encode-toolkit 0.3.0b10__tar.gz → 0.3.2__tar.gz

{encode_toolkit-0.3.0b10 → encode_toolkit-0.3.2}/.gitignore

@@ -37,9 +37,16 @@ node_modules/
 *.swp
 *.swo
 
-# Claude Code local files
-.claude/settings.local.json
-.claude/*.local.md
+# AI assistant configuration and notes (never commit)
+.claude/
+CLAUDE.md
+CLAUDE.local.md
+AGENTS.md
+GEMINI.md
+.mcp.json
+!plugin/.mcp.json
+.cursorrules
+.aider*
 
 # Runtime data
 *.db

{encode_toolkit-0.3.0b10 → encode_toolkit-0.3.2}/CHANGELOG.md

@@ -5,6 +5,51 @@ All notable changes to the ENCODE Toolkit will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.3.2] - 2026-09-20
+
+Maintenance release. The Python package is functionally identical to 0.3.1.
+
+### Fixed
+
+- `bioinformatics-installer` skill: the ChIP-seq walkthrough pointed at `scripts/chipseq-env.yml`
+  (the file lives in `environments/`) and at an `annotation-env.yml` that did not exist. The first
+  path is corrected and the second is replaced with an explicit `conda create` command.
+
+### Changed
+
+- Removed local tooling configuration files from the repository and ignored them going forward.
+- `CONTRIBUTING.md` and `docs/SHOWCASE.md` now use the ENCODE Toolkit name and the current skill
+  count (47).
+
+## [0.3.1] - 2026-09-20
+
+### Fixed
+
+- **Server failed to start on fresh installs.** The `mcp` dependency had no upper bound, so new
+  environments resolved `mcp` 2.x, which removed `mcp.server.fastmcp`. Startup then crashed with
+  `ModuleNotFoundError: No module named 'mcp.server.fastmcp'`. The dependency is now capped at
+  `mcp[cli]>=1.0,<2`. Existing installs that already had `mcp` 1.x were not affected.
+
+  If you hit this error, uv may have cached the broken environment. Refresh it once with
+  `uvx --refresh encode-toolkit` (or `uv cache clean encode-toolkit`); pip users can run
+  `pip install --upgrade encode-toolkit`.
+
+### Security
+
+- The ChIP-seq, ATAC-seq, and RNA-seq pipeline Dockerfiles now download the UCSC
+  `bedGraphToBigWig` executable over HTTPS instead of plain HTTP.
+
+### Changed
+
+- The source distribution now contains only the Python package, tests, and project documents.
+  It previously bundled the whole repository, including editor configuration and a duplicate
+  copy of the plugin tree (1.6 MB down to 118 KB). The wheel is unchanged.
+- Updated dead GREAT links in the `peak-annotation` and `multi-omics-integration` skills.
+
+### Added
+
+- Packaging regression test that fails if the `mcp` dependency loses its upper bound.
+
 ## [0.3.0-beta.1] - 2026-03-08
 
 Initial public beta release.
@@ -34,7 +79,7 @@ Initial public beta release.
 - **OS keyring credential management** with Fernet-encrypted file fallback
 - **Thread-safe SQLite tracker** with full transaction safety
 - **Streaming downloads** with 64KB chunks and SSRF-safe redirect validation
-- **506 tests** with 98% code coverage
+- **568 tests** with 98% code coverage
 - **34 literature reference documents** (~320 papers cataloged with DOI, PMID, key findings)
 - **9 scientist-facing vignettes** with real ENCODE API output
 - **GitHub Actions CI/CD** (pytest across Python 3.10–3.13, ruff lint, plugin validation)

encode_toolkit-0.3.2/CITATION.cff

@@ -0,0 +1,23 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+type: software
+title: "ENCODE Toolkit"
+abstract: "A Model Context Protocol server for programmatic access to ENCODE functional genomics data."
+authors:
+  - family-names: Mawla
+    given-names: Alex M.
+    orcid: "https://orcid.org/0000-0003-0907-464X"
+    affiliation: "Independent Researcher"
+version: 0.3.2
+date-released: "2026-09-20"
+license: AGPL-3.0-only
+repository-code: "https://github.com/ammawla/encode-toolkit"
+url: "https://github.com/ammawla/encode-toolkit"
+doi: "10.5281/zenodo.18917511"
+keywords:
+  - bioinformatics
+  - genomics
+  - ENCODE
+  - epigenomics
+  - MCP
+  - functional genomics