scitex-dev 0.3.2__tar.gz → 0.4.0__tar.gz

scitex_dev-0.4.0/.gitignore

@@ -0,0 +1,32 @@
+__pycache__/
+*.py[cod]
+*$py.class
+*.egg-info/
+*.egg
+dist/
+build/
+.eggs/
+.pytest_cache/
+*.so
+.tox/
+.coverage
+htmlcov/
+.mypy_cache/
+.ruff_cache/
+logs/
+GITIGNORED/
+.env
+.last-hpc-job
+.venv/
+.claude/
+
+# Pre-built docs (generated by sphinx-build)
+src/*/_sphinx_html/
+
+# WIP directories
+scitex/
+src/scitex_dev/app/
+
+# Hook logs and pending
+docs/to_claude/hooks/**/*.log
+docs/to_claude/hooks/**/.pending/

scitex_dev-0.4.0/PKG-INFO

@@ -0,0 +1,266 @@
+Metadata-Version: 2.4
+Name: scitex-dev
+Version: 0.4.0
+Summary: Shared developer utilities for the SciTeX ecosystem
+Author-email: Yusuke Watanabe <ywatanabe@scitex.ai>
+License-Expression: AGPL-3.0-only
+Project-URL: Homepage, https://github.com/ywatanabe1989/scitex-dev
+Project-URL: Repository, https://github.com/ywatanabe1989/scitex-dev
+Project-URL: Documentation, https://scitex-dev.readthedocs.io/
+Keywords: scitex,developer-tools,documentation,llm-friendly,mcp
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Provides-Extra: cli
+Requires-Dist: click>=8.0.0; extra == "cli"
+Provides-Extra: mcp
+Requires-Dist: fastmcp>=2.0.0; extra == "mcp"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: sphinx>=7.0; extra == "docs"
+Requires-Dist: sphinx-rtd-theme>=2.0; extra == "docs"
+Requires-Dist: myst-parser>=2.0; extra == "docs"
+Requires-Dist: sphinx-copybutton>=0.5; extra == "docs"
+Requires-Dist: sphinx-autodoc-typehints>=1.25; extra == "docs"
+Provides-Extra: all
+Requires-Dist: scitex-dev[cli]; extra == "all"
+Requires-Dist: scitex-dev[mcp]; extra == "all"
+Requires-Dist: scitex-dev[dev]; extra == "all"
+Requires-Dist: scitex-dev[docs]; extra == "all"
+Dynamic: license-file
+
+# SciTeX Dev (`scitex-dev`)
+
+<p align="center">
+  <a href="https://scitex.ai">
+    <img src="docs/scitex-logo-blue-cropped.png" alt="SciTeX" width="400">
+  </a>
+</p>
+
+<p align="center"><b>Shared developer utilities for the SciTeX ecosystem</b></p>
+
+<p align="center">
+  <a href="https://badge.fury.io/py/scitex-dev"><img src="https://badge.fury.io/py/scitex-dev.svg" alt="PyPI version"></a>
+  <a href="https://scitex-dev.readthedocs.io/"><img src="https://readthedocs.org/projects/scitex-dev/badge/?version=latest" alt="Documentation"></a>
+  <a href="https://github.com/ywatanabe1989/scitex-dev/actions/workflows/test.yml"><img src="https://github.com/ywatanabe1989/scitex-dev/actions/workflows/test.yml/badge.svg" alt="Tests"></a>
+  <a href="https://www.gnu.org/licenses/agpl-3.0"><img src="https://img.shields.io/badge/License-AGPL--3.0-blue.svg" alt="License: AGPL-3.0"></a>
+</p>
+
+<p align="center">
+  <a href="https://scitex-dev.readthedocs.io/">Full Documentation</a> · <code>pip install scitex-dev</code>
+</p>
+
+---
+
+## Problem
+
+The SciTeX ecosystem spans multiple packages (scitex-clew, scitex-writer, scitex-stats, figrecipe, etc.), each with their own documentation, versions, APIs, and CLI commands. Keeping them in sync, discovering what's available, and maintaining consistency across the ecosystem becomes increasingly difficult as it grows.
+
+## Solution
+
+`scitex-dev` provides a unified toolkit for developing and maintaining the SciTeX ecosystem:
+
+- **Docs aggregation** — discover, build, and search documentation across all packages from a single entry point
+- **Unified search** — search Python APIs, CLI commands, MCP tools, and docs with fuzzy matching and Google-like syntax
+- **Version management** — track, compare, and fix version mismatches across pyproject.toml, `__init__.py`, git tags, PyPI, and RTD
+- **Bulk rename** — safe, preview-able renaming with cross-reference updates across the entire codebase
+- **LLM-friendly types** — `Result`, `ErrorCode`, `@supports_return_as` for consistent structured responses
+
+Zero runtime dependencies. Pure stdlib.
+
+## Installation
+
+```bash
+pip install scitex-dev
+
+# With CLI support:
+pip install scitex-dev[cli]
+
+# With MCP server:
+pip install scitex-dev[mcp]
+
+# Everything:
+pip install scitex-dev[all]
+```
+
+## Quick Start
+
+```python
+import scitex_dev
+
+# Unified search across the ecosystem
+results = scitex_dev.search("save figure")
+
+# Version management
+versions = scitex_dev.list_versions()
+mismatches = scitex_dev.get_mismatches()
+
+# Documentation aggregation
+docs = scitex_dev.get_docs(package="scitex-writer", format="json")
+```
+
+## Four Interfaces
+
+<details>
+<summary><b>Python API</b></summary>
+
+```python
+import scitex_dev
+
+# Search
+scitex_dev.search("ttest", scope="api")
+scitex_dev.search('+required -excluded "exact phrase"')
+
+# Docs
+scitex_dev.get_docs()
+scitex_dev.get_docs(package="scitex-writer", format="json")
+scitex_dev.build_docs(package="scitex-writer")
+scitex_dev.search_docs("installation")
+
+# Versions
+scitex_dev.list_versions()
+scitex_dev.check_versions(["scitex", "figrecipe"])
+scitex_dev.get_mismatches()
+scitex_dev.fix_mismatches(dry_run=True)
+
+# LLM-friendly types
+from scitex_dev import Result, supports_return_as
+
+@supports_return_as
+def my_function(x: int) -> int:
+    return x * 2
+
+result = my_function(5, return_as="result")
+# Result(success=True, data=10)
+```
+
+</details>
+
+<details>
+<summary><b>CLI Commands</b></summary>
+
+```bash
+# Ecosystem management
+scitex-dev ecosystem list
+scitex-dev ecosystem list --versions
+scitex-dev ecosystem fix-mismatches --dry-run
+scitex-dev ecosystem sync
+
+# Documentation
+scitex-dev docs --package scitex-writer
+scitex-dev search "save figure"
+
+# Bulk rename
+scitex-dev rename old_name new_name --dry-run
+
+# See all commands
+scitex-dev --help
+scitex-dev --help-recursive
+```
+
+</details>
+
+<details>
+<summary><b>MCP Server</b></summary>
+
+```bash
+# Start server
+scitex-dev mcp start
+
+# Check setup
+scitex-dev mcp doctor
+scitex-dev mcp list-tools
+
+# Installation info
+scitex-dev mcp installation
+```
+
+**Claude Code Setup** — add `.mcp.json` to your project root. Use `SCITEX_DEV_ENV_SRC` to load configuration from a `.src` file:
+
+```json
+{
+  "mcpServers": {
+    "scitex-dev": {
+      "command": "scitex-dev",
+      "args": ["mcp", "start"],
+      "env": {
+        "SCITEX_DEV_ENV_SRC": "${SCITEX_DEV_ENV_SRC}"
+      }
+    }
+  }
+}
+```
+
+Switch environments via your shell profile:
+
+```bash
+# Local machine
+export SCITEX_DEV_ENV_SRC=~/.scitex/dev/local.src
+
+# Remote server
+export SCITEX_DEV_ENV_SRC=~/.scitex/dev/remote.src
+```
+
+</details>
+
+<details>
+<summary><strong>Skills — for AI Agent Discovery</strong></summary>
+
+<br>
+
+Skills provide workflow-oriented guides that AI agents query to discover capabilities and usage patterns.
+
+```bash
+scitex-dev skills list              # List available skill pages
+scitex-dev skills get SKILL         # Show main skill page
+scitex-dev skills export --package scitex-dev  # Export to Claude Code
+```
+
+| Skill | Content |
+|-------|---------|
+| `result-types` | `Result`, `ErrorCode`, `@supports_return_as` for LLM-friendly responses |
+| `cli-mcp-utils` | CLI and MCP utility helpers |
+| `versions` | Version management, mismatch detection and fixing |
+| `ecosystem` | Ecosystem list, sync, and commit workflows |
+| `rename` | Safe bulk rename with cross-reference updates |
+| `docs-search` | Documentation aggregation and unified search |
+| `test-runner` | Local and HPC test execution |
+| `config` | Package configuration and priority config patterns |
+
+</details>
+
+## Part of SciTeX
+
+`scitex-dev` is part of [SciTeX](https://scitex.ai). It provides the shared infrastructure that keeps the ecosystem consistent and discoverable. When used with the orchestrator package `scitex`, it enables unified version management and documentation across all modules:
+
+```python
+import scitex_dev
+
+# See the entire ecosystem at a glance
+versions = scitex_dev.list_versions()
+mismatches = scitex_dev.get_mismatches()
+
+# Search across all installed SciTeX packages
+scitex_dev.search("statistical test")
+```
+
+The SciTeX system follows the Four Freedoms for Research below, inspired by [the Free Software Definition](https://www.gnu.org/philosophy/free-sw.en.html):
+
+>Four Freedoms for Research
+>
+>0. The freedom to **run** your research anywhere — your machine, your terms.
+>1. The freedom to **study** how every step works — from raw data to final manuscript.
+>2. The freedom to **redistribute** your workflows, not just your papers.
+>3. The freedom to **modify** any module and share improvements with the community.
+>
+>AGPL-3.0 — because we believe research infrastructure deserves the same freedoms as the software it runs on.
+
+---
+
+<p align="center">
+  <a href="https://scitex.ai">
+    <img src="docs/scitex-icon-navy-inverted.png" alt="SciTeX" width="40">
+  </a>
+</p>

scitex_dev-0.4.0/README.md

@@ -0,0 +1,233 @@
+# SciTeX Dev (`scitex-dev`)
+
+<p align="center">
+  <a href="https://scitex.ai">
+    <img src="docs/scitex-logo-blue-cropped.png" alt="SciTeX" width="400">
+  </a>
+</p>
+
+<p align="center"><b>Shared developer utilities for the SciTeX ecosystem</b></p>
+
+<p align="center">
+  <a href="https://badge.fury.io/py/scitex-dev"><img src="https://badge.fury.io/py/scitex-dev.svg" alt="PyPI version"></a>
+  <a href="https://scitex-dev.readthedocs.io/"><img src="https://readthedocs.org/projects/scitex-dev/badge/?version=latest" alt="Documentation"></a>
+  <a href="https://github.com/ywatanabe1989/scitex-dev/actions/workflows/test.yml"><img src="https://github.com/ywatanabe1989/scitex-dev/actions/workflows/test.yml/badge.svg" alt="Tests"></a>
+  <a href="https://www.gnu.org/licenses/agpl-3.0"><img src="https://img.shields.io/badge/License-AGPL--3.0-blue.svg" alt="License: AGPL-3.0"></a>
+</p>
+
+<p align="center">
+  <a href="https://scitex-dev.readthedocs.io/">Full Documentation</a> · <code>pip install scitex-dev</code>
+</p>
+
+---
+
+## Problem
+
+The SciTeX ecosystem spans multiple packages (scitex-clew, scitex-writer, scitex-stats, figrecipe, etc.), each with their own documentation, versions, APIs, and CLI commands. Keeping them in sync, discovering what's available, and maintaining consistency across the ecosystem becomes increasingly difficult as it grows.
+
+## Solution
+
+`scitex-dev` provides a unified toolkit for developing and maintaining the SciTeX ecosystem:
+
+- **Docs aggregation** — discover, build, and search documentation across all packages from a single entry point
+- **Unified search** — search Python APIs, CLI commands, MCP tools, and docs with fuzzy matching and Google-like syntax
+- **Version management** — track, compare, and fix version mismatches across pyproject.toml, `__init__.py`, git tags, PyPI, and RTD
+- **Bulk rename** — safe, preview-able renaming with cross-reference updates across the entire codebase
+- **LLM-friendly types** — `Result`, `ErrorCode`, `@supports_return_as` for consistent structured responses
+
+Zero runtime dependencies. Pure stdlib.
+
+## Installation
+
+```bash
+pip install scitex-dev
+
+# With CLI support:
+pip install scitex-dev[cli]
+
+# With MCP server:
+pip install scitex-dev[mcp]
+
+# Everything:
+pip install scitex-dev[all]
+```
+
+## Quick Start
+
+```python
+import scitex_dev
+
+# Unified search across the ecosystem
+results = scitex_dev.search("save figure")
+
+# Version management
+versions = scitex_dev.list_versions()
+mismatches = scitex_dev.get_mismatches()
+
+# Documentation aggregation
+docs = scitex_dev.get_docs(package="scitex-writer", format="json")
+```
+
+## Four Interfaces
+
+<details>
+<summary><b>Python API</b></summary>
+
+```python
+import scitex_dev
+
+# Search
+scitex_dev.search("ttest", scope="api")
+scitex_dev.search('+required -excluded "exact phrase"')
+
+# Docs
+scitex_dev.get_docs()
+scitex_dev.get_docs(package="scitex-writer", format="json")
+scitex_dev.build_docs(package="scitex-writer")
+scitex_dev.search_docs("installation")
+
+# Versions
+scitex_dev.list_versions()
+scitex_dev.check_versions(["scitex", "figrecipe"])
+scitex_dev.get_mismatches()
+scitex_dev.fix_mismatches(dry_run=True)
+
+# LLM-friendly types
+from scitex_dev import Result, supports_return_as
+
+@supports_return_as
+def my_function(x: int) -> int:
+    return x * 2
+
+result = my_function(5, return_as="result")
+# Result(success=True, data=10)
+```
+
+</details>
+
+<details>
+<summary><b>CLI Commands</b></summary>
+
+```bash
+# Ecosystem management
+scitex-dev ecosystem list
+scitex-dev ecosystem list --versions
+scitex-dev ecosystem fix-mismatches --dry-run
+scitex-dev ecosystem sync
+
+# Documentation
+scitex-dev docs --package scitex-writer
+scitex-dev search "save figure"
+
+# Bulk rename
+scitex-dev rename old_name new_name --dry-run
+
+# See all commands
+scitex-dev --help
+scitex-dev --help-recursive
+```
+
+</details>
+
+<details>
+<summary><b>MCP Server</b></summary>
+
+```bash
+# Start server
+scitex-dev mcp start
+
+# Check setup
+scitex-dev mcp doctor
+scitex-dev mcp list-tools
+
+# Installation info
+scitex-dev mcp installation
+```
+
+**Claude Code Setup** — add `.mcp.json` to your project root. Use `SCITEX_DEV_ENV_SRC` to load configuration from a `.src` file:
+
+```json
+{
+  "mcpServers": {
+    "scitex-dev": {
+      "command": "scitex-dev",
+      "args": ["mcp", "start"],
+      "env": {
+        "SCITEX_DEV_ENV_SRC": "${SCITEX_DEV_ENV_SRC}"
+      }
+    }
+  }
+}
+```
+
+Switch environments via your shell profile:
+
+```bash
+# Local machine
+export SCITEX_DEV_ENV_SRC=~/.scitex/dev/local.src
+
+# Remote server
+export SCITEX_DEV_ENV_SRC=~/.scitex/dev/remote.src
+```
+
+</details>
+
+<details>
+<summary><strong>Skills — for AI Agent Discovery</strong></summary>
+
+<br>
+
+Skills provide workflow-oriented guides that AI agents query to discover capabilities and usage patterns.
+
+```bash
+scitex-dev skills list              # List available skill pages
+scitex-dev skills get SKILL         # Show main skill page
+scitex-dev skills export --package scitex-dev  # Export to Claude Code
+```
+
+| Skill | Content |
+|-------|---------|
+| `result-types` | `Result`, `ErrorCode`, `@supports_return_as` for LLM-friendly responses |
+| `cli-mcp-utils` | CLI and MCP utility helpers |
+| `versions` | Version management, mismatch detection and fixing |
+| `ecosystem` | Ecosystem list, sync, and commit workflows |
+| `rename` | Safe bulk rename with cross-reference updates |
+| `docs-search` | Documentation aggregation and unified search |
+| `test-runner` | Local and HPC test execution |
+| `config` | Package configuration and priority config patterns |
+
+</details>
+
+## Part of SciTeX
+
+`scitex-dev` is part of [SciTeX](https://scitex.ai). It provides the shared infrastructure that keeps the ecosystem consistent and discoverable. When used with the orchestrator package `scitex`, it enables unified version management and documentation across all modules:
+
+```python
+import scitex_dev
+
+# See the entire ecosystem at a glance
+versions = scitex_dev.list_versions()
+mismatches = scitex_dev.get_mismatches()
+
+# Search across all installed SciTeX packages
+scitex_dev.search("statistical test")
+```
+
+The SciTeX system follows the Four Freedoms for Research below, inspired by [the Free Software Definition](https://www.gnu.org/philosophy/free-sw.en.html):
+
+>Four Freedoms for Research
+>
+>0. The freedom to **run** your research anywhere — your machine, your terms.
+>1. The freedom to **study** how every step works — from raw data to final manuscript.
+>2. The freedom to **redistribute** your workflows, not just your papers.
+>3. The freedom to **modify** any module and share improvements with the community.
+>
+>AGPL-3.0 — because we believe research infrastructure deserves the same freedoms as the software it runs on.
+
+---
+
+<p align="center">
+  <a href="https://scitex.ai">
+    <img src="docs/scitex-icon-navy-inverted.png" alt="SciTeX" width="40">
+  </a>
+</p>

scitex_dev-0.4.0/docs/to_claude/commands/s.md

@@ -0,0 +1 @@
+Load and apply the skill(s): @ARGUMENTS

scitex_dev-0.4.0/docs/to_claude/commands/speak-and-call.md

@@ -0,0 +1,16 @@
+## Skills to Load (Required)
+skill:quality-guards
+skill:speak-and-signature
+
+## Override:
+- Continue working on the task.
+  - Until requirements have satisfied and confirmed visually and functionally, 
+
+- No false positive reports.
+
+- Make a phone call to the user if you speak seven times but the user does not respond
+
+## Requirements are below:
+$ARGUMENTS
+
+(If no requirements shown here, please estimate requests based on the tasks so far)