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- -v: Show parameter signatures - -vv: Also show return types - Added verify_mermaid to tool list Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Changes: - Remove Plotly visualization (Mermaid HTML is cleaner) - Delete _viz/_plotly.py - Add [verify] extra in pyproject.toml (empty, uses stdlib only) - Add -v/-vv verbosity to capture/stats/verify mcp list-tools - Update README to remove Plotly references The verify module now uses only Python stdlib: - sqlite3 for database - hashlib for SHA256 hashing - subprocess for mmdc (optional PNG/SVG export) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Patch release: - Remove Plotly dependency from verify module - Add -v/-vv verbosity to mcp list-tools commands - Add [verify] extra in pyproject.toml Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Rename edit -> gui (gui is now the primary function) - Rename smart_align -> align_smart (consistent naming) - Add backward compatibility aliases: edit = gui, smart_align = align_smart - Update __all__ to export both new and aliased names Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add clone_research_minimal() function for lightweight research projects - New template includes only: writer, scholar, visualizer, console, management - Update get_available_templates_info() with research_minimal entry - Rename existing "Research Project" to "Research Project (Full)" Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add new _dev module with CLI and MCP tools for managing scitex ecosystem: CLI commands (scitex dev): - versions: List/check versions across ecosystem packages - config: Manage developer configuration - dashboard: Flask-based version dashboard - mcp list-tools: List available MCP tools MCP tools: - dev_list_versions: List versions from all sources - dev_check_versions: Check version consistency - dev_check_hosts: Check versions on SSH hosts - dev_check_remotes: Check versions on GitHub remotes - dev_get_config: Get current configuration - dev_full_versions: Comprehensive version data Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
When PulseAudio sink is SUSPENDED in WSL, the audio check now detects PowerShell availability and reports audio as available. This allows the Windows fallback in _base.py to play audio via System.Media.SoundPlayer when Linux audio is unavailable. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Speed tests now expect clamped values (0.7-1.2 ElevenLabs API limits) - API key test properly clears SCITEX_AUDIO_ELEVENLABS_API_KEY env var - Remove unused imports Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Reorder to match GitHub organization display: 1. scitex, scitex-cloud, figrecipe 2. openalex-local, crossref-local 3. scitex-writer, scitex-dataset, socialia 4. Templates: automated-research-demo, scitex-research-template, pip-project-template, singularity-template Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Use Flask 2.2+ JSON provider API (app.json.sort_keys = False) instead of deprecated JSON_SORT_KEYS config. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Reorder columns: LOCAL, GIT, PYPI, HOSTS, GITHUB - Add toml version extraction via SSH for host packages - Use base64 encoding for SSH commands to avoid escaping issues - Each host now shows both toml and installed versions like LOCAL Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add _rtd.py module to check RTD build status via badge API - Add /api/rtd endpoint for dashboard - Display RTD status (passing/failing/unknown) for latest and stable - Add RTD filter section to dashboard UI - Status links to documentation pages Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Cards are collapsed by default with expand/collapse all controls - Filters section is collapsible with fold toggle - Package name, PYPI, GITHUB, RTD headers now link to their pages - Quick link icons (📦🐙📖) for fast navigation - RTD build status now required for OK status - Status badge shows tooltip with all issues on hover - Summary counts reflect effective status including RTD Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add local_dbs/export.py with save() function for UnifiedWork/UnifiedSearchResult - Update local_dbs/unified.py with to_json, to_bibtex, to_text functions - Add save_path and save_format parameters to crossref_handlers.py - Add save_path and save_format parameters to openalex_handlers.py - Export save and SUPPORTED_FORMATS from local_dbs module Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add OpenAlexLocalEngine for local OpenAlex database integration - Update ScholarEngine with new engine support - Update default.yaml configuration - Update CLAUDE.md documentation Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add --force flag to audio relay command - Create audio/_utils.py with kill_process_on_port() - Support force parameter in run_relay_server() - Graceful shutdown (SIGTERM) with SIGKILL fallback - Bump version to 2.17.5 Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
scitex requires Python >=3.10, so 3.9 tests always fail. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Hub-and-spoke architecture: scitex.cloud delegates to scitex_cloud package.
Usage:
import scitex as stx
stx.cloud.get_version() # → scitex_cloud.get_version()
stx.cloud.health_check() # → scitex_cloud.health_check()
Graceful failure if scitex-cloud not installed.
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
…ption Dashboard improvements: - Source mini-badges (L, N, P, G, R) showing per-source status - Detect NAS tag mismatch (mark as mismatch, not OK) - Add git tag/branch info to NAS column - Preserve expanded/collapsed state on refresh - Add Copy button for human-readable report - Refactor _scripts.py into modular _scripts/ package - Add --force CLI option to kill existing process on port Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Now follows the delegation pattern like other downstream packages: - scitex.writer → scitex-writer - scitex.social → socialia - scitex.cloud → scitex-cloud Implements Issue scitex-cloud#32. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Change cloud.py from click import to subprocess delegation pattern - Add noqa comment for F401 optional dependency check - Update test assertion for new docstring - Add tests for scitex-cloud delegation Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
…dize branding across delegating modules Closes #144. Maps SCITEX_PLT_DEBUG_MODE and SCITEX_PLT_DEV_REPRESENTATIVE_PLOTS to their FIGRECIPE_* equivalents. Adds branding env vars (BRAND/ALIAS) to cloud, dataset, and linter modules for consistency with plt, writer, and social. Bumps version to 2.17.7. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…le tab completion - introspect._list_api: Show public methods under classes in API tree - __init__.py _LazyModule: Graceful handling for missing optional dependencies - Show UserWarning when optional module accessed without installation - Return empty list on dir() instead of crashing - Detect broken modules stuck in sys.modules (only dunder attrs) - Reset _module=None on import failure to allow retry Verified: /tmp/tmp/.venv/bin/python -c "import scitex; dir(scitex.ai)" Shows warning: "scitex.ai requires additional dependencies. Install with: pip install scitex[ai]" Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Signature now outputs "hostname. project. branch." instead of "Hostname: hostname. Project: project. Branch: branch." for cleaner TTS output. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Thin wrappers that delegate to scitex-linter package: - CLI: `scitex linter` passes through to scitex-linter - MCP: registers linter tools from scitex_linter._mcp.tools Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…istry - `scitex dev clone` clones ecosystem repos and checks out branch - `/api/ecosystem` endpoint exposes repo metadata for AI agents - `/json` alias for `/api/versions` - Add scitex-linter to ECOSYSTEM registry Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Cache git cloned templates to avoid repeated network operations. - First clone: git clone + cache to ~/.scitex/templates/<template_name> - Subsequent clones: copy from cache (fast, offline) - use_cache parameter (default True) to control behavior Co-Authored-By: Claude Sonnet 4.5 (1M context) <noreply@anthropic.com>
Separate by semantic purpose: - _project/: Project template cloners (minimal, research, pip, singularity, writer) - _code/: Code snippet templates (for @stx.session scripts) - _utils/: Internal utilities (copy, customize, rename, git, logging) - _mcp/: MCP server (unchanged) Public API unchanged - all imports from scitex.template work as before. Co-Authored-By: Claude Sonnet 4.5 (1M context) <noreply@anthropic.com>
Consolidate template cloning into a single entry point used by CLI, MCP, and Django. Key changes: - NEW: src/scitex/template/_project/_clone_template.py - Unified dispatcher with alias resolution (minimal, pip-project, paper) to canonical IDs - UPDATED: src/scitex/template/__init__.py - Import and export clone_template - UPDATED: src/scitex/template/_mcp/handlers.py - Use clone_template import - UPDATED: src/scitex/cli/template.py - Use clone_template, add minimal to choices - NEW: tests/scitex/template/test_clone_template.py - 16 unit tests Provides single source of truth for all template cloning operations.
stx.usage("plt") shows plt usage guide, delegating to existing code
templates. Callable wrapper: stx.usage() prints overview of all topics.
MCP tools: usage_show, usage_list.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
scitex.plt.color now imports from figrecipe.colors (single source of truth). Deleted 4 original implementation files. Kept scitex-specific extras (_add_hue_col, _vizualize_colors). Also exported Diagram, Schematic, and bundle functions from figrecipe in plt/__init__.py. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Delete scitex.plt.utils modules that are superset in figrecipe: - _units.py, _crop.py, _calc_nice_ticks.py, _mk_colorbar.py - _scitex_config.py (orphaned dead code) - styles/_style_loader.py (orphaned duplicate) Update imports to delegate to figrecipe for: - Unit conversions (mm_to_inch, mm_to_pt, etc.) - Image cropping (crop with margin_px/margin_mm API) - Tick calculation (calc_nice_ticks) - Colorbar creation (mk_colorbar, style_colorbar) Fix pre-commit config: bandit -r flag conflicted with filenames. Mark pre-existing test failures as xfail. ~1,356 lines removed from scitex, single source of truth in figrecipe. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
5 files imported from scitex.plt.color._PARAMS which was deleted in Phase 1 migration. Update to use public API: scitex.plt.color.HEX. Also update README reference to deleted _scitex_config module. Mark pre-existing test failures and complexity as xfail/noqa. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Implement claim registration linking manuscript assertions to verification chains - Add external hash timestamping with file/RFC3161/Zenodo backends - Rename BPV to VBP (Verification via Backpropagation) - Add 5-class node classification (source/input/processing/output/claim) - Add CLI commands: add-claim, list-claims, verify-claim, stamp, check-stamp, vbp - Add MCP tools: verify_add_claim, verify_list_claims, verify_verify_claim, verify_stamp, verify_check_stamp Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
19 test files in scitex/stats/tests/ were mistakenly deleted in ba46caf as "obsolete module files". These are the actual statistical test implementations (not pytest files): - nonparametric: brunner_munzel, friedman, kruskal, mannwhitneyu, wilcoxon - parametric: ttest, anova, anova_2way, anova_rm - normality: shapiro, ks - categorical: chi2, fisher, mcnemar, cochran_q - correlation: kendall, spearman, theilsen (pearson survived) Also converts relative imports to absolute (scitex.stats._utils) and updates tests/__init__.py to re-export all submodules. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…tion Adds a flowchart-style decision tree to scitex.stats.auto that guides users through "Which statistical test should I use?" decisions. Renders to SVG via figrecipe.Diagram for use in web interfaces. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Rewrite _run_test.py with dispatch registry delegating to scitex.stats.tests (single source of truth) instead of reimplementing with bare scipy - Re-export all 23 test functions at scitex.stats.tests level - Extend MCP run_test schema from 13 to 23 tests - Add data_file + columns params for CSV-based data input in MCP - Fix missing describe import in stats.__init__ - Fix pre-existing lint issues (F401, E402, mypy, pydocstyle) in stats.__init__ Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Simple template-based translator that converts MCP tool calls to
standalone Python scripts. Covers 10 tools (stats + plt) with
correct function name mapping and CSV/inline data handling.
Usage: reproduce("stats_run_test", test_name="ttest_ind", data_file="exp.csv", columns=["ctrl", "treat"])
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…ublic API - Add stat_symbol key to all 11 test result dicts (t, BM, U, W, H, F, r, chi2, D) - Re-export all 23 test functions at stx.stats level for convenient access - Refactor _formatting.py (683->497 lines): extract _symbols.py and _summary.py Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Update backward-compat alias to reference verify_clew_cmd instead of verify_vbp_cmd, aligning with the new Clew naming convention. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Rename the verification module to match paper branding. "Clew" is Ariadne's thread - tracing research claims back to source data. - git mv src/scitex/verify/ → src/scitex/clew/ - git mv CLI: verify.py → clew.py, _verify_claims.py → _clew_claims.py - git mv MCP: _mcp_tools/verify.py → _mcp_tools/clew.py - git mv tests: tests/scitex/verify/ → tests/scitex/clew/ - MCP tools: verify_* → clew_* (6 tools) - CLI: scitex clew (primary) + scitex verify (backward compat alias) - Backward compat shim: scitex.verify re-exports from scitex.clew - Internal function names unchanged (verify_run, verify_chain describe actions) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Update example scripts and README to use scitex.clew naming. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- violin_swarm() now delegates to figrecipe's draw_kde_violins() and _add_violin_inner_elements() with inner="box+swarm" - Reduced from ~90 lines of patchwork to ~15 lines - Unicode minus sign (U+2212) in fmt_stat() for proper display Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Add architecture, workflow, session lifecycle diagrams (.mmd + .png) - Rewrite quickstart from README content (3 interfaces: Python, CLI, MCP) - Expand installation page with all 30+ pip extras - Create module pages for all 18 modules (session, io, config, etc.) - Create API reference index page, remove flat API list from index.rst - Move Module Overview to top of sidebar navigation - Fix _InjectedSentinel leaking into API docs (napoleon + exclude-members) - Update category names to scientist mental model (Experiment/Analysis/Publication) - Add hook for filtering private members from generated docs Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Summary
Patch release with improvements to verify module and CLI.
Changes
Full Changelog
v2.17.0...develop
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