fix: dag mermaid-js edges (bug:#3556) #3669
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I noticed that `DAG._dot()` renders the edges correctly, but `DAG._mermaid_js()` makes a mess out of it. - I copied the bit from the _dot part to the _mermaid_js part - modified the f"" stretch to use the correct numbers This fixed the mermaid output so it matches the dor one.
📝 WalkthroughWalkthroughThe internal logic of the Additionally, a new test workflow and corresponding Mermaid diagram were added to verify the correct behavior related to GitHub issues #3556 and #946. A new test function was introduced to run Snakemake with the Mermaid.js DAG output for this workflow. Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant DAG
participant MermaidJS
User->>DAG: Request Mermaid.js graph
DAG->>DAG: Map nodes to indices (ids)
DAG->>DAG: Iterate over nodes and dependencies
DAG->>MermaidJS: Generate edges as dep --> node using ids
DAG->>User: Return Mermaid.js graph string
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src/snakemake/dag.py (1)
2668-2674: Avoid triple enumeration ofgraphfor index consistency & micro-perf
graphis enumerated three times (headers, styles,ids). Any mutation of the dict between calls would desynchronise indices. A single pass keeps things deterministic and shaves a bit of work:- nodes_headers = [ - f"\tid{index}[{node2label(node)}]" for index, node in enumerate(graph) - ] - nodes_styles = [ - f"\tstyle id{index} fill:{rulecolor[str(node)]},stroke-width:2px,color:#333333{node2style(node)}" - for index, node in enumerate(graph) - ] - # node ids - ids = {node: i for i, node in enumerate(graph)} + nodes = list(graph.keys()) + ids = {node: i for i, node in enumerate(nodes)} + nodes_headers = [f"\tid{ids[node]}[{node2label(node)}]" for node in nodes] + nodes_styles = [ + f"\tstyle id{ids[node]} " + f"fill:{rulecolor[str(node)]},stroke-width:2px,color:#333333{node2style(node)}" + for node in nodes + ]Keeps all index look-ups consistent and makes intent clearer.
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📓 Common learnings
Learnt from: johanneskoester
PR: snakemake/snakemake#3148
File: snakemake/dag.py:1332-1336
Timestamp: 2024-11-12T12:08:20.342Z
Learning: In `snakemake/dag.py`, when code is outdated and will disappear upon resolving merge conflicts, avoid making code review suggestions on that code.
Learnt from: johanneskoester
PR: snakemake/snakemake#3140
File: snakemake/dag.py:1308-1308
Timestamp: 2024-10-14T09:42:11.571Z
Learning: In `snakemake/dag.py`, avoid flagging missing lines or indentation issues when there is no clear syntax or logical error to prevent false positives.
Learnt from: leoschwarz
PR: snakemake/snakemake#3176
File: tests/test_output_index.py:99-157
Timestamp: 2025-01-17T12:00:09.368Z
Learning: New test dependencies for Snakemake should be introduced in separate PRs rather than being added as part of feature or refactoring PRs.
src/snakemake/dag.py (2)
<retrieved_learning>
Learnt from: johanneskoester
PR: #3148
File: snakemake/dag.py:1332-1336
Timestamp: 2024-11-12T12:08:20.342Z
Learning: In snakemake/dag.py, when code is outdated and will disappear upon resolving merge conflicts, avoid making code review suggestions on that code.
</retrieved_learning>
<retrieved_learning>
Learnt from: johanneskoester
PR: #3140
File: snakemake/dag.py:1308-1308
Timestamp: 2024-10-14T09:42:11.571Z
Learning: In snakemake/dag.py, avoid flagging missing lines or indentation issues when there is no clear syntax or logical error to prevent false positives.
</retrieved_learning>
🔇 Additional comments (1)
src/snakemake/dag.py (1)
2671-2673: Edge direction now matches DOT output – good fix
Changing the arrow toid{ids[dep]} --> id{ids[node]}aligns Mermaid with the DOT representation and renders dependencies in the expected upstream → downstream direction.
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I have managed to get a test that passes with the fix and fails without the fix. I don't know how to integrate it using PRs, but here is the link to my commit: b-brankovics/snakemake@e715f3e |
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@b-brankovics just commit your test to the same branch as that of this PR. Then, it will automatically appear here. |
Add the test for the issue and fix
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Thank you @johanneskoester! Merged the test commit and updated the PR to show that there is a test included. |
🤖 I have created a release *beep* *boop* --- ## [9.9.0](v9.8.2...v9.9.0) (2025-07-29) ### Features * python 3.13 support ([#3602](#3602)) ([429cff4](429cff4)) ### Bug Fixes * dag mermaid-js edges (bug:[#3556](#3556)) ([#3669](#3669)) ([c6e2e71](c6e2e71)) * if asset is present and no sha256 provided assume pass ([#3685](#3685)) ([7731175](7731175)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).
fixes #3556
I noticed that
DAG._dot()renders the edges correctly, butDAG._mermaid_js()makes a mess out of it.This fixed the mermaid output so it matches the dot one.
QC
docs/) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).Summary by CodeRabbit