encode-toolkit 0.3.0b5__tar.gz → 0.3.0b6__tar.gz

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Files changed (283) hide show
  1. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/.claude-plugin/plugin.json +1 -1
  2. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/.gitignore +12 -0
  3. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/PKG-INFO +1 -1
  4. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/package.json +1 -1
  5. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/pyproject.toml +1 -1
  6. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/server.json +3 -3
  7. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/.claude/settings.json +0 -0
  8. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/.claude-plugin/marketplace.json +0 -0
  9. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/.env.example +0 -0
  10. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/.github/ISSUE_TEMPLATE/bug_report.yml +0 -0
  11. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/.github/ISSUE_TEMPLATE/feature_request.yml +0 -0
  12. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/.github/PULL_REQUEST_TEMPLATE.md +0 -0
  13. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/.github/dependabot.yml +0 -0
  14. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/.github/workflows/lint.yml +0 -0
  15. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/.github/workflows/release.yml +0 -0
  16. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/.github/workflows/test.yml +0 -0
  17. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/.github/workflows/validate.yml +0 -0
  18. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/.mcp.json +0 -0
  19. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/.pre-commit-config.yaml +0 -0
  20. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/CHANGELOG.md +0 -0
  21. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/CLAUDE.md +0 -0
  22. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/CONTRIBUTING.md +0 -0
  23. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/Dockerfile +0 -0
  24. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/LICENSE +0 -0
  25. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/PRIVACY.md +0 -0
  26. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/README.md +0 -0
  27. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/SECURITY.md +0 -0
  28. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/conftest.py +0 -0
  29. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/SHOWCASE.md +0 -0
  30. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/api-reference.md +0 -0
  31. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/icon.svg +0 -0
  32. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/integrations.md +0 -0
  33. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/security.md +0 -0
  34. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/accessibility-aggregation.md +0 -0
  35. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/batch-analysis.md +0 -0
  36. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/cellxgene-context.md +0 -0
  37. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/cite-encode.md +0 -0
  38. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/clinvar-annotation.md +0 -0
  39. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/compare-biosamples.md +0 -0
  40. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/cross-reference.md +0 -0
  41. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/data-provenance.md +0 -0
  42. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/disease-research.md +0 -0
  43. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/download-encode.md +0 -0
  44. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/ensembl-annotation.md +0 -0
  45. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/epigenome-profiling.md +0 -0
  46. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/geo-connector.md +0 -0
  47. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/gnomad-variants.md +0 -0
  48. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/gtex-expression.md +0 -0
  49. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/gwas-catalog.md +0 -0
  50. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/hic-aggregation.md +0 -0
  51. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/histone-aggregation.md +0 -0
  52. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/integrative-analysis.md +0 -0
  53. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/jaspar-motifs.md +0 -0
  54. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/methylation-aggregation.md +0 -0
  55. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/motif-analysis.md +0 -0
  56. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/multi-omics-integration.md +0 -0
  57. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/peak-annotation.md +0 -0
  58. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/pipeline-atacseq.md +0 -0
  59. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/pipeline-chipseq.md +0 -0
  60. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/pipeline-cutandrun.md +0 -0
  61. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/pipeline-dnaseseq.md +0 -0
  62. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/pipeline-guide.md +0 -0
  63. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/pipeline-hic.md +0 -0
  64. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/pipeline-rnaseq.md +0 -0
  65. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/pipeline-wgbs.md +0 -0
  66. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/publication-trust.md +0 -0
  67. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/quality-assessment.md +0 -0
  68. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/regulatory-elements.md +0 -0
  69. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/scrna-meta-analysis.md +0 -0
  70. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/search-encode.md +0 -0
  71. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/setup.md +0 -0
  72. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/single-cell-encode.md +0 -0
  73. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/track-experiments.md +0 -0
  74. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/ucsc-browser.md +0 -0
  75. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/variant-annotation.md +0 -0
  76. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/skill-vignettes/visualization-workflow.md +0 -0
  77. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/submission-examples.md +0 -0
  78. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/vignettes/01-discovery-and-search.md +0 -0
  79. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/vignettes/02-download-and-track.md +0 -0
  80. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/vignettes/03-epigenomics-workflow.md +0 -0
  81. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/vignettes/04-variant-and-disease.md +0 -0
  82. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/vignettes/05-expression-and-single-cell.md +0 -0
  83. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/vignettes/06-motif-and-regulatory.md +0 -0
  84. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/vignettes/07-3d-genome-and-methylation.md +0 -0
  85. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/vignettes/08-pipeline-execution.md +0 -0
  86. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/vignettes/09-cross-reference-and-integration.md +0 -0
  87. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/vignettes/_captured_output.md +0 -0
  88. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/docs/walkthrough.md +0 -0
  89. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/glama.json +0 -0
  90. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/index.js +0 -0
  91. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/accessibility-aggregation/SKILL.md +0 -0
  92. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/accessibility-aggregation/references/atac-vs-dnase.md +0 -0
  93. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/accessibility-aggregation/references/literature.md +0 -0
  94. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/accessibility-aggregation/scripts/validate_peaks.py +0 -0
  95. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/batch-analysis/SKILL.md +0 -0
  96. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/batch-analysis/references/literature.md +0 -0
  97. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/bioinformatics-installer/SKILL.md +0 -0
  98. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/bioinformatics-installer/environments/atacseq-env.yml +0 -0
  99. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/bioinformatics-installer/environments/chipseq-env.yml +0 -0
  100. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/bioinformatics-installer/environments/cutandrun-env.yml +0 -0
  101. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/bioinformatics-installer/environments/dnaseseq-env.yml +0 -0
  102. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/bioinformatics-installer/environments/hic-env.yml +0 -0
  103. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/bioinformatics-installer/environments/rnaseq-env.yml +0 -0
  104. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/bioinformatics-installer/environments/wgbs-env.yml +0 -0
  105. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/bioinformatics-installer/references/literature.md +0 -0
  106. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/bioinformatics-installer/scripts/install-nextflow.sh +0 -0
  107. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/bioinformatics-installer/scripts/install-python-packages.sh +0 -0
  108. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/bioinformatics-installer/scripts/install-r-packages.R +0 -0
  109. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/cellxgene-context/SKILL.md +0 -0
  110. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/cellxgene-context/references/literature.md +0 -0
  111. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/cite-encode/SKILL.md +0 -0
  112. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/cite-encode/references/literature.md +0 -0
  113. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/clinvar-annotation/SKILL.md +0 -0
  114. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/clinvar-annotation/references/literature.md +0 -0
  115. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/compare-biosamples/SKILL.md +0 -0
  116. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/compare-biosamples/references/literature.md +0 -0
  117. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/cross-reference/SKILL.md +0 -0
  118. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/cross-reference/references/literature.md +0 -0
  119. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/data-provenance/SKILL.md +0 -0
  120. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/data-provenance/references/literature.md +0 -0
  121. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/disease-research/SKILL.md +0 -0
  122. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/disease-research/references/literature.md +0 -0
  123. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/download-encode/SKILL.md +0 -0
  124. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/download-encode/references/literature.md +0 -0
  125. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/ensembl-annotation/SKILL.md +0 -0
  126. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/ensembl-annotation/references/literature.md +0 -0
  127. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/epigenome-profiling/SKILL.md +0 -0
  128. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/epigenome-profiling/references/literature.md +0 -0
  129. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/functional-screen-analysis/SKILL.md +0 -0
  130. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/functional-screen-analysis/references/literature.md +0 -0
  131. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/geo-connector/SKILL.md +0 -0
  132. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/geo-connector/references/literature.md +0 -0
  133. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/gnomad-variants/SKILL.md +0 -0
  134. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/gnomad-variants/references/literature.md +0 -0
  135. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/gtex-expression/SKILL.md +0 -0
  136. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/gtex-expression/references/literature.md +0 -0
  137. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/gwas-catalog/SKILL.md +0 -0
  138. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/gwas-catalog/references/literature.md +0 -0
  139. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/hic-aggregation/SKILL.md +0 -0
  140. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/hic-aggregation/references/literature.md +0 -0
  141. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/hic-aggregation/references/loop-caller-comparison.md +0 -0
  142. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/hic-aggregation/scripts/validate_loops.py +0 -0
  143. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/histone-aggregation/SKILL.md +0 -0
  144. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/histone-aggregation/references/broad-vs-narrow.md +0 -0
  145. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/histone-aggregation/references/histone-marks-reference.md +0 -0
  146. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/histone-aggregation/references/literature.md +0 -0
  147. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/histone-aggregation/references/signal-filtering.md +0 -0
  148. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/histone-aggregation/scripts/validate_peaks.py +0 -0
  149. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/integrative-analysis/SKILL.md +0 -0
  150. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/integrative-analysis/references/literature.md +0 -0
  151. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/jaspar-motifs/SKILL.md +0 -0
  152. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/jaspar-motifs/references/literature.md +0 -0
  153. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/liftover-coordinates/SKILL.md +0 -0
  154. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/liftover-coordinates/references/literature.md +0 -0
  155. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/methylation-aggregation/SKILL.md +0 -0
  156. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/methylation-aggregation/references/hmr-definitions.md +0 -0
  157. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/methylation-aggregation/references/literature.md +0 -0
  158. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/methylation-aggregation/scripts/validate_methylation.py +0 -0
  159. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/motif-analysis/SKILL.md +0 -0
  160. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/motif-analysis/references/literature.md +0 -0
  161. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/multi-omics-integration/SKILL.md +0 -0
  162. {encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/skills/multi-omics-integration/references/literature.md +0 -0
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{encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/.claude-plugin/plugin.json RENAMED
@@ -1,7 +1,7 @@
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  {
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  "name": "encode-toolkit",
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  "description": "20 ENCODE API tools + 48 expert skills for genomics research. Search experiments, download files with MD5 verification, run pipelines, and cross-reference 14 databases.",
4
- "version": "0.3.0-beta.5",
4
+ "version": "0.3.0-beta.6",
5
5
  "author": {
6
6
  "name": "Dr. Alex M. Mawla, PhD",
7
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  "email": "ammawla@ucdavis.edu"
{encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/.gitignore RENAMED
@@ -51,6 +51,18 @@ data/
51
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  # MCP Registry tokens
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  .mcpregistry_*
53
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54
+ # Generated PDFs
55
+ *.pdf
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+
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+ # PDF build artifacts
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+ docs/pdf-build/
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+
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+ # Smithery
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+ .smithery/
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+
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+ # npm lock (thin wrapper, no deps to lock)
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+ package-lock.json
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+
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  # OS
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  .DS_Store
56
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  Thumbs.db
{encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: encode-toolkit
3
- Version: 0.3.0b5
3
+ Version: 0.3.0b6
4
4
  Summary: MCP server for querying and downloading ENCODE Project genomics data directly from Claude
5
5
  Project-URL: Homepage, https://github.com/ammawla/encode-toolkit
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  Project-URL: Repository, https://github.com/ammawla/encode-toolkit
{encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/package.json RENAMED
@@ -1,6 +1,6 @@
1
1
  {
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  "name": "encode-toolkit",
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- "version": "0.3.0-beta.5",
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+ "version": "0.3.0-beta.6",
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  "mcpName": "io.github.ammawla/encode-toolkit",
5
5
  "description": "ENCODE Toolkit — Genomics research infrastructure with 20 MCP tools, 47 skills, 14 database integrations, and 7 pipelines for Claude Code",
6
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  "main": "index.js",
{encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/pyproject.toml RENAMED
@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
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  [project]
6
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  name = "encode-toolkit"
7
- version = "0.3.0b5"
7
+ version = "0.3.0b6"
8
8
  description = "MCP server for querying and downloading ENCODE Project genomics data directly from Claude"
9
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  readme = "README.md"
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  license = "CC-BY-NC-ND-4.0"
{encode_toolkit-0.3.0b5 → encode_toolkit-0.3.0b6}/server.json RENAMED
@@ -7,12 +7,12 @@
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  "url": "https://github.com/ammawla/encode-toolkit",
8
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  "source": "github"
9
9
  },
10
- "version": "0.3.0-beta.5",
10
+ "version": "0.3.0-beta.6",
11
11
  "packages": [
12
12
  {
13
13
  "registryType": "npm",
14
14
  "identifier": "encode-toolkit",
15
- "version": "0.3.0-beta.5",
15
+ "version": "0.3.0-beta.6",
16
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  "transport": {
17
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  "type": "stdio"
18
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  }
@@ -20,7 +20,7 @@
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  {
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  "registryType": "pypi",
22
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  "identifier": "encode-toolkit",
23
- "version": "0.3.0b5",
23
+ "version": "0.3.0b6",
24
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  "transport": {
25
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  "type": "stdio"
26
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  }