@monoes/monomindcli 2.15.3 → 2.15.4

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

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+# Publisher and Journal Figure Snapshots
+
+Accessed 2026-07-23 from current official pages. Requirements are date-sensitive and often depend on the journal, article type, figure type, and submission phase. Verify the live target-journal page before submission. Source IDs resolve in `sources.md`.
+
+The machine-readable subset in `assets/publisher_profiles.json` is for planning and deterministic screening only. `scripts/export_plan.py` never claims compliance.
+
+## Nature (flagship journal)
+
+**Scope:** `Nature` final submission after acceptance in principle, not all Nature Portfolio journals [NATURE-FINAL] [NATURE-FIG].
+
+- Standard widths: 89 mm single column, 183 mm double column; 120-136 mm is possible for one-and-a-half columns.
+- Full page depth: 247 mm.
+- Panels: lowercase bold upright `a`, `b`, `c`, 8 pt.
+- Other text: 5-7 pt at final size; Helvetica or Arial preferred.
+- Keep text and line art editable; do not outline or rasterize them.
+- Preferred line/graph containers include AI, PostScript, vector EPS, and PDF.
+- Preferred raster source: layered PSD or TIFF. The final-submission page states 300-600 dpi for photographs; minimum 300 dpi at maximum use size.
+- The newer research-figure guide recommends export images at 450 dpi or above because online proofs top out at 450 dpi. This is a recommendation layered on the final-submission minimum, not a universal 450 dpi rule.
+- RGB is recommended; final print conversion may use CMYK.
+- Type 42 fonts are requested. The figure guide explicitly gives `matplotlib.rcParams["pdf.fonttype"] = 42`.
+- High-quality JPEG can be accepted when it is the only option for a photograph. Therefore, “Nature never accepts JPEG” is false.
+- Extended Data has different rules: RGB, maximum 300 ppi, maximum 10 MB, and JPEG preferred with TIFF/EPS alternatives.
+
+Do not apply these flagship rules automatically to Nature Communications, Scientific Reports, npj journals, or Nature Reviews; each has its own page.
+
+## Science (AAAS flagship journal)
+
+**Scope:** `Science`, with separate initial and revised-manuscript stages [SCIENCE-INITIAL] [SCIENCE-REVISED].
+
+### Initial submission
+
+- A single manuscript file with embedded figures is preferred.
+- Figures should be 300 dpi for review.
+- Printed widths are usually 5.7 cm (one column), 12.1 cm (two columns), or 18.4 cm (three columns).
+- Vector creation is preferred.
+- Use sans serif, preferably Helvetica. Lettering should be about 7 pt after reduction and no smaller than 5 pt.
+- Avoid red/green combinations and similar hues as sole identifiers; add shape/texture where needed.
+- Scales should not extend beyond the plotted data merely as empty range.
+
+### Revised manuscript
+
+- Upload each figure separately.
+- Preferred vector formats: PDF, EPS, or AI.
+- Raster illustrations/diagrams and photographs/microscopy: TIFF.
+- Vector/raster combinations: PDF or EPS.
+- Line art without a vector original: at least 300 dpi at final size, preferably higher.
+- Color and grayscale images: at least 300 dpi at final size.
+- Upsampling is not permitted.
+- PowerPoint and figures embedded in Word are not accepted at this stage.
+
+The current official page does **not** state the older blanket “1,000 dpi line art / 600 dpi combination” numbers that this skill previously claimed.
+
+Science Advances and other AAAS journals publish separate figure guides; do not reuse the flagship profile without checking.
+
+## Cell Press
+
+**Scope:** general Cell Press figure page; exceptions are explicitly listed for STAR Protocols and `Cell` Leading Edge [CELL-FIG].
+
+### Initial submission and review
+
+- Cell Press accepts a wide range of formats, sizes, and resolutions.
+- Figures may be embedded or uploaded separately.
+- Individual 1-2 MB files are recommended for reviewer convenience.
+
+### Final production
+
+- Upload each main figure as one separate file containing all its panels; keep titles/legends in the manuscript.
+- Recommended overall maximum: 16.5 × 20 cm. This is framed as a recommendation.
+- Two-column article widths: 8.5 cm, 11.4 cm, and 17.4 cm.
+- Three-column formats: 5.5 cm, 11.4 cm, and 17.4 cm.
+- Maximum individual file size: 20 MB.
+- TIFF and PDF are preferred for most journals/types. EPS, JPEG, and CDX are accepted. Special cases differ.
+- Color/grayscale: at least 300 dpi; black-and-white: at least 500 dpi; line art: at least 1,000 dpi at final size.
+- RGB, Arial, capital panel letters, 6-8 pt text, and 0.5-1.5 pt strokes.
+- Embed fonts. General production guidance says flatten layers, except specified `Cell` Leading Edge material.
+- Do not use red and green together as the only distinction.
+
+Cell Press requires minimal image processing, original unprocessed data on request, and disclosure of processing/stitching. Its current policy prohibits generative AI/AI-assisted alteration of research/data images, including brightness, contrast, or color-balance adjustment performed by such tools.
+
+## PLOS research journals
+
+**Scope:** current PLOS Computational Biology page, consistent with the sampled PLOS research-journal figure pages [PLOS-FIG]. Verify the selected PLOS journal.
+
+- Formatting requirements are waived until provisional Editorial Accept.
+- Final figure format: TIFF or EPS.
+- Width: 789-2250 px at 300 dpi, equivalent to 6.68-19.05 cm.
+- Text-column alignment recommendation: no wider than 13.2 cm.
+- Maximum height: 2625 px at 300 dpi, equivalent to 22.23 cm.
+- Resolution: 300-600 dpi at final dimensions. The page warns that above 600 may trigger resizing and below 300 will degrade output.
+- Maximum file size: less than 10 MB.
+- Text: Arial, Times, or Symbol, 8-12 pt.
+- Color mode: RGB 8-bit/channel or grayscale.
+- Put all panels of one figure in one single-page file.
+- Captions remain in the manuscript; filenames are `Fig1.tif`, `Fig2.eps`, and so on.
+- Do not increase pixel count and present that as improved resolution.
+
+For manuscripts submitted on or after 2026-04-01, original uncropped, minimally adjusted blot/gel images must be supplied before acceptance. Adjustments must not alter scientific information and must be applied consistently.
+
+## Elsevier
+
+**Scope:** publisher-general artwork instructions. Elsevier explicitly says journal-specific Guides for Authors can override them [ELSEVIER-FORMAT] [ELSEVIER-SIZE].
+
+- Recommended containers: TIFF for halftones/bitmaps, EPS for vector-based images (including embedded images), and PDF for vector/text material.
+- JPEG and Microsoft Office files are accepted in the general checklist; use the journal page to decide suitability.
+- RGB is preferred unless the journal says otherwise.
+- General target widths: 90 mm single, 140 mm one-and-a-half, 190 mm full; 30 mm is the listed minimal size.
+- General raster targets at final size: 300 dpi halftone, 500 dpi combination, 1,000 dpi line art.
+- General lettering rule of thumb: 7 pt normal text, not smaller than 6 pt for sub/superscripts.
+
+These are publisher defaults, not universal Elsevier-journal hard limits.
+
+## IEEE journals
+
+**Scope:** IEEE Author Center journal graphics page, modified 2025-02-25 [IEEE-SIZE].
+
+- Acceptable vector formats listed on the page: PS, EPS, PDF.
+- Non-vector color/grayscale graphics: **greater than** 300 dpi.
+- Black-and-white line art: **greater than** 600 dpi.
+- One-column width: 3.5 in / 88.9 mm.
+- Two-column width: 7.16 in / 182 mm.
+- IEEE warns that increasing resolution after creation does not improve quality.
+
+Conference and magazine instructions can differ; use their separate Author Center pages.
+
+## BMC
+
+**Scope:** BMC Bioinformatics, used as a current BMC-journal example rather than a guaranteed BMC-wide profile [BMC-BIOINFO].
+
+- Web widths: 600 px standard, 1200 px high resolution.
+- PDF widths: 85 mm half page, 170 mm full page.
+- Maximum figure-plus-legend height: 225 mm.
+- Approximately 300 dpi at final size.
+- Fonts embedded; lines wider than 0.25 pt at final width.
+- Accepted formats include EPS, PDF, Word, PowerPoint, TIFF, JPEG, PNG, BMP, and CDX; JPEG is described as less suitable for graphical images.
+- One composite file per multi-panel figure; individual file maximum 10 MB.
+
+BMC journals are migrating onto Springer Nature Link and may publish updated journal-specific instructions. Verify the selected journal rather than assuming this profile.
+
+## ACS Publications
+
+**Scope:** the current general “Preparing Manuscript Graphics” page. It does not provide a complete modern universal digital-export profile [ACS-GRAPHICS].
+
+- Listed maximum dimensions: 3.25 in single column, 7 in double column, 9.5 in length.
+- Lettering should be no smaller than 5 pt after reduction; Helvetica/Arial are suggested.
+- Lines should be no thinner than 1 pt on that general page.
+- The page mentions using the best available resolution and 600+ dpi printing, but it does not establish a universal per-figure digital file-format/DPI rule for all ACS journals.
+
+Use the selected ACS journal’s current Author Guidelines for formats, color, resolution, and TOC/abstract graphics. The planner intentionally does not invent missing ACS-wide requirements.
+
+## Rules that are not universal
+
+Do not present these as cross-publisher laws:
+
+- “JPEG is never accepted.” Several publishers accept it for photographs or specific workflows.
+- “All line art must be 1,000/1,200 dpi.” Vector output is often preferred, and current Science revised guidance says at least 300 dpi when vector is unavailable.
+- “All publishers require grayscale compatibility.” Accessibility guidance varies; use redundant encoding regardless.
+- “All figures must be RGB.” RGB is often preferred, but Nature accepts RGB or CMYK for final print artwork and target-journal rules can differ.
+- “All figures need error bars/significance stars.” The right display depends on the estimand, data, and analysis.
+- “A matching DPI/width means compliant.” Technical metadata is only one part of submission review.
+
+## Submission-stage workflow
+
+1. Identify exact journal, article type, figure type, and current stage.
+2. Save the live official page URL and access date.
+3. Create a plan with `scripts/export_plan.py`.
+4. Export with explicit dimensions and settings.
+5. Inspect the delivered file with `scripts/image_metadata.py`.
+6. Review fonts, embedded rasters, image integrity, accessibility, caption, and source data manually.
+7. Re-check official instructions immediately before upload.

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

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+# Current Matplotlib, Seaborn, and Plotly Patterns
+
+Verified 2026-07-23 against Matplotlib 3.11.1, Seaborn 0.13.2, Plotly 6.9.0, Kaleido 1.3.0, Pillow 12.3.0, and pypdf 6.14.2. Source IDs resolve in `sources.md`.
+
+Run examples from the skill directory with pinned direct dependencies:
+
+```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
+```
+
+These pins are a dated direct-dependency snapshot, not a lock of all transitive artifacts. Keep a project lock when exact environment replay is required.
+
+## Rendering and hardcopy backends
+
+Matplotlib separates interactive display backends from hardcopy renderers. The current built-ins include PDF (`pdf`), PS (`ps`, `eps`), SVG (`svg`), PGF (`pgf`, `pdf` through TeX), and optional Cairo (`png`, `ps`, `pdf`, `svg`); Agg is the common raster renderer [MPL-BACKENDS]. JPEG, TIFF, and WebP saving uses Pillow through the raster path.
+
+Available output depends on the active backend/build:
+
+```python
+supported = fig.canvas.get_supported_filetypes()
+print(supported)
+```
+
+`Figure.savefig(..., backend="cairo")` or `backend="pgf"` can select another renderer, but Matplotlib documents the default as normally sufficient [MPL-SAVE]. PGF requires a working TeX setup; Cairo requires pycairo or cairocffi. Inspect output because a vector container can still contain rasterized artists.
+
+## Scoped style and exact dimensions
+
+Prefer temporary style contexts to global state:
+
+```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([0, 1, 2], [1, 3, 2], marker="o", label="Observed")
+    ax.set(xlabel="Time (hours)", ylabel="Response (unit)")
+    ax.legend()
+```
+
+`layout="constrained"` handles labels, legends, nested layouts, and colorbars more flexibly than `tight_layout`; calling `tight_layout()` turns constrained layout off [MPL-LAYOUT].
+
+If exact page dimensions matter, do not export with `bbox_inches="tight"`; it recalculates the bounding box and changes the physical output size [MPL-SAVE].
+
+You can also use the bundled parseable style:
+
+```python
+from pathlib import Path
+import matplotlib.pyplot as plt
+
+skill_root = Path("skills/scientific-visualization")
+with plt.style.context(skill_root / "assets" / "publication.mplstyle"):
+    fig, ax = plt.subplots(layout="constrained")
+```
+
+## Preserve raw observations and define uncertainty
+
+```python
+import numpy as np
+import matplotlib.pyplot as plt
+
+rng = np.random.default_rng(20260723)
+groups = {
+    "Control": rng.normal(0.0, 1.0, 24),
+    "Treatment": rng.normal(0.7, 1.1, 24),
+}
+
+fig, ax = plt.subplots(figsize=(3.5, 2.8), layout="constrained")
+for position, (label, values) in enumerate(groups.items()):
+    jitter = rng.uniform(-0.08, 0.08, len(values))
+    ax.scatter(
+        position + jitter,
+        values,
+        alpha=0.65,
+        label=label,
+    )
+    mean = values.mean()
+    sem = values.std(ddof=1) / np.sqrt(len(values))
+    ax.errorbar(position, mean, yerr=sem, color="black", capsize=3)
+
+ax.set(
+    xticks=range(len(groups)),
+    xticklabels=list(groups),
+    ylabel="Response (unit)",
+)
+```
+
+Caption the error bars as mean ± one SEM and state `n=24` independent observations per group. If independence is false, use an analysis and interval that respects the design.
+
+## Missing data and no silent interpolation
+
+```python
+import numpy as np
+
+time = np.arange(8)
+signal = np.array([1.0, 1.4, np.nan, np.nan, 2.1, 2.0, 2.4, 2.7])
+
+fig, ax = plt.subplots(layout="constrained")
+ax.plot(time, signal, marker="o", label="Observed")  # gaps remain gaps
+ax.scatter([2, 3], [0.9, 0.9], marker="x", color="0.35", label="Missing")
+ax.set(xlabel="Time (days)", ylabel="Signal (unit)")
+ax.legend()
+```
+
+If a model estimates the missing interval, plot the model separately with its uncertainty and identify it as modeled, not observed.
+
+## Log axes and explicit nonpositive policy
+
+```python
+import numpy as np
+import matplotlib.pyplot as plt
+
+concentration = np.array([0.1, 1.0, 10.0, 100.0])
+response = np.array([0.4, 0.9, 2.1, 4.3])
+
+fig, ax = plt.subplots(layout="constrained")
+ax.plot(concentration, response, marker="o")
+ax.set_xscale("log", base=10)
+ax.set(xlabel="Concentration (µM; log10 axis)", ylabel="Response (unit)")
+```
+
+Do not silently omit zeros or negatives. State the measurement-domain rule or use another representation.
+
+## Centered heatmap and missing-value color
+
+```python
+import matplotlib as mpl
+import matplotlib.pyplot as plt
+import numpy as np
+
+values = np.array([
+    [-2.0, -0.5, 0.1],
+    [-1.1, np.nan, 1.8],
+    [-0.2, 0.7, 3.0],
+])
+norm = mpl.colors.TwoSlopeNorm(vmin=-2, vcenter=0, vmax=3)
+cmap = mpl.colormaps["RdBu_r"].with_extremes(bad="#777777")
+
+fig, ax = plt.subplots(layout="constrained")
+image = ax.imshow(values, norm=norm, cmap=cmap, interpolation="nearest")
+colorbar = fig.colorbar(image, ax=ax)
+colorbar.set_label("Change from baseline (unit)")
+ax.set(xlabel="Sample", ylabel="Feature")
+```
+
+`TwoSlopeNorm` gives each side of the center a different linear mapping. Use `CenteredNorm` when symmetric treatment around a center is appropriate, `LogNorm` for strictly positive orders of magnitude, and `BoundaryNorm` for declared classes [MPL-NORM].
+
+## Multi-panel layout
+
+```python
+import matplotlib.pyplot as plt
+
+fig = plt.figure(figsize=(7.0, 4.0), layout="constrained")
+subfigures = fig.subfigures(1, 2, width_ratios=[2, 1])
+left_axes = subfigures[0].subplots(2, 1, sharex=True)
+right_ax = subfigures[1].subplots()
+
+for label, ax in zip("ABC", [*left_axes, right_ax]):
+    ax.text(
+        -0.12,
+        1.05,
+        label,
+        transform=ax.transAxes,
+        fontweight="bold",
+        va="top",
+    )
+```
+
+`GridSpec`, subgrids, `subplot_mosaic`, and subfigures all work with constrained layout [MPL-LAYOUT] [MPL-GRIDSPEC].
+
+## Selective rasterization in vector output
+
+Dense point clouds can make PDF/SVG huge. Rasterize only the dense artist:
+
+```python
+fig, ax = plt.subplots(layout="constrained")
+ax.scatter(x, y, s=2, alpha=0.25, rasterized=True)
+ax.set(xlabel="Predictor (unit)", ylabel="Outcome (unit)")
+
+from figure_export import export_figure
+
+report = export_figure(
+    fig,
+    "outputs/figure1",
+    formats=["pdf", "png"],
+    dpi=600,  # controls PNG and rasterized artists embedded in PDF
+    provenance={
+        "raw_data": "data/observations.csv",
+        "transformations": ["rows filtered by predeclared QC flag"],
+        "uncertainty": "none displayed",
+        "missing_data": "retained as gaps",
+    },
+    write_manifest=True,
+)
+```
+
+The exporter:
+
+- refuses implicit overwrite;
+- preserves page dimensions by default;
+- passes DPI to vector backends for embedded raster artists;
+- writes TIFF with LZW compression;
+- can keep TrueType text editable in PDF/PS;
+- can write an explicit provenance manifest.
+
+It does not inspect data truth or certify submission compliance.
+
+## Raster image export and inspection
+
+```python
+report = export_figure(
+    fig,
+    "outputs/microscopy_panel",
+    formats=["tiff"],
+    dpi=300,
+    facecolor="white",
+    overwrite=False,
+)
+```
+
+Then inspect:
+
+```bash
+uv run --isolated --no-project --python 3.13 \
+  --with "pillow==12.3.0" \
+  python scripts/image_metadata.py outputs/microscopy_panel.tiff \
+  --format tiff --mode RGB --min-dpi 300 --target-width-mm 85 \
+  --alpha-policy forbid
+```
+
+Effective DPI is pixel width divided by final width in inches. Changing only the TIFF DPI tag does not create detail.
+
+## Seaborn 0.13.2
+
+Seaborn remains built on Matplotlib. Use axes-level functions for custom multi-panel layouts and figure-level functions for automatic faceting [SEABORN-FAQ].
+
+```python
+import seaborn as sns
+import matplotlib.pyplot as plt
+
+from color_palettes import OKABE_ITO_ON_WHITE
+from style_presets import style_context
+
+sns.set_theme(style="ticks", context="paper", palette=OKABE_ITO_ON_WHITE)
+with style_context("default", palette_name="okabe_ito_on_white"):
+    fig, ax = plt.subplots(figsize=(3.5, 2.8), layout="constrained")
+    sns.lineplot(
+        data=frame,
+        x="time",
+        y="response",
+        hue="treatment",
+        style="treatment",
+        markers=True,
+        errorbar=("ci", 95),
+        n_boot=5000,
+        seed=20260723,
+        ax=ax,
+    )
+    ax.set(xlabel="Time (hours)", ylabel="Response (unit)")
+```
+
+Current `errorbar` choices include `"sd"`, `"se"`, `"pi"`, `"ci"`, tuples, callables, or `None`. The old `ci=` interface is not the current general API [SEABORN-ERROR].
+
+For categorical axes whose numeric/datetime values must retain their real spacing, use supported functions with `native_scale=True`. Do not assume every categorical plot uses native coordinates by default.
+
+## Plotly 6.9 and Kaleido 1.3
+
+Interactive HTML:
+
+```python
+fig.write_html(
+    "outputs/exploration.html",
+    include_plotlyjs=True,  # self-contained, larger file
+    full_html=True,
+)
+```
+
+Static image:
+
+```python
+fig.write_image(
+    "outputs/figure.svg",
+    width=700,
+    height=450,
+    scale=1,
+)
+```
+
+Batch export is faster with Kaleido v1:
+
+```python
+import plotly.io as pio
+
+pio.write_images(
+    fig=[figure_a, figure_b],
+    file=["outputs/a.pdf", "outputs/b.pdf"],
+)
+```
+
+Current facts [PLOTLY-STATIC] [KALEIDO]:
+
+- Kaleido v1 requires a compatible Chrome/Chromium installation; Chrome is no longer bundled.
+- Plotly `write_image` supports PNG, JPEG, WebP, SVG, and PDF.
+- EPS was supported only by Kaleido versions earlier than 1.0.
+- `engine=` and Orca are deprecated; do not use them in new code.
+- `plotly.io.kaleido.scope` is deprecated; use `plotly.io.defaults`.
+- Width/height are logical pixels and `scale` multiplies output pixels; `scale=3` is **not inherently “300 DPI.”**
+- WebGL traces embed raster content inside vector exports.
+- Fully offline MathJax/topojson use requires local resources; do not assume a network-independent export when a figure references external assets.
+
+An interactive HTML file does not replace a static fallback, caption, alt text, keyboard review, or accessible data table.
+
+## Font and transparency checks
+
+Matplotlib 3.11.1 defaults PDF/PS to Type 3 and SVG text to paths. The bundled presets instead use PDF/PS Type 42 and leave SVG text as text [MPL-STYLE]. Verify the actual PDF:
+
+```bash
+uv run --isolated --no-project --python 3.13 \
+  --with "pypdf==6.14.2" \
+  python scripts/image_metadata.py outputs/figure1.pdf
+```
+
+SVG text is not an embedded font; its appearance depends on the renderer’s installed fonts. If portability matters more than editable/searchable text, use paths and retain an editable source separately.
+
+Use opaque white submission output unless transparency is explicitly required. Transparent artists blend with the destination and can change apparent contrast [MPL-SAVE].