CHANGELOG.md

Changelog

All notable changes to SciTeX will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

Changed

• _LazyModule error messages now name the canonical attribute home when one exists. When scitex.<short>.<attr> lookup fails because <short> is not installed (extras gate) or because <short> is installed but doesn't carry <attr> (the "phantom" case), the resulting error now routes through a curated redirect map (scitex._canonical_redirects). Example: scitex.gen.load_configs (which doesn't exist in scitex_gen) used to raise ImportError: scitex.gen requires additional dependencies. Install with: pip install scitex[gen] — telling the user to pip-install a heavy extras package (torch + CUDA + …) that doesn't even contain the function. Now it raises ImportError: scitex.gen.load_configs is not available here; the canonical location is scitex.io.load_configs (already installed by the umbrella core — no extra needed). Change your import to from scitex.io import load_configs``. Same upgrade for the AttributeError path when the module loaded fine but doesn't have the attribute. Seed redirect entries (gen → io / session / dict / str / etc / context / types) come from proj-paper-ripple-wm's PR#4a misdirected- callsite audit (2026-06-07) — the mngs.gen kitchen-sink namespace was split across multiple scitex peers, leaving hundreds of callsites pointing at `scitex.gen.` for `X` that now lives elsewhere.
• pip install hints now use {sys.executable} -m pip. The previous bare pip install scitex[...] hint risked installing into a system-level Python when the user had an active virtualenv. Switched to {sys.executable} -m pip install 'scitex[<extras>]' so the install lands in the venv the user is currently running. Quotes the extras spec so shells that glob square brackets (zsh) don't choke. Applied to both _LazyModule.__getattr__'s ImportError fallback and the __dir__() missing-module warning.
• scitex.security repointed to scitex_audit.github per ADR-0001 (scitex-dev #139, Accepted 2026-06-07). scitex-security was absorbed into scitex-audit 0.2.0; the 5 public symbols (check_github_alerts, save_alerts_to_file, get_latest_alerts_file, format_alerts_report, GitHubSecurityError) now live in scitex_audit.github. The umbrella _LazyModule("security", external="scitex_audit.github") resolution
  • the external_alias_map "security" entry both move atomically. (#322)
• click promoted to a hard core dependency (click>=8.0.0 in [project.dependencies]). The scitex-pkg console-script (scitex.cli.pkg:pkg) does an unguarded module-load import click, so PS-213 (console-script-deps-must-be-core, scitex-dev v0.17.10+) requires click in core — bare pip install scitex followed by scitex-pkg --help no longer raises ModuleNotFoundError. (#328)
• Umbrella sub-package pins bumped to PyPI latest to satisfy PS-170 (audit-umbrella-pins freshness gate) — unblocks the tests matrix that was red on main since 2026-06-09: scitex-dev 0.17.4 → 0.17.10, scitex-io 0.2.20 → 0.3.1, scitex-stats 0.2.23 → 0.2.24, scitex-db 0.1.11 → 0.1.12, scitex-msword 0.2.0 → 0.3.2, scitex-dataset 0.3.10 → 0.4.0, scitex-writer 2.17.3 → 2.17.5, scitex-agent-container 0.21.9 → 0.21.11. 18 occurrences updated across [project.dependencies], module extras, [dev], and tooling extras. (#329)

Added

• scitex._canonical_redirects module — private helper carrying the (short, attr) → canonical_short map and the two hint builders (missing_extras_hint, phantom_attr_hint). Extracted from scitex.re_export to keep the latter under the 512-line file cap. Pinned by 27 tests across tests/scitex/test_canonical_redirects.py and tests/scitex/test_lazymodule_redirects.py.
• [security] extra now installs scitex-audit>=0.2.0 (was empty). Brings the umbrella extras into compliance with skill 03 §8 "every module MUST have an extra listing its standalone package". (#322)
• scitex-audit pinned to ==0.2.0 in main deps, [audit], [dev], and [all]. (#322)

Removed

• scitex-security==0.1.4 from main deps and [all] — absorbed into scitex-audit. The deprecated scitex-security 0.2.0 PyPI shim is NOT pulled by the umbrella; users who explicitly depend on the old package still get a DeprecationWarning redirecting them to scitex_audit.github. (#322)

Migration

• from scitex_security import X → from scitex_audit.github import X, or just scitex.security.X (now resolves to the same SSOT).
• scitex-security check OWNER/REPO --save → scitex-audit github --repo OWNER/REPO --save. The legacy console-script hard-errors with a redirect per CLI-deprecation skill 11 §5.
• ~/.scitex/security/ auto-symlinks to ~/.scitex/audit/github-alerts/ on first import of scitex_audit (one-shot, marker-gated).

[2.30.0] - 2026-05-31

Changed

• Umbrella decomposition campaign: scitex.<x> modules are now thin branded aliases to their owning standalone packages instead of in-tree shim directories. Dropped the in-tree shim dirs for errors (→ scitex_logging), torch (→ scitex_linalg), stats (→ scitex_stats), diagram (→ figrecipe.diagram), clew (→ scitex_clew), tunnel (→ scitex_ssh), rng/verify. scitex.utils is now a thin re-export aggregator that distributes implementations to their owning packages. Env-loading delegates to scitex-config.
• Linter: scitex.linter (and the more-consistent scitex.dev.linter) now resolve to the real engine scitex_dev.linter. Two stale registrations that kept routing to the archived scitex_linter distribution were removed (#306).

Removed

• scitex-core dependency: dropped from pyproject.toml; all former scitex-core contents are standalonized. Enables public-archiving of scitex-core. (#299)
• scitex.utils.verify_scitex_format: removed; superseded by the scitex-dev linter. (#300)
• Dropped 10 redundant legacy MCP bridge files now covered by registry auto-mount.

Fixed

• CI test matrix: greened the chronic-red umbrella matrix — switched to uv resolver, CPU-only torch, dropped coverage-triggered segfaults, and added a retry-on-incomplete-report guard for the non-deterministic C-extension shutdown segfault. (#303, #304, #305)
• Bumped sibling pins for PS-170 freshness (scitex-dev 0.15.0, et al.).

[2.29.3] - 2026-05-23

Fixed

• Dependency pins: Restore >= minima for sibling scitex-* deps (was exact ==, which referenced unpublished versions like scitex-config==0.3.3 and broke pip install scitex with ResolutionImpossible). Fixes #282. The 2.29.0 and 2.29.1 PyPI releases shipped the broken == pins; 2.29.3 is the corrected release.

[2.28.13] - 2026-04-30

Changed

• Umbrella simplification (Tier 2 batch 6): Collapsed 8 leaf-duplicate dirs (benchmark, context, cv, introspect, msword, os, security, tex) into eager-mounted external pointers. Trimmed ~hundreds of LOC from src/scitex/.

Fixed

• Import-path regression: Re-added 4 tiny shim dirs (ml, reproduce, rng, verify) so import scitex.ml etc. continue to work alongside the existing scitex.<aliased> proxy. Each shim emits a DeprecationWarning then re-exports from the canonical location (scitex.ai, scitex.repro, scitex.clew).

[2.28.5 – 2.28.12] - 2026-04-30

Changed

• Umbrella simplification (Tier 1 + Tier 2 batches 1–5): Collapsed 21 pure re-export directories — dt, etc, gists, audit, compat, repro, app, scholar, dict, notebook, str, logging, browser, parallel, path, db, audio, types, template, plus 4 deprecated alias dirs — into eager-mounted external pointers in src/scitex/__init__.py. ~8,000 lines removed across 8 PyPI releases.
• Pin tightening: Tightened >= floors for ~30 standalone packages whose APIs are now load-bearing for the umbrella (one PyPI install pulls a known-compatible matrix).

[2.28.0 – 2.28.4] - 2026-04-28

Fixed

• License classifier: Drop legacy License :: OSI Approved trove classifier — PEP 639 + setuptools ≥80 reject it (E5C13).
• DSP/gen edge cases: gen.to_even handles 0-d numpy/torch arrays via .item(); dsp.design_filter coerces tensor fs to scalar before int(); Hilbert + signal_fn cascade preserves float64 dtype.
• Stats compatibility shim: Register scitex_stats._utils at scitex.stats._utils sys.modules path so downstream from scitex.stats._utils import X keeps working post-extraction.

[2.27.0 – 2.27.3] - 2026-03-25 — 2026-03-29

Added

• Module-level _skills/: 302 sub-skill files across 70 modules, surfacing per-API guidance to MCP clients.
• Skills CLI: scitex skills get all dumps every sub-skill, not just SKILL.md.
• Notebook: Unified migration mode for Jupyter → SciTeX conversion.
• Template: list-code-templates CLI command.

Changed

• Skills layout: Cleaned legacy skills/ directory; module-level _skills/<short>/ is now the source of truth (later moved to scitex-dev in 2.28.x).
• CLI skills export: Clean --param handling, frontmatter normalised.

[2.26.0] - 2026-03-23

Added

• Browser: save-as-pdf tool with cookie-banner dismissal; playwright-cli runtime detection.
• Browser skills: First-class _skills/browser/ set.

Fixed

• FastMCP compatibility: mount(..., namespace=) for FastMCP 3.x and mount(..., prefix=) for 2.x via _compat.safe_mount.

[2.25.0 – 2.25.10] - 2026-03 (multiple patches)

Added

• Lazy-loaded module skeletons for introspect, sh, os, cv, ui, git, schema, canvas, security, benchmark, bridge, browser, compat, cli.
• scitex-pkg audit CLI for venv drift detection + auto-fix.

Fixed

• Numerous lazy-loader, optional-dep, and deprecation-warning fixes (see git log between v2.25.0 and v2.26.0 for the full punch list).

[2.22.0 – 2.24.0] - 2026-03

Added

• First wave of standalone-package extractions (#51, #206): etc, compat, audit, parallel, types, gists, path, repro, db, scholar, dict, logging, browser, str and others — umbrella now delegates to dedicated PyPI packages with try/except fallbacks for unpublished ones.
• Notebook unified migration mode, template list-code-templates, scholar clean_abstract re-export.

Fixed

• Default autolayout=False in plt + session (#214); CLI warns when top-level --json is given with a subcommand (#211); session final-message differentiated by exit_status (#145); decorators lazy-import joblib; io lazy-imports flask (#441); LazyGroup tolerant of optional-dep leaks (#279).

[2.21.0] - 2026-02-27

Added

• Media classify: Add graphviz (.dot, .gv) and .mermaid extensions to media type detection
• MCP handlers: Project handler improvements

[2.19.3] - 2026-02-24

Added

• scitex.git.ls_remote(): Get remote ref commit hash via git ls-remote
• scitex.git.get_head_hash(): Get local repo HEAD commit hash
• Smart template cache: Validates cache by comparing local vs remote commit hashes; auto-invalidates stale cache

[2.19.0] - 2026-02-22

Added

• build_from_dois(): Build citation networks from multiple seed DOIs with batch scoring
• build_from_query(): Build citation networks from text queries via local DB search
• Batch SQL optimization: get_combined_similarity_scores_batch() — O(4) queries instead of O(4N)
• HTTP parallel batch: ThreadPoolExecutor parallelism for HTTP-mode batch scoring (up to 20 workers)
• is_seed flag: PaperNode now tracks whether it's a seed paper
• seed_dois field: CitationGraph stores all seed DOIs for multi-seed graphs

[Unreleased]

Changed

• Module Refactoring: Cleaned up root-level namespace, moved items to appropriate modules
  • INJECTED sentinel → scitex.session.INJECTED (backward-compatible with deprecation warning)
  • show_install_guide() → scitex.dev.show_install_guide() (backward-compatible with deprecation warning)
  • Diagram class → scitex.diagram.Diagram (backward-compatible with deprecation warning)
  • ci() (confidence interval) → scitex.stats.descriptive.ci (also available via stx.gen.ci)

Added

• New Lazy Modules: Added missing modules to root namespace
  • introspect, sh, os, cv, ui, git, schema, canvas, security, benchmark, bridge, browser, compat, cli

Migration Map

Before (Deprecated)	After (Recommended)
stx.INJECTED	stx.session.INJECTED
stx.show_install_guide()	stx.dev.show_install_guide()
stx.Diagram	stx.diagram.Diagram
stx.gen.ci()	stx.stats.descriptive.ci()
stx.gen.inspect_module()	stx.introspect.inspect_module()
stx.gen.check_host()	stx.os.check_host()
stx.gen.is_host()	stx.os.is_host()
stx.gen.verify_host()	stx.os.verify_host()
stx.gen.detect_environment()	stx.context.detect_environment()
stx.gen.is_notebook()	stx.context.is_notebook()
stx.gen.is_script()	stx.context.is_script()
stx.gen.get_notebook_path()	stx.context.get_notebook_path()
stx.gen.run_shellcommand()	stx.sh.run_shellcommand()
stx.gen.run_shellscript()	stx.sh.run_shellscript()
stx.gen.title_case()	stx.str.title_case()

[2.14.0] - 2026-01-15

Added

• Unified MCP Server: Single FastMCP server with 106 tools across 10 modules
  • scitex mcp list: List all tools with column-aligned output
  • scitex mcp doctor: Check server health and configuration
  • scitex mcp serve: Start server (stdio/sse/http transports)
  • scitex mcp help-recursive: Show help for all MCP commands
• Scholar Module: Expanded from 5 to 23 MCP tools
  • Added: enrich_bibtex, download_pdf, download_pdfs_batch, parse_bibtex
  • Added: validate_pdfs, resolve_openurls, authenticate, check_auth_status
  • Added: logout, export_papers, add_papers_to_project, parse_pdf_content
  • Added job handlers: fetch_papers, list_jobs, get_job_status, start_job, cancel_job, get_job_result
• MCP CLI Tests: 10 new tests for mcp CLI commands

Changed

• MCP Architecture: Consolidated into _mcp_tools/ subpackage
• Test Naming: Renamed MCP tests to module-prefixed convention (e.g., test_audio_handlers.py)

Removed

• Legacy module-specific MCP files (consolidated into unified server)

Fixed

• Release workflow: Simplified version check (pyproject.toml only)
• Gitignore: Added script_out/, .monitor_repository.sh.log

[2.13.0] - 2026-01-08

Changed

• Renamed rng_manager → rng: Shorter, NumPy-aligned naming convention
  • stx.session.start() now returns rng instead of rng_manager
  • All examples, docs, and tests updated to use new naming
• MCP Servers: Added graceful dependency handling with MCP_AVAILABLE flag
  • Servers now provide helpful installation instructions when mcp package missing

Added

• GitHub Actions: Install time benchmark workflow with GitHub Pages deployment
  • Dynamic shields.io badges for all modules at badges/<module>.json
  • Weekly scheduled benchmarks and release-triggered runs
• README: Per-module install time badges in all module tables

Fixed

• README: Removed stray </details> tag, fixed stx.io.load example

[2.12.0] - 2026-01-08

Added

• MCP Servers: Integrated MCP (Model Context Protocol) servers for LLM integration
  • scholar: Literature management with BibTeX operations, DOI resolution (11 tools)
  • stats: Statistical testing with auto-recommendation, power analysis (10 tools)
  • template: Project scaffolding from templates (4 tools)
  • plt: Publication-quality plotting with style management (6 tools)
  • canvas: Multi-panel figure composition (7 tools)
  • diagram: Paper-optimized diagram generation with Mermaid/Graphviz (7 tools)
• CLI Commands: 7 new CLI command groups (113 new tests)
  • audio: Text-to-speech (speak, backends, check, stop)
  • capture: Screenshot/monitoring (snap, start, stop, gif, info, window)
  • repro: Reproducibility tools (gen-id, gen-timestamp, hash, seed)
  • resource: System monitoring (specs, usage, monitor)
  • stats: Statistical analysis (recommend, describe, save, load, tests)
  • template: Project scaffolding (list, clone, info)
  • tex: LaTeX operations (compile, preview, to-vec, check)
• Web Module: New download_images function for batch image downloading with size filtering

Removed

• Obsolete MCP Servers: Removed standalone src/mcp_servers/ directory (18 servers, ~44K lines)
  • Replaced by integrated module structure at src/scitex/<module>/mcp_server.py

Changed

• MCP server entry points now follow pattern: scitex-<module> (e.g., scitex-scholar, scitex-stats)

[2.11.0] - 2026-01-08

Breaking Changes

• Removed Modules: Deprecated fig, fts, and compat modules have been removed
• Canvas API: position/size parameters renamed to xy_mm/size_mm for clarity

Changed

• Removed legacy Pltz* aliases and terminology
• Reorganized maintenance scripts into dependencies/ directory
• Simplified path module implementations
• Added installation time benchmark scripts

Documentation

• Updated README with uv recommendations
• Consolidated visualization documentation into docs/visualization/

[2.10.3] - 2026-01-06

Fixed

• Dependency: Add direct llvmlite>=0.39.0 constraint to force Python 3.11+ compatible version
  • umap-learn>=0.5.4 alone was insufficient; pynndescent still pulled old llvmlite==0.36.0

[2.10.2] - 2026-01-06

Fixed

• Dependency: Pin umap-learn>=0.5.4 for Python 3.11+ compatibility (llvmlite issue)

[2.10.1] - 2026-01-06

Fixed

• Documentation: Updated README to recommend scitex[all] as primary installation

[2.10.0] - 2026-01-05

Added

• CI/CD Infrastructure: Separate workflow files for all 41 modules
• Datetime Module: New datetime module with dt alias for time operations
• Comprehensive Test Suites: Major test improvements across modules
  • AI module: 577 tests passing
  • NN module: 498 tests passing
  • IO module: 506 tests passing
  • Writer module: 414 tests (expanded from 276)
  • CLI module: 201 tests
  • SH module: 149 tests
  • Scholar module: Core and storage tests

Changed

• License: Updated to AGPL-3.0
• Updated README with improved installation section
• Reorganized project structure (removed unused externals directory)

Fixed

• HTML tag order and markdown link syntax in README
• DSP module test failures (reduced from 154 to 78)
• Resource module test failures and source bugs
• Repro module JAX circular import bug
• Web module tests and source bugs
• Gen module tests improvements

Security

• Added .env.zenrows to .gitignore to prevent credential commits

[2.9.0] - 2025-12-28

Added

• FTS Bundle System: New node kinds for annotations and images
  • text kind for text annotations with fontsize, fontweight, alignment
  • shape kind for shapes (rectangle, ellipse, arrow, line) with styling
  • image kind for embedded images
• Node Categories: Clear categorization of node kinds
  • DATA_LEAF_KINDS: plot, table, stats (require payload data files)
  • ANNOTATION_LEAF_KINDS: text, shape (no payload required)
  • IMAGE_LEAF_KINDS: image (require payload image file)
  • COMPOSITE_KINDS: figure (contain children)
• Theme Enhancements: FigureTitle and Caption dataclasses for attribute access
• Matplotlib Analysis Tools: Signature analysis tools in dev/plt/mpl/
• CI/CD Improvements: Added module-specific coverage targets

Changed

• Reorganized demo plotters to dev/plt/demo_plotters/ subdirectory
• Updated FTS examples to use new kind attribute instead of type
• Theme figure_title and caption now use dataclass attribute access

Fixed

• Various import and attribute access fixes across modules
• Stats module now has optional torch dependency with numpy fallback

Removed

• Deprecated VIS planning documentation (now in .gitignore)

[2.8.1] - 2025-12-27

Changed

• Made torch optional in stats module with numpy fallback
• Added cross-process FIFO queue for MCP audio server

[2.8.0] - 2025-12-20

Added

• FTS bundle examples
• Updated existing examples for FTS compatibility
• Tests for FTS refactoring

Changed

• Core modules updated for FTS integration
• Consolidated error and warning classes in logging module