FigRecipe (scitex-plt)

Reproducible scientific figures as first-class objects

Full Documentation · pip install figrecipe

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Installation

Requires Python >= 3.10.

pip install figrecipe

For the GUI editor:

pip install figrecipe[editor]

SciTeX users: pip install scitex[plt] already includes FigRecipe.

Quickstart

import figrecipe as fr
import numpy as np

x = np.linspace(0, 2 * np.pi, 100)

fig, ax = fr.subplots()
ax.plot(x, np.sin(x), id="sine")
fr.save(fig, "figure.png")
# Produces: figure.png, figure.yaml, figure_data/sine.csv

Reload and edit from the saved recipe:

fig, ax = fr.reproduce("figure.yaml")
fr.gui(fig)  # Launch visual editor at http://127.0.0.1:5050

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Role in SciTeX Ecosystem

FigRecipe is the first app built on the SciTeX platform -- it proves the app pattern that other apps follow. It works standalone (figrecipe gui) AND embedded inside scitex-cloud.

scitex (orchestrator) -- re-exports figrecipe as scitex.plt
  |-- scitex-app        -- runtime SDK (FigRecipe inherits ScitexAppConfig)
  |-- scitex-ui         -- React/TS components (FigRecipe consumes these)
  +-- figrecipe (this package) -- reference app
        |-- figrecipe           -- standalone Python package (pip install figrecipe)
        +-- figrecipe._django   -- Django integration for scitex-cloud embedding

What this package owns:

• Figure creation, reproduction, and composition engine
• YAML recipe format and data provenance
• Diagram system (box-and-arrow with mm-based coordinates)
• GUI editor (figrecipe gui)
• Django integration via figrecipe._django package

What this package does NOT own:

• App runtime SDK -- inherits from scitex-app
• UI components -- consumes from scitex-ui
• Templates and scaffolding -- managed by scitex

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FigRecipe -- Reproducible, editable, publication-ready scientific figures. Part of SciTeX.

The SciTeX system follows the Four Freedoms for Research below, inspired by the Free Software Definition:

Four Freedoms for Research

0. The freedom to run your research anywhere -- your machine, your terms.
1. The freedom to study how every step works -- from raw data to final manuscript.
2. The freedom to redistribute your workflows, not just your papers.
3. The freedom to modify any module and share improvements with the community.

AGPL-3.0 -- because we believe research infrastructure deserves the same freedoms as the software it runs on.

SciTeX users: pip install scitex[plt] includes FigRecipe. scitex.plt delegates to figrecipe -- they share the same API.

Overview

FigRecipe treats recipe, data, and style as first-class attributes of every figure. This enables data governance and style editing without losing scientific rigor.

_{Created with Diagrams}

Styling

FigRecipe provides millimeter-precise control over every visual element. The SCITEX style preset is applied by default, producing publication-ready figures with standard matplotlib plotting.

Millimeter-based Layout

fig, ax = fr.subplots(
    axes_width_mm=60,
    axes_height_mm=40,
    margin_left_mm=15,
)

Style Presets

fr.load_style("SCITEX")       # Publication defaults
fr.load_style("SCITEX_DARK")  # Dark theme
fr.load_style("MATPLOTLIB")   # Pure Matplotlib

GUI Editor

For precise adjustments, GUI editor is available.

Migration from Matplotlib

Matplotlib-compatibility

Details

FigRecipe is a drop-in replacement for matplotlib -- just change your import:

# Before
import matplotlib.pyplot as plt
fig, ax = plt.subplots()
ax.plot(x, y)
plt.savefig("fig.png")

# After
import figrecipe as fr
fig, ax = fr.subplots()
ax.plot(x, y, id="my_trace")
fr.save(fig, "fig.png")  # -> fig.png + fig.yaml + fig_data/

Systematic Migration

scitex-linter detects and auto-fixes matplotlib patterns into mm-based FigRecipe equivalents (check, format, python). It also works as a pre-commit hook, ensuring AI agents follow FigRecipe conventions.

Diagrams

Create publication-quality box-and-arrow diagrams with mm-based coordinates. See Overview for an example output.

Usage

from figrecipe import Diagram

d = Diagram(title="EEG Pipeline", gap_mm=10)

# Boxes
d.add_box(
    "raw", "Raw EEG", subtitle="64 ch", emphasis="muted", shape="cylinder"
)
d.add_box("filter", "Bandpass", subtitle="0.5-45 Hz", emphasis="primary")
d.add_box("ica", "ICA", subtitle="Artifact removal", emphasis="primary")

# Arrows
d.add_arrow("raw", "filter")
d.add_arrow("filter", "ica")

d.save(
    "pipeline.png"
)  # -> pipeline.png + pipeline.yaml + pipeline_hitmap.png + pipeline_debug.png

Containers & Flex Layout

Use gap_mm on the Diagram for automatic flex layout (no manual x/y needed):

d = Diagram(title="System Overview", gap_mm=10)

d.add_box("a", "Module A")
d.add_box("b", "Module B")
d.add_container("grp", title="Core", children=["a", "b"], direction="row")
d.add_box("out", "Output", shape="document")
d.add_arrow("grp", "out")
d.save("overview.png")

Auto-Fix & Save Options

auto_fix=True automatically resolves layout violations (overlaps, container enclosure, canvas bounds, arrow collisions):

fig, ax = d.render(auto_fix=True)

# d.save() renders, auto-crops, and optionally watermarks:
d.save("out.png", watermark=True)  # "Plotted by FigRecipe" stamp

Output files from d.save():

File	Content
out.png	Auto-cropped diagram
out.yaml	Recipe for reproduction
out_hitmap.png	Click-target regions for GUI editing
out_debug.png	Debug overlay showing positions and anchors

Shapes & Anchors

Shapes: rounded (default), box, stadium, cylinder, document, file, codeblock. Use node_class for semantic defaults: "code" -> codeblock, "input" -> cylinder, "claim" -> document.

Anchors: top, bottom, left, right, top-left, top-right, bottom-left, bottom-right, center, or auto (default). Aliases like n/s/e/w, tl/tr/bl/br are normalized automatically.

Validation Rules

All rules are enforced on render. Failed figures are saved with a _FAILED suffix for inspection.

Rule	Check	Severity
W	Width exceeds 185 mm (double-column max)	Warning
R1	Container must enclose all children	Error
R2	No two boxes may overlap	Error
R3	Container title must clear children (5 mm zone)	Warning
R4	Box text must fit within padded inner area	Warning
R5	Text-to-text margin >= 2 mm	Error
R6	Text-to-edge margin >= 2 mm	Error
R7	Arrow visible-length ratio >= 90%	Error
R8	Curved-arrow label on same side as arc	Error
R9	All elements within canvas bounds	Error

Three Interfaces

Python API

Create and save -- standard matplotlib API with auto-recording:

import figrecipe as fr
import numpy as np

fig, ax = fr.subplots()
ax.plot(np.sin(np.linspace(0, 10, 100)), id="sine")
fr.save(fig, "figure.png")  # Saves + validates pixel-identical reproduction

Output:

figure.png                # Publication-ready image
figure.yaml               # Reproducible recipe (validated on save)
figure_data/
  sine.csv                # Plot data (one CSV per trace)

Save / Load Formats -- from recipe or bundle:

fr.save(fig, "fig.png")     # fig.png + fig.yaml
fr.save(fig, "fig.zip")     # self-contained zip bundle
fr.load("fig.png")          # reload from any format

Format	Save	Load
PNG / PDF / SVG	Y	Y
YAML	Y	Y
Directory / ZIP	Y	Y

Reproduce and edit -- from recipe or bundle:

fig, ax = fr.reproduce("figure.yaml")
fr.gui(fig)  # Launch visual editor (at http://127.0.0.1:5050 by default)

Compose -- multi-panel figures:

fr.compose(
    sources=["panel_a.yaml", "panel_b.yaml"],
    output_path="composed.png",
    layout="horizontal",
)

Statistics -- significance brackets:

ax.add_stat_annotation(x1=0, x2=1, p_value=0.01, style="stars")

Full API reference

CLI Commands

figrecipe --help-recursive            # Show all commands
figrecipe reproduce fig.yaml          # Recreate figure from recipe
figrecipe gui figure.png              # Launch visual editor
figrecipe validate fig.yaml           # Verify pixel-identical reproduction
figrecipe extract fig.yaml            # Extract plotted data as CSV
figrecipe compose a.yaml b.yaml       # Compose multi-panel figure
figrecipe crop figure.png             # Auto-crop whitespace
figrecipe info fig.yaml               # Show recipe metadata

Full CLI reference

MCP Server -- for AI Agents

AI agents can create, compose, and reproduce publication-ready figures autonomously via the Model Context Protocol.

Tool	Description
plot	Create figure from declarative YAML spec
reproduce	Recreate figure from recipe
compose	Combine panels into multi-panel layout
crop	Auto-crop whitespace
info	Inspect recipe metadata
validate	Verify reproduction fidelity
diagram_compile_mermaid	Compile diagram spec to Mermaid
diagram_render	Render diagram to PNG/SVG/PDF
audio_speak	Text-to-speech relay to user's speakers

Audio relay: The audio_speak tool enables AI agents to provide auditory feedback through the user's local speakers -- the agent generates text, the MCP server synthesizes speech on the host machine. This keeps the human in the loop without requiring them to watch the terminal.

Claude Code Setup

Add .mcp.json to your project root. Use SCITEX_ENV_SRC to load all configuration from a .src file -- this keeps .mcp.json static across environments:

{
  "mcpServers": {
    "scitex": {
      "command": "scitex",
      "args": ["mcp", "start"],
      "env": {
        "SCITEX_ENV_SRC": "${SCITEX_ENV_SRC}"
      }
    }
  }
}

Then switch environments via your shell profile:

# Local machine
export SCITEX_ENV_SRC=~/.scitex/scitex/local.src

# Remote server
export SCITEX_ENV_SRC=~/.scitex/scitex/remote.src

Generate a template .src file:

scitex env-template -o ~/.scitex/scitex/local.src

Or install globally:

scitex mcp install

Full MCP specification

Lint Rules

Detected by scitex-linter when this package is installed.

Rule	Severity	Message
STX-FM001	warning	figsize= detected -- inch-based figure sizing is imprecise for publications
STX-FM002	warning	tight_layout() detected -- layout is unpredictable across plot types
STX-FM003	warning	bbox_inches="tight" detected -- can crop important elements unpredictably
STX-FM004	info	constrained_layout=True detected -- conflicts with mm-based layout control
STX-FM005	info	subplots_adjust() with hardcoded fractions -- fragile across figure sizes
STX-FM006	info	plt.savefig() detected -- no provenance tracking
STX-FM007	info	rcParams direct modification detected -- hard to maintain across figures
STX-FM008	warning	set_size_inches() detected -- bypasses mm-based layout control
STX-FM009	warning	ax.set_position() detected -- conflicts with mm-based layout control
STX-P001	info	ax.plot() -- consider ax.stx_line() for automatic CSV data export
STX-P002	info	ax.scatter() -- consider ax.stx_scatter() for automatic CSV data export
STX-P003	info	ax.bar() -- consider ax.stx_bar() for automatic sample size annotation
STX-P004	info	plt.show() is non-reproducible in batch/CI environments
STX-P005	info	print() inside @stx.session -- use logger for tracked logging

47 matplotlib plot types supported

Details

Category	Plot Types
Line & Curve	plot, step, fill, fill_between, fill_betweenx, errorbar, stackplot, stairs
Scatter & Points	scatter
Bar & Categorical	bar, barh
Distribution	hist, hist2d, boxplot, violinplot, ecdf
2D Image & Matrix	imshow, matshow, pcolor, pcolormesh, hexbin, spy
Contour & Surface	contour, contourf, tricontour, tricontourf, tripcolor, triplot
Spectral & Signal	specgram, psd, csd, cohere, angle_spectrum, magnitude_spectrum, phase_spectrum, acorr, xcorr
Vector & Flow	quiver, barbs, streamplot
Special	pie, stem, eventplot, loglog, semilogx, semilogy, graph

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