Issues

• Observations from one agent build: a complete mirror of the sources, but no structure for the questions the graph must answer

  biocypher/biotope#85 · Filter by author VladSam42 opened on Oct 30, 2026

• Two new identical files in one dataset are described once

  biocypher/biotope#84 · Filter by author VladSam42 opened on Oct 27, 2026

• A dataset added inside another dataset's folder is described twice

  biocypher/biotope#83 · Filter by author VladSam42 opened on Oct 27, 2026

• Nothing reports records extracted from an older version of a document

  biocypher/biotope#82 · Filter by author VladSam42 opened on Oct 27, 2026

• The .gitignore that init writes does not ignore .env

  biocypher/biotope#81 · Filter by author VladSam42 opened on Oct 27, 2026

• Extraction marks empty and implausible records as supported

  biocypher/biotope#80 · Filter by author VladSam42 opened on Oct 27, 2026
  1

• One-dimensional JSON lists generate as opaque fields

  biocypher/biotope#78 · Filter by author VladSam42 opened on Oct 27, 2026

• A rebake rewrites dateCreated, and the generated citeAs cites Unknown

  biocypher/biotope#77 · Filter by author VladSam42 opened on Oct 27, 2026

• Small problems found in the InTRAC build: whitespace IDs, missing-value tokens, duplicate columns, annotate validate

  biocypher/biotope#76 · Filter by author VladSam42 opened on Oct 26, 2026
  1

• extract run cannot keep one document of a dataset away from the model

  biocypher/biotope#75 · Filter by author VladSam42 opened on Oct 26, 2026
  1

• Extraction reports carry no token counts or cost

  biocypher/biotope#74 · Filter by author VladSam42 opened on Oct 26, 2026

• A JSON object keyed by data values puts those values into committed descriptions and source code

  biocypher/biotope#73 · Filter by author VladSam42 opened on Oct 26, 2026
  2

• Rebake fails when a file is named like one of croissant-baker's position IDs

  biocypher/biotope#72 · Filter by author VladSam42 opened on Oct 26, 2026

• Baker describes each Parquet partition as its own file beside the FileSet

  biocypher/biotope#71 · Filter by author VladSam42 opened on Oct 26, 2026

• Annotation requirements set by biotope config are no longer checked

  biocypher/biotope#70 · Filter by author VladSam42 opened on Oct 26, 2026
  1

• Scaffold and docs pin biotope[graph]<0.11, which rejects the release B2 makes

  biocypher/biotope#69 · Filter by author VladSam42 opened on Oct 26, 2026

• Extraction adds top-level extraction/ and extracted/ folders to the project

  biocypher/biotope#66 · Filter by author VladSam42 opened on Oct 26, 2026

• biotope add: warn when Git ignores a manifest it writes

  biocypher/biotope#57 · Filter by author VladSam42 opened on Oct 23, 2026

• Roadmap: unstructured data and REACH sprint

  biocypher/biotope#53 · Filter by author VladSam42 opened on Oct 22, 2026

• Decisions left open in #46: skipped copies, dependency lists, reserved names

  biocypher/biotope#50 · Filter by author VladSam42 opened on Sep 28, 2026

• fix: files Baker describes in a directory manifest are reported untracked

  biocypher/biotope#48 · Filter by author VladSam42 opened on Sep 28, 2026

• fix(add): distinct unclaimed files can share one FileObject @id

  biocypher/biotope#47 · Filter by author VladSam42 opened on Sep 28, 2026

• Add biotope audit for cluster-side compliance scans

  biocypher/biotope#26 · Filter by author slobentanzer opened on May 25, 2026

• [Feature] Split annotate.py to smaller files

  enhancement
  biocypher/biotope#17 · Filter by author peymanvahidi opened on Dec 2, 2025
  1

• [Feature] Checksum algorithm: auto

  enhancement
  biocypher/biotope#12 · Filter by author slobentanzer opened on Aug 5, 2025