sources.md
84 lines · skills/scientific-visualization/references/sources.md at 5f2bc03
Sources and Version Snapshot
Reviewed 2026-10-01 using official documentation, release source, current PyPI metadata, native synthetic fixtures, and fresh extraction for blocked publisher pages. Science remains a historical snapshot because both retrieval routes failed. ACS is an explicitly dated legacy page, not a current journal rule. No submission, authentication, or publication API is called by these network-free tools.
Raw lines 1 to 4Tested direct package snapshot
- Matplotlib 3.11.2, Python >=3.11 [MPL-PYPI].
- Seaborn 0.13.2, Python >=3.8 [SEABORN-PYPI].
- Plotly 7.1.0, Python >=3.8 [PLOTLY-PYPI].
- Kaleido 1.4.0, Python >=3.8; compatible Chrome/Chromium required [KALEIDO-PYPI].
- Pillow 12.3.0, Python >=3.10 [PIL-PYPI].
- pypdf 6.19.0, Python >=3.9 [PYPDF-PYPI].
Native tests use Python 3.13, synthetic data, and local Matplotlib/Pillow/pypdf outputs. Plotly HTML and Kaleido exports are checked separately; the isolated baseline manifest does not install optional Kaleido. These direct pins are not a transitive lock. GUI, TeX/PGF, optional Cairo, color-managed printing, authenticated journal submission, and arbitrary external-asset rendering are not established by these checks.
Raw lines 5 to 15Matplotlib
- [MPL-PYPI] matplotlib on PyPI — current package version and release history.
- [MPL-RELEASE] Matplotlib release notes — 3.11 release/API changes.
- [MPL-SAVE] [
matplotlib.figure.Figure.savefig](https://matplotlib.org/stable/api/_as_gen/matplotlib.figure.Figure.savefig.html) — 3.11.2 signature; format inference, DPI, metadata, bounding boxes, transparency, backends, Pillow kwargs. - [MPL-BACKENDS] Backends — interactive versus static renderers; PDF/PS/SVG/PGF/Cairo formats.
- [MPL-STYLE] Customizing Matplotlib with style sheets and rcParams —
rc_context, style composition, save settings, PDF/PS/SVG font types. - [MPL-LAYOUT] Constrained layout guide —
layout="constrained", colorbars, subfigures, GridSpec, interaction withtight_layout. - [MPL-GRIDSPEC] [
matplotlib.gridspec](https://matplotlib.org/stable/api/gridspec_api.html) — current grid layout API. - [MPL-NORM] Colormap normalization —
Normalize,LogNorm,CenteredNorm,SymLogNorm,PowerNorm,BoundaryNorm,TwoSlopeNorm. - [MPL-CMAP] Choosing colormaps — data classes and perceived lightness.
Seaborn
- [SEABORN-PYPI] seaborn on PyPI — 0.13.2 package metadata and release history.
- [SEABORN-ERROR] Statistical estimation and error bars — current
errorbarmethods, callable intervals, bootstrapping,seed, andn_boot. - [SEABORN-FAQ] Frequently asked questions — axes-level versus figure-level functions, Matplotlib object-oriented integration, DPI/SVG notes.
- [SEABORN-PALETTE] Choosing color palettes — qualitative, sequential, and diverging palette APIs.
- [SEABORN-THEME] [
seaborn.set_theme](https://seaborn.pydata.org/generated/seaborn.set_theme.html) — style, context, palette, font, scale, and rc parameters.
Plotly and Kaleido
- [PLOTLY-PYPI] plotly on PyPI — 7.1.0 package metadata.
- [PLOTLY-STATIC] Static image export in Python — Kaleido/Chrome setup, formats,
write_image,write_images, dimensions/scale, WebGL rasterization, offline assets, defaults, EPS/Orca/engine deprecations; page dated 2026. - [PLOTLY-HTML] Interactive HTML export —
write_html,to_html,include_plotlyjs,full_html; page dated 2026. - [PLOTLY-CHANGES] Static image generation changes in Plotly.py 6.1 — Kaleido v1 migration and deprecations.
- [KALEIDO] Plotly Kaleido repository — Chrome requirement, v1 migration, direct APIs, and offline/page behavior.
- [KALEIDO-PYPI] kaleido on PyPI — 1.4.0 package metadata.
- [PLOTLY-7] Plotly 7.0 release — removal of Orca, Kaleido v0, and
engine; MathJax 2 removal and Share Chart button. - [KALEIDO-14] Kaleido 1.4 release — MathJax default moves to v3.
Accessibility and color
- [WCAG22] Web Content Accessibility Guidelines (WCAG) 2.2 — W3C Recommendation; normative SC 1.1.1, 1.4.1, 1.4.3, 1.4.5, and 1.4.11.
- [WCAG-NONTEXT] Understanding SC 1.4.11: Non-text Contrast — informative chart/graph examples and testing principles; not itself normative.
- [WCAG-COLOR] Understanding SC 1.4.1: Use of Color — informative non-color cue guidance.
- [COLORBREWER] ColorBrewer 2.0 — Cynthia Brewer, Mark Harrower, and Penn State; scheme type, data-class count, colorblind/print/photocopy filters, and exports.
- [TOL-HOME] Paul Tol’s Notes — canonical site; page states the move from SRON on 2026-07-07.
- [TOL] Paul Tol, “Colour Schemes” — SRON/EPS/TN/09-002, issue 3.2, 2021-08-18; exact sRGB palettes, intended uses, color-vision checks, and grayscale analysis.
- [WONG] Bang Wong, “Color blindness” — Nature Methods 8, 441 (2011); source commonly used for the eight-color palette.
Publishers and journals
Most publisher content was verified 2026-10-01. Nature final submission and Cell Press needed fresh extraction after direct access failed. Science initial/revised pages remained blocked; their 2026-07-23 values are explicitly historical. ACS is a legacy source updated 2006-01-21. Dates label access separately from publication dates.
- [NATURE-FINAL] [
Naturefinal submission](https://www.nature.com/nature/for-authors/final-submission) — flagship final files, dimensions, fonts, formats, raster resolution, RGB/CMYK, Extended Data distinctions. - [NATURE-FIG] [
Natureresearch figure specifications](https://research-figure-guide.nature.com/figures/preparing-figures-our-specifications) — graphs, accessibility, RGB, 300/450 dpi discussion, editable Type 42 text, export. - [SCIENCE-INITIAL] [
Scienceinitial manuscript instructions](https://www.science.org/content/page/instructions-preparing-initial-manuscript) — historical snapshot: initial figure embedding, 300 dpi, widths, fonts, color/contrast, source data. - [SCIENCE-REVISED] [
Sciencerevised manuscript instructions](https://www.science.org/content/page/instructions-preparing-revised-manuscript) — historical snapshot: separate files, formats, minimum resolution, dimensions, no upsampling. - [CELL-FIG] Cell Press figure guidelines — initial versus final stages, formats, widths, file size, DPI, RGB, fonts, image integrity, AI-assisted image policy.
- [PLOS-FIG] PLOS Computational Biology figures — provisional-accept waiver, TIFF/EPS, dimensions, 300-600 dpi, RGB/grayscale, file size, image integrity, 2026-04-01 blot/gel requirement.
- [ELSEVIER-FORMAT] Elsevier artwork formats checklist — general formats, RGB preference, separate files, journal override.
- [ELSEVIER-SIZE] Elsevier artwork sizing — general widths, 300/500/1,000 dpi, typography, and explicit journal variability.
- [IEEE-SIZE] IEEE Resolution and Size — modified 2025-02-25; PS/EPS/PDF, >300/>600 dpi, 88.9/182 mm.
- [BMC-BIOINFO] BMC Bioinformatics: preparing your manuscript — journal-specific formats, 85/170 mm, approximately 300 dpi, 10 MB, embedded fonts.
- [ACS-GRAPHICS] ACS Preparing Manuscript Graphics — legacy dimensions/typography, page updated 2006-01-21; target-journal rules govern.
Optional inspection backends
- [PIL-PYPI] Pillow on PyPI — 12.3.0 package metadata; released 2026-07-01.
- [PYPDF-PYPI] pypdf on PyPI — 6.19.0 package metadata.
- [PIL-IMAGE] Pillow Image API — lazy open, verify versus decoding, channel conversion, pixel limits.
- [PIL-TIFF] Pillow TIFF format — LZW compression, DPI, ICC, multiple frames.
- [PYPDF-PAGE] pypdf PageObject —
user_unit,rotation,mediabox, andcropbox; page coordinates alone are not physical size. - [SEABORN-LINE] seaborn.lineplot —
unitswithestimator=Nonefor individual trajectories; missing rows can be dropped before line construction, so use explicit Matplotlib gaps for missing observations.
Native checks verify technical behavior, not truth of data, inferential calibration, full-file accessibility, or publisher acceptance. The PDF inspector reports only first-page declared font resources; it does not traverse nested XObjects or all pages. Source artifacts and smoke outputs stay outside the shipped skill.
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