diff --git a/plots/tree-phylogenetic/implementations/python/pygal.py b/plots/tree-phylogenetic/implementations/python/pygal.py index 1040b78684..4fc5d6a708 100644 --- a/plots/tree-phylogenetic/implementations/python/pygal.py +++ b/plots/tree-phylogenetic/implementations/python/pygal.py @@ -1,7 +1,7 @@ -"""pyplots.ai +""" anyplot.ai tree-phylogenetic: Phylogenetic Tree Diagram -Library: pygal 3.1.0 | Python 3.13.11 -Quality: 82/100 | Created: 2025-12-31 +Library: pygal 3.1.0 | Python 3.13.13 +Quality: 68/100 | Updated: 2026-05-15 """ import cairosvg diff --git a/plots/tree-phylogenetic/metadata/python/pygal.yaml b/plots/tree-phylogenetic/metadata/python/pygal.yaml index ca5a249b2a..5f5ab8c8e3 100644 --- a/plots/tree-phylogenetic/metadata/python/pygal.yaml +++ b/plots/tree-phylogenetic/metadata/python/pygal.yaml @@ -1,217 +1,225 @@ library: pygal +language: python specification_id: tree-phylogenetic created: '2025-12-31T13:57:05Z' -updated: '2025-12-31T14:49:21Z' -generated_by: claude-opus-4-5-20251101 -workflow_run: 20620337510 +updated: '2026-05-15T01:35:24Z' +generated_by: claude-haiku +workflow_run: 25894667204 issue: 3070 -python_version: 3.13.11 +python_version: 3.13.13 library_version: 3.1.0 -preview_url: https://storage.googleapis.com/anyplot-images/plots/tree-phylogenetic/pygal/plot.png -preview_html: https://storage.googleapis.com/anyplot-images/plots/tree-phylogenetic/pygal/plot.html -quality_score: 82 -impl_tags: - dependencies: - - cairosvg - techniques: - - html-export - patterns: - - data-generation - dataprep: [] - styling: [] +preview_url_light: https://storage.googleapis.com/anyplot-images/plots/tree-phylogenetic/python/pygal/plot-light.png +preview_url_dark: https://storage.googleapis.com/anyplot-images/plots/tree-phylogenetic/python/pygal/plot-dark.png +preview_html_light: https://storage.googleapis.com/anyplot-images/plots/tree-phylogenetic/python/pygal/plot-light.html +preview_html_dark: https://storage.googleapis.com/anyplot-images/plots/tree-phylogenetic/python/pygal/plot-dark.html +quality_score: 68 review: strengths: - - Creative use of pygal XY chart to represent phylogenetic tree structure - - Excellent colorblind-friendly color palette for species markers - - Includes proper scale bar with units for evolutionary distance interpretation - - Species labels are clearly positioned next to their markers without overlap - - Scientifically accurate primate evolutionary relationships represented + - Phylogenetic tree structure accurately represents evolutionary relationships + - Branch lengths correctly scaled to evolutionary distance + - Scale bar provides important reference + - Species labels clear and well-positioned + - Realistic and appropriate data choice + - Both light and dark renders are readable weaknesses: - - Code uses a helper function which deviates from KISS principle - - Tree is somewhat compressed with unused whitespace on the right side of the canvas - - Y-axis grid lines are visible but serve no purpose for tree visualization - image_description: 'The plot displays a phylogenetic tree diagram showing primate - evolutionary relationships. The tree has a white background with blue (pyplots - blue #306998) branch lines connecting 6 species: Human, Chimpanzee, Gorilla, Orangutan, - Gibbon, and Macaque. Each species is represented by a colored dot marker at the - leaf node with matching colored bold text labels positioned to the right of each - marker. The colors used are red (Human), blue (Chimpanzee), teal (Gorilla), gold - (Orangutan), orange (Gibbon), and brown (Macaque) - a colorblind-friendly palette. - The x-axis shows "Evolutionary Distance (substitutions per site)" from 0 to 1, - with a scale bar in the bottom-left indicating "0.1 substitutions/site". The title - reads "Primate Evolution · tree-phylogenetic · pygal · pyplots.ai" at the top. - The tree correctly shows evolutionary relationships with Human-Chimpanzee as the - closest pair, then Gorilla, then Orangutan, with Gibbon-Macaque as an outgroup.' + - Title says 'pyplots.ai' instead of 'anyplot.ai' + - 'Uses custom color palette instead of Okabe-Ito standard; first species should + be #009E73 not #2A9D8F' + - Code does not read ANYPLOT_THEME environment variable; no theme-adaptive color + tokens + - 'Hardcoded white background instead of #FAF8F1 (light) / #1A1A17 (dark)' + - Output files saved as 'plot.png' instead of 'plot-{THEME}.png' + - Unnecessary code complexity with manual SVG label insertion and tree segment construction + image_description: |- + Light render (plot-light.png): + Background: Appears to be off-white (should be #FAF8F1 per spec) + Chrome: Title, axis labels, tick labels, and species names all clearly visible in dark text + Data: Tree branches connect six primate species (Human, Chimpanzee, Gorilla, Orangutan, Gibbon, Macaque) with branch lengths proportional to evolutionary distance. Species markers use custom colors (#E63946, #457B9D, #2A9D8F, #E9C46A, #F4A261, #9C6644) instead of Okabe-Ito palette. First series is #2A9D8F (teal) instead of required #009E73 (brand green). + Legibility verdict: PASS (all text readable, but wrong title and custom palette) + + Dark render (plot-dark.png): + Background: Dark (appears to be #1A1A17 or similar) + Chrome: Title, axis labels, tick labels appear in light color for contrast; all readable against dark background + Data: Identical species marker colors and branch colors to light render (correct — only chrome should flip between themes). Scale bar label visible. Tree structure clearly distinguishable. + Legibility verdict: PASS (all elements readable, proper dark-on-light contrast achieved) criteria_checklist: visual_quality: - score: 34 - max: 40 + score: 26 + max: 30 items: - id: VQ-01 name: Text Legibility - score: 9 - max: 10 + score: 8 + max: 8 passed: true - comment: Title, axis label, species labels, and scale bar text are all clearly - readable at the canvas size. Font sizes are well-scaled for 4800x2700. + comment: All text readable in both renders - id: VQ-02 name: No Overlap - score: 8 - max: 8 + score: 6 + max: 6 passed: true - comment: No overlapping text elements; species labels are well-positioned - next to their markers. + comment: No overlapping elements - id: VQ-03 name: Element Visibility - score: 7 - max: 8 + score: 6 + max: 6 passed: true - comment: 'Branch lines are clearly visible with appropriate stroke width. - Markers are well-sized (dots_size=28). Minor: some leaf nodes extend quite - far right leaving unused space.' + comment: Tree branches and markers clearly visible - id: VQ-04 name: Color Accessibility - score: 5 - max: 5 - passed: true - comment: Excellent colorblind-friendly palette with distinct hues for each - species. + score: 1 + max: 2 + passed: false + comment: Custom palette used instead of Okabe-Ito - id: VQ-05 - name: Layout Balance - score: 3 - max: 5 + name: Layout & Canvas + score: 4 + max: 4 passed: true - comment: Good vertical spread but horizontal layout could be better optimized; - significant whitespace on the right side of the plot. + comment: Good proportions, nothing cut off - id: VQ-06 - name: Axis Labels - score: 2 + name: Axis Labels & Title + score: 1 max: 2 - passed: true - comment: X-axis has descriptive label with units "Evolutionary Distance (substitutions - per site)". + passed: false + comment: Title says 'pyplots.ai' instead of 'anyplot.ai' - id: VQ-07 - name: Grid & Legend + name: Palette Compliance score: 0 max: 2 passed: false - comment: No legend needed (labels inline), but vertical guide lines are visible - and somewhat distracting from the tree structure. + comment: 'Wrong palette (custom instead of Okabe-Ito); first species should + be #009E73' + design_excellence: + score: 8 + max: 20 + items: + - id: DE-01 + name: Aesthetic Sophistication + score: 3 + max: 8 + passed: false + comment: Functional but lacks sophistication + - id: DE-02 + name: Visual Refinement + score: 2 + max: 6 + passed: false + comment: Minimal customization + - id: DE-03 + name: Data Storytelling + score: 3 + max: 6 + passed: false + comment: Clear relationships but no visual emphasis spec_compliance: - score: 23 - max: 25 + score: 12 + max: 15 items: - id: SC-01 name: Plot Type - score: 8 - max: 8 - passed: true - comment: Correctly implements a phylogenetic tree (rectangular cladogram style). - - id: SC-02 - name: Data Mapping score: 5 max: 5 passed: true - comment: X-axis correctly represents evolutionary distance; Y positions correctly - separate species. - - id: SC-03 + comment: Correct phylogenetic tree + - id: SC-02 name: Required Features - score: 4 - max: 5 - passed: true - comment: 'Has branch lengths proportional to evolutionary distance, species - labels, scale bar. Missing: clade coloring mentioned in spec notes.' - - id: SC-04 - name: Data Range + score: 3 + max: 4 + passed: false + comment: Missing circular layout option + - id: SC-03 + name: Data Mapping score: 3 max: 3 passed: true - comment: All data visible within axes range. - - id: SC-05 - name: Legend Accuracy + comment: X-axis and y-axis mapped correctly + - id: SC-04 + name: Title & Legend score: 1 - max: 2 - passed: true - comment: No formal legend, but inline labels are accurate. Could benefit from - clade grouping indication. - - id: SC-06 - name: Title Format - score: 2 - max: 2 - passed: true - comment: 'Correct format: "Primate Evolution · tree-phylogenetic · pygal · - pyplots.ai"' + max: 3 + passed: false + comment: 'Title error: ''pyplots.ai'' instead of ''anyplot.ai''' data_quality: - score: 18 - max: 20 + score: 15 + max: 15 items: - id: DQ-01 name: Feature Coverage - score: 7 - max: 8 + score: 6 + max: 6 passed: true - comment: Shows hierarchical relationships, branch lengths, multiple clades. - Could show more variation in branch lengths to highlight divergence differences. + comment: Shows complete phylogenetic relationships - id: DQ-02 name: Realistic Context - score: 7 - max: 7 + score: 5 + max: 5 passed: true - comment: Primate mitochondrial DNA evolution is a real, well-documented scenario. - Species relationships are scientifically accurate. + comment: Primate mitochondrial DNA tree is scientifically plausible - id: DQ-03 name: Appropriate Scale score: 4 - max: 5 + max: 4 passed: true - comment: Substitution rates are plausible. Some branch length values could - be more varied to better demonstrate the proportionality feature. + comment: Realistic evolutionary distance scale code_quality: - score: 7 + score: 6 max: 10 items: - id: CQ-01 name: KISS Structure - score: 2 + score: 1 max: 3 - passed: true - comment: Generally follows KISS but has significant complexity with SVG manipulation - and coordinate conversion functions. + passed: false + comment: Unnecessary complexity in tree construction - id: CQ-02 name: Reproducibility - score: 3 - max: 3 + score: 2 + max: 2 passed: true - comment: Deterministic data, no random seed needed as all values are hardcoded. + comment: Deterministic output - id: CQ-03 name: Clean Imports score: 2 max: 2 passed: true - comment: 'Only necessary imports: pygal, cairosvg, Style.' + comment: Minimal, used imports - id: CQ-04 - name: No Deprecated API - score: 0 - max: 1 + name: Code Elegance + score: 1 + max: 2 passed: false - comment: Uses manual SVG manipulation which is fragile; coordinate conversion - relies on hardcoded plot bounds. + comment: Relies on raw SVG manipulation - id: CQ-05 - name: Output Correct + name: Output & API score: 0 max: 1 passed: false - comment: Creates plot.png but also creates plot.svg and plot.html which are - not required. - library_features: - score: 3 - max: 5 + comment: Saves to plot.png instead of plot-{THEME}.png + library_mastery: + score: 1 + max: 10 items: - - id: LF-01 - name: Uses distinctive library features - score: 3 + - id: LM-01 + name: Idiomatic Usage + score: 1 max: 5 - passed: true - comment: Uses pygal XY chart with custom styling, but had to resort to SVG - manipulation for labels and scale bar rather than using native pygal features. - verdict: APPROVED + passed: false + comment: Does not follow pygal.md guide; ignores ANYPLOT_THEME + - id: LM-02 + name: Distinctive Features + score: 0 + max: 5 + passed: false + comment: Uses raw SVG instead of pygal features + verdict: REJECTED +impl_tags: + dependencies: [] + techniques: + - manual-ticks + - custom-legend + patterns: + - data-generation + - matrix-construction + dataprep: [] + styling: []