chore(main): release 0.1.0

[github-actions]

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0.1.0 (2026-07-21)

Features

• /assembly/intent endpoint returns YAML format (626e844)
• add assembly_run abstraction, referencing unique github_repo + git_commit pair (fef74c9)
• add base_url to reads schema and assembly manifest, update tests (e3f5c52)
• add batch broker endpoint to request multiple objects by id (609b704)
• add bulk upsert taxonomy-info endpoint, add assembly_id to manifest (2f42b1b)
• add dependency for requests library (20274c9)
• add endpoint to bulk insert specimens, update sample table to only require bpa_sample_id for derived samples (248de31)
• add endpoint to cancel an assembly_run (e12ea65)
• add endpoint to look up specimen by specimen_id + tax_id (96910e8)
• add function to determine data_type for an assembly, and a matching endpoint (c1f54a8)
• add migration for timestamptz and tolid and a migration doc (69ee3bf)
• add ncbi taxonomy information for organisms (a4c621f)
• add new organism fields (6bbef3a)
• add new organism fields and improve broker endpoints (cc804f5)
• add POST /claim endpoint to lease individual sample/experiments/reads objs (no organism_key required) (da14705)
• add project_id fk to sample_submission table (b35c2b1)
• add project_id fk to sample_submission table (c2154ca)
• add rna-seq data type (illumina only) (471c214)
• add sample metadata to manifest (846baf0)
• add shim for legacy data structure, until data mapper is updated (dbf9bb1)
• add source reads to qc_reads (4177cf2)
• add source reads to qc_reads (a019d0f)
• add source reads to qc_reads (db58c93)
• add source_read_file_checksums to qc_reads, validating this and bpa_package_id (786af65)
• add specimen-level samples (0d61033)
• add specimen/derived samples to the db schema, models, endpoints (bf2840c)
• add support for tolids (cfd4797)
• add taxon_info rows iff ncbi fetch succeeds, log ncbi failures in taxon_info/bulk-insert (459115c)
• add taxonomic information about organisms (5a80236)
• add taxonomy data from data mapper into database, incl CRUD and bulk-ingest endpoints (36946ee)
• add taxonomy info from data mapper to assembly pipelines manifest (b683e3a)
• add taxonomy lookup code (0b59f73)
• add tol_id to assembly schema and models etc. (00fe18c)
• add tolid table and endpoints for handling tolid requests (1d6989c)
• add tolid table and endpoints for handling tolid requests (30ce8f9)
• add uniqueness constraint on tax_id + specimen_id for specimen samples (2dcbf1a)
• add version endpoint (a45650f)
• allow multiple hi-c specimens in assembly manifest (ee216ae)
• archive old migrations (24e8e93)
• backfill mitohifi_reference_species with values from mito_ref (ddc1df2)
• consolidate references to project and study accessions, which are usually used interchangeably (0ac67c5)
• create new submission draft after failed submission to ENA (2b527b6)
• create new submission object when submission fails to ENA (1c017a8)
• docs (a7450e0)
• fix ncbi lookup logic, add ncbi lookup to bulk-insert ops, add tests (d4cc0bd)
• generate assembly manifest (for pacbio and hi-C reads) (665a633)
• get all samples, experiments and reads for specimen_id (a219de1)
• get all samples, experiments and reads for specimen_id (70389af)
• handle accessino pre-reqs for broker endpoints (ee5c69d)
• handle accession pre-reqs for broker endpoints (baa0d1d)
• implement genome notes with versioning (b865bac)
• improve error messaging for bulk-insert endpoints (c5aca3e)
• include assembly_run.id in manifests, and require assembly_run id for for /cancel (bc1dcac)
• include qc_reads in aggregate endpoint (dbe44c0)
• make assembly runs unique on github_repo + git_commit, and improve debugging (83bcca4)
• make assembly runs unique on github_repo + git_commit, and improve debugging (15ecc50)
• make scientific_name optional in schema (this may be changed when we fetch data from NCBI) (e190dd5)
• new data (01f0766)
• normalise fk references for submissioon objects, denormalise accession fields (14e5c03)
• only require attempt_id as path param in /broker/report endpoint (affb397)
• re-introduce o.scientific_name, populate from ti.ncbi_sci.._name or else o.bpa_sci.._name (b801470)
• rebase update to support qc reads (31b9c02)
• redesign genome notes and assemblies (dd7115e)
• refactor migrations (afaa9bc)
• remove backwards compatibility shim (8398098)
• remove external_run_id from stage_runs (3329e01)
• remove file extension validation for pacbio files, since no equivalent check on ont or hi-c (b2fe161)
• remove sample_id param for /intent endpoint - canopy will select optimal sample for tax_id (dbf32eb)
• remove study_accession references (0b4dd81)
• remove unnecessary function, remove repeated db lookup (78e3ca4)
• remove validation_hints from broker endpoint, broker can decide this (b6aa696)
• return meaningful error when reporting entities whose accessions already exist in registry (d988950)
• return sample.kind from /broker/claim endpoint (e9b3b53)
• return scientific_name (83eca1b)
• returns meaningful error for duplicate reports - same stage and assembly run (64284e1)
• seperate broker contract endpoints and add tests (270657d)
• set organism_part to WHOLE ORGANISM for specimen samples (88deee4)
• sync schema with database, update AssemblyStageRun model (107fe6a)
• tighten access token expiration time (7934e7a)
• tighten auth and update outdated projects crud endpoints (4d394f9)
• update accession registry references (efae4c4)
• update assembly flow from requesting manifest to reporting results (5db2cc0)
• update assembly models to meet new requirements (ee75d58)
• update assembly models to meet new(est) requirements (f936379)
• update broker (33915eb)
• update broker (e62cc53)
• update manifest fields (3d1ecac)
• update manifest request flow (49590ed)
• update manifest, bpa base url field (831a48c)
• update ncbi information for taxonomy info objects that already exist (0c19c04)
• update organism schema and refine assembly versioning (e016da5)
• update organism.scientific_name after importing taxonomy_info (b6503ef)
• update policies, update naming, add CRUD endpoints for qc_reads (7fa2c24)
• update qc_read_file fields (2d317cd)
• update references from submission tables (56bd98a)
• update reporting process for qc reads and assembly pipelines (rebased) (bd794d2)
• update response from broker endpoints (f50a38a)
• update results reporting and assembly manifest generation (18a4564)
• update shape of body for bulk-insert specimen samples endpoint to match mapper output (c38fba2)
• update submission table references (2f9ba27)
• update taxonomy and organism fields in schemas and models (b50566f)
• update taxonomy_info and organism schema, adding taxonomy details from ncbi (12a8335)
• update versioning strategy, use json for manifests, require specimen_ids for assemblies (514370c)
• updates assembly stage run to rmv "status" and rename "stats" to "data" (0c437db)
• uplift error handling, tests, auth policy (9120188)

Bug Fixes

• /claim endpoint to accept experiments and read ids (28d2681)
• address codepilot review (9f8253b)
• allow no request body on endpoint where all request body fields are optional (95bfdb3)
• catch error thrown from determine_assembly_data_types in assembly/intent endpoint (81da31a)
• consolidate auth policy, add centralised error handling module and pagination (9df3b9f)
• consolidate auth policy, add centralised error handling module and pagination (1db5e59)
• Dockerfile (01f1be5)
• enforce 72-byte limit at user create/update (44b9bbb)
• enforce expiry of leased items on before new lease request (91dbbbc)
• fix db readiness probe (175f9d2)
• fix migration (575f060)
• fix migration, specimen lookup and add logging (305b1a5)
• import if an experiment already exists in the db, still add any valid related runs to the db (b053cee)
• improve error message (c547d04)
• improve errors returned from ingestion endpoints (32161f4)
• improve test for the 72 byte password limitation in bcrypt (974b29d)
• linting (866797d)
• make references to entity ids and entity submission ids consistent for broker endpoints (660e132)
• make references to entity ids and entity submission ids consistent for broker endpoints (c931fd0)
• remove qc_reads from specimens discovery endpoint (33f4465)
• remove redundant or outdated taxonomy columns (1f6e0d2)
• rename testing files (30bb35d)
• resolve passlib + bcrypt incompatibility (6ad8cd0)
• shorten migration name to meet alembic constraint of 32 chars (cb875bb)
• shorten migration version label (14bd6b3)
• shorten migration version label (546fdef)
• shorten migration version label, linting (77a58a6)
• some incorrect fields and move default value from db schema to code (5329976)
• update accepted file types for assemblies (05c44b6)
• update data types check, update tests, allow same specimen_id for hi-c + long read data (9f87c13)
• update data types check, update tests, allow same specimen_id for hi-c + long read data (e81716d)
• update read field from "base_url" to "bioplatforms_base_url" to match atol schema (4034aa2)
• update references to organism key, and resolve conflicting status field (6b3bdc4)
• update stale CRUD endpoints (3ce1982)
• update tests (f85fe77)
• uplift testing, tighten auth policies, fix stale CRUD endpoints (951cb20)

Performance Improvements

• parallelize NCBI API calls in bulk taxonomy import (6ce8f7f)
• parallelize parent and organelle lookups within each organism (11dcbba)

Documentation

• add PR template for repo (7a4d695)
• known_issues (c344476)
• known_issues (30a0fdf)
• organism.scientific_name and taxonomy_info.last_synced_at behaviour (711659a)
• update docs (7f89c24)
• update docs (5e5e2b3)
• update docs (cb6c67c)
• update docs (52bcb18)
• update handover docs (58cee85)
• update handover docs (46b5199)
• update handover docs (d4f9e98)

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