@monoes/monomindcli 2.15.3 → 2.15.5

package/org-skills/scientific-visualization/SKILL.md

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+---
+name: scientific-visualization
+description: "Create and audit truthful, accessible, publication-ready scientific figures with Matplotlib, Seaborn, or Plotly. Use for figure design, multi-panel layouts, uncertainty and missing-data displays, color/contrast review, image metadata validation, and journal export planning."
+tags: ["data","science","design"]
+tools: []
+license: MIT
+source: https://github.com/K-Dense-AI/scientific-agent-skills
+source_path: "skills/scientific-visualization"
+source_commit: 49c6e97775eaa18ba791bebe23162a70ae601c18
+---
+# Scientific Visualization
+
+Build figures that preserve scientific meaning before optimizing appearance. Separate universal principles from dated publisher rules, preserve raw data and transformations, use color redundantly, and inspect delivered files rather than trusting plotting defaults.
+
+## Non-negotiable guardrails
+
+- Never alter, hide, invent, or selectively enhance data to improve a figure.
+- Preserve raw tables/images, exclusions, missing-value codes, analysis code, normalization, binning, image adjustments, and random seeds.
+- Do not infer journal requirements. Identify the exact journal, article type, figure type, and submission phase; verify its live official guidance.
+- Do not claim that a palette, DPI value, format, or automated report makes a figure accessible or journal-compliant.
+- Do not silently connect missing observations, suppress inconvenient points, upsample images as if detail increased, or tune axes/dual axes to exaggerate a conclusion.
+- Keep interactive and static outputs as distinct deliverables. Interactive hover is not a substitute for labels, alt text, keyboard access, an accessible data table, or a static fallback.
+
+Read `references/publication_guidelines.md` for deceptive-encoding and integrity checks. Read `references/journal_requirements.md` only after the target and phase are known.
+
+## Workflow
+
+### 1. Define the evidence and destination
+
+Record:
+
+- audience and medium: manuscript, web, slide, poster, supplement;
+- exact publisher/journal, article type, submission phase, and intended final width;
+- variable semantics, units, sample/replicate structure, missing/censored values;
+- estimator and uncertainty definition;
+- transformations: filtering, aggregation, normalization, smoothing, bins, image processing;
+- source-data paths/identifiers and output provenance.
+
+If requirements are not known, create a provisional general figure and label all publisher choices as pending verification.
+
+### 2. Choose an honest encoding
+
+Prefer position on a common scale. Before coding, check:
+
+- **Bars/areas:** normally include zero because length/area is measured from a baseline.
+- **Points/lines:** nonzero limits can be valid; show context and disclose breaks.
+- **Uncertainty:** name SD, SE, CI, percentile, posterior, or another interval; state `n` and the unit of replication.
+- **Raw observations:** show them when feasible; do not let jitter obscure categories/values.
+- **Missing data:** distinguish missing, zero, censored, and excluded; use gaps or explicit model/interpolation styling.
+- **Area/volume:** scale area/volume, not radius/diameter; avoid decorative 3D.
+- **Log axes:** label the base/transform and declare how zero/negative values are handled.
+- **Binning/smoothing:** record edges, bandwidth/window, method, and sensitivity.
+- **Normalization:** state formula/reference and keep limits consistent across compared panels.
+- **Dual axes:** prefer aligned panels; if unavoidable, justify units and do not engineer apparent correlation.
+- **Images:** preserve originals, disclose whole-image adjustments, show scale bars, and avoid clipped/erased background.
+
+### 3. Design accessibility in, not after
+
+- Use color plus marker, line style, hatching, direct label, or panel separation.
+- Choose qualitative, sequential, diverging, or cyclic color according to data semantics.
+- Audit foreground/background contrast at the rendered size.
+- Make missing and out-of-range values explicit.
+- Provide alt text, a longer description for complex figures, and underlying data for web delivery.
+- Treat WCAG 2.2 as web guidance: 4.5:1 normal text, 3:1 large text, and 3:1 for graphical objects required for understanding; color cannot be the only cue. Applicability and exceptions matter.
+
+See `references/color_palettes.md`. A grayscale screen is useful but is not a complete color-vision or accessibility test.
+
+### 4. Implement with scoped styles
+
+Use Matplotlib's object-oriented API and temporary style contexts:
+
+```python
+import matplotlib.pyplot as plt
+
+from style_presets import style_context
+
+with style_context("default", palette_name="okabe_ito_on_white"):
+    fig, ax = plt.subplots(
+        figsize=(89 / 25.4, 60 / 25.4),
+        layout="constrained",
+    )
+    ax.plot(x, y, marker="o", label="Observed")
+    ax.set(xlabel="Time (hours)", ylabel="Response (unit)")
+    ax.legend()
+```
+
+`layout="constrained"` supports colorbars, nested GridSpec, subfigures, and `subplot_mosaic`. Do not call `tight_layout()` afterward; it disables constrained layout.
+
+For exact physical dimensions, do not use `bbox_inches="tight"` unless the changed page size is intentional.
+
+#### Color normalization
+
+```python
+import matplotlib as mpl
+
+norm = mpl.colors.TwoSlopeNorm(vmin=-2, vcenter=0, vmax=5)
+cmap = mpl.colormaps["RdBu_r"].with_extremes(bad="#777777")
+image = ax.imshow(values, norm=norm, cmap=cmap, interpolation="nearest")
+fig.colorbar(image, ax=ax, label="Change (unit)")
+```
+
+Use `LogNorm`, `CenteredNorm`, `SymLogNorm`, `BoundaryNorm`, or `TwoSlopeNorm` only when its mapping matches the scientific meaning.
+
+#### Seaborn
+
+Seaborn 0.13.2 uses the current `errorbar` API:
+
+```python
+sns.lineplot(
+    data=frame,
+    x="time",
+    y="response",
+    hue="treatment",
+    style="treatment",
+    markers=True,
+    errorbar=("ci", 95),
+    n_boot=5000,
+    seed=20260723,
+    ax=ax,
+)
+```
+
+Axes-level functions fit custom Matplotlib layouts; figure-level functions create their own figures/facets. Do not customize Seaborn's internal artist lists as if they were stable API.
+
+#### Plotly
+
+- Use `write_html()` for interaction and `write_image()`/`plotly.io.write_images()` for static output.
+- Kaleido 1.3.0 requires Chrome/Chromium; it no longer bundles Chrome.
+- Current static formats: PNG, JPEG, WebP, SVG, PDF. EPS is Kaleido v0-only.
+- Do not pass deprecated `engine=` or use Orca/`plotly.io.kaleido.scope`.
+- `width`, `height`, and `scale` control pixels; `scale=3` is not inherently “300 DPI.”
+- WebGL traces embed raster content in PDF/SVG.
+- Fully offline exports need local external assets when a figure references MathJax/topojson/tiles.
+
+### 5. Export explicitly and record provenance
+
+```python
+from figure_export import export_figure
+
+report = export_figure(
+    fig,
+    "outputs/figure1",
+    formats=["pdf", "png"],
+    dpi=600,
+    bbox_inches=None,  # preserve figure page dimensions
+    provenance={
+        "raw_data": "data/source.csv",
+        "transformations": ["predeclared QC filter", "group mean"],
+        "uncertainty": "95% bootstrap CI; seed 20260723",
+        "missing_data": "retained as gaps",
+    },
+    write_manifest=True,
+)
+```
+
+The exporter refuses implicit overwrite, writes atomically, keeps vector DPI for embedded rasters, uses TIFF LZW, and can use PDF/PS Type 42 fonts. It does not validate scientific content or publisher acceptance.
+
+For editable fonts:
+
+- PDF/PS Type 42 embeds TrueType fonts.
+- `svg.fonttype="none"` keeps text editable/searchable but does not embed fonts; appearance depends on installed fonts.
+- `svg.fonttype="path"` preserves glyph appearance as paths but loses editable/searchable text.
+
+Use an opaque explicit background unless transparency is required; blending against another background changes apparent contrast.
+
+### 6. Inspect, compare, and review
+
+1. Inspect file metadata.
+2. Audit palette contrast/grayscale separation.
+3. Compare against a dated publisher snapshot.
+4. View at final size in the manuscript/web context.
+5. Manually review fonts, embedded rasters, clipping, legends, scale bars, image integrity, caption, alt text, and source data.
+6. Re-check the live target-journal page immediately before upload.
+
+## Pinned snapshot
+
+The examples and smoke tests use direct package pins current on 2026-07-23:
+
+```bash
+uv run --isolated --no-project --python 3.13 \
+  --with "matplotlib==3.11.1" \
+  --with "seaborn==0.13.2" \
+  --with "plotly==6.9.0" \
+  --with "kaleido==1.3.0" \
+  --with "pillow==12.3.0" \
+  --with "pypdf==6.14.2" \
+  python your_figure.py
+```
+
+This is a dated direct-dependency snapshot, not a transitive lock. Use the project's uv lock for exact replay; this skill intentionally ships no dependency lock.
+
+## Bundled CLIs
+
+All helpers are deterministic, network-free, bounded, reject symlink inputs/destinations where relevant, and refuse overwrite unless `--force` is explicit.
+
+### Inspect raster/vector metadata
+
+```bash
+uv run --isolated --no-project --python 3.13 \
+  --with "pillow==12.3.0" \
+  python scripts/image_metadata.py figure.tiff \
+  --format tiff --mode RGB --min-dpi 300 --target-width-mm 85 \
+  --alpha-policy forbid
+```
+
+Supports raster images (Pillow), SVG, PDF (pypdf), and EPS/PS. Reports dimensions, DPI/effective DPI, mode, alpha, ICC presence, compression, page size, and conservative first-page PDF font resources. It does not inspect every embedded raster in a vector container.
+
+### Audit palette contrast and grayscale
+
+```bash
+uv run --isolated --no-project --python 3.13 \
+  python scripts/palette_audit.py \
+  --palette okabe_ito_on_white \
+  --background FFFFFF \
+  --role graphical
+```
+
+Reports exact WCAG sRGB contrast plus pairwise CIE L* grayscale screening. The grayscale threshold is a heuristic, not a standard.
+
+### Plan/screen publisher export
+
+```bash
+uv run --isolated --no-project --python 3.13 \
+  python scripts/export_plan.py \
+  --publisher nature \
+  --figure-type combination \
+  --width single \
+  --phase final
+```
+
+Add `--input figure.pdf` to screen machine-readable properties. Profiles are official-source snapshots accessed 2026-07-23, not automatic compliance rules.
+
+### Preview styles
+
+```bash
+uv run --isolated --no-project --python 3.13 \
+  --with "matplotlib==3.11.1" \
+  python scripts/style_preview.py \
+  --output outputs/style-preview \
+  --style default \
+  --palette okabe_ito_on_white \
+  --formats png,svg
+```
+
+### Inspect/write styles and smoke-test export
+
+```bash
+uv run --isolated --no-project --python 3.13 \
+  python scripts/style_presets.py --list
+uv run --isolated --no-project --python 3.13 \
+  python scripts/style_presets.py --show nature
+uv run --isolated --no-project --python 3.13 \
+  --with "matplotlib==3.11.1" \
+  python scripts/figure_export.py --demo outputs/export-smoke --manifest
+```
+
+## Assets
+
+- `assets/publication.mplstyle`: general print starting point.
+- `assets/nature.mplstyle`: dated flagship Nature visual starting point, not a compliance preset.
+- `assets/presentation.mplstyle`: larger projected-display style.
+- `assets/color_palettes.py`: importable Okabe-Ito and Paul Tol values with metadata.
+- `assets/publisher_profiles.json`: dated, machine-readable planning snapshots.
+
+Matplotlib style files omit `#` in hex colors because `#` begins comments in `.mplstyle` parsing.
+
+## References
+
+- `references/publication_guidelines.md`: integrity, deceptive encodings, accessibility, static/interactive output.
+- `references/color_palettes.md`: palette semantics, exact values, WCAG contrast, grayscale caveats, color management.
+- `references/journal_requirements.md`: phase-specific official publisher snapshots.
+- `references/matplotlib_examples.md`: current, runnable Matplotlib/Seaborn/Plotly patterns.
+- `references/sources.md`: official URLs, dates, versions, and research basis.
+
+## Final review checklist
+
+- [ ] Raw data/images and transformation code are preserved.
+- [ ] Missing values, exclusions, bins, normalization, and uncertainty are explicit.
+- [ ] Baselines, scales, limits, and area/volume encodings are honest.
+- [ ] Color is redundant and rendered contrast was reviewed.
+- [ ] Figure has an accessible description/data alternative where applicable.
+- [ ] Physical dimensions, DPI, format, fonts, transparency, and file size were inspected after export.
+- [ ] Publisher rules were verified for the exact journal and phase.
+- [ ] No automated report is presented as a scientific, accessibility, or compliance certification.
+
+## Citing Scientific Agent Skills
+
+This skill is part of Scientific Agent Skills by K-Dense. If it materially contributed to a
+manuscript, report, presentation, or code release, add the paper to the references or
+software section and tell the user you did so:
+
+> Kassis, T., Agarwal, V., He, Y., Patel, D., & Brueckner, A. M. (2026). Scientific Agent
+> Skills: A Library of Procedural Knowledge for Research Agents. arXiv:2609.00065.
+> https://doi.org/10.48550/arXiv.2609.00065
+
+Always cite the current version. The DOI and https://arxiv.org/abs/2609.00065 resolve to the
+latest arXiv version, so never append a version suffix such as `v1`. When network access is
+available, fetch https://arxiv.org/abs/2609.00065 (or
+http://export.arxiv.org/api/query?id_list=2609.00065) before writing the reference and take
+the author list, year, and version from that record. If the record lists a journal reference
+or publisher DOI, cite the published version instead.

package/org-skills/scientific-visualization/references/color_palettes.md

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+# Color, Contrast, and Palette Selection
+
+Reviewed 2026-07-23. Source IDs resolve in `sources.md`. A named “colorblind-safe” palette is not a guarantee that a rendered figure is accessible: background, line thickness, adjacency, text, category count, display/print conversion, and redundant encoding all matter.
+
+## Start with data semantics
+
+- **Qualitative:** unordered categories. Hue can separate groups; lightness should not imply an unintended ranking.
+- **Sequential:** ordered low-to-high values. Use monotonic perceived lightness.
+- **Diverging:** departure around a meaningful center. Use a neutral midpoint and document the normalization.
+- **Cyclic:** periodic values where endpoints meet.
+
+Do not use a diverging map merely because values contain positive and negative numbers; the center must have scientific meaning. Do not use a rainbow map as a generic ordered scale. Paul Tol documents false visual transitions, lack of inherent magnitude ordering, and color-vision problems in ordinary rainbow schemes [TOL].
+
+With Matplotlib, colormap and normalization are separate:
+
+```python
+import matplotlib as mpl
+
+norm = mpl.colors.TwoSlopeNorm(vmin=-2, vcenter=0, vmax=5)
+image = ax.imshow(values, cmap="RdBu_r", norm=norm)
+fig.colorbar(image, ax=ax, label="Change (unit)")
+```
+
+Use `LogNorm` for strictly positive orders of magnitude, `SymLogNorm` for signed data with a disclosed linear zone, `BoundaryNorm` for meaningful classes, and `TwoSlopeNorm` for unequal ranges around a center [MPL-NORM].
+
+## Okabe-Ito / Wong colors
+
+The eight colors commonly reproduced from Wong’s Nature Methods article are [WONG]:
+
+```python
+OKABE_ITO = [
+    "#E69F00",  # orange
+    "#56B4E9",  # sky blue
+    "#009E73",  # bluish green
+    "#F0E442",  # yellow
+    "#0072B2",  # blue
+    "#D55E00",  # vermillion
+    "#CC79A7",  # reddish purple
+    "#000000",  # black
+]
+```
+
+Several light colors do not reach 3:1 against white. For thin lines or required graphical objects on white, start with the bundled five-color subset:
+
+```python
+OKABE_ITO_ON_WHITE = [
+    "#0072B2",
+    "#D55E00",
+    "#009E73",
+    "#CC79A7",
+    "#000000",
+]
+```
+
+This subset is derived by WCAG sRGB contrast calculation; it is not a published palette or a compliance certification. Use marker/line-style redundancy and audit the actual rendering.
+
+## Paul Tol qualitative schemes
+
+Paul Tol’s canonical site moved to `sronpersonalpages.nl` in July 2026. The current technical note remains SRON/EPS/TN/09-002, issue 3.2, dated 2021-08-18 [TOL] [TOL-HOME].
+
+The note states that the bright, high-contrast, vibrant, muted, and medium-contrast qualitative schemes are color-blind safe under its design/testing assumptions. It also states:
+
+- high-contrast is the strongest choice for grayscale/monochrome separation;
+- medium-contrast provides three pairs but weaker grayscale separation;
+- light is reasonably distinct and intended mainly for labeled cell fills;
+- pale/dark are not sufficiently distinct for multi-series lines or maps and are meant for text backgrounds/foregrounds;
+- most multi-color qualitative schemes do not remain fully separable in grayscale.
+
+Bundled fixed-order values:
+
+```python
+TOL_BRIGHT = [
+    "#4477AA", "#EE6677", "#228833", "#CCBB44",
+    "#66CCEE", "#AA3377", "#BBBBBB",
+]
+
+TOL_HIGH_CONTRAST = ["#004488", "#DDAA33", "#BB5566"]
+
+TOL_VIBRANT = [
+    "#EE7733", "#0077BB", "#33BBEE", "#EE3377",
+    "#CC3311", "#009988", "#BBBBBB",
+]
+
+TOL_MUTED = [
+    "#CC6677", "#332288", "#DDCC77", "#117733", "#88CCEE",
+    "#882255", "#44AA99", "#999933", "#AA4499",
+]
+
+TOL_MEDIUM_CONTRAST = [
+    "#6699CC", "#004488", "#EECC66",
+    "#994455", "#997700", "#EE99AA",
+]
+```
+
+The maximum intended series counts are 7, 3, 7, 9, and 6 respectively. Do not interpolate qualitative palettes.
+
+## ColorBrewer
+
+ColorBrewer 2.0 is an authoritative interactive resource for sequential, diverging, and qualitative cartographic schemes. It allows filtering by “colorblind safe,” “print friendly,” and “photocopy safe,” and exposes the supported number of data classes [COLORBREWER].
+
+Use the exact class count shown by ColorBrewer. A scheme marked safe at one class count may not be marked safe at another. ColorBrewer’s flags are design guidance for its intended mapping context, not a WCAG conformance result for arbitrary line widths, backgrounds, or text.
+
+Matplotlib exposes many ColorBrewer-derived maps. Verify the exact map direction and class count rather than relying on its name.
+
+## Perceptually uniform continuous maps
+
+Matplotlib recommends selecting maps based on data semantics and discusses lightness behavior in its colormap guide [MPL-CMAP]. Common continuous candidates:
+
+- `viridis`, `plasma`, `inferno`, `magma`: perceptually uniform sequential families;
+- `cividis`: designed with color-vision deficiencies in mind;
+- `RdBu_r`, `PuOr`, `BrBG`: possible diverging candidates after checking the center, direction, contrast, and grayscale behavior.
+
+No list is universally safe. A map can be perceptually uniform yet still fail to distinguish a narrow feature at the chosen size, or lose detail during RGB-to-CMYK conversion.
+
+## WCAG contrast: what to test
+
+WCAG 2.2 is normative for web content [WCAG22]:
+
+- normal text: 4.5:1 against its background (SC 1.4.3 AA);
+- large text: 3:1 (SC 1.4.3 AA);
+- graphical objects required to understand content: 3:1 against adjacent colors (SC 1.4.11 AA);
+- color must not be the only visual means of conveying information (SC 1.4.1 A).
+
+W3C’s understanding document uses line and pie charts as examples and explains that required graphical objects are tested against adjacent colors; all data-series colors do not automatically need 3:1 against each other when they do not overlap [WCAG-NONTEXT].
+
+Run:
+
+```bash
+uv run --isolated --no-project --python 3.13 \
+  python scripts/palette_audit.py \
+  --palette okabe_ito_on_white \
+  --background FFFFFF \
+  --role graphical
+```
+
+The CLI reports:
+
+- exact WCAG sRGB contrast against the chosen background;
+- pairwise contrast;
+- pairwise CIE L* separation after removing hue.
+
+Its default grayscale threshold (ΔL* 10) is a heuristic. It is not a WCAG threshold and does not simulate every color-vision deficiency, printer, profile, or viewing condition.
+
+## Redundant encoding
+
+Use at least one non-color cue:
+
+```python
+colors = ["#0072B2", "#D55E00", "#009E73"]
+linestyles = ["-", "--", "-."]
+markers = ["o", "s", "^"]
+
+for index, series in enumerate(series_list):
+    ax.plot(
+        x,
+        series,
+        color=colors[index],
+        linestyle=linestyles[index],
+        marker=markers[index],
+        markevery=5,
+        label=labels[index],
+    )
+```
+
+For bars, use edge contrast, labels, and restrained hatching. For images, consider accessible channel combinations plus separate grayscale panels. Direct labels often outperform distant legends.
+
+## Missing and out-of-range colors
+
+Assign explicit colors to missing and out-of-range values:
+
+```python
+import matplotlib as mpl
+
+cmap = mpl.colormaps["viridis"].with_extremes(
+    bad="#777777",
+    under="#222222",
+    over="#FDE725",
+)
+```
+
+Label these states in the colorbar/legend. Never let missing values default to the low end of a quantitative scale.
+
+## Seaborn and Plotly
+
+Seaborn 0.13.2 accepts palette names, lists, and dictionaries through `palette=`/`set_palette()`. Apply a Matplotlib style before Seaborn only if the subsequent `sns.set_theme()` call will not overwrite the intended rc settings; pass `rc=` explicitly when needed [SEABORN-PALETTE] [SEABORN-THEME].
+
+```python
+import seaborn as sns
+
+sns.set_theme(style="ticks", context="paper")
+sns.set_palette(OKABE_ITO_ON_WHITE)
+```
+
+For Plotly, set categorical colors explicitly and add symbols/dashes:
+
+```python
+fig = px.scatter(
+    frame,
+    x="x",
+    y="y",
+    color="group",
+    symbol="group",
+    color_discrete_sequence=OKABE_ITO_ON_WHITE,
+)
+```
+
+Check the static export too. Interactive hover does not replace contrast, labels, keyboard operation, alt text, or a static fallback.
+
+## Color management
+
+- Work in sRGB unless the publisher or calibrated workflow requires another space.
+- Preserve ICC profiles in scientific raster images when relevant.
+- Preview print conversion when the publisher converts RGB to CMYK.
+- Do not alter raw intensity data merely to obtain attractive colors.
+- Record channel mappings, color limits, normalization, and any color-space conversion.
+- Avoid transparency when blending with an unknown background can change contrast.
+
+## Review checklist
+
+- [ ] Palette type matches data semantics.
+- [ ] Center, limits, normalization, and missing-value color are explicit.
+- [ ] Foreground/background contrast was audited at final size.
+- [ ] Color is redundant with shape, line style, hatching, labels, or layout.
+- [ ] Grayscale was inspected without treating it as a complete accessibility test.
+- [ ] Print/profile conversion was reviewed when relevant.
+- [ ] Palette and category mapping are consistent across figures.
+- [ ] Underlying values and an accessible text/table alternative are available.