encode-toolkit 0.3.1__tar.gz → 0.3.2__tar.gz

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Files changed (34) hide show
  1. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/.gitignore +10 -3
  2. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/CHANGELOG.md +16 -0
  3. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/CITATION.cff +1 -1
  4. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/PKG-INFO +2 -2
  5. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/README.md +1 -1
  6. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/pyproject.toml +1 -1
  7. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/src/encode_connector/client/constants.py +1 -1
  8. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/LICENSE +0 -0
  9. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/PRIVACY.md +0 -0
  10. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/SECURITY.md +0 -0
  11. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/conftest.py +0 -0
  12. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/src/encode_connector/__init__.py +0 -0
  13. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/src/encode_connector/__main__.py +0 -0
  14. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/src/encode_connector/client/__init__.py +0 -0
  15. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/src/encode_connector/client/auth.py +0 -0
  16. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/src/encode_connector/client/downloader.py +0 -0
  17. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/src/encode_connector/client/encode_client.py +0 -0
  18. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/src/encode_connector/client/models.py +0 -0
  19. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/src/encode_connector/client/tracker.py +0 -0
  20. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/src/encode_connector/client/validation.py +0 -0
  21. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/src/encode_connector/server/__init__.py +0 -0
  22. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/src/encode_connector/server/__main__.py +0 -0
  23. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/src/encode_connector/server/main.py +0 -0
  24. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/tests/__init__.py +0 -0
  25. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/tests/test_auth.py +0 -0
  26. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/tests/test_bioinformatics_audit.py +0 -0
  27. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/tests/test_client.py +0 -0
  28. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/tests/test_downloader.py +0 -0
  29. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/tests/test_models.py +0 -0
  30. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/tests/test_packaging.py +0 -0
  31. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/tests/test_server.py +0 -0
  32. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/tests/test_tool_responses.py +0 -0
  33. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/tests/test_tracker.py +0 -0
  34. {encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/tests/test_validation.py +0 -0
{encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/.gitignore RENAMED
@@ -37,9 +37,16 @@ node_modules/
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  *.swp
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  *.swo
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- # Claude Code local files
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- .claude/settings.local.json
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- .claude/*.local.md
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+ # AI assistant configuration and notes (never commit)
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+ .claude/
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+ CLAUDE.md
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+ CLAUDE.local.md
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+ AGENTS.md
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+ GEMINI.md
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+ .mcp.json
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+ !plugin/.mcp.json
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+ .cursorrules
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+ .aider*
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  # Runtime data
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  *.db
{encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/CHANGELOG.md RENAMED
@@ -5,6 +5,22 @@ All notable changes to the ENCODE Toolkit will be documented in this file.
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  The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
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  and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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+ ## [0.3.2] - 2026-09-20
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+
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+ Maintenance release. The Python package is functionally identical to 0.3.1.
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+
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+ ### Fixed
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+
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+ - `bioinformatics-installer` skill: the ChIP-seq walkthrough pointed at `scripts/chipseq-env.yml`
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+ (the file lives in `environments/`) and at an `annotation-env.yml` that did not exist. The first
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+ path is corrected and the second is replaced with an explicit `conda create` command.
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+
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+ ### Changed
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+
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+ - Removed local tooling configuration files from the repository and ignored them going forward.
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+ - `CONTRIBUTING.md` and `docs/SHOWCASE.md` now use the ENCODE Toolkit name and the current skill
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+ count (47).
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+
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  ## [0.3.1] - 2026-09-20
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  ### Fixed
{encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/CITATION.cff RENAMED
@@ -8,7 +8,7 @@ authors:
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  given-names: Alex M.
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  orcid: "https://orcid.org/0000-0003-0907-464X"
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  affiliation: "Independent Researcher"
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- version: 0.3.1
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+ version: 0.3.2
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  date-released: "2026-09-20"
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  license: AGPL-3.0-only
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  repository-code: "https://github.com/ammawla/encode-toolkit"
{encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.5
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  Name: encode-toolkit
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- Version: 0.3.1
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+ Version: 0.3.2
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  Summary: MCP server for querying and downloading ENCODE Project genomics data directly from Claude
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  Project-URL: Homepage, https://github.com/ammawla/encode-toolkit
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  Project-URL: Repository, https://github.com/ammawla/encode-toolkit
@@ -37,7 +37,7 @@ Description-Content-Type: text/markdown
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  [![License: AGPL-3.0](https://img.shields.io/badge/license-AGPL--3.0-green.svg)](LICENSE)
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  [![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
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- [![Version](https://img.shields.io/badge/version-0.3.1-green)](CHANGELOG.md)
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+ [![Version](https://img.shields.io/badge/version-0.3.2-green)](CHANGELOG.md)
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  [![Status](https://img.shields.io/badge/status-beta-yellow)]()
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  [![Skills](https://img.shields.io/badge/skills-47-orange)](docs/skill-vignettes/)
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  [![Tools](https://img.shields.io/badge/MCP_tools-20-purple)](src/encode_connector/server/main.py)
{encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/README.md RENAMED
@@ -4,7 +4,7 @@
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  [![License: AGPL-3.0](https://img.shields.io/badge/license-AGPL--3.0-green.svg)](LICENSE)
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  [![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
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- [![Version](https://img.shields.io/badge/version-0.3.1-green)](CHANGELOG.md)
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+ [![Version](https://img.shields.io/badge/version-0.3.2-green)](CHANGELOG.md)
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  [![Status](https://img.shields.io/badge/status-beta-yellow)]()
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  [![Skills](https://img.shields.io/badge/skills-47-orange)](docs/skill-vignettes/)
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  [![Tools](https://img.shields.io/badge/MCP_tools-20-purple)](src/encode_connector/server/main.py)
{encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/pyproject.toml RENAMED
@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
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  [project]
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  name = "encode-toolkit"
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- version = "0.3.1"
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+ version = "0.3.2"
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  description = "MCP server for querying and downloading ENCODE Project genomics data directly from Claude"
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  readme = "README.md"
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  license = "AGPL-3.0-only"
{encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/src/encode_connector/client/constants.py RENAMED
@@ -17,7 +17,7 @@ try:
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  _version = importlib.metadata.version("encode-toolkit")
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  except importlib.metadata.PackageNotFoundError:
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- _version = "0.3.1"
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+ _version = "0.3.2"
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  USER_AGENT = f"encode-toolkit/{_version} (MCP; +https://github.com/ammawla/encode-toolkit)"
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  # Keyring service name for credential storage
{encode_toolkit-0.3.1 → encode_toolkit-0.3.2}/LICENSE RENAMED
File without changes