Web API Documentation

v0.12.19

Alpha Release — API endpoints and rate limits are provisional.
Campaign API Key: scitex-cloud-campaign-20260101-20261231-alpha

🤖 MCP Server

MCP Server Overview #

SciTeX exposes a Model Context Protocol (MCP) server at https://scitex.ai/mcp. Connect any MCP-compatible AI client — Claude Desktop, Claude Code, or your own agent — to get direct access to 204 scientific tools: plotting, statistics, literature management, LaTeX compilation, and more.

Requires an API key with MCP tools or Full Access scope. Generate one at Settings → API Keys.

Connect a Client #

No API key needed. Install scitex locally and get all 204 tools for free, running on your own machine.

1. Install

Shell

pip install scitex[all]     # Full installation (recommended)
pip install scitex[plt,stats,scholar]  # Typical research setup
pip install scitex          # Core only (minimal)

2. Configure Claude Desktop / Claude Code

Add the following to ~/.claude/settings.json or claude_desktop_config.json:

JSON

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

3. That's it

Your AI client now has access to all 204 SciTeX tools — plotting, statistics, LaTeX compilation, literature management, and more — running entirely on your local machine.

Connect to the hosted MCP server at https://scitex.ai/mcp. Requires an API key.

Claude Desktop / Claude Code (`claude_desktop_config.json`)

JSON

{
  "mcpServers": {
    "scitex": {
      "type": "streamable-http",
      "url": "https://scitex.ai/mcp",
      "headers": { "Authorization": "Bearer YOUR_API_KEY" }
    }
  }
}

Python (fastmcp client)

Python

from fastmcp import Client
async with Client(
    "https://scitex.ai/mcp",
    headers={"Authorization": "Bearer YOUR_API_KEY"},
) as client:
    tools = await client.list_tools()
    result = await client.call_tool("stats_run_test", {
        "test_name": "ttest_ind",
        "data": [[1, 2, 3], [4, 5, 6]],
    })
    print(result)

Authentication #

All requests to /mcp require a Bearer token in the Authorization header.

Header	Value
`Authorization`	`Bearer YOUR_API_KEY`

Required Scope

The API key must have the mcp scope or * (Full Access). Keys with only project:read or scholar:read will be rejected with 401 Unauthorized.

Keep your key secret. API keys are shown only once at creation. If compromised, deactivate or delete it from Settings → API Keys.

Configuration #

Control which tool groups the MCP server exposes using environment variables. Set SCITEX_MCP_USE_<GROUP>=0 to disable a group. All groups are enabled by default.

Tool Group Toggles

Variable	Group
`SCITEX_MCP_USE_PLT`	Plotting & visualization
`SCITEX_MCP_USE_DIAGRAM`	Mermaid / Graphviz diagrams
`SCITEX_MCP_USE_STATS`	Statistical tests & analysis
`SCITEX_MCP_USE_SCHOLAR`	Literature & PDF management
`SCITEX_MCP_USE_DATASET`	Dataset search & fetch
`SCITEX_MCP_USE_WRITER`	LaTeX manuscript compilation
`SCITEX_MCP_USE_INTROSPECT`	Python API introspection
`SCITEX_MCP_USE_PROJECT`	Project file management
`SCITEX_MCP_USE_TEMPLATE`	Project templates
`SCITEX_MCP_USE_CLEW`	Experiment tracking
`SCITEX_MCP_USE_AUDIO`	Text-to-speech
`SCITEX_MCP_USE_CAPTURE`	Screenshot capture
`SCITEX_MCP_USE_SOCIAL`	Social media posting
`SCITEX_MCP_USE_UI`	Desktop notifications
`SCITEX_MCP_USE_DEV`	Developer tools
`SCITEX_MCP_USE_LINTER`	Code linting
`SCITEX_MCP_USE_USAGE`	Usage tracking

Example: Minimal Setup

Shell

# Only enable plotting and statistics
export SCITEX_MCP_USE_PLT=1
export SCITEX_MCP_USE_STATS=1

# Disable everything else
export SCITEX_MCP_USE_SCHOLAR=0
export SCITEX_MCP_USE_WRITER=0
export SCITEX_MCP_USE_DIAGRAM=0
# ... set other groups to 0

Using .env.d Files

For persistent configuration, copy the example env files and source them:

Shell

# Copy examples to your local config
cp -r .env.d.examples .env.d
# Edit toggles
$EDITOR .env.d/02_mcp.env
# Source all config
source .env.d/entry.src

These toggles only affect the MCP server. Python imports (import scitex) and CLI commands (scitex plt ...) are unaffected.

Available Tools #

204 tools across 18 categories. Click tool rows to expand parameters & return types. Call client.list_tools() for the live list, or fetch /api/mcp/tools/ for the full JSON catalog.

Audio — `audio_` (1 tools)

Tool Description

audio_speak

Convert text to speech with smart routing.

Parameters & Returns ▸

Name	Type	Default
`text`	`string`	required
`backend`	`string`	`None`
`voice`	`string`	`None`
`rate`	`integer`	`150`
`speed`	`number`	`1.5`
`play`	`boolean`	`True`
`save`	`boolean`	`False`
`output_path`	`string`	`None`
`fallback`	`boolean`	`True`
`agent_id`	`string`	`None`
`wait`	`boolean`	`True`
`signature`	`boolean`	`False`

Returns: str

Capture — `capture_` (1 tools)

Tool Description

capture_capture_screenshot

Capture screenshot - monitor, window, browser, or everything.

Parameters & Returns ▸

Name	Type	Default
`monitor_id`	`integer`	`0`
`all`	`boolean`	`False`
`quality`	`integer`	`85`
`message`	`string`	`None`
`return_base64`	`boolean`	`False`
`url`	`string`	`None`
`app`	`string`	`None`

Returns: str

CLEW Pipelines — `clew_` (6 tools)

Tool Description

clew_chain

Verify the dependency chain for a target file.

Parameters & Returns ▸

Name	Type	Default
`target_file`	`string`	required

Returns: str

clew_list

List all tracked runs with verification status.

Parameters & Returns ▸

Name	Type	Default
`limit`	`integer`	`50`
`status_filter`	`string`	`None`

Returns: str

clew_mermaid

Generate Mermaid diagram for verification DAG.

Parameters & Returns ▸

Name	Type	Default
`session_id`	`string`	`None`
`target_file`	`string`	`None`

Returns: str

clew_run

Verify a specific session run by checking all file hashes.

Parameters & Returns ▸

Name	Type	Default
`session_or_path`	`string`	required

Returns: str

clew_stats Show verification database statistics.

clew_status Show verification status summary (like git status).

Crossref — `crossref_` (15 tools)

Tool Description

crossref_cache_citation_summary

Get citation statistics for cached papers.

Parameters & Returns ▸

Name	Type	Default
`name`	`string`	required

Returns: str

crossref_cache_create

Create a paper cache from search query.

Parameters & Returns ▸

Name	Type	Default
`name`	`string`	required
`query`	`string`	required
`limit`	`integer`	`1000`

Returns: str

crossref_cache_export

Export cache to file.

Parameters & Returns ▸

Name	Type	Default
`name`	`string`	required
`output_path`	`string`	required
`format`	`string`	`'json'`
`fields`	`array`	`None`

Returns: str

crossref_cache_list List all available caches.

crossref_cache_plot_network

Generate citation network visualization.

Parameters & Returns ▸

Name	Type	Default
`name`	`string`	required
`output`	`string`	required
`max_nodes`	`integer`	`100`

Returns: str

crossref_cache_plot_scatter

Generate year vs citations scatter plot.

Parameters & Returns ▸

Name	Type	Default
`name`	`string`	required
`output`	`string`	required
`top_n`	`integer`	`10`

Returns: str

crossref_cache_query

Query cached papers with field filtering.

Parameters & Returns ▸

Name	Type	Default
`name`	`string`	required
`fields`	`array`	`None`
`include_abstract`	`boolean`	`False`
`include_references`	`boolean`	`False`
`include_citations`	`boolean`	`False`
`year_min`	`integer`	`None`
`year_max`	`integer`	`None`
`journal`	`string`	`None`
`limit`	`integer`	`None`

Returns: str

crossref_cache_stats

Get cache statistics.

Parameters & Returns ▸

Name	Type	Default
`name`	`string`	required

Returns: str

crossref_cache_top_cited

Get top cited papers from cache.

Parameters & Returns ▸

Name	Type	Default
`name`	`string`	required
`n`	`integer`	`20`
`year_min`	`integer`	`None`
`year_max`	`integer`	`None`

Returns: str

crossref_check_bibtex_file

Check all citations in a BibTeX file against the local database.

Parameters & Returns ▸

Name	Type	Default
`file_path`	`string`	required
`validate_metadata`	`boolean`	`True`
`suggest_enrichment`	`boolean`	`True`

Returns: str

crossref_check_citations

Check citations against the local CrossRef database.

Parameters & Returns ▸

Name	Type	Default
`identifiers`	`array`	required
`validate_metadata`	`boolean`	`True`
`suggest_enrichment`	`boolean`	`True`

Returns: str

crossref_enrich_dois

Enrich DOIs with full metadata including citation counts and references.

Parameters & Returns ▸

Name	Type	Default
`dois`	`array`	required

Returns: str

crossref_search

Search for academic works by title, abstract, or authors.

Parameters & Returns ▸

Name	Type	Default
`query`	`string`	required
`limit`	`integer`	`10`
`offset`	`integer`	`0`
`with_abstracts`	`boolean`	`False`
`save_path`	`string`	`None`
`save_format`	`string`	`'json'`

Returns: str

crossref_search_by_doi

Get detailed information about a work by DOI.

Parameters & Returns ▸

Name	Type	Default
`doi`	`string`	required
`as_citation`	`boolean`	`False`
`save_path`	`string`	`None`
`save_format`	`string`	`'json'`

Returns: str

crossref_status Get database statistics and status.

Datasets — `dataset_` (1 tools)

Tool	Description
`dataset_usage`	Get usage guide for SciTeX Dataset (not installed).

Developer — `dev_` (9 tools)

Tool Description

dev_bulk_rename

Bulk rename files, contents, directories, and symlinks.

Parameters & Returns ▸

Name	Type	Default
`pattern`	`string`	required
`replacement`	`string`	required
`directory`	`string`	`'.'`
`confirm`	`boolean`	`False`
`django_safe`	`boolean`	`True`
`extra_excludes`	`array`	`None`

Returns: str

dev_config_show Get current developer configuration.

dev_test_hpc

Run project tests on HPC (Spartan) via Slurm.

Parameters & Returns ▸

Name	Type	Default
`module`	`string`	`''`
`fast`	`boolean`	`False`
`hpc_cpus`	`integer`	`8`
`hpc_partition`	`string`	`'sapphire'`
`hpc_time`	`string`	`'00:10:00'`
`hpc_mem`	`string`	`'16G'`
`async_mode`	`boolean`	`False`

Returns: str

dev_test_hpc_poll

Check HPC test job status.

Parameters & Returns ▸

Name	Type	Default
`job_id`	`string`	`None`

Returns: str

dev_test_hpc_result

Fetch full HPC test output.

Parameters & Returns ▸

Name	Type	Default
`job_id`	`string`	`None`

Returns: str

dev_test_local

Run project tests locally via pytest.

Parameters & Returns ▸

Name	Type	Default
`module`	`string`	`''`
`fast`	`boolean`	`False`
`coverage`	`boolean`	`False`
`exitfirst`	`boolean`	`True`
`pattern`	`string`	`''`
`parallel`	`string`	`'auto'`

Returns: str

dev_versions_list

List versions across the scitex ecosystem.

Parameters & Returns ▸

Name	Type	Default
`packages`	`array`	`None`

Returns: str

dev_versions_sync

Sync ecosystem packages to remote hosts (git stash, pull, pip install).

Parameters & Returns ▸

Name	Type	Default
`hosts`	`array`	`None`
`packages`	`array`	`None`
`install`	`boolean`	`True`
`confirm`	`boolean`	`False`

Returns: str

dev_versions_sync_local

Install all local editable packages (pip install -e).

Parameters & Returns ▸

Name	Type	Default
`packages`	`array`	`None`
`confirm`	`boolean`	`False`

Returns: str

Introspect — `introspect_` (12 tools)

Tool Description

introspect_api

List the API tree of a module recursively.

Parameters & Returns ▸

Name	Type	Default
`dotted_path`	`string`	required
`max_depth`	`integer`	`5`
`docstring`	`boolean`	`False`
`root_only`	`boolean`	`False`

Returns: str

introspect_call_graph

Get function call graph (with timeout protection).

Parameters & Returns ▸

Name	Type	Default
`dotted_path`	`string`	required
`max_depth`	`integer`	`2`
`timeout_seconds`	`integer`	`10`
`internal_only`	`boolean`	`True`

Returns: str

introspect_class_hierarchy

Get class inheritance hierarchy (MRO + subclasses).

Parameters & Returns ▸

Name	Type	Default
`dotted_path`	`string`	required
`include_builtins`	`boolean`	`False`
`max_depth`	`integer`	`10`

Returns: str

introspect_dependencies

Get module dependencies (what it imports).

Parameters & Returns ▸

Name	Type	Default
`dotted_path`	`string`	required
`recursive`	`boolean`	`False`
`max_depth`	`integer`	`3`

Returns: str

introspect_dir

List members of module/class (like dir()). filter: all|public|private|dunder.

Parameters & Returns ▸

Name	Type	Default
`dotted_path`	`string`	required
`filter`	`string`	`'public'`
`kind`	`string`	`None`
`include_inherited`	`boolean`	`False`

Returns: str

introspect_docstring

Get docstring of a Python object. format: raw|parsed|summary.

Parameters & Returns ▸

Name	Type	Default
`dotted_path`	`string`	required
`format`	`string`	`'raw'`

Returns: str

introspect_examples

Find usage examples in tests/examples directories.

Parameters & Returns ▸

Name	Type	Default
`dotted_path`	`string`	required
`search_paths`	`string`	`None`
`max_results`	`integer`	`10`

Returns: str

introspect_exports

Get __all__ exports of a module.

Parameters & Returns ▸

Name	Type	Default
`dotted_path`	`string`	required

Returns: str

introspect_imports

Get all imports from a module (AST-based static analysis).

Parameters & Returns ▸

Name	Type	Default
`dotted_path`	`string`	required
`categorize`	`boolean`	`True`

Returns: str

introspect_signature

Get function/class signature with parameters and types.

Parameters & Returns ▸

Name	Type	Default
`dotted_path`	`string`	required
`include_defaults`	`boolean`	`True`
`include_annotations`	`boolean`	`True`

Returns: str

introspect_source

Get source code of a Python object.

Parameters & Returns ▸

Name	Type	Default
`dotted_path`	`string`	required
`max_lines`	`integer`	`None`
`include_decorators`	`boolean`	`True`

Returns: str

introspect_type_hints

Get detailed type hint analysis for function/class.

Parameters & Returns ▸

Name	Type	Default
`dotted_path`	`string`	required
`include_extras`	`boolean`	`True`

Returns: str

Linter — `linter_` (1 tools)

Tool	Description
`linter_usage`	Get usage guide for SciTeX Linter (not installed).

OpenAlex — `openalex_` (4 tools)

Tool Description

openalex_enrich_ids

Enrich OpenAlex IDs or DOIs with full metadata.

Parameters & Returns ▸

Name	Type	Default
`identifiers`	`array`	required

Returns: str

openalex_search

Search for academic works by title, abstract, or authors.

Parameters & Returns ▸

Name	Type	Default
`query`	`string`	required
`limit`	`integer`	`10`
`offset`	`integer`	`0`
`with_abstracts`	`boolean`	`False`
`save_path`	`string`	`None`
`save_format`	`string`	`'json'`

Returns: str

openalex_search_by_id

Get detailed information about a work by OpenAlex ID or DOI.

Parameters & Returns ▸

Name	Type	Default
`identifier`	`string`	required
`as_citation`	`boolean`	`False`
`save_path`	`string`	`None`
`save_format`	`string`	`'json'`

Returns: str

openalex_status Get database statistics and status.

Plotting — `plt_` (71 tools)

Tool Description

plt_acorr

Plot autocorrelation (ax.acorr).

Parameters & Returns ▸

Name	Type	Default
`x`	`array`	required
`output_path`	`string`	required
`data_file`	`string`	`None`
`maxlags`	`integer`	`10`
`color`	`string`	`None`
`label`	`string`	`None`
`linestyle`	`string`	`'-'`
`marker`	`string`	`'o'`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_angle_spectrum

Plot angle spectrum (ax.angle_spectrum).

Parameters & Returns ▸

Name	Type	Default
`x`	`array`	required
`output_path`	`string`	required
`data_file`	`string`	`None`
`Fs`	`number`	`2.0`
`Fc`	`number`	`0.0`
`color`	`string`	`None`
`label`	`string`	`None`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_bar

Create a bar chart (ax.bar).

Parameters & Returns ▸

Name	Type	Default
`output_path`	`string`	required
`x`	`array`	required
`height`	`array`	required
`data_file`	`string`	`None`
`yerr`	`array`	`None`
`capsize`	`number`	`4.0`
`color`	`string`	`None`
`label`	`string`	`None`
`alpha`	`number`	`1.0`
`width`	`number`	`0.8`
`edgecolor`	`string`	`None`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_barh

Create a horizontal bar chart (ax.barh).

Parameters & Returns ▸

Name	Type	Default
`output_path`	`string`	required
`y`	`array`	required
`width`	`array`	required
`data_file`	`string`	`None`
`xerr`	`array`	`None`
`capsize`	`number`	`4.0`
`color`	`string`	`None`
`label`	`string`	`None`
`alpha`	`number`	`1.0`
`height`	`number`	`0.8`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_boxplot

Create a box plot (ax.boxplot).

Parameters & Returns ▸

Name	Type	Default
`data`	`array`	required
`output_path`	`string`	required
`labels`	`array`	`None`
`notch`	`boolean`	`False`
`vert`	`boolean`	`True`
`showfliers`	`boolean`	`True`
`color`	`string`	`None`
`colors`	`array`	`None`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_cohere

Plot coherence between two signals (ax.cohere).

Parameters & Returns ▸

Name	Type	Default
`x`	`array`	required
`y`	`array`	required
`output_path`	`string`	required
`data_file`	`string`	`None`
`Fs`	`number`	`2.0`
`NFFT`	`integer`	`256`
`color`	`string`	`None`
`label`	`string`	`None`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_compose

Compose multiple figures into a single figure with panel labels.

Parameters & Returns ▸

Name	Type	Default
`sources`	`array`	required
`output_path`	`string`	required
`layout`	`string`	`'horizontal'`
`gap_mm`	`number`	`5.0`
`dpi`	`integer`	`300`
`panel_labels`	`boolean`	`True`
`label_style`	`string`	`'uppercase'`
`caption`	`string`	`None`
`create_symlinks`	`boolean`	`True`
`canvas_size_mm`	`array`	`None`
`save_recipe`	`boolean`	`True`

Returns: Dict

plt_conf_mat

Plot a confusion matrix (ax.stx_conf_mat).

Parameters & Returns ▸

Name	Type	Default
`conf_mat`	`array`	required
`output_path`	`string`	required
`x_labels`	`array`	`None`
`y_labels`	`array`	`None`
`cmap`	`string`	`'Blues'`
`fmt`	`string`	`'.2f'`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_contour

Create contour lines (ax.contour).

Parameters & Returns ▸

Name	Type	Default
`X`	`array`	required
`Y`	`array`	required
`Z`	`array`	required
`output_path`	`string`	required
`levels`	`integer`	`10`
`cmap`	`string`	`'viridis'`
`colors`	`string`	`None`
`linewidths`	`number`	`1.0`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_contourf

Create a filled contour plot (ax.contourf).

Parameters & Returns ▸

Name	Type	Default
`X`	`array`	required
`Y`	`array`	required
`Z`	`array`	required
`output_path`	`string`	required
`levels`	`integer`	`10`
`cmap`	`string`	`'viridis'`
`alpha`	`number`	`1.0`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_crop

Crop whitespace from a figure image.

Parameters & Returns ▸

Name	Type	Default
`input_path`	`string`	required
`output_path`	`string`	`None`
`margin_mm`	`number`	`1.0`
`overwrite`	`boolean`	`False`

Returns: Dict

plt_csd

Plot cross-spectral density (ax.csd).

Parameters & Returns ▸

Name	Type	Default
`x`	`array`	required
`y`	`array`	required
`output_path`	`string`	required
`data_file`	`string`	`None`
`Fs`	`number`	`2.0`
`NFFT`	`integer`	`256`
`color`	`string`	`None`
`label`	`string`	`None`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_diagram_compile_graphviz

Compile diagram specification to Graphviz DOT format.

Parameters & Returns ▸

Name	Type	Default
`spec_dict`	`object`	`None`
`spec_path`	`string`	`None`
`output_path`	`string`	`None`

Returns: Dict

plt_diagram_compile_mermaid

Compile diagram specification to Mermaid format.

Parameters & Returns ▸

Name	Type	Default
`spec_dict`	`object`	`None`
`spec_path`	`string`	`None`
`output_path`	`string`	`None`

Returns: Dict

plt_diagram_create

Create a diagram from a YAML specification file or dictionary.

Parameters & Returns ▸

Name	Type	Default
`spec_dict`	`object`	`None`
`spec_path`	`string`	`None`

Returns: Dict

plt_diagram_get_backends List available rendering backends and their status.

plt_diagram_get_paper_modes Get available paper layout modes and their constraints.

plt_diagram_get_preset

Get a diagram preset configuration by name.

Parameters & Returns ▸

Name	Type	Default
`preset_name`	`string`	required

Returns: Dict

plt_diagram_list_presets List available diagram presets (workflow, decision, pipeline, scientific).

plt_diagram_render

Render diagram to image file (PNG, SVG, PDF).

Parameters & Returns ▸

Name	Type	Default
`spec_dict`	`object`	`None`
`spec_path`	`string`	`None`
`output_path`	`string`	`''`
`format`	`string`	`'png'`
`backend`	`string`	`'auto'`
`scale`	`number`	`2.0`

Returns: Dict

plt_diagram_split

Split a large diagram into smaller parts for multi-column layouts.

Parameters & Returns ▸

Name	Type	Default
`spec_path`	`string`	required
`max_nodes_per_part`	`integer`	`10`
`strategy`	`string`	`'by_groups'`

Returns: Dict

plt_ecdf

Plot empirical CDF (ax.stx_ecdf).

Parameters & Returns ▸

Name	Type	Default
`values`	`array`	required
`output_path`	`string`	required
`data_file`	`string`	`None`
`color`	`string`	`None`
`label`	`string`	`None`
`linewidth`	`number`	`1.5`
`complementary`	`boolean`	`False`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_errorbar

Create an error-bar plot (ax.errorbar).

Parameters & Returns ▸

Name	Type	Default
`output_path`	`string`	required
`x`	`array`	required
`y`	`array`	required
`data_file`	`string`	`None`
`yerr`	`array`	`None`
`xerr`	`array`	`None`
`capsize`	`number`	`4.0`
`color`	`string`	`None`
`label`	`string`	`None`
`linestyle`	`string`	`'-'`
`marker`	`string`	`'o'`
`alpha`	`number`	`1.0`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_eventplot

Create a spike raster / event plot (ax.eventplot).

Parameters & Returns ▸

Name	Type	Default
`positions`	`array`	required
`output_path`	`string`	required
`orientation`	`string`	`'horizontal'`
`lineoffsets`	`number`	`1.0`
`linelengths`	`number`	`0.8`
`linewidths`	`number`	`1.0`
`colors`	`array`	`None`
`label`	`string`	`None`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_extract_data

Extract plotted data arrays from a saved recipe.

Parameters & Returns ▸

Name	Type	Default
`recipe_path`	`string`	required

Returns: Dict

plt_fill

Fill a closed polygon (ax.fill).

Parameters & Returns ▸

Name	Type	Default
`x`	`array`	required
`y`	`array`	required
`output_path`	`string`	required
`color`	`string`	`None`
`label`	`string`	`None`
`alpha`	`number`	`0.5`
`edgecolor`	`string`	`None`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_fill_between

Create a filled region plot (ax.fill_between).

Parameters & Returns ▸

Name	Type	Default
`x`	`array`	required
`y1`	`array`	required
`output_path`	`string`	required
`data_file`	`string`	`None`
`y2`	`array`	`None`
`color`	`string`	`None`
`label`	`string`	`None`
`alpha`	`number`	`0.3`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_fill_betweenx

Create a horizontal fill-between region (ax.fill_betweenx).

Parameters & Returns ▸

Name	Type	Default
`y`	`array`	required
`x1`	`array`	required
`output_path`	`string`	required
`x2`	`array`	`None`
`color`	`string`	`None`
`label`	`string`	`None`
`alpha`	`number`	`0.3`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_fillv

Fill vertical spans between start/end x-values (ax.stx_fillv).

Parameters & Returns ▸

Name	Type	Default
`starts`	`array`	required
`ends`	`array`	required
`output_path`	`string`	required
`data_file`	`string`	`None`
`color`	`string`	`'red'`
`alpha`	`number`	`0.2`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_get_plot_types Get list of supported plot types.

plt_heatmap

Heatmap with smart annotation colors (ax.stx_heatmap).

Parameters & Returns ▸

Name	Type	Default
`values_2d`	`array`	required
`output_path`	`string`	required
`cmap`	`string`	`'viridis'`
`vmin`	`number`	`None`
`vmax`	`number`	`None`
`annot`	`boolean`	`True`
`fmt`	`string`	`'.2f'`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_hexbin

Create a 2D hexagonal binning plot (ax.hexbin).

Parameters & Returns ▸

Name	Type	Default
`x`	`array`	required
`y`	`array`	required
`output_path`	`string`	required
`data_file`	`string`	`None`
`gridsize`	`integer`	`20`
`cmap`	`string`	`'Blues'`
`bins`	`integer`	`None`
`mincnt`	`integer`	`1`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_hist

Create a histogram (ax.hist).

Parameters & Returns ▸

Name	Type	Default
`x`	`array`	required
`output_path`	`string`	required
`data_file`	`string`	`None`
`bins`	`integer`	`'auto'`
`color`	`string`	`None`
`label`	`string`	`None`
`alpha`	`number`	`0.7`
`density`	`boolean`	`False`
`histtype`	`string`	`'bar'`
`edgecolor`	`string`	`None`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_hist2d

Create a 2D histogram (ax.hist2d).

Parameters & Returns ▸

Name	Type	Default
`x`	`array`	required
`y`	`array`	required
`output_path`	`string`	required
`bins`	`integer`	`20`
`cmap`	`string`	`'Blues'`
`vmin`	`number`	`None`
`vmax`	`number`	`None`
`density`	`boolean`	`False`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_image

Display 2D array as image with correct orientation (ax.stx_image).

Parameters & Returns ▸

Name	Type	Default
`arr_2d`	`array`	required
`output_path`	`string`	required
`cmap`	`string`	`'gray'`
`vmin`	`number`	`None`
`vmax`	`number`	`None`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_imshow

Display a 2D array as an image / heatmap (ax.imshow).

Parameters & Returns ▸

Name	Type	Default
`data`	`array`	required
`output_path`	`string`	required
`cmap`	`string`	`'viridis'`
`aspect`	`string`	`'auto'`
`vmin`	`number`	`None`
`vmax`	`number`	`None`
`interpolation`	`string`	`'nearest'`
`origin`	`string`	`'upper'`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_info

Get information about a recipe file.

Parameters & Returns ▸

Name	Type	Default
`recipe_path`	`string`	required
`verbose`	`boolean`	`False`

Returns: Dict

plt_line

Plot a 1D array as a line (ax.stx_line).

Parameters & Returns ▸

Name	Type	Default
`values`	`array`	required
`output_path`	`string`	required
`data_file`	`string`	`None`
`xx`	`array`	`None`
`color`	`string`	`None`
`label`	`string`	`None`
`linewidth`	`number`	`1.5`
`alpha`	`number`	`1.0`
`linestyle`	`string`	`'-'`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_list_styles List available figure style presets.

plt_loglog

Line plot with both axes on log scale (ax.loglog).

Parameters & Returns ▸

Name	Type	Default
`x`	`array`	required
`y`	`array`	required
`output_path`	`string`	required
`data_file`	`string`	`None`
`color`	`string`	`None`
`label`	`string`	`None`
`linestyle`	`string`	`'-'`
`linewidth`	`number`	`1.5`
`marker`	`string`	`None`
`alpha`	`number`	`1.0`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_magnitude_spectrum

Plot magnitude spectrum (ax.magnitude_spectrum).

Parameters & Returns ▸

Name	Type	Default
`x`	`array`	required
`output_path`	`string`	required
`data_file`	`string`	`None`
`Fs`	`number`	`2.0`
`Fc`	`number`	`0.0`
`scale`	`string`	`'linear'`
`color`	`string`	`None`
`label`	`string`	`None`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_matshow

Display a 2D matrix with row/column ticks (ax.matshow).

Parameters & Returns ▸

Name	Type	Default
`data`	`array`	required
`output_path`	`string`	required
`cmap`	`string`	`'viridis'`
`vmin`	`number`	`None`
`vmax`	`number`	`None`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_mean_ci

Plot mean with CI shading (ax.stx_mean_ci).

Parameters & Returns ▸

Name	Type	Default
`values_2d`	`array`	required
`output_path`	`string`	required
`data_file`	`string`	`None`
`xx`	`array`	`None`
`perc`	`number`	`95.0`
`color`	`string`	`None`
`label`	`string`	`None`
`alpha`	`number`	`0.3`
`linewidth`	`number`	`1.5`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_mean_std

Plot mean ± sd with shaded region (ax.stx_mean_std).

Parameters & Returns ▸

Name	Type	Default
`values_2d`	`array`	required
`output_path`	`string`	required
`data_file`	`string`	`None`
`xx`	`array`	`None`
`sd`	`number`	`1.0`
`color`	`string`	`None`
`label`	`string`	`None`
`alpha`	`number`	`0.3`
`linewidth`	`number`	`1.5`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_median_iqr

Plot median with IQR shading (ax.stx_median_iqr).

Parameters & Returns ▸

Name	Type	Default
`values_2d`	`array`	required
`output_path`	`string`	required
`data_file`	`string`	`None`
`xx`	`array`	`None`
`color`	`string`	`None`
`label`	`string`	`None`
`alpha`	`number`	`0.3`
`linewidth`	`number`	`1.5`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_pcolor

Create a pseudocolor plot (ax.pcolor).

Parameters & Returns ▸

Name	Type	Default
`X`	`array`	required
`Y`	`array`	required
`C`	`array`	required
`output_path`	`string`	required
`cmap`	`string`	`'viridis'`
`vmin`	`number`	`None`
`vmax`	`number`	`None`
`shading`	`string`	`'auto'`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_pcolormesh

Create a pseudocolor mesh plot (ax.pcolormesh).

Parameters & Returns ▸

Name	Type	Default
`X`	`array`	required
`Y`	`array`	required
`C`	`array`	required
`output_path`	`string`	required
`cmap`	`string`	`'viridis'`
`vmin`	`number`	`None`
`vmax`	`number`	`None`
`shading`	`string`	`'auto'`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_phase_spectrum

Plot phase spectrum (ax.phase_spectrum).

Parameters & Returns ▸

Name	Type	Default
`x`	`array`	required
`output_path`	`string`	required
`data_file`	`string`	`None`
`Fs`	`number`	`2.0`
`Fc`	`number`	`0.0`
`color`	`string`	`None`
`label`	`string`	`None`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_pie

Create a pie chart (ax.pie).

Parameters & Returns ▸

Name	Type	Default
`x`	`array`	required
`output_path`	`string`	required
`data_file`	`string`	`None`
`labels`	`array`	`None`
`colors`	`array`	`None`
`autopct`	`string`	`None`
`startangle`	`number`	`90.0`
`counterclock`	`boolean`	`False`
`explode`	`array`	`None`
`shadow`	`boolean`	`False`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_plot

Create a matplotlib figure from a declarative specification.

Parameters & Returns ▸

Name	Type	Default
`spec`	`object`	required
`output_path`	`string`	required
`dpi`	`integer`	`300`
`save_recipe`	`boolean`	`True`

Returns: Dict

plt_psd

Plot power spectral density (ax.psd).

Parameters & Returns ▸

Name	Type	Default
`x`	`array`	required
`output_path`	`string`	required
`data_file`	`string`	`None`
`Fs`	`number`	`1.0`
`NFFT`	`integer`	`256`
`noverlap`	`integer`	`128`
`color`	`string`	`None`
`label`	`string`	`None`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_quiver

Create a vector field (ax.quiver).

Parameters & Returns ▸

Name	Type	Default
`X`	`array`	required
`Y`	`array`	required
`U`	`array`	required
`V`	`array`	required
`output_path`	`string`	required
`scale`	`number`	`None`
`color`	`string`	`None`
`cmap`	`string`	`None`
`alpha`	`number`	`1.0`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_raster

Plot a raster/event plot (ax.stx_raster).

Parameters & Returns ▸

Name	Type	Default
`spike_times`	`array`	required
`output_path`	`string`	required
`color`	`string`	`None`
`label`	`string`	`None`
`linelengths`	`number`	`1.0`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_rectangle

Add rectangle patches to a plot (ax.stx_rectangle).

Parameters & Returns ▸

Name	Type	Default
`xx`	`array`	required
`yy`	`array`	required
`ww`	`array`	required
`hh`	`array`	required
`output_path`	`string`	required
`color`	`string`	`None`
`alpha`	`number`	`0.5`
`fill`	`boolean`	`True`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_reproduce

Reproduce a figure from a saved YAML recipe.

Parameters & Returns ▸

Name	Type	Default
`recipe_path`	`string`	required
`output_path`	`string`	`None`
`format`	`string`	`'png'`
`dpi`	`integer`	`300`

Returns: Dict

plt_scatter

Create a scatter plot (ax.scatter).

Parameters & Returns ▸

Name	Type	Default
`output_path`	`string`	required
`x`	`array`	required
`y`	`array`	required
`data_file`	`string`	`None`
`color`	`string`	`None`
`label`	`string`	`None`
`marker`	`string`	`'o'`
`s`	`number`	`None`
`alpha`	`number`	`1.0`
`edgecolors`	`string`	`None`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_scatter_hist

Scatter plot with marginal histograms (ax.stx_scatter_hist).

Parameters & Returns ▸

Name	Type	Default
`x`	`array`	required
`y`	`array`	required
`output_path`	`string`	required
`data_file`	`string`	`None`
`color`	`string`	`None`
`alpha`	`number`	`0.7`
`bins`	`integer`	`20`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_semilogx

Line plot with x-axis on log scale (ax.semilogx).

Parameters & Returns ▸

Name	Type	Default
`x`	`array`	required
`y`	`array`	required
`output_path`	`string`	required
`data_file`	`string`	`None`
`color`	`string`	`None`
`label`	`string`	`None`
`linestyle`	`string`	`'-'`
`linewidth`	`number`	`1.5`
`marker`	`string`	`None`
`alpha`	`number`	`1.0`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_semilogy

Line plot with y-axis on log scale (ax.semilogy).

Parameters & Returns ▸

Name	Type	Default
`x`	`array`	required
`y`	`array`	required
`output_path`	`string`	required
`data_file`	`string`	`None`
`color`	`string`	`None`
`label`	`string`	`None`
`linestyle`	`string`	`'-'`
`linewidth`	`number`	`1.5`
`marker`	`string`	`None`
`alpha`	`number`	`1.0`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_shaded_line

Plot line(s) with shaded uncertainty regions (ax.stx_shaded_line).

Parameters & Returns ▸

Name	Type	Default
`xs`	`array`	required
`y_lower`	`array`	required
`y_middle`	`array`	required
`y_upper`	`array`	required
`output_path`	`string`	required
`data_file`	`string`	`None`
`color`	`string`	`None`
`label`	`string`	`None`
`alpha`	`number`	`0.3`
`linewidth`	`number`	`1.5`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_specgram

Create a spectrogram (ax.specgram).

Parameters & Returns ▸

Name	Type	Default
`x`	`array`	required
`output_path`	`string`	required
`data_file`	`string`	`None`
`Fs`	`number`	`1.0`
`NFFT`	`integer`	`256`
`noverlap`	`integer`	`128`
`cmap`	`string`	`'viridis'`
`scale`	`string`	`'dB'`
`vmin`	`number`	`None`
`vmax`	`number`	`None`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_spy

Visualize sparsity of a 2D matrix (ax.spy).

Parameters & Returns ▸

Name	Type	Default
`data`	`array`	required
`output_path`	`string`	required
`marker`	`string`	`'.'`
`markersize`	`number`	`3.0`
`color`	`string`	`None`
`precision`	`number`	`0.0`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`title`	`string`	`None`
`caption`	`string`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_stackplot

Create a stacked area chart (ax.stackplot).

Parameters & Returns ▸

Name	Type	Default
`x`	`array`	required
`y_stacks`	`array`	required
`output_path`	`string`	required
`labels`	`array`	`None`
`colors`	`array`	`None`
`alpha`	`number`	`1.0`
`baseline`	`string`	`'zero'`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`True`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_stairs

Create a staircase (step histogram) plot (ax.stairs).

Parameters & Returns ▸

Name	Type	Default
`values`	`array`	required
`output_path`	`string`	required
`data_file`	`string`	`None`
`edges`	`array`	`None`
`color`	`string`	`None`
`label`	`string`	`None`
`linewidth`	`number`	`1.5`
`fill`	`boolean`	`False`
`alpha`	`number`	`1.0`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_stem

Create a stem plot (ax.stem).

Parameters & Returns ▸

Name	Type	Default
`y`	`array`	required
`output_path`	`string`	required
`x`	`array`	`None`
`data_file`	`string`	`None`
`linefmt`	`string`	`'C0-'`
`markerfmt`	`string`	`'C0o'`
`basefmt`	`string`	`'C0-'`
`label`	`string`	`None`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_step

Create a step plot (ax.step).

Parameters & Returns ▸

Name	Type	Default
`x`	`array`	required
`y`	`array`	required
`output_path`	`string`	required
`data_file`	`string`	`None`
`where`	`string`	`'mid'`
`color`	`string`	`None`
`label`	`string`	`None`
`linestyle`	`string`	`'-'`
`linewidth`	`number`	`1.5`
`alpha`	`number`	`1.0`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_streamplot

Create a streamline plot of a vector field (ax.streamplot).

Parameters & Returns ▸

Name	Type	Default
`X`	`array`	required
`Y`	`array`	required
`U`	`array`	required
`V`	`array`	required
`output_path`	`string`	required
`density`	`number`	`1.0`
`color`	`string`	`None`
`cmap`	`string`	`None`
`linewidth`	`number`	`None`
`arrowsize`	`number`	`1.0`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_validate

Validate that a recipe can reproduce its original figure.

Parameters & Returns ▸

Name	Type	Default
`recipe_path`	`string`	required
`mse_threshold`	`number`	`100.0`

Returns: Dict

plt_violin

Plot violins from a list of arrays (ax.stx_violin).

Parameters & Returns ▸

Name	Type	Default
`values_list`	`array`	required
`output_path`	`string`	required
`color`	`string`	`None`
`alpha`	`number`	`0.7`
`positions`	`array`	`None`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_violinplot

Create a violin plot (ax.violinplot).

Parameters & Returns ▸

Name	Type	Default
`dataset`	`array`	required
`output_path`	`string`	required
`labels`	`array`	`None`
`showmeans`	`boolean`	`False`
`showmedians`	`boolean`	`True`
`showextrema`	`boolean`	`True`
`vert`	`boolean`	`True`
`color`	`string`	`None`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

plt_xcorr

Plot cross-correlation of two signals (ax.xcorr).

Parameters & Returns ▸

Name	Type	Default
`x`	`array`	required
`y`	`array`	required
`output_path`	`string`	required
`data_file`	`string`	`None`
`maxlags`	`integer`	`10`
`color`	`string`	`None`
`label`	`string`	`None`
`linestyle`	`string`	`'-'`
`marker`	`string`	`'o'`
`width_mm`	`number`	`40.0`
`height_mm`	`number`	`28.0`
`style`	`string`	`'SCITEX'`
`dpi`	`integer`	`300`
`xlabel`	`string`	`None`
`ylabel`	`string`	`None`
`title`	`string`	`None`
`caption`	`string`	`None`
`legend`	`boolean`	`False`
`xlim`	`array`	`None`
`ylim`	`array`	`None`
`stat_annotations`	`array`	`None`
`stats_results`	`array`	`None`

Returns: Dict

Project Files — `project_` (4 tools)

Tool Description

project_list_files

List files and directories in a project directory.

Parameters & Returns ▸

Name	Type	Default
`root_path`	`string`	required
`relative_path`	`string`	`'.'`
`max_depth`	`integer`	`3`

Returns: str

project_read_file

Read the content of a file in a project.

Parameters & Returns ▸

Name	Type	Default
`root_path`	`string`	required
`relative_path`	`string`	required

Returns: str

project_search_files

Search project files by name glob and/or content substring.

Parameters & Returns ▸

Name	Type	Default
`root_path`	`string`	required
`name_pattern`	`string`	`''`
`content_pattern`	`string`	`''`
`relative_path`	`string`	`'.'`
`max_results`	`integer`	`50`

Returns: str

project_write_file

Write or create a file in a project.

Parameters & Returns ▸

Name	Type	Default
`root_path`	`string`	required
`relative_path`	`string`	required
`content`	`string`	required

Returns: str

Scholar — `scholar_` (22 tools)

Tool Description

scholar_add_papers_to_project

Add papers to a project by DOI or from BibTeX file.

Parameters & Returns ▸

Name	Type	Default
`project`	`string`	required
`dois`	`array`	`None`
`bibtex_path`	`string`	`None`

Returns: str

scholar_authenticate

Start SSO login for institutional access (OpenAthens, Shibboleth). Call without confirm first to check requirements, ...

Parameters & Returns ▸

Name	Type	Default
`method`	`string`	required
`institution`	`string`	`None`
`force`	`boolean`	`False`
`confirm`	`boolean`	`False`

Returns: str

scholar_cancel_job

Cancel a running or pending job.

Parameters & Returns ▸

Name	Type	Default
`job_id`	`string`	required

Returns: str

scholar_check_auth_status

Check current authentication status without starting login. Returns whether a valid session exists.

Parameters & Returns ▸

Name	Type	Default
`method`	`string`	`'openathens'`
`verify_live`	`boolean`	`False`

Returns: str

scholar_create_project

Create a new scholar project for organizing papers.

Parameters & Returns ▸

Name	Type	Default
`project_name`	`string`	required
`description`	`string`	`None`

Returns: str

scholar_download_pdfs_batch

Download PDFs for multiple papers with progress tracking. Supports resumable operation.

Parameters & Returns ▸

Name	Type	Default
`dois`	`array`	`None`
`bibtex_path`	`string`	`None`
`project`	`string`	`None`
`output_dir`	`string`	`None`
`max_concurrent`	`integer`	`3`
`resume`	`boolean`	`True`

Returns: str

scholar_enrich_bibtex

Enrich BibTeX entries with metadata: DOIs, abstracts, citation counts, impact factors.

Parameters & Returns ▸

Name	Type	Default
`bibtex_path`	`string`	required
`output_path`	`string`	`None`
`add_abstracts`	`boolean`	`True`
`add_citations`	`boolean`	`True`
`add_impact_factors`	`boolean`	`True`

Returns: str

scholar_export_papers

Export papers to various formats (BibTeX, RIS, JSON, CSV).

Parameters & Returns ▸

Name	Type	Default
`output_path`	`string`	required
`project`	`string`	`None`
`format`	`string`	`'bibtex'`
`filter_has_pdf`	`boolean`	`False`

Returns: str

scholar_fetch_papers

Fetch papers to your library. Supports async mode (default) which returns immediately with a job_id for tracking.

Parameters & Returns ▸

Name	Type	Default
`papers`	`array`	`None`
`bibtex_path`	`string`	`None`
`project`	`string`	`None`
`workers`	`integer`	`None`
`browser_mode`	`string`	`'stealth'`
`chrome_profile`	`string`	`'system'`
`force`	`boolean`	`False`
`output`	`string`	`None`
`async_mode`	`boolean`	`True`

Returns: str

scholar_get_job_result

Get the result of a completed job.

Parameters & Returns ▸

Name	Type	Default
`job_id`	`string`	required

Returns: str

scholar_get_job_status

Get detailed status of a specific job including progress.

Parameters & Returns ▸

Name	Type	Default
`job_id`	`string`	required

Returns: str

scholar_get_library_status

Get status of the paper library: download progress, missing PDFs, validation status.

Parameters & Returns ▸

Name	Type	Default
`project`	`string`	`None`
`include_details`	`boolean`	`False`

Returns: str

scholar_list_jobs

List all background jobs with their status.

Parameters & Returns ▸

Name	Type	Default
`status`	`string`	`None`
`limit`	`integer`	`20`

Returns: str

scholar_list_projects List all scholar projects in the library.

scholar_logout

Logout from institutional authentication and clear session cache.

Parameters & Returns ▸

Name	Type	Default
`method`	`string`	`'openathens'`
`clear_cache`	`boolean`	`True`

Returns: str

scholar_parse_bibtex

Parse a BibTeX file and return paper objects.

Parameters & Returns ▸

Name	Type	Default
`bibtex_path`	`string`	required

Returns: str

scholar_parse_pdf_content

Parse PDF content to extract text, sections (IMRaD), tables, images, and metadata.

Parameters & Returns ▸

Name	Type	Default
`pdf_path`	`string`	`None`
`doi`	`string`	`None`
`project`	`string`	`None`
`mode`	`string`	`'scientific'`
`extract_sections`	`boolean`	`True`
`extract_tables`	`boolean`	`False`
`extract_images`	`boolean`	`False`
`max_pages`	`integer`	`None`

Returns: str

scholar_resolve_dois

Resolve DOIs from paper titles using Crossref API. Supports resumable operation for large batches.

Parameters & Returns ▸

Name	Type	Default
`titles`	`array`	`None`
`bibtex_path`	`string`	`None`
`project`	`string`	`None`
`resume`	`boolean`	`True`

Returns: str

scholar_resolve_openurls

Resolve publisher URLs via OpenURL resolver for institutional access.

Parameters & Returns ▸

Name	Type	Default
`dois`	`array`	required
`resolver_url`	`string`	`None`
`resume`	`boolean`	`True`

Returns: str

scholar_search_papers

Search for scientific papers. Supports local library search and external databases (CrossRef, Semantic Scholar, PubMe...

Parameters & Returns ▸

Name	Type	Default
`query`	`string`	required
`limit`	`integer`	`20`
`year_min`	`integer`	`None`
`year_max`	`integer`	`None`
`search_mode`	`string`	`'local'`
`sources`	`array`	`None`

Returns: str

scholar_start_job

Start a pending job that was submitted with async mode.

Parameters & Returns ▸

Name	Type	Default
`job_id`	`string`	required

Returns: str

scholar_validate_pdfs

Validate PDF files in library for completeness and readability.

Parameters & Returns ▸

Name	Type	Default
`project`	`string`	`None`
`pdf_paths`	`array`	`None`

Returns: str

Social — `social_` (1 tools)

Tool	Description
`social_status`	Get social media status (not installed).

Statistics — `stats_` (10 tools)

Tool Description

stats_correct_pvalues

Apply multiple comparison correction to p-values.

Parameters & Returns ▸

Name	Type	Default
`pvalues`	`array`	required
`method`	`string`	`'fdr_bh'`
`alpha`	`number`	`0.05`

Returns: str

stats_describe

Calculate descriptive statistics for data.

Parameters & Returns ▸

Name	Type	Default
`data`	`array`	required
`percentiles`	`array`	`None`

Returns: str

stats_effect_size

Calculate effect size between groups.

Parameters & Returns ▸

Name	Type	Default
`group1`	`array`	required
`group2`	`array`	required
`measure`	`string`	`'cohens_d'`
`pooled`	`boolean`	`True`

Returns: str

stats_format_results

Format statistical results in journal style (APA, Nature, etc.).

Parameters & Returns ▸

Name	Type	Default
`test_name`	`string`	required
`statistic`	`number`	required
`p_value`	`number`	required
`df`	`number`	`None`
`effect_size`	`number`	`None`
`effect_size_name`	`string`	`None`
`style`	`string`	`'apa'`
`ci_lower`	`number`	`None`
`ci_upper`	`number`	`None`

Returns: str

stats_normality_test

Test whether data follows a normal distribution.

Parameters & Returns ▸

Name	Type	Default
`data`	`array`	required
`method`	`string`	`'shapiro'`

Returns: str

stats_p_to_stars

Convert p-value to significance stars (*, **, ***, ns).

Parameters & Returns ▸

Name	Type	Default
`p_value`	`number`	required
`thresholds`	`array`	`None`

Returns: str

stats_posthoc_test

Run post-hoc pairwise comparisons after significant ANOVA/Kruskal.

Parameters & Returns ▸

Name	Type	Default
`groups`	`array`	required
`group_names`	`array`	`None`
`method`	`string`	`'tukey'`
`control_group`	`integer`	`0`

Returns: str

stats_power_analysis

Calculate statistical power or required sample size.

Parameters & Returns ▸

Name	Type	Default
`test_type`	`string`	`'ttest'`
`effect_size`	`number`	`None`
`alpha`	`number`	`0.05`
`power`	`number`	`0.8`
`n`	`integer`	`None`
`n_groups`	`integer`	`2`
`ratio`	`number`	`1.0`

Returns: str

stats_recommend_tests

Recommend appropriate statistical tests based on data characteristics.

Parameters & Returns ▸

Name	Type	Default
`n_groups`	`integer`	`2`
`sample_sizes`	`array`	`None`
`outcome_type`	`string`	`'continuous'`
`design`	`string`	`'between'`
`paired`	`boolean`	`False`
`has_control_group`	`boolean`	`False`
`top_k`	`integer`	`3`

Returns: str

stats_run_test

Execute a statistical test on provided data.

Parameters & Returns ▸

Name	Type	Default
`test_name`	`string`	required
`data`	`array`	`None`
`data_file`	`string`	`None`
`columns`	`array`	`None`
`alternative`	`string`	`'two-sided'`

Returns: str

Templates — `template_` (4 tools)

Tool Description

template_clone_template

Create a new project by cloning a template.

Parameters & Returns ▸

Name	Type	Default
`template_id`	`string`	required
`project_name`	`string`	required
`target_dir`	`string`	`None`
`git_strategy`	`string`	`'child'`
`branch`	`string`	`None`
`tag`	`string`	`None`

Returns: str

template_get_code_template

Get a code template for scripts and modules. Core: session, io, config. Module usage: plt, stats, scholar, audio, cap...

Parameters & Returns ▸

Name	Type	Default
`template_id`	`string`	required
`filepath`	`string`	`None`
`docstring`	`string`	`None`

Returns: str

template_list_code_templates List all available code templates for scripts and modules.

template_list_git_strategies List available git initialization strategies for template cloning.

UI / Notifications — `ui_` (2 tools)

Tool Description

ui_get_notification_config Get current notification configuration.

ui_notify

Send a notification via configured backends.

Parameters & Returns ▸

Name	Type	Default
`message`	`string`	required
`title`	`string`	`None`
`level`	`string`	`'info'`
`backend`	`string`	`None`
`backends`	`array`	`None`
`timeout`	`number`	`5.0`

Returns: str

Usage — `usage_` (2 tools)

Tool Description

usage_list List available usage topics.

usage_show

Show usage examples for a scitex module (plt, stats, session, etc.).

Parameters & Returns ▸

Name	Type	Default
`topic`	`string`	`''`

Returns: str

Writer / LaTeX — `writer_` (38 tools)

Tool Description

writer_add_bibentry

Add a BibTeX entry to a bibliography file.

Parameters & Returns ▸

Name	Type	Default
`project_dir`	`string`	required
`bibtex_entry`	`string`	required
`bibfile`	`string`	`'custom.bib'`
`deduplicate`	`boolean`	`True`

Returns: dict

writer_add_claim

Add or update a claim in 00_shared/claims.json.

Parameters & Returns ▸

Name	Type	Default
`project_dir`	`string`	required
`claim_id`	`string`	required
`claim_type`	`string`	required
`value`	`object`	required
`context`	`string`	`None`
`session_id`	`string`	`None`
`output_file`	`string`	`None`
`output_hash`	`string`	`None`
`test`	`string`	`None`

Returns: dict

writer_add_figure

Add a figure (copy image + create caption) to the project.

Parameters & Returns ▸

Name	Type	Default
`project_dir`	`string`	required
`name`	`string`	required
`image_path`	`string`	required
`caption`	`string`	required
`label`	`string`	`None`
`doc_type`	`string`	`'manuscript'`

Returns: dict

writer_add_table

Add a new table (CSV + caption) to the project.

Parameters & Returns ▸

Name	Type	Default
`project_dir`	`string`	required
`name`	`string`	required
`csv_content`	`string`	required
`caption`	`string`	required
`label`	`string`	`None`
`doc_type`	`string`	`'manuscript'`

Returns: dict

writer_clone_project

Create a new LaTeX manuscript project from template.

Parameters & Returns ▸

Name	Type	Default
`project_dir`	`string`	required
`git_strategy`	`string`	`'child'`
`branch`	`string`	`None`
`tag`	`string`	`None`

Returns: dict

writer_compile_content

Compile raw LaTeX content to PDF with color mode support.

Parameters & Returns ▸

Name	Type	Default
`latex_content`	`string`	required
`project_dir`	`string`	`None`
`color_mode`	`string`	`'light'`
`name`	`string`	`'content'`
`timeout`	`integer`	`60`
`keep_aux`	`boolean`	`False`

Returns: dict

writer_compile_manuscript

Compile manuscript LaTeX document to PDF.

Parameters & Returns ▸

Name	Type	Default
`project_dir`	`string`	required
`timeout`	`integer`	`300`
`no_figs`	`boolean`	`False`
`no_tables`	`boolean`	`False`
`no_diff`	`boolean`	`False`
`draft`	`boolean`	`False`
`dark_mode`	`boolean`	`False`
`quiet`	`boolean`	`False`
`verbose`	`boolean`	`False`
`engine`	`string`	`None`

Returns: dict

writer_compile_revision

Compile revision document to PDF with optional change tracking.

Parameters & Returns ▸

Name	Type	Default
`project_dir`	`string`	required
`track_changes`	`boolean`	`False`
`timeout`	`integer`	`300`
`no_diff`	`boolean`	`True`
`draft`	`boolean`	`False`
`dark_mode`	`boolean`	`False`
`quiet`	`boolean`	`False`
`engine`	`string`	`None`

Returns: dict

writer_compile_supplementary

Compile supplementary materials LaTeX document to PDF.

Parameters & Returns ▸

Name	Type	Default
`project_dir`	`string`	required
`timeout`	`integer`	`300`
`no_figs`	`boolean`	`False`
`no_tables`	`boolean`	`False`
`no_diff`	`boolean`	`False`
`draft`	`boolean`	`False`
`dark_mode`	`boolean`	`False`
`quiet`	`boolean`	`False`
`engine`	`string`	`None`

Returns: dict

writer_convert_figure

Convert figure between formats (e.g., PDF to PNG).

Parameters & Returns ▸

Name	Type	Default
`input_path`	`string`	required
`output_path`	`string`	required
`dpi`	`integer`	`300`
`quality`	`integer`	`95`

Returns: dict

writer_csv_to_latex

Convert CSV file to LaTeX table format.

Parameters & Returns ▸

Name	Type	Default
`csv_path`	`string`	required
`output_path`	`string`	`None`
`caption`	`string`	`None`
`label`	`string`	`None`
`longtable`	`boolean`	`False`

Returns: dict

writer_export_manuscript

Export manuscript as arXiv-ready tarball.

Parameters & Returns ▸

Name	Type	Default
`project_dir`	`string`	required
`output_dir`	`string`	`None`
`format`	`string`	`'arxiv'`

Returns: dict

writer_export_overleaf

Export a scitex-writer project as Overleaf-compatible ZIP.

Parameters & Returns ▸

Name	Type	Default
`project_dir`	`string`	`'.'`
`output_path`	`string`	`None`
`dry_run`	`boolean`	`False`

Returns: dict

writer_format_claim

Render a claim as a formatted LaTeX string.

Parameters & Returns ▸

Name	Type	Default
`project_dir`	`string`	required
`claim_id`	`string`	required
`style`	`string`	`'nature'`

Returns: dict

writer_get_bibentry

Get a specific BibTeX entry by citation key.

Parameters & Returns ▸

Name	Type	Default
`project_dir`	`string`	required
`citation_key`	`string`	required

Returns: dict

writer_get_claim

Get full details of a specific claim including all style renderings.

Parameters & Returns ▸

Name	Type	Default
`project_dir`	`string`	required
`claim_id`	`string`	required

Returns: dict

writer_get_pdf

Get path to compiled PDF for a document type.

Parameters & Returns ▸

Name	Type	Default
`project_dir`	`string`	required
`doc_type`	`string`	`'manuscript'`

Returns: dict

writer_get_project_info

Get writer project structure and status information.

Parameters & Returns ▸

Name	Type	Default
`project_dir`	`string`	required

Returns: dict

writer_guideline_build

Build editing prompt by combining guideline with draft text.

Parameters & Returns ▸

Name	Type	Default
`section`	`string`	required
`draft`	`string`	required

Returns: str

writer_guideline_get

Get IMRAD writing guideline for a manuscript section.

Parameters & Returns ▸

Name	Type	Default
`section`	`string`	required

Returns: str

writer_guideline_list List available IMRAD writing guideline sections.

writer_import_overleaf

Import an Overleaf ZIP export into a scitex-writer project.

Parameters & Returns ▸

Name	Type	Default
`zip_path`	`string`	required
`output_dir`	`string`	`None`
`project_name`	`string`	`None`
`dry_run`	`boolean`	`False`
`force`	`boolean`	`False`

Returns: dict

writer_latex_to_csv

Convert LaTeX table to CSV format.

Parameters & Returns ▸

Name	Type	Default
`latex_path`	`string`	required
`output_path`	`string`	`None`
`table_index`	`integer`	`0`

Returns: dict

writer_list_bibentries

List all BibTeX entries in the project or specific file.

Parameters & Returns ▸

Name	Type	Default
`project_dir`	`string`	required
`bibfile`	`string`	`None`

Returns: dict

writer_list_bibfiles

List all bibliography files in the project.

Parameters & Returns ▸

Name	Type	Default
`project_dir`	`string`	required

Returns: dict

writer_list_claims

List all claims in the project.

Parameters & Returns ▸

Name	Type	Default
`project_dir`	`string`	required

Returns: dict

writer_list_document_types List available document types in a writer project.

writer_list_figures

List all figures in a writer project directory.

Parameters & Returns ▸

Name	Type	Default
`project_dir`	`string`	required
`extensions`	`array`	`None`

Returns: dict

writer_list_tables

List all tables in a writer project.

Parameters & Returns ▸

Name	Type	Default
`project_dir`	`string`	required
`doc_type`	`string`	`'manuscript'`

Returns: dict

writer_merge_bibfiles

Merge all .bib files into one, with optional deduplication.

Parameters & Returns ▸

Name	Type	Default
`project_dir`	`string`	required
`output_file`	`string`	`'bibliography.bib'`
`deduplicate`	`boolean`	`True`

Returns: dict

writer_pdf_to_images

Render PDF pages as images.

Parameters & Returns ▸

Name	Type	Default
`pdf_path`	`string`	required
`output_dir`	`string`	`None`
`pages`	`integer`	`None`
`dpi`	`integer`	`600`
`format`	`string`	`'png'`

Returns: dict

writer_prompts_asta

Generate AI2 Asta prompt for finding related papers or collaborators.

Parameters & Returns ▸

Name	Type	Default
`project_path`	`string`	`'.'`
`search_type`	`string`	`'related'`

Returns: str

writer_remove_bibentry

Remove a BibTeX entry by citation key.

Parameters & Returns ▸

Name	Type	Default
`project_dir`	`string`	required
`citation_key`	`string`	required

Returns: dict

writer_remove_claim

Remove a claim from 00_shared/claims.json.

Parameters & Returns ▸

Name	Type	Default
`project_dir`	`string`	required
`claim_id`	`string`	required

Returns: dict

writer_remove_figure

Remove a figure (image + caption) from the project.

Parameters & Returns ▸

Name	Type	Default
`project_dir`	`string`	required
`name`	`string`	required
`doc_type`	`string`	`'manuscript'`

Returns: dict

writer_remove_table

Remove a table (CSV + caption) from the project.

Parameters & Returns ▸

Name	Type	Default
`project_dir`	`string`	required
`name`	`string`	required
`doc_type`	`string`	`'manuscript'`

Returns: dict

writer_render_claims

Generate 00_shared/claims_rendered.tex from claims.json.

Parameters & Returns ▸

Name	Type	Default
`project_dir`	`string`	required

Returns: dict

writer_update_project

Update engine files of a scitex-writer project to the latest version.

Parameters & Returns ▸

Name	Type	Default
`project_dir`	`string`	required
`branch`	`string`	`None`
`tag`	`string`	`None`
`dry_run`	`boolean`	`False`
`force`	`boolean`	`False`

Returns: dict

🤖 MCP Server

MCP Server Overview #

Connect a Client #

1. Install

2. Configure Claude Desktop / Claude Code

3. That's it

Claude Desktop / Claude Code (claude_desktop_config.json)

Python (fastmcp client)

Authentication #

Required Scope

Configuration #

Tool Group Toggles

Example: Minimal Setup

Using .env.d Files

Available Tools #

Audio — audio_ (1 tools)

Capture — capture_ (1 tools)

CLEW Pipelines — clew_ (6 tools)

Crossref — crossref_ (15 tools)

Datasets — dataset_ (1 tools)

Developer — dev_ (9 tools)

Introspect — introspect_ (12 tools)

Linter — linter_ (1 tools)

OpenAlex — openalex_ (4 tools)

Plotting — plt_ (71 tools)

Project Files — project_ (4 tools)

Scholar — scholar_ (22 tools)

Social — social_ (1 tools)

Statistics — stats_ (10 tools)

Templates — template_ (4 tools)

UI / Notifications — ui_ (2 tools)

Usage — usage_ (2 tools)

Writer / LaTeX — writer_ (38 tools)

Claude Desktop / Claude Code (`claude_desktop_config.json`)

Audio — `audio_` (1 tools)

Capture — `capture_` (1 tools)

CLEW Pipelines — `clew_` (6 tools)

Crossref — `crossref_` (15 tools)

Datasets — `dataset_` (1 tools)

Developer — `dev_` (9 tools)

Introspect — `introspect_` (12 tools)

Linter — `linter_` (1 tools)

OpenAlex — `openalex_` (4 tools)

Plotting — `plt_` (71 tools)

Project Files — `project_` (4 tools)

Scholar — `scholar_` (22 tools)

Social — `social_` (1 tools)

Statistics — `stats_` (10 tools)

Templates — `template_` (4 tools)

UI / Notifications — `ui_` (2 tools)

Usage — `usage_` (2 tools)

Writer / LaTeX — `writer_` (38 tools)