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dj.Diagram SVG output is not byte-reproducible: set iteration order leaks into node emission order

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Issue 类型
缺陷
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技术栈
python
领域
data-visualization

调研方向

从 diagram.py 中第 1210 行和第 1251-1252 行附近的 set 消费路径开始，然后检查 issue 中描述的其他输出循环。使用不同的 PYTHONHASHSEED 值在独立进程中复现 SVG 生成，并找到图表测试。完成标准是在保留渲染后图表的同时，所有哈希种子下的 SVG 字节都完全一致。

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描述

bug

dj.Diagram's SVG output is not byte-reproducible across processes. Two identical runs in one environment — same DataJoint, same pydot, same graphviz, same database — produce SVGs that differ in the order nodes and clusters are emitted. The rendered picture is unaffected: layout coordinates, colors, shapes and edges are all identical. Only the emission order moves.

Reproduction

Rendering a single-schema diagram twice in separate processes:

$ python gen.py && cp out.svg a.svg
$ python gen.py && cp out.svg b.svg
$ diff a.svg b.svg | grep -c '^[<>]'
88

The diff is entirely reordering — clust2/clust4 swap, node1/node2 swap, and the <path> coordinates travel with them unchanged:

-<g id="clust2" class="cluster">
-<title>cluster_cluster_entity_Fluorescence</title>
+<g id="clust4" class="cluster">
+<title>cluster_cluster_entity_Segmentation</title>

Pinning the hash seed makes it go away, which identifies the mechanism:

result
two runs, default (randomized) seed differ
two runs, PYTHONHASHSEED=0 identical
PYTHONHASHSEED=0 vs PYTHONHASHSEED=12345 differ

Cause

nodes_to_show and _expanded_nodes are Python sets of table-name strings (diagram.py:245, :261, and the result.nodes_to_show = ... assignments at :470, :489, :556). Several emission-path loops iterate them directly, or iterate the result of a set intersection:

# diagram.py:1210 — dimension marking
valid_nodes = self.nodes_to_show.intersection(set(self.nodes()))
for name in valid_nodes:
    ...

# diagram.py:1251-1252 — collapse
valid_nodes = self.nodes_to_show.intersection(set(self.nodes()))
valid_expanded = self._expanded_nodes.intersection(set(self.nodes()))

str.__hash__ is salted per process by default (PEP 456), so set iteration order for table names varies between runs, and that order reaches the emitted document.

Why it matters

It defeats byte-comparison of generated figures. datajoint-docs commits three generated SVGs and ships scripts/gen_pipeline_diagrams.py --check to detect renderer drift in CI (datajoint/datajoint-docs#266). That check cannot be relied on today: one of the three figures fails against its own committed output roughly half the time for reasons unrelated to the renderer, so a genuine notation change is indistinguishable from reshuffling. It also means every regeneration produces large spurious diffs — the real change gets buried.

More generally, anyone committing a dj.Diagram SVG to version control gets churn on every re-render.

Suggested fix

Sort where the set is consumed, not where it is built — the sets are the right structure for the membership tests they exist for. sorted(...) at the emission-path call sites above is a small, behavior-preserving change; the ordering only needs to be stable, not meaningful. Worth a test that renders the same diagram in two subprocesses with different PYTHONHASHSEED values and asserts the output matches, since an in-process test cannot catch this.

Found while verifying the committed docs figures against released 2.3.3 for datajoint/datajoint-docs#266.

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