From de1ded2a0dcd568d4a3a232b8e2ed2c6794b1f79 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Fri, 15 May 2026 01:12:46 +0000 Subject: [PATCH 1/5] chore(pygal): add metadata for tree-phylogenetic --- .../metadata/python/pygal.yaml | 226 ++---------------- 1 file changed, 15 insertions(+), 211 deletions(-) diff --git a/plots/tree-phylogenetic/metadata/python/pygal.yaml b/plots/tree-phylogenetic/metadata/python/pygal.yaml index ca5a249b2a..81a94eddea 100644 --- a/plots/tree-phylogenetic/metadata/python/pygal.yaml +++ b/plots/tree-phylogenetic/metadata/python/pygal.yaml @@ -1,217 +1,21 @@ +# Per-library metadata for pygal implementation of tree-phylogenetic +# Auto-generated by impl-generate.yml + 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: '2026-05-15T01:12:46Z' +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: null 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 - 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.' - criteria_checklist: - visual_quality: - score: 34 - max: 40 - items: - - id: VQ-01 - name: Text Legibility - score: 9 - max: 10 - 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. - - id: VQ-02 - name: No Overlap - score: 8 - max: 8 - passed: true - comment: No overlapping text elements; species labels are well-positioned - next to their markers. - - id: VQ-03 - name: Element Visibility - score: 7 - max: 8 - 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.' - - id: VQ-04 - name: Color Accessibility - score: 5 - max: 5 - passed: true - comment: Excellent colorblind-friendly palette with distinct hues for each - species. - - id: VQ-05 - name: Layout Balance - score: 3 - max: 5 - passed: true - comment: Good vertical spread but horizontal layout could be better optimized; - significant whitespace on the right side of the plot. - - id: VQ-06 - name: Axis Labels - score: 2 - max: 2 - passed: true - comment: X-axis has descriptive label with units "Evolutionary Distance (substitutions - per site)". - - id: VQ-07 - name: Grid & Legend - 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. - spec_compliance: - score: 23 - max: 25 - 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 - 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: 3 - passed: true - comment: All data visible within axes range. - - id: SC-05 - name: Legend Accuracy - 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"' - data_quality: - score: 18 - max: 20 - items: - - id: DQ-01 - name: Feature Coverage - score: 7 - max: 8 - passed: true - comment: Shows hierarchical relationships, branch lengths, multiple clades. - Could show more variation in branch lengths to highlight divergence differences. - - id: DQ-02 - name: Realistic Context - score: 7 - max: 7 - passed: true - comment: Primate mitochondrial DNA evolution is a real, well-documented scenario. - Species relationships are scientifically accurate. - - id: DQ-03 - name: Appropriate Scale - score: 4 - max: 5 - passed: true - comment: Substitution rates are plausible. Some branch length values could - be more varied to better demonstrate the proportionality feature. - code_quality: - score: 7 - max: 10 - items: - - id: CQ-01 - name: KISS Structure - score: 2 - max: 3 - passed: true - comment: Generally follows KISS but has significant complexity with SVG manipulation - and coordinate conversion functions. - - id: CQ-02 - name: Reproducibility - score: 3 - max: 3 - passed: true - comment: Deterministic data, no random seed needed as all values are hardcoded. - - id: CQ-03 - name: Clean Imports - score: 2 - max: 2 - passed: true - comment: 'Only necessary imports: pygal, cairosvg, Style.' - - id: CQ-04 - name: No Deprecated API - score: 0 - max: 1 - passed: false - comment: Uses manual SVG manipulation which is fragile; coordinate conversion - relies on hardcoded plot bounds. - - id: CQ-05 - name: Output Correct - 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 - items: - - id: LF-01 - name: Uses distinctive library features - score: 3 - 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 + strengths: [] + weaknesses: [] From 493cc02d5d0c1c96a2542c00124c04b80bd0a273 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Fri, 15 May 2026 01:16:59 +0000 Subject: [PATCH 2/5] chore(pygal): update quality score 75 and review feedback for tree-phylogenetic --- .../implementations/python/pygal.py | 6 +- .../metadata/python/pygal.yaml | 211 +++++++++++++++++- 2 files changed, 207 insertions(+), 10 deletions(-) diff --git a/plots/tree-phylogenetic/implementations/python/pygal.py b/plots/tree-phylogenetic/implementations/python/pygal.py index 1040b78684..84c8d6ce99 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: 75/100 | 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 81a94eddea..3ac0fbfaa5 100644 --- a/plots/tree-phylogenetic/metadata/python/pygal.yaml +++ b/plots/tree-phylogenetic/metadata/python/pygal.yaml @@ -1,11 +1,8 @@ -# Per-library metadata for pygal implementation of tree-phylogenetic -# Auto-generated by impl-generate.yml - library: pygal language: python specification_id: tree-phylogenetic created: '2025-12-31T13:57:05Z' -updated: '2026-05-15T01:12:46Z' +updated: '2026-05-15T01:16:59Z' generated_by: claude-haiku workflow_run: 25894667204 issue: 3070 @@ -15,7 +12,207 @@ preview_url_light: https://storage.googleapis.com/anyplot-images/plots/tree-phyl 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: null +quality_score: 75 review: - strengths: [] - weaknesses: [] + strengths: + - Visually perfect output in both light and dark renders + - Clear phylogenetic tree structure with proper relationships + - Scientifically credible example (primate evolution) + - Excellent text legibility at full 4800x2700 resolution + - No accessibility issues in rendered outputs + weaknesses: + - Code does not read ANYPLOT_THEME environment variable + - Output filenames not theme-aware (plot.png instead of plot-{THEME}.png) + - Manual SVG label positioning is brittle and not maintainable + - Text colors hardcoded (#333) would be unreadable on dark background + - Generic design with minimal refinement beyond basic structure + image_description: |- + Light render (plot-light.png): + Background: Warm off-white (#FAF8F1) - correct for light theme + Chrome: Title "tree-phylogenetic · pygal · anyplot.ai" is dark and readable; axis label "Evolutionary Distance (substitutions per site)" clearly visible; species labels in corresponding colors next to leaf nodes; scale bar "0.1 substitutions/site" at bottom left all in dark text against light background + Data: Phylogenetic tree with 6 primates (Human, Chimpanzee, Gorilla, Orangutan, Gibbon, Macaque) shown with teal/cyan branches connecting to colored species markers. Colors are Okabe-Ito compliant and distinct. + Legibility verdict: PASS - All text is clearly readable against the light background with excellent contrast. + + Dark render (plot-dark.png): + Background: Warm near-black (#1A1A17) - correct for dark theme + Chrome: Title, axis labels, and species labels are now in light text. All remain fully readable against dark background with good contrast. No dark-on-dark failures detected. + Data: Phylogenetic tree structure and colors are IDENTICAL to light render - species marker colors and branch colors are unchanged, only the background and text chrome has flipped from dark to light. This confirms proper theme-adaptive design with data-color invariance. + Legibility verdict: PASS - All text is readable against dark background. No "dark-on-dark" failures observed (e.g., black text on near-black background). + + Both renders successfully demonstrate proper light/dark theme adaptation with correct background colors (#FAF8F1 and #1A1A17), readable text in all elements, and identical data representation across themes. + criteria_checklist: + visual_quality: + score: 28 + max: 30 + items: + - id: VQ-01 + name: Text Legibility + score: 8 + max: 8 + passed: true + comment: All text readable in both themes at proper font sizes + - id: VQ-02 + name: No Overlap + score: 6 + max: 6 + passed: true + comment: Species labels positioned without collision + - id: VQ-03 + name: Element Visibility + score: 6 + max: 6 + passed: true + comment: Tree branches and markers clearly visible + - id: VQ-04 + name: Color Accessibility + score: 2 + max: 2 + passed: true + comment: Colorblind-safe palette used + - id: VQ-05 + name: Layout & Canvas + score: 4 + max: 4 + passed: true + comment: Good proportions on 4800x2700 canvas + - id: VQ-07 + name: Palette Compliance + score: 0 + max: 2 + passed: false + comment: Code hardcodes background and text colors without reading ANYPLOT_THEME + design_excellence: + score: 12 + max: 20 + items: + - id: DE-01 + name: Aesthetic Sophistication + score: 4 + max: 8 + passed: false + comment: Functional but minimal design refinement + - id: DE-02 + name: Visual Refinement + score: 3 + max: 6 + passed: false + comment: Clean structure but generic styling + - id: DE-03 + name: Data Storytelling + score: 5 + max: 6 + passed: true + comment: Clear visual hierarchy and species differentiation + spec_compliance: + score: 15 + max: 15 + items: + - id: SC-01 + name: Plot Type + score: 5 + max: 5 + passed: true + comment: Correct phylogenetic tree diagram + - id: SC-02 + name: Required Features + score: 4 + max: 4 + passed: true + comment: Hierarchical relationships, branch lengths, labels, scale bar all + present + - id: SC-03 + name: Data Mapping + score: 3 + max: 3 + passed: true + comment: X-axis and Y-axis mapped correctly + - id: SC-04 + name: Title & Legend + score: 3 + max: 3 + passed: true + comment: Title format correct; legend N/A for tree diagram + data_quality: + score: 15 + max: 15 + items: + - id: DQ-01 + name: Feature Coverage + score: 6 + max: 6 + passed: true + comment: Shows hierarchical relationships, branch lengths, leaf labels + - id: DQ-02 + name: Realistic Context + score: 5 + max: 5 + passed: true + comment: Primate phylogenetic tree is scientifically plausible + - id: DQ-03 + name: Appropriate Scale + score: 4 + max: 4 + passed: true + comment: Evolutionary distances and species count appropriate + code_quality: + score: 3 + max: 10 + items: + - id: CQ-01 + name: KISS Structure + score: 3 + max: 3 + passed: true + comment: Straightforward code + - id: CQ-02 + name: Reproducibility + score: 2 + max: 2 + passed: true + comment: Deterministic output + - id: CQ-03 + name: Clean Imports + score: 2 + max: 2 + passed: true + comment: Only necessary imports + - id: CQ-04 + name: Code Elegance + score: 0 + max: 2 + passed: false + comment: Manual SVG positioning is brittle + - id: CQ-05 + name: Output & API + score: 0 + max: 1 + passed: false + comment: Does not read ANYPLOT_THEME; saves to plot.png instead of plot-{THEME}.png + library_mastery: + score: 2 + max: 10 + items: + - id: LM-01 + name: Idiomatic Usage + score: 2 + max: 5 + passed: false + comment: Does not follow pygal.md theme-aware pattern + - id: LM-02 + name: Distinctive Features + score: 0 + max: 5 + passed: false + comment: Generic usage without library-specific features + verdict: REJECTED +impl_tags: + dependencies: + - cairosvg + techniques: + - annotations + - html-export + patterns: + - data-generation + - matrix-construction + dataprep: [] + styling: [] From caad108a025a2a09245662b12d00420b7f86c048 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Fri, 15 May 2026 01:23:06 +0000 Subject: [PATCH 3/5] chore(pygal): update quality score 71 and review feedback for tree-phylogenetic --- .../implementations/python/pygal.py | 2 +- .../metadata/python/pygal.yaml | 127 +++++++++--------- 2 files changed, 67 insertions(+), 62 deletions(-) diff --git a/plots/tree-phylogenetic/implementations/python/pygal.py b/plots/tree-phylogenetic/implementations/python/pygal.py index 84c8d6ce99..4bfe540595 100644 --- a/plots/tree-phylogenetic/implementations/python/pygal.py +++ b/plots/tree-phylogenetic/implementations/python/pygal.py @@ -1,7 +1,7 @@ """ anyplot.ai tree-phylogenetic: Phylogenetic Tree Diagram Library: pygal 3.1.0 | Python 3.13.13 -Quality: 75/100 | Updated: 2026-05-15 +Quality: 71/100 | 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 3ac0fbfaa5..4ac291cf8f 100644 --- a/plots/tree-phylogenetic/metadata/python/pygal.yaml +++ b/plots/tree-phylogenetic/metadata/python/pygal.yaml @@ -2,7 +2,7 @@ library: pygal language: python specification_id: tree-phylogenetic created: '2025-12-31T13:57:05Z' -updated: '2026-05-15T01:16:59Z' +updated: '2026-05-15T01:23:06Z' generated_by: claude-haiku workflow_run: 25894667204 issue: 3070 @@ -12,34 +12,34 @@ preview_url_light: https://storage.googleapis.com/anyplot-images/plots/tree-phyl 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: 75 +quality_score: 71 review: strengths: - - Visually perfect output in both light and dark renders - - Clear phylogenetic tree structure with proper relationships - - Scientifically credible example (primate evolution) - - Excellent text legibility at full 4800x2700 resolution - - No accessibility issues in rendered outputs + - Both light and dark renders visually correct with proper backgrounds and theme-adapted + text + - Tree structure is clear and well-spaced with no overlaps or legibility issues + - Species labels and scale bar are properly positioned + - Scientific data (primate phylogeny) is realistic and educational weaknesses: - - Code does not read ANYPLOT_THEME environment variable - - Output filenames not theme-aware (plot.png instead of plot-{THEME}.png) - - Manual SVG label positioning is brittle and not maintainable - - Text colors hardcoded (#333) would be unreadable on dark background - - Generic design with minimal refinement beyond basic structure + - 'Title format violation: contains ''Primate Evolution'' and says ''pyplots.ai'' + instead of ''anyplot.ai''' + - 'No theme adaptation in code: does not read ANYPLOT_THEME or adapt Style parameters + per pygal.md' + - Output filenames hardcoded to 'plot.png' instead of 'plot-light.png'/'plot-dark.png' + - Generic design with no visual sophistication or data storytelling emphasis + - Manual coordinate-to-pixel conversions are brittle and error-prone image_description: |- Light render (plot-light.png): - Background: Warm off-white (#FAF8F1) - correct for light theme - Chrome: Title "tree-phylogenetic · pygal · anyplot.ai" is dark and readable; axis label "Evolutionary Distance (substitutions per site)" clearly visible; species labels in corresponding colors next to leaf nodes; scale bar "0.1 substitutions/site" at bottom left all in dark text against light background - Data: Phylogenetic tree with 6 primates (Human, Chimpanzee, Gorilla, Orangutan, Gibbon, Macaque) shown with teal/cyan branches connecting to colored species markers. Colors are Okabe-Ito compliant and distinct. - Legibility verdict: PASS - All text is clearly readable against the light background with excellent contrast. + Background: Warm off-white (#FAF8F1) - correct + Chrome: Title "Primate Evolution · tree-phylogenetic · pygal · pyplots.ai" in dark text (#333), X-axis label "Evolutionary Distance (substitutions per site)", tick labels on both axes - all readable + Data: Tree branches in teal color, six species with distinct colored markers (green, red, blue, pink, gold, light blue), species labels positioned right of markers, scale bar "0.1 substitutions/site" at bottom left + Legibility verdict: PASS - all text readable against light background Dark render (plot-dark.png): - Background: Warm near-black (#1A1A17) - correct for dark theme - Chrome: Title, axis labels, and species labels are now in light text. All remain fully readable against dark background with good contrast. No dark-on-dark failures detected. - Data: Phylogenetic tree structure and colors are IDENTICAL to light render - species marker colors and branch colors are unchanged, only the background and text chrome has flipped from dark to light. This confirms proper theme-adaptive design with data-color invariance. - Legibility verdict: PASS - All text is readable against dark background. No "dark-on-dark" failures observed (e.g., black text on near-black background). - - Both renders successfully demonstrate proper light/dark theme adaptation with correct background colors (#FAF8F1 and #1A1A17), readable text in all elements, and identical data representation across themes. + Background: Warm near-black (#1A1A17) - correct + Chrome: Title, axis labels, tick labels in light text - all readable against dark background, no dark-on-dark failures + Data: Tree branches and species markers identical in color to light render (only chrome adapted), species labels same color as markers + Legibility verdict: PASS - all text readable, data colors consistent with light render, no theme-adaptation failures criteria_checklist: visual_quality: score: 28 @@ -50,39 +50,45 @@ review: score: 8 max: 8 passed: true - comment: All text readable in both themes at proper font sizes + comment: All text readable in both themes - id: VQ-02 name: No Overlap score: 6 max: 6 passed: true - comment: Species labels positioned without collision + comment: Species labels well-positioned, no collisions - id: VQ-03 name: Element Visibility score: 6 max: 6 passed: true - comment: Tree branches and markers clearly visible + comment: All elements clearly visible and distinguishable - id: VQ-04 name: Color Accessibility score: 2 max: 2 passed: true - comment: Colorblind-safe palette used + comment: Distinct colors with adequate contrast - id: VQ-05 name: Layout & Canvas score: 4 max: 4 passed: true - comment: Good proportions on 4800x2700 canvas + comment: Good proportions and spacing + - id: VQ-06 + name: Axis Labels & Title + score: 2 + max: 2 + passed: true + comment: X-axis labeled with units - id: VQ-07 name: Palette Compliance score: 0 max: 2 passed: false - comment: Code hardcodes background and text colors without reading ANYPLOT_THEME + comment: Title says 'pyplots.ai' not 'anyplot.ai' - branding violation design_excellence: - score: 12 + score: 8 max: 20 items: - id: DE-01 @@ -90,21 +96,21 @@ review: score: 4 max: 8 passed: false - comment: Functional but minimal design refinement + comment: Generic design with no special visual touches - id: DE-02 name: Visual Refinement - score: 3 + score: 2 max: 6 passed: false - comment: Clean structure but generic styling + comment: Minimal customization - id: DE-03 name: Data Storytelling - score: 5 + score: 2 max: 6 - passed: true - comment: Clear visual hierarchy and species differentiation + passed: false + comment: No visual hierarchy or emphasis spec_compliance: - score: 15 + score: 12 max: 15 items: - id: SC-01 @@ -112,26 +118,26 @@ review: score: 5 max: 5 passed: true - comment: Correct phylogenetic tree diagram + comment: Correct phylogenetic tree - id: SC-02 name: Required Features - score: 4 + score: 3 max: 4 passed: true - comment: Hierarchical relationships, branch lengths, labels, scale bar all - present + comment: All features present, only rectangular layout used - id: SC-03 name: Data Mapping score: 3 max: 3 passed: true - comment: X-axis and Y-axis mapped correctly + comment: X/Y axes correctly mapped - id: SC-04 name: Title & Legend - score: 3 + score: 1 max: 3 - passed: true - comment: Title format correct; legend N/A for tree diagram + passed: false + comment: Title must be 'tree-phylogenetic · pygal · anyplot.ai', not 'Primate + Evolution · ... · pyplots.ai' data_quality: score: 15 max: 15 @@ -141,35 +147,35 @@ review: score: 6 max: 6 passed: true - comment: Shows hierarchical relationships, branch lengths, leaf labels + comment: Shows all phylogenetic tree aspects - id: DQ-02 name: Realistic Context score: 5 max: 5 passed: true - comment: Primate phylogenetic tree is scientifically plausible + comment: Primate phylogeny is realistic - id: DQ-03 name: Appropriate Scale score: 4 max: 4 passed: true - comment: Evolutionary distances and species count appropriate + comment: Reasonable values for domain code_quality: - score: 3 + score: 5 max: 10 items: - id: CQ-01 name: KISS Structure - score: 3 + score: 1 max: 3 - passed: true - comment: Straightforward code + passed: false + comment: No theme adaptation, manual tree construction is complex - id: CQ-02 name: Reproducibility score: 2 max: 2 passed: true - comment: Deterministic output + comment: Deterministic, reproducible - id: CQ-03 name: Clean Imports score: 2 @@ -178,18 +184,18 @@ review: comment: Only necessary imports - id: CQ-04 name: Code Elegance - score: 0 + score: 1 max: 2 passed: false - comment: Manual SVG positioning is brittle + comment: Coordinate conversions are inelegant - id: CQ-05 name: Output & API score: 0 max: 1 passed: false - comment: Does not read ANYPLOT_THEME; saves to plot.png instead of plot-{THEME}.png + comment: Saves as 'plot.png' not 'plot-light.png'/'plot-dark.png' library_mastery: - score: 2 + score: 3 max: 10 items: - id: LM-01 @@ -197,22 +203,21 @@ review: score: 2 max: 5 passed: false - comment: Does not follow pygal.md theme-aware pattern + comment: Fails to follow pygal.md theme-adaptation pattern - id: LM-02 name: Distinctive Features - score: 0 + score: 1 max: 5 passed: false - comment: Generic usage without library-specific features + comment: Uses cairosvg but otherwise generic XY plotting verdict: REJECTED impl_tags: dependencies: - cairosvg techniques: - - annotations - html-export + - annotations patterns: - data-generation - - matrix-construction dataprep: [] styling: [] From 1a37a449f9c9941208a052b12a937cf095b90978 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Fri, 15 May 2026 01:28:52 +0000 Subject: [PATCH 4/5] chore(pygal): update quality score 65 and review feedback for tree-phylogenetic --- .../implementations/python/pygal.py | 2 +- .../metadata/python/pygal.yaml | 136 +++++++++--------- 2 files changed, 72 insertions(+), 66 deletions(-) diff --git a/plots/tree-phylogenetic/implementations/python/pygal.py b/plots/tree-phylogenetic/implementations/python/pygal.py index 4bfe540595..98725ae4df 100644 --- a/plots/tree-phylogenetic/implementations/python/pygal.py +++ b/plots/tree-phylogenetic/implementations/python/pygal.py @@ -1,7 +1,7 @@ """ anyplot.ai tree-phylogenetic: Phylogenetic Tree Diagram Library: pygal 3.1.0 | Python 3.13.13 -Quality: 71/100 | Updated: 2026-05-15 +Quality: 65/100 | 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 4ac291cf8f..7c44e4cee0 100644 --- a/plots/tree-phylogenetic/metadata/python/pygal.yaml +++ b/plots/tree-phylogenetic/metadata/python/pygal.yaml @@ -2,7 +2,7 @@ library: pygal language: python specification_id: tree-phylogenetic created: '2025-12-31T13:57:05Z' -updated: '2026-05-15T01:23:06Z' +updated: '2026-05-15T01:28:51Z' generated_by: claude-haiku workflow_run: 25894667204 issue: 3070 @@ -12,105 +12,111 @@ preview_url_light: https://storage.googleapis.com/anyplot-images/plots/tree-phyl 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: 71 +quality_score: 65 review: strengths: - - Both light and dark renders visually correct with proper backgrounds and theme-adapted - text - - Tree structure is clear and well-spaced with no overlaps or legibility issues - - Species labels and scale bar are properly positioned - - Scientific data (primate phylogeny) is realistic and educational + - Accurate phylogenetic tree representation with correct evolutionary relationships + - Realistic primate dataset with appropriate scale and legible rendering + - Proper canvas size (4800×2700) and overall layout proportions + - Helpful scale bar for branch length interpretation + - Both renders display data completely and visibly weaknesses: - - 'Title format violation: contains ''Primate Evolution'' and says ''pyplots.ai'' - instead of ''anyplot.ai''' - - 'No theme adaptation in code: does not read ANYPLOT_THEME or adapt Style parameters - per pygal.md' - - Output filenames hardcoded to 'plot.png' instead of 'plot-light.png'/'plot-dark.png' - - Generic design with no visual sophistication or data storytelling emphasis - - Manual coordinate-to-pixel conversions are brittle and error-prone + - 'Uses custom color palette instead of Okabe-Ito; first series must be #009E73 + (brand green) not #E63946' + - Missing ANYPLOT_THEME environment variable handling - code must read theme and + adapt Style object accordingly + - Wrong output filenames - saves plot.png instead of plot-{THEME}.png and plot-{THEME}.html + - Hardcoded Style colors (foreground=#333, background=white) won't adapt to dark + theme in actual workflow execution + - 'Code-image mismatch: implementation lacks theme logic yet images show proper + theming, suggesting images are from previous version' + - Minimal design refinement - no custom spine styling, grid customization, or typography + hierarchy image_description: |- Light render (plot-light.png): - Background: Warm off-white (#FAF8F1) - correct - Chrome: Title "Primate Evolution · tree-phylogenetic · pygal · pyplots.ai" in dark text (#333), X-axis label "Evolutionary Distance (substitutions per site)", tick labels on both axes - all readable - Data: Tree branches in teal color, six species with distinct colored markers (green, red, blue, pink, gold, light blue), species labels positioned right of markers, scale bar "0.1 substitutions/site" at bottom left - Legibility verdict: PASS - all text readable against light background + Background: Warm off-white (#FAF8F1), correctly rendered + Chrome: Title "tree-phylogenetic · pygal · anyplot.ai" in dark text, x-axis label "Evolutionary Distance (substitutions per site)" clearly readable, scale bar "0.1 substitutions/site" visible at bottom-left + Data: Primate species (Human, Chimpanzee, Gorilla, Orangutan, Gibbon, Macaque) positioned at leaf nodes with colored circular markers; hierarchical tree branches show evolutionary relationships with proportional spacing + Legibility verdict: PASS - all text and data elements readable on light surface Dark render (plot-dark.png): - Background: Warm near-black (#1A1A17) - correct - Chrome: Title, axis labels, tick labels in light text - all readable against dark background, no dark-on-dark failures - Data: Tree branches and species markers identical in color to light render (only chrome adapted), species labels same color as markers - Legibility verdict: PASS - all text readable, data colors consistent with light render, no theme-adaptation failures + Background: Warm near-black (#1A1A17), correctly rendered + Chrome: Title, x-axis label, and scale bar text appear in light colors, adequate contrast and readable + Data: Species markers and tree branches visible; data colors appear identical to light render (only chrome inverted, not data colors which is correct per spec) + Legibility verdict: PASS for visual output, but CODE does not support this - hardcoded white background and dark foreground would fail. Images likely from previous attempt. + + CRITICAL CODE-IMAGE MISMATCH: Implementation code shows no ANYPLOT_THEME usage or theme-adaptive Style creation, yet both renders show proper theme adaptation. This inconsistency must be resolved. criteria_checklist: visual_quality: - score: 28 + score: 22 max: 30 items: - id: VQ-01 name: Text Legibility - score: 8 + score: 7 max: 8 passed: true - comment: All text readable in both themes + comment: Both renders readable but concern about code-image mismatch - id: VQ-02 name: No Overlap score: 6 max: 6 passed: true - comment: Species labels well-positioned, no collisions + comment: Species labels positioned without collision - id: VQ-03 name: Element Visibility score: 6 max: 6 passed: true - comment: All elements clearly visible and distinguishable + comment: All markers, branches, labels clearly visible - id: VQ-04 name: Color Accessibility - score: 2 + score: 1 max: 2 - passed: true - comment: Distinct colors with adequate contrast + passed: false + comment: Colors distinct but not Okabe-Ito safe palette - id: VQ-05 name: Layout & Canvas score: 4 max: 4 passed: true - comment: Good proportions and spacing + comment: Correct 4800x2700, good proportions - id: VQ-06 name: Axis Labels & Title score: 2 max: 2 passed: true - comment: X-axis labeled with units + comment: Descriptive labels with units - id: VQ-07 name: Palette Compliance score: 0 max: 2 passed: false - comment: Title says 'pyplots.ai' not 'anyplot.ai' - branding violation + comment: 'CRITICAL: Custom palette #E63946 instead of Okabe-Ito #009E73' design_excellence: - score: 8 + score: 9 max: 20 items: - id: DE-01 name: Aesthetic Sophistication - score: 4 + score: 3 max: 8 passed: false - comment: Generic design with no special visual touches + comment: Generic styling, no custom palette or design thought - id: DE-02 name: Visual Refinement score: 2 max: 6 passed: false - comment: Minimal customization + comment: No spine customization, minimal refinement - id: DE-03 name: Data Storytelling - score: 2 + score: 4 max: 6 - passed: false - comment: No visual hierarchy or emphasis + passed: true + comment: Clear evolutionary hierarchy shown spec_compliance: - score: 12 + score: 14 max: 15 items: - id: SC-01 @@ -118,26 +124,25 @@ review: score: 5 max: 5 passed: true - comment: Correct phylogenetic tree + comment: Correct phylogenetic tree visualization - id: SC-02 name: Required Features - score: 3 + score: 4 max: 4 passed: true - comment: All features present, only rectangular layout used + comment: Tree structure, branch lengths, species labels, scale bar all present - id: SC-03 name: Data Mapping score: 3 max: 3 passed: true - comment: X/Y axes correctly mapped + comment: X-axis shows evolutionary distance correctly - id: SC-04 name: Title & Legend - score: 1 + score: 2 max: 3 - passed: false - comment: Title must be 'tree-phylogenetic · pygal · anyplot.ai', not 'Primate - Evolution · ... · pyplots.ai' + passed: true + comment: Title present, legend appropriately omitted for single series data_quality: score: 15 max: 15 @@ -147,77 +152,78 @@ review: score: 6 max: 6 passed: true - comment: Shows all phylogenetic tree aspects + comment: Shows hierarchical relationships and divergence patterns - id: DQ-02 name: Realistic Context score: 5 max: 5 passed: true - comment: Primate phylogeny is realistic + comment: Primate mitochondrial DNA is authentic and neutral - id: DQ-03 name: Appropriate Scale score: 4 max: 4 passed: true - comment: Reasonable values for domain + comment: Evolutionary distance values realistic for primates code_quality: - score: 5 + score: 2 max: 10 items: - id: CQ-01 name: KISS Structure - score: 1 + score: 3 max: 3 - passed: false - comment: No theme adaptation, manual tree construction is complex + passed: true + comment: No unnecessary functions or classes - id: CQ-02 name: Reproducibility score: 2 max: 2 passed: true - comment: Deterministic, reproducible + comment: Hardcoded data is deterministic - id: CQ-03 name: Clean Imports score: 2 max: 2 passed: true - comment: Only necessary imports + comment: Only necessary imports used - id: CQ-04 name: Code Elegance score: 1 max: 2 passed: false - comment: Coordinate conversions are inelegant + comment: Manual coordinate conversion is repetitive - id: CQ-05 name: Output & API score: 0 max: 1 passed: false - comment: Saves as 'plot.png' not 'plot-light.png'/'plot-dark.png' + comment: 'CRITICAL: Saves plot.png instead of plot-{THEME}.png' library_mastery: score: 3 max: 10 items: - id: LM-01 name: Idiomatic Usage - score: 2 + score: 1 max: 5 passed: false - comment: Fails to follow pygal.md theme-adaptation pattern + comment: 'CRITICAL: Missing ANYPLOT_THEME environment variable; no theme-adaptive + Style' - id: LM-02 name: Distinctive Features - score: 1 + score: 2 max: 5 passed: false - comment: Uses cairosvg but otherwise generic XY plotting + comment: XY chart for tree is unconventional, not leveraging library strengths verdict: REJECTED impl_tags: dependencies: - cairosvg techniques: - html-export - - annotations patterns: - data-generation + - matrix-construction dataprep: [] styling: [] From 26f03ab5d00b241b9eaab71a73a3db039a0632a4 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Fri, 15 May 2026 01:35:24 +0000 Subject: [PATCH 5/5] chore(pygal): update quality score 68 and review feedback for tree-phylogenetic --- .../implementations/python/pygal.py | 2 +- .../metadata/python/pygal.yaml | 142 +++++++++--------- 2 files changed, 70 insertions(+), 74 deletions(-) diff --git a/plots/tree-phylogenetic/implementations/python/pygal.py b/plots/tree-phylogenetic/implementations/python/pygal.py index 98725ae4df..4fc5d6a708 100644 --- a/plots/tree-phylogenetic/implementations/python/pygal.py +++ b/plots/tree-phylogenetic/implementations/python/pygal.py @@ -1,7 +1,7 @@ """ anyplot.ai tree-phylogenetic: Phylogenetic Tree Diagram Library: pygal 3.1.0 | Python 3.13.13 -Quality: 65/100 | Updated: 2026-05-15 +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 7c44e4cee0..5f5ab8c8e3 100644 --- a/plots/tree-phylogenetic/metadata/python/pygal.yaml +++ b/plots/tree-phylogenetic/metadata/python/pygal.yaml @@ -2,7 +2,7 @@ library: pygal language: python specification_id: tree-phylogenetic created: '2025-12-31T13:57:05Z' -updated: '2026-05-15T01:28:51Z' +updated: '2026-05-15T01:35:24Z' generated_by: claude-haiku workflow_run: 25894667204 issue: 3070 @@ -12,89 +12,86 @@ preview_url_light: https://storage.googleapis.com/anyplot-images/plots/tree-phyl 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: 65 +quality_score: 68 review: strengths: - - Accurate phylogenetic tree representation with correct evolutionary relationships - - Realistic primate dataset with appropriate scale and legible rendering - - Proper canvas size (4800×2700) and overall layout proportions - - Helpful scale bar for branch length interpretation - - Both renders display data completely and visibly + - 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: - - 'Uses custom color palette instead of Okabe-Ito; first series must be #009E73 - (brand green) not #E63946' - - Missing ANYPLOT_THEME environment variable handling - code must read theme and - adapt Style object accordingly - - Wrong output filenames - saves plot.png instead of plot-{THEME}.png and plot-{THEME}.html - - Hardcoded Style colors (foreground=#333, background=white) won't adapt to dark - theme in actual workflow execution - - 'Code-image mismatch: implementation lacks theme logic yet images show proper - theming, suggesting images are from previous version' - - Minimal design refinement - no custom spine styling, grid customization, or typography - hierarchy + - 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: Warm off-white (#FAF8F1), correctly rendered - Chrome: Title "tree-phylogenetic · pygal · anyplot.ai" in dark text, x-axis label "Evolutionary Distance (substitutions per site)" clearly readable, scale bar "0.1 substitutions/site" visible at bottom-left - Data: Primate species (Human, Chimpanzee, Gorilla, Orangutan, Gibbon, Macaque) positioned at leaf nodes with colored circular markers; hierarchical tree branches show evolutionary relationships with proportional spacing - Legibility verdict: PASS - all text and data elements readable on light surface + 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: Warm near-black (#1A1A17), correctly rendered - Chrome: Title, x-axis label, and scale bar text appear in light colors, adequate contrast and readable - Data: Species markers and tree branches visible; data colors appear identical to light render (only chrome inverted, not data colors which is correct per spec) - Legibility verdict: PASS for visual output, but CODE does not support this - hardcoded white background and dark foreground would fail. Images likely from previous attempt. - - CRITICAL CODE-IMAGE MISMATCH: Implementation code shows no ANYPLOT_THEME usage or theme-adaptive Style creation, yet both renders show proper theme adaptation. This inconsistency must be resolved. + 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: 22 + score: 26 max: 30 items: - id: VQ-01 name: Text Legibility - score: 7 + score: 8 max: 8 passed: true - comment: Both renders readable but concern about code-image mismatch + comment: All text readable in both renders - id: VQ-02 name: No Overlap score: 6 max: 6 passed: true - comment: Species labels positioned without collision + comment: No overlapping elements - id: VQ-03 name: Element Visibility score: 6 max: 6 passed: true - comment: All markers, branches, labels clearly visible + comment: Tree branches and markers clearly visible - id: VQ-04 name: Color Accessibility score: 1 max: 2 passed: false - comment: Colors distinct but not Okabe-Ito safe palette + comment: Custom palette used instead of Okabe-Ito - id: VQ-05 name: Layout & Canvas score: 4 max: 4 passed: true - comment: Correct 4800x2700, good proportions + comment: Good proportions, nothing cut off - id: VQ-06 name: Axis Labels & Title - score: 2 + score: 1 max: 2 - passed: true - comment: Descriptive labels with units + passed: false + comment: Title says 'pyplots.ai' instead of 'anyplot.ai' - id: VQ-07 name: Palette Compliance score: 0 max: 2 passed: false - comment: 'CRITICAL: Custom palette #E63946 instead of Okabe-Ito #009E73' + comment: 'Wrong palette (custom instead of Okabe-Ito); first species should + be #009E73' design_excellence: - score: 9 + score: 8 max: 20 items: - id: DE-01 @@ -102,21 +99,21 @@ review: score: 3 max: 8 passed: false - comment: Generic styling, no custom palette or design thought + comment: Functional but lacks sophistication - id: DE-02 name: Visual Refinement score: 2 max: 6 passed: false - comment: No spine customization, minimal refinement + comment: Minimal customization - id: DE-03 name: Data Storytelling - score: 4 + score: 3 max: 6 - passed: true - comment: Clear evolutionary hierarchy shown + passed: false + comment: Clear relationships but no visual emphasis spec_compliance: - score: 14 + score: 12 max: 15 items: - id: SC-01 @@ -124,25 +121,25 @@ review: score: 5 max: 5 passed: true - comment: Correct phylogenetic tree visualization + comment: Correct phylogenetic tree - id: SC-02 name: Required Features - score: 4 + score: 3 max: 4 - passed: true - comment: Tree structure, branch lengths, species labels, scale bar all present + passed: false + comment: Missing circular layout option - id: SC-03 name: Data Mapping score: 3 max: 3 passed: true - comment: X-axis shows evolutionary distance correctly + comment: X-axis and y-axis mapped correctly - id: SC-04 name: Title & Legend - score: 2 + score: 1 max: 3 - passed: true - comment: Title present, legend appropriately omitted for single series + passed: false + comment: 'Title error: ''pyplots.ai'' instead of ''anyplot.ai''' data_quality: score: 15 max: 15 @@ -152,55 +149,55 @@ review: score: 6 max: 6 passed: true - comment: Shows hierarchical relationships and divergence patterns + comment: Shows complete phylogenetic relationships - id: DQ-02 name: Realistic Context score: 5 max: 5 passed: true - comment: Primate mitochondrial DNA is authentic and neutral + comment: Primate mitochondrial DNA tree is scientifically plausible - id: DQ-03 name: Appropriate Scale score: 4 max: 4 passed: true - comment: Evolutionary distance values realistic for primates + comment: Realistic evolutionary distance scale code_quality: - score: 2 + score: 6 max: 10 items: - id: CQ-01 name: KISS Structure - score: 3 + score: 1 max: 3 - passed: true - comment: No unnecessary functions or classes + passed: false + comment: Unnecessary complexity in tree construction - id: CQ-02 name: Reproducibility score: 2 max: 2 passed: true - comment: Hardcoded data is deterministic + comment: Deterministic output - id: CQ-03 name: Clean Imports score: 2 max: 2 passed: true - comment: Only necessary imports used + comment: Minimal, used imports - id: CQ-04 name: Code Elegance score: 1 max: 2 passed: false - comment: Manual coordinate conversion is repetitive + comment: Relies on raw SVG manipulation - id: CQ-05 name: Output & API score: 0 max: 1 passed: false - comment: 'CRITICAL: Saves plot.png instead of plot-{THEME}.png' + comment: Saves to plot.png instead of plot-{THEME}.png library_mastery: - score: 3 + score: 1 max: 10 items: - id: LM-01 @@ -208,20 +205,19 @@ review: score: 1 max: 5 passed: false - comment: 'CRITICAL: Missing ANYPLOT_THEME environment variable; no theme-adaptive - Style' + comment: Does not follow pygal.md guide; ignores ANYPLOT_THEME - id: LM-02 name: Distinctive Features - score: 2 + score: 0 max: 5 passed: false - comment: XY chart for tree is unconventional, not leveraging library strengths + comment: Uses raw SVG instead of pygal features verdict: REJECTED impl_tags: - dependencies: - - cairosvg + dependencies: [] techniques: - - html-export + - manual-ticks + - custom-legend patterns: - data-generation - matrix-construction