pip install scitex                     # Core only (minimal)
pip install scitex[plt,stats,scholar]  # Typical research setup
pip install scitex[plt]                # Publication-ready figures (figrecipe)
pip install scitex[stats]              # Statistical testing (23+ tests)
pip install scitex[scholar]            # Literature search, PDF download, BibTeX enrichment
pip install scitex[writer]             # LaTeX manuscript compilation
pip install scitex[audio]              # Text-to-speech
pip install scitex[ai]                 # LLM APIs (OpenAI, Anthropic, Google) + ML tools
pip install scitex[dataset]            # Scientific datasets (DANDI, OpenNeuro, PhysioNet)
pip install scitex[browser]            # Web automation (Playwright)
pip install scitex[capture]            # Screenshot capture and monitoring
pip install scitex[cloud]              # Cloud platform integration

Requires Python 3.10+. We recommend uv for fast installs.

pip install scitex[all] pulls the full 33-package ecosystem plus heavy extras (playwright browsers, torch, jax, pymupdf, Apptainer/Docker integrations, etc.). On a typical connection it can take 30–90 minutes — more if PyPI is slow. Common fixes:

# 1. Extend pip's socket timeout (default 15s) — stops big wheel pulls from aborting mid-stream
pip install --timeout 600 --retries 5 "scitex[all]"

# 2. Use uv — 10-30× faster resolver, far better retry behaviour
pip install uv && uv pip install "scitex[all]"

# 3. Install in groups if a single run keeps failing
pip install scitex[io,stats,plt]         # core analysis layer first
pip install scitex[scholar,writer]       # research layer
pip install scitex[audio,browser,dataset,cloud]   # heavy extras last

# 4. Mirror — for networks where pypi.org is unreliable
pip install -i https://pypi.tuna.tsinghua.edu.cn/simple "scitex[all]"

If a single dep hangs, identify it with pip install -v and install that package alone with --no-deps, then resume the full install.

One decorator gives you: auto-CLI, YAML config injection, random seed fixation, structured output, and logging.

import scitex as stx
import numpy as np

@stx.session
def main(
    data_path: str = "./data.csv",   # --data-path data.csv
    n_samples: int = 100,            # --n-samples 200
    CONFIG=stx.session.INJECTED,     # Aggregated ./config/*.yaml
    plt=stx.session.INJECTED,        # Pre-configured matplotlib
    logger=stx.session.INJECTED,     # Session logger
):
    """Analyze data. Docstring becomes --help text."""
    
    # Load
    data = stx.io.load(data_path)
    
    # Demo data
    x = np.linspace(0, 2 * np.pi, n_samples)
    y = np.sin(x) + np.random.randn(n_samples) * 0.1
    
    # FigRecipe Plot
    fig, ax = stx.plt.subplots()
    ax.plot(x, y)
    ax.set_xyt("Time", "Amplitude", "Noisy Sine Wave")
    
    # Save sine.png + sine.csv with logging message
    stx.io.save(fig, "sine.png")
    
    return 0

if __name__ == "__main__":
    main()

$ python script.py --data-path experiment.csv --n-samples 200
$ python script.py --help
# usage: script.py [-h] [--data-path DATA_PATH] [--n-samples N_SAMPLES]
# Analyze data. Docstring becomes --help text.

script_out/FINISHED_SUCCESS/2026-03-18_14-30-00_Z5MR/
├── sine.png, sine.csv         # Figure + auto-exported plot data
├── CONFIGS/CONFIG.yaml        # Frozen parameters
└── logs/{stdout,stderr}.log   # Execution logs

The injected CONFIG is a DotDict merging YAML user configs with session-resolved keys:

Use CONFIG.SDIR_RUN / "results.csv" to re-load a file saved earlier in the same session. A frozen copy of CONFIG is persisted to CONFIG.SDIR_RUN/CONFIGS/{CONFIG.yaml,CONFIG.pkl} so any run is fully auditable. See the Session config docs for the full reference.

import scitex as stx

# Save and load -- format detected from extension.
# symlink_from_cwd=True drops a symlink at cwd so round-trip by filename works;
# without it, save() routes to <script>_out/ and load() must use an absolute path.
stx.io.save(df, "results.csv", symlink_from_cwd=True)
df = stx.io.load("results.csv")

stx.io.save(arr, "data.npy", symlink_from_cwd=True)
arr = stx.io.load("data.npy")

stx.io.save(fig, "figure.png")       # Also exports figure data as CSV
stx.io.save(config, "config.yaml")
stx.io.save(model, "model.pkl")

# Aggregate ./config/*.yaml into a single DotDict
CONFIG = stx.io.load_configs(config_dir="./config")
print(CONFIG.MODEL.hidden_size)      # Dot-notation access

# Register custom formats
@stx.io.register_saver(".custom")
def save_custom(obj, path, **kw):
    with open(path, "w") as f:
        f.write(str(obj))

@stx.io.register_loader(".custom")
def load_custom(path, **kw):
    with open(path) as f:
        return f.read()

Supports: CSV, JSON, YAML, TOML, HDF5, NPY, NPZ, PKL, PNG, JPG, SVG, PDF, Excel, Parquet, Zarr, INI, TXT, MAT, WAV, MP3, BibTeX, and more.

Built-in features: Auto directory creation, path resolution to <script_name>_out/, symlinks (symlink_from_cwd=True), save logging with file size, and Clew hash tracking.

Powered by figrecipe. Figures are reproducible nodes in the Clew verification DAG -- scientific data and visual style are decomposed, so figures can be restyled (fonts, colors, layout) without altering the underlying data hash. Every figure auto-exports its data as CSV + a YAML recipe for exact reproduction.

import scitex as stx
fig, axes = stx.plt.subplots(1, 3)
axes[0].stx_line(x, y)
axes[0].set_xyt("Time", "Value", "Line")

axes[1].stx_violin([g1, g2, g3])
axes[1].set_xyt("Group", "Score", "Violin")

axes[2].stx_heatmap(corr_matrix)
axes[2].set_xyt("X", "Y", "Heatmap")
stx.io.save(fig, "analysis.png")  # Saves analysis.png + analysis.csv + analysis.yaml

# Restyle without changing data (hash stays valid for Clew verification)
stx.plt.reproduce("analysis.yaml", style="nature")

import scitex as stx
result = stx.stats.run_test("ttest_ind", group1, group2, return_as="dataframe")
# Returns: p-value, effect size (Cohen's d), CI, normality check, power
recommendations = stx.stats.recommend_tests(data)
stx.stats.annotate(ax, test=result, style="apa")   # stars + "t(58) = 2.34, p = .021, d = 0.60" on a matplotlib Axes

Search, download, enrich papers. Backed by local CrossRef (167M+) and OpenAlex (250M+) databases.

import scitex as stx
scholar = stx.scholar.Scholar()                             # lazy-load library
papers = scholar.process_papers(["neural oscillations working memory"])
scholar.download_pdfs_from_dois(["10.1038/s41586-024-07804-3"])
scholar.enrich_papers(bibtex_path="references.bib")

scitex scholar crossref-scitex search "neural oscillations" --abstracts
scitex scholar fetch --from-bibtex references.bib --project myproject

import scitex as stx
stx.writer.compile.manuscript("paper/")                     # latexmk wrapper
stx.writer.figures.add("paper/", "results.png", caption="Main results")
stx.writer.tables.add("paper/", "stats.csv", caption="Statistical summary")

Get notified when experiments finish -- via desktop, phone call, SMS, or email -- with automatic fallback.

import scitex as stx
stx.notification.alert("Experiment complete: accuracy = 94.2%")
stx.notification.call("Training diverged -- loss is NaN")
stx.notification.sms("GPU job finished on node-42")

@stx.session(notify=True)   # Notifies on completion or failure
def main(CONFIG=stx.session.INJECTED): ...

As AI agents produce research at scale, the question shifts from "could this be reproduced?" to "has this been verified?". Clew builds a SHA-256 hash-chain DAG linking every manuscript claim back to source data.

import scitex as stx

# Every stx.io.load/save automatically records file hashes -- zero config
stx.clew.status()                          # {'verified': 12, 'mismatched': 0, 'missing': 0}
stx.clew.chain("results/figure1.png")      # Trace one file back to source data
stx.clew.dag(claims=True)                  # Verify all manuscript claims

# Register traceable assertions
stx.clew.add_claim(
    file_path="paper/main.tex", claim_type="statistic", line_number=142,
    claim_value="t(58) = 2.34, p = .021",
    source_session="2026-03-18_14-30-00_Z5MR", source_file="results/stats.csv",
)

stx.clew.mermaid(claims=True)              # Visualize provenance DAG

L1 hash comparison (ms) / L2 sandbox re-execution (min) / L3 registered timestamp proof (optional).

_{Figure 2. Clew verification DAG -- green nodes are verified (hash match), red nodes have mismatches. Each node shows its SHA-256 hash prefix.}

import scitex as stx
stx.audio.speak("Training complete. Accuracy ninety-four percent.")
stx.audio.speak("Offline only", backend="pyttsx3")                  # force offline
stx.audio.speak("Report", output_path="report.mp3", play=False)     # TTS → file

Backends fall back automatically: ElevenLabs (paid, highest) → LuxTTS (offline, 48 kHz, voice-cloning) → gTTS (free online) → pyttsx3 (offline espeak).

import scitex as stx
ds = stx.dataset.neuroscience.openneuro.fetch_all_datasets(max_datasets=10)
stx.dataset.neuroscience.dandi.fetch_all_datasets(max_datasets=10)
hits = stx.dataset.search_datasets(ds, text_query="phase-amplitude coupling")

Uniform API across neuroscience / biomedical / clinical-trial repositories.

import scitex as stx
stx.container.apptainer.build(def_name="recipe")        # versioned SIF
stx.container.apptainer.switch_version("2.19.5")        # atomic active-SIF flip
stx.container.apptainer.rollback()                      # revert to previous
snap = stx.container.env_snapshot()                     # full env for papers

Reproducible HPC containers — build, version, rollback, env-snapshot for manuscripts.

import scitex as stx
stx.tunnel.setup(port=8888, bastion_server="gw.example.com")
stx.tunnel.status()                                     # {"8888": "active"}

NAT traversal for lab machines — autossh-backed systemd service.

import scitex as stx
issues = stx.linter.lint_file("src/")
for i in issues:
    print(f"{i.filepath}:{i.line} [{i.rule.id}] {i.message}")

Lints SciTeX projects for ecosystem conventions (stx.io.save usage, CONFIGS naming, matplotlib prefs, import hygiene). Complements ruff/flake8.

import scitex as stx
rng = stx.repro.RandomStateManager(seed=42)             # seeds random + numpy + torch + tf
run_id = stx.repro.gen_ID()                             # "20260423_2155_abc12345"
digest = stx.repro.hash_array(np_array)                 # deterministic SHA

One call seeds every RNG; generates experiment-run IDs; hashes arrays for fingerprinting.

import scitex as stx
results = stx.parallel.run(download, [(u,) for u in urls], n_jobs=-1)

Drop-in parallel map for I/O-bound work — HTTP fetches, file reads, API calls. tqdm progress bar built-in.

import scitex as stx
root = stx.path.find_git_root()                     # walk up for .git/
out = stx.path.get_spath("results.csv")             # → {script}_out/results.csv
stx.path.create_relative_symlink(src, dst)          # relative (portable) symlink
latest = stx.path.find_latest(".", "model_", ".pt") # model_v003.pt (highest version)
stx.path.fix_broken_symlinks("dir/", remove=True)   # cleanup dangling links

Auto-routes saves to {script}_out/ and resolves session-scoped paths so @stx.session scripts produce dated, hash-trackable output dirs with no boilerplate.

import scitex as stx
logger = stx.logging.getLogger(__name__)
logger.success("Training converged at epoch 87")    # SUCCESS level (custom)
logger.fail("Validation loss diverged")             # FAIL level (custom)

# Structured warnings with SciTeX categories
stx.logging.warn_deprecated("old_api", replacement="new_api", version="3.0")
stx.logging.warn_data_loss("NaN values dropped in column 'bp'")

# Typed exceptions (30+ subclasses of SciTeXError)
raise stx.logging.ShapeError("expected (N, 2), got (N, 3)")

# Tee stdout/stderr to a log file
with stx.logging.Tee("run.log"):
    main()                                           # prints go to screen + file

Extends stdlib logging with SUCCESS/FAIL levels, a 30+ class exception tree (IOError/ShapeError/ConfigKeyError/...), structured warning categories, and tee-to-file. SCITEX_LOGGING_LEVEL env var sets default at import.

import scitex as stx, numpy as np

db = stx.db.SQLite3("experiments.db")
with db:                                             # context-manager transaction
    db.execute("CREATE TABLE IF NOT EXISTS runs (id TEXT, acc REAL)")
    db.save_array("weights_epoch_87", np.random.rand(1024, 1024))   # compressed BLOB

df = db.to_df("runs")                                # pandas round-trip
w = db.load_array("weights_epoch_87")                # typed ndarray back
db.check_health()                                    # integrity + schema drift
stx.db.delete_duplicates(conn, "runs", columns=["id"])

SQLite / PostgreSQL clients with first-class compressed-ndarray BLOBs, dataframe round-trips, health checks, and duplicate removal. Drop-in replacement for hand-rolling pickle → BLOB storage or SQLAlchemy Core when you don't need an ORM.

import scitex as stx, asyncio

async def grab_pdf():
    async with stx.browser.SyncBrowserSession() as session:
        page = await session.new_page()
        await page.goto("https://journal.example/article/123")
        await stx.browser.click_with_fallbacks_async(
            page, ["button.download-pdf", "a[href$='.pdf']"]   # fall through selectors
        )
        await stx.browser.save_as_pdf_async(page, "article.pdf")

asyncio.run(grab_pdf())

Playwright wrappers with: Chrome-PDF-viewer download helper, popup/cookie dismissers (close_popups_async, PopupHandler), cursor/click/step overlays for debug video recording, console-log collectors, test-failure artifact capture. Drop-in replacement for raw Playwright scripts + stealth plugins.

See docs/05_ADDITIONAL_MODULES.md for full examples.

scitex --help-recursive                  # Show all commands
scitex scholar crossref-scitex search "topic"   # Search literature (CrossRef 167M+)
scitex scholar fetch "10.1038/..."       # Download paper by DOI
scitex stats recommend                   # Suggest statistical tests
scitex clew status                       # Project verification overview
scitex clew dag --claims                 # Verify all manuscript claims
scitex audio speak "Analysis complete"   # Text-to-speech
scitex notification send "Job finished"  # Multi-backend notification
scitex template clone research my_proj   # Scaffold a project
scitex dev ecosystem list                # Check ecosystem versions
scitex mcp list-tools                    # List all MCP tools (323)

Full CLI reference

Turn AI agents into autonomous researchers via MCP.

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

Full MCP reference

Each package exposes the ecosystem via up to six interfaces: Python library, CLI, MCP tools, Claude Code skills, hooks, and HTTP. Ratings: ⭐⭐⭐ = primary / canonical surface, ⭐⭐ = strong secondary, ⭐ = thin, — = not provided. Packages are grouped by their primary interface — the one users should reach for first.

Python-first (library API is primary)

CLI-first

MCP-first

Hook-first

Mixed (multiple equally-primary interfaces)