encode-toolkit 0.3.1__tar.gz → 0.3.3__tar.gz

{encode_toolkit-0.3.1 → encode_toolkit-0.3.3}/.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-0.3.3/CHANGELOG.md

@@ -0,0 +1,159 @@
+# Changelog
+
+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).
+
+## [0.3.3] - 2026-09-20
+
+Pipeline skills release. The Python package (MCP server) is functionally identical to 0.3.2.
+
+### Fixed
+
+- **All seven Nextflow pipelines now run on current Nextflow (validated on 26.04.6).** The
+  workflows mixed top-level statements with process definitions and four configs defined a
+  function, both of which the strict parser rejects. Validation and channel setup moved into the
+  `workflow` block, and `check_max` was replaced by `process.resourceLimits`.
+- **ChIP-seq**: the workflow called each process twice (samples, then controls), which Nextflow
+  does not allow, so it could not start. Controls now go through the same calls and are split
+  off before peak calling, where they are pooled. `--control` is optional. Signal tracks now
+  receive the sample ID they were missing.
+- **CUT&RUN**: SEACR was given the control BAM instead of a control bedGraph; spike-in scale
+  factors were computed but never applied to the signal track; `--seacr_mode` was ignored;
+  MACS2 peak calling always failed on a no-op `mv`; fragments were extracted from a
+  coordinate-sorted BAM, which drops most read pairs; `--control` and chromosome sizes were
+  not staged into tasks.
+- **DNase-seq**: Hotspot2 was called with options it does not have and without its mandatory
+  center-sites file; the image pinned a Hotspot2 tag that does not exist and lacked `modwt`
+  and `bc`. Footprinting could pair a BAM with another sample's peaks. `--hotspot_index` is
+  replaced by `--hotspot_center_sites` and `--hotspot_mappable`.
+  HINT footprinting needs an RGT data directory that the container's unprivileged user could
+  never find; it is now an explicit input, `--rgt_data`, checked before the run starts.
+- **WGBS**: the bedMethyl conversion divided by zero on MethylDackel's header line, so
+  extraction always failed; only CpG was converted although CHG and CHH were promised;
+  `--no_overlap` toggled `--mergeContext`, which is unrelated to mate overlap (renamed
+  `--merge_context`). bedMethyl score and strand now follow the ENCODE format.
+- **RNA-seq**: the RSEM reference is a file prefix but was required to be a directory.
+- **ATAC-seq**: the BAM index was not passed to the Tn5 shift step, which `alignmentSieve`
+  requires; the mitochondrial fraction used `bc`, which the image lacked, and silently wrote an
+  empty value; duplication metrics were never published. The workflow now states that it needs
+  paired-end reads instead of filtering every single-end read away.
+- **Hi-C**: `pairtools sort` was given a temporary directory that was never created. HiCCUPS
+  now runs its CPU mode by default, because the image has no CUDA runtime (`--hiccups_gpu`).
+- **IDR** (ChIP-seq, ATAC-seq) picked two peak files in arbitrary order and crashed with a
+  single replicate. The pair is now sorted, and IDR is skipped below two replicates.
+- **Pipeline images had never been built.** Beyond missing `build-essential`, `unzip`, `bc`, and
+  Boost: `idr`, `trim-galore`, and `phantompeakqualtools` are not PyPI packages; `deeptools
+  3.5.4` was never published; BWA 0.7.17 does not link with current GCC (now 0.7.18); Picard 3
+  needs Java 17; MethylDackel needs libBigWig; SEACR could not find its R script through a
+  symlink; RGT 0.13.2 and pairtools 1.0.3 no longer install (now 1.0.2 and 1.1.2). Index
+  prefixes are resolved from staged files, so cloud executors work.
+- **Conda environment files** pinned packages that do not exist (`hotspot2`, `hint`, `f-seq2`)
+  or cannot be installed together. All seven now solve, and the Anaconda `defaults` channel is
+  no longer used.
+- Pipelines referenced container images that do not exist. Each config now uses an image built
+  from the skill's own Dockerfile, with a fixed tag and a `--container` override.
+- `gcp` profiles used the retired `google-lifesciences` executor; they now use `google-batch`.
+- QC references: `samtools view` needs `-L` for a BED file; the WGBS coverage one-liner never
+  counted bases at 5x or more.
+
+### Changed
+
+- **Removed parameters that had no effect**: `--aligner` and `--lambda_genome` (WGBS),
+  `--motif_db` (DNase-seq), `--restriction_site` (Hi-C), `--gtf` (RNA-seq). The skills now
+  describe what the workflows actually do.
+- `install-nextflow.sh` installs a pinned Nextflow release and verifies its SHA-256 before use,
+  instead of piping a remote script into a shell. It no longer fails when the install
+  directory is not on the `PATH`.
+- `install-python-packages.sh` installs against `constraints.txt`, a lock file with exact
+  versions for Python 3.10+, generated from `requirements.in`.
+- The pipeline guide now separates the official ENCODE WDL pipelines from this toolkit's own
+  Nextflow implementations, and no longer cites repositories or images that do not exist.
+  Pipeline images are no longer labelled as maintained by the ENCODE DCC.
+
+### Added
+
+- `Pipelines` CI workflow: `nextflow lint`, `nextflow run -preview` across parameter
+  combinations, profile resolution, a Docker build of every pipeline image with checks that
+  the tools each workflow calls are present and actually start, a dry-run solve of every conda
+  environment, shellcheck, and a `skills/` vs `plugin/skills/` identity check.
+
+## [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.
+
+### Features
+
+- **20 MCP tools** for searching, downloading, and tracking ENCODE data
+  - Search experiments and files with comprehensive filters and pagination
+  - Download files with MD5 verification, concurrent downloads, and directory organization
+  - Local experiment tracking with SQLite (publications, pipelines, quality metrics)
+  - Cross-reference with PubMed, bioRxiv, ClinicalTrials.gov, GEO
+  - Citation export (BibTeX, RIS) for reference managers
+  - Data provenance chain for derived files
+  - Batch download with dry-run preview
+
+- **47 skills** across 10 categories
+  - Core: setup, search, download, track, cross-reference
+  - Analysis: quality assessment, integrative analysis, regulatory elements, epigenome profiling, compare biosamples, visualization, motif analysis, peak annotation, batch analysis
+  - Functional genomics: CRISPR/MPRA/STARR-seq screen analysis
+  - Data aggregation: histone, accessibility, Hi-C, methylation
+  - External databases: UCSC, GEO, gnomAD, Ensembl, GTEx, ClinVar, CELLxGENE, GWAS Catalog, JASPAR
+  - Workflows: provenance, citations, variant annotation, pipelines, single-cell, disease research, publication trust, bioinformatics installer, scientific writing, liftover coordinates
+  - Pipeline execution: ChIP-seq, ATAC-seq, RNA-seq, WGBS, Hi-C, DNase-seq, CUT&RUN (Nextflow + Docker)
+  - Meta-analysis: scRNA-seq meta-analysis, multi-omics integration
+
+- **Async ENCODE API client** with retry logic, 1-hour TTL cache, and rate limiting
+- **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
+- **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-0.3.1 → encode_toolkit-0.3.3}/CITATION.cff

@@ -8,7 +8,7 @@ authors:
     given-names: Alex M.
     orcid: "https://orcid.org/0000-0003-0907-464X"
     affiliation: "Independent Researcher"
-version: 0.3.1
+version: 0.3.3
 date-released: "2026-09-20"
 license: AGPL-3.0-only
 repository-code: "https://github.com/ammawla/encode-toolkit"

{encode_toolkit-0.3.1 → encode_toolkit-0.3.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: encode-toolkit
-Version: 0.3.1
+Version: 0.3.3
 Summary: MCP server for querying and downloading ENCODE Project genomics data directly from Claude
 Project-URL: Homepage, https://github.com/ammawla/encode-toolkit
 Project-URL: Repository, https://github.com/ammawla/encode-toolkit
@@ -37,7 +37,7 @@ Description-Content-Type: text/markdown
 
 [![License: AGPL-3.0](https://img.shields.io/badge/license-AGPL--3.0-green.svg)](LICENSE)
 [![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
-[![Version](https://img.shields.io/badge/version-0.3.1-green)](CHANGELOG.md)
+[![Version](https://img.shields.io/badge/version-0.3.3-green)](CHANGELOG.md)
 [![Status](https://img.shields.io/badge/status-beta-yellow)]()
 [![Skills](https://img.shields.io/badge/skills-47-orange)](docs/skill-vignettes/)
 [![Tools](https://img.shields.io/badge/MCP_tools-20-purple)](src/encode_connector/server/main.py)

{encode_toolkit-0.3.1 → encode_toolkit-0.3.3}/README.md

@@ -4,7 +4,7 @@
 
 [![License: AGPL-3.0](https://img.shields.io/badge/license-AGPL--3.0-green.svg)](LICENSE)
 [![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
-[![Version](https://img.shields.io/badge/version-0.3.1-green)](CHANGELOG.md)
+[![Version](https://img.shields.io/badge/version-0.3.3-green)](CHANGELOG.md)
 [![Status](https://img.shields.io/badge/status-beta-yellow)]()
 [![Skills](https://img.shields.io/badge/skills-47-orange)](docs/skill-vignettes/)
 [![Tools](https://img.shields.io/badge/MCP_tools-20-purple)](src/encode_connector/server/main.py)

{encode_toolkit-0.3.1 → encode_toolkit-0.3.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "encode-toolkit"
-version = "0.3.1"
+version = "0.3.3"
 description = "MCP server for querying and downloading ENCODE Project genomics data directly from Claude"
 readme = "README.md"
 license = "AGPL-3.0-only"

{encode_toolkit-0.3.1 → encode_toolkit-0.3.3}/src/encode_connector/client/constants.py

@@ -17,7 +17,7 @@ try:
 
     _version = importlib.metadata.version("encode-toolkit")
 except importlib.metadata.PackageNotFoundError:
-    _version = "0.3.1"
+    _version = "0.3.3"
 USER_AGENT = f"encode-toolkit/{_version} (MCP; +https://github.com/ammawla/encode-toolkit)"
 
 # Keyring service name for credential storage

encode_toolkit-0.3.1/CHANGELOG.md

@@ -1,69 +0,0 @@
-# Changelog
-
-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).
-
-## [0.3.1] - 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.
-
-### Features
-
-- **20 MCP tools** for searching, downloading, and tracking ENCODE data
-  - Search experiments and files with comprehensive filters and pagination
-  - Download files with MD5 verification, concurrent downloads, and directory organization
-  - Local experiment tracking with SQLite (publications, pipelines, quality metrics)
-  - Cross-reference with PubMed, bioRxiv, ClinicalTrials.gov, GEO
-  - Citation export (BibTeX, RIS) for reference managers
-  - Data provenance chain for derived files
-  - Batch download with dry-run preview
-
-- **47 skills** across 10 categories
-  - Core: setup, search, download, track, cross-reference
-  - Analysis: quality assessment, integrative analysis, regulatory elements, epigenome profiling, compare biosamples, visualization, motif analysis, peak annotation, batch analysis
-  - Functional genomics: CRISPR/MPRA/STARR-seq screen analysis
-  - Data aggregation: histone, accessibility, Hi-C, methylation
-  - External databases: UCSC, GEO, gnomAD, Ensembl, GTEx, ClinVar, CELLxGENE, GWAS Catalog, JASPAR
-  - Workflows: provenance, citations, variant annotation, pipelines, single-cell, disease research, publication trust, bioinformatics installer, scientific writing, liftover coordinates
-  - Pipeline execution: ChIP-seq, ATAC-seq, RNA-seq, WGBS, Hi-C, DNase-seq, CUT&RUN (Nextflow + Docker)
-  - Meta-analysis: scRNA-seq meta-analysis, multi-omics integration
-
-- **Async ENCODE API client** with retry logic, 1-hour TTL cache, and rate limiting
-- **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
-- **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)