodeo03 · Pull Request #195 · deepforestsci/DeepRetro

redrodeo03 · 2026-04-09T15:59:58Z

Description

Fix #(issue)

This PR adds a function to generate images of pathways generated by DeepRetro
todo: add SVG

Bug fix (non-breaking change which fixes an issue)
New feature (non-breaking change which adds functionality)
Breaking change (fix or feature that would cause existing functionality to not work as expected)
- In this case, we recommend to discuss your modification on GitHub issues before creating the PR
Documentations (modification for documents)

Checklist

I have performed a self-review of my own code
I have commented my code, particularly in hard-to-understand areas
I have made corresponding changes to the documentation
I have added tests that prove my fix is effective or that my feature works
New unit tests pass locally with my changes
I have checked my code and corrected any misspellings

ARY2260 · 2026-04-20T14:50:52Z

+    return root
+
+
+def node_height(node: Node) -> int:


Please docstrings, unit tests, fix linting and type annotations

also add rst docs

ARY2260

docstrings and lint needed

ARY2260 · 2026-04-20T14:51:37Z

+    return root
+
+
+def node_height(node: Node) -> int:


also add rst docs

riya-singh28

@redrodeo03 I have left a few comments regarding doctests and suggested some changes in pytests.

riya-singh28 · 2026-04-22T16:50:08Z

+        "product_metadata": {"chemical_formula": "C2H6O", "mass": 46.07},
+    })
+    assert formula == "C2H6O"
+    assert "46" in mass_str


@redrodeo03
assert "46" in mass_str is too loose a check. This may pass for incorrect values; consider asserting an exact value or using approximate float comparison.

riya-singh28 · 2026-04-22T16:51:59Z

+    assert "46" in mass_str
+
+
+def test_mol_metadata_falls_back_to_rdkit() -> None:


@redrodeo03 Can you add a docstring explaining the test here?

riya-singh28 · 2026-04-22T16:58:01Z

+    assert img.mode == "RGB"
+
+
+def test_visualize_pathway_smoke() -> None:


@redrodeo03, consider adding a test comparing the rendered image to a baseline image (preferably with tolerance to avoid brittle failures)

riya-singh28 · 2026-04-22T16:58:25Z

@@ -0,0 +1,523 @@
+"""Synthesis pathway visualization.
+
+Renders retrosynthesis output from :class:`~deepretro.algorithms.autosolve.AutoSolver`


Please shift these doctrings to rst docs.

riya-singh28 · 2026-04-22T17:01:09Z

+    Node or None
+        Root node of the tree, or ``None`` if *result* has no steps.
+
+    Examples


@redrodeo03 Please run doctests locally; the current examples are missing required import statements

riya-singh28 · 2026-04-22T17:02:37Z

+        is_target=True,
+    )
+
+    def recurse(step_id: str) -> Node:


Please add docstrings

riya-singh28 · 2026-04-22T17:03:22Z

+
+    Examples
+    --------
+    >>> leaf = Node(label="Step 1", molecules=[{"smiles": "CCO"}])


missing required import statements

riya-singh28 · 2026-04-22T17:04:03Z

+
+    Examples
+    --------
+    >>> root = Node(label="Step 0", molecules=[], is_target=True)


Missing import statements

riya-singh28 · 2026-04-22T17:04:25Z

+
+    Examples
+    --------
+    >>> img = render_mol("CCO", 200)   # doctest: +SKIP


missing required import statements

feat: add synthesis pathway visualization utility

06c70fe

redrodeo03 temporarily deployed to testing April 9, 2026 16:00 — with GitHub Actions Inactive

type check

74bbce1

redrodeo03 temporarily deployed to testing April 9, 2026 16:07 — with GitHub Actions Inactive

ARY2260 mentioned this pull request Apr 20, 2026

draft autosolve #183

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ARY2260 reviewed Apr 20, 2026

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ARY2260 requested changes Apr 20, 2026

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tests and docstrings

4db7fdc

redrodeo03 temporarily deployed to testing April 20, 2026 17:07 — with GitHub Actions Inactive

riya-singh28 marked this pull request as ready for review April 22, 2026 16:35

riya-singh28 requested changes Apr 22, 2026

View reviewed changes

redrodeo03 marked this pull request as draft April 22, 2026 17:26

docs and tests cleanuo

a1bbf0a

redrodeo03 temporarily deployed to testing April 24, 2026 17:23 — with GitHub Actions Inactive

		assert "46" in mass_str


		def test_mol_metadata_falls_back_to_rdkit() -> None:

		assert img.mode == "RGB"


		def test_visualize_pathway_smoke() -> None:

		@@ -0,0 +1,523 @@
		"""Synthesis pathway visualization.

		Renders retrosynthesis output from :class:`~deepretro.algorithms.autosolve.AutoSolver`

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redrodeo03 commented Apr 9, 2026

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