From 38452267cd6a2bf64593f0a843d11c939127896b Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Tue, 21 Jul 2026 03:45:31 +0000
Subject: [PATCH] chore(main): release 0.1.0

---
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+# Changelog
+
+## 0.1.0 (2026-07-21)
+
+
+### Features
+
+* /assembly/intent endpoint returns YAML format ([626e844](https://github.com/AustralianBioCommons/atol-canopy/commit/626e84479d36c9e7b656dae920f106b1151fc990))
+* add assembly_run abstraction, referencing unique github_repo + git_commit pair ([fef74c9](https://github.com/AustralianBioCommons/atol-canopy/commit/fef74c9a6cf1d049a05f46db5650395d8500b947))
+* add base_url to reads schema and assembly manifest, update tests ([e3f5c52](https://github.com/AustralianBioCommons/atol-canopy/commit/e3f5c525e7369428505b0138845da3cab7eb1239))
+* add batch broker endpoint to request multiple objects by id ([609b704](https://github.com/AustralianBioCommons/atol-canopy/commit/609b7045c6d40983bbf440188c5dcbc10a3e57e9))
+* add bulk upsert taxonomy-info endpoint, add assembly_id to manifest ([2f42b1b](https://github.com/AustralianBioCommons/atol-canopy/commit/2f42b1b5c228707b29fab17c140c8b3824c3ff54))
+* add dependency for requests library ([20274c9](https://github.com/AustralianBioCommons/atol-canopy/commit/20274c90675f2d4395939c5a971bed2f93b767ae))
+* add endpoint to bulk insert specimens, update sample table to only require bpa_sample_id for derived samples ([248de31](https://github.com/AustralianBioCommons/atol-canopy/commit/248de31a587b8142512fe21a8d43a47968833c52))
+* add endpoint to cancel an assembly_run ([e12ea65](https://github.com/AustralianBioCommons/atol-canopy/commit/e12ea6594589141ba4d36e700eadf5842940f877))
+* add endpoint to look up specimen by specimen_id + tax_id ([96910e8](https://github.com/AustralianBioCommons/atol-canopy/commit/96910e87daf446538264022fdd417852047fcb98))
+* add function to determine data_type for an assembly, and a matching endpoint ([c1f54a8](https://github.com/AustralianBioCommons/atol-canopy/commit/c1f54a852ff16c55bd9ed6cbb19df6f97fa40d82))
+* add migration for timestamptz and tolid and a migration doc ([69ee3bf](https://github.com/AustralianBioCommons/atol-canopy/commit/69ee3bf5289c52d254f234ed97384b866543606d))
+* add ncbi taxonomy information for organisms ([a4c621f](https://github.com/AustralianBioCommons/atol-canopy/commit/a4c621fe414e0481e2411ef530c772c658e8cf82))
+* add new organism fields ([6bbef3a](https://github.com/AustralianBioCommons/atol-canopy/commit/6bbef3ae92a96128c975926b9a58252343affc13))
+* add new organism fields and improve broker endpoints ([cc804f5](https://github.com/AustralianBioCommons/atol-canopy/commit/cc804f5dfc7a3e94629618c7195c64b85a0599d3))
+* add POST /claim endpoint to lease individual sample/experiments/reads objs (no organism_key required) ([da14705](https://github.com/AustralianBioCommons/atol-canopy/commit/da147059ae6c5200b35d04f9e332f8764b89ed14))
+* add project_id fk to sample_submission table ([b35c2b1](https://github.com/AustralianBioCommons/atol-canopy/commit/b35c2b1340da95a18aab3a2f64b9863e76603007))
+* add project_id fk to sample_submission table ([c2154ca](https://github.com/AustralianBioCommons/atol-canopy/commit/c2154ca0dcbaa4d8e98e26f31c8a9a00879d6d0e))
+* add rna-seq data type (illumina only) ([471c214](https://github.com/AustralianBioCommons/atol-canopy/commit/471c214d33616651ba1bbf5f7467a137b3250b45))
+* add sample metadata to manifest ([846baf0](https://github.com/AustralianBioCommons/atol-canopy/commit/846baf09bc71cce6fa2ecb73bc116437a7418755))
+* add shim for legacy data structure, until data mapper is updated ([dbf9bb1](https://github.com/AustralianBioCommons/atol-canopy/commit/dbf9bb1806f74ebce59c577f0f6b1d05e4d143cc))
+* add source reads to qc_reads ([4177cf2](https://github.com/AustralianBioCommons/atol-canopy/commit/4177cf2e604b4fa8036d59c56d6d761d1391d2f4))
+* add source reads to qc_reads ([a019d0f](https://github.com/AustralianBioCommons/atol-canopy/commit/a019d0fdb081f53be0e7e7a3f380b35142be9267))
+* add source reads to qc_reads ([db58c93](https://github.com/AustralianBioCommons/atol-canopy/commit/db58c93546cbabd17500bf6f3eb9c79ef2929915))
+* add source_read_file_checksums to qc_reads, validating this and bpa_package_id ([786af65](https://github.com/AustralianBioCommons/atol-canopy/commit/786af65937bf4d6dc95e50ff995c1aed153879b2))
+* add specimen-level samples ([0d61033](https://github.com/AustralianBioCommons/atol-canopy/commit/0d61033a0887b2bd1bf075884e360d3501fa56af))
+* add specimen/derived samples to the db schema, models, endpoints ([bf2840c](https://github.com/AustralianBioCommons/atol-canopy/commit/bf2840cd4bac8aa78dcecf461059bebc80419fa2))
+* add support for tolids ([cfd4797](https://github.com/AustralianBioCommons/atol-canopy/commit/cfd4797c9bb58d423e885a4bce8e40e6f297b986))
+* add taxon_info rows iff ncbi fetch succeeds, log ncbi failures in taxon_info/bulk-insert ([459115c](https://github.com/AustralianBioCommons/atol-canopy/commit/459115cc22bf96d2b3e70d72e8e62b207e9d0e35))
+* add taxonomic information about organisms ([5a80236](https://github.com/AustralianBioCommons/atol-canopy/commit/5a80236e1518100bc6e14b967f0cac28fe416829))
+* add taxonomy data from data mapper into database, incl CRUD and bulk-ingest endpoints ([36946ee](https://github.com/AustralianBioCommons/atol-canopy/commit/36946ee7d0fe0c274192912188c60b231d26c9c1))
+* add taxonomy info from data mapper to assembly pipelines manifest ([b683e3a](https://github.com/AustralianBioCommons/atol-canopy/commit/b683e3a26e03118121cd7afbb9810e71125c002e))
+* add taxonomy lookup code ([0b59f73](https://github.com/AustralianBioCommons/atol-canopy/commit/0b59f73a3ea89bfdc3c10f0d9f797cb6de1c4cd2))
+* add tol_id to assembly schema and models etc. ([00fe18c](https://github.com/AustralianBioCommons/atol-canopy/commit/00fe18cb144de24eaeee0a870930302bd5e1519e))
+* add tolid table and endpoints for handling tolid requests ([1d6989c](https://github.com/AustralianBioCommons/atol-canopy/commit/1d6989cde30967d48ab49352697b0b483e85551e))
+* add tolid table and endpoints for handling tolid requests ([30ce8f9](https://github.com/AustralianBioCommons/atol-canopy/commit/30ce8f9466459ac7371e07cc5e4d77ffe10293b3))
+* add uniqueness constraint on tax_id + specimen_id for specimen samples ([2dcbf1a](https://github.com/AustralianBioCommons/atol-canopy/commit/2dcbf1af19b62c7f01451fe5cd79c472824035b8))
+* add version endpoint ([a45650f](https://github.com/AustralianBioCommons/atol-canopy/commit/a45650f58bbb3b36cb122b8b6fde9e5d62b4c45a))
+* allow multiple hi-c specimens in assembly manifest ([ee216ae](https://github.com/AustralianBioCommons/atol-canopy/commit/ee216ae6690db5a3fae3a54d794ecc1ac087c4ac))
+* archive old migrations ([24e8e93](https://github.com/AustralianBioCommons/atol-canopy/commit/24e8e931c1d7f6b9529984203f5d78032923dcc0))
+* backfill mitohifi_reference_species with values from mito_ref ([ddc1df2](https://github.com/AustralianBioCommons/atol-canopy/commit/ddc1df2ef0521eff187a8bc17585ed83d8d4594b))
+* consolidate references to project and study accessions, which are usually used interchangeably ([0ac67c5](https://github.com/AustralianBioCommons/atol-canopy/commit/0ac67c53e7747ffd9732112816b3545eabe328d1))
+* create new submission draft after failed submission to ENA ([2b527b6](https://github.com/AustralianBioCommons/atol-canopy/commit/2b527b6739d08dfd01f96ad2881eba0f41132785))
+* create new submission object when submission fails to ENA ([1c017a8](https://github.com/AustralianBioCommons/atol-canopy/commit/1c017a8a4096b6fffdf6ba50b9c8938ee13342ea))
+* docs ([a7450e0](https://github.com/AustralianBioCommons/atol-canopy/commit/a7450e096c221139ec3d5c2156ccf81eeb22f7bf))
+* fix ncbi lookup logic, add ncbi lookup to bulk-insert ops, add tests ([d4cc0bd](https://github.com/AustralianBioCommons/atol-canopy/commit/d4cc0bd2d6892b8724a6032c04b67007658527a1))
+* generate assembly manifest (for pacbio and hi-C reads) ([665a633](https://github.com/AustralianBioCommons/atol-canopy/commit/665a63351b739a6533b44dffdecc2bceee09fbeb))
+* get all samples, experiments and reads for specimen_id ([a219de1](https://github.com/AustralianBioCommons/atol-canopy/commit/a219de1358c5148e6f1d2ff271202eaad27c3a85))
+* get all samples, experiments and reads for specimen_id ([70389af](https://github.com/AustralianBioCommons/atol-canopy/commit/70389afeead2c6c044f5c1680882c4a1fd1b8333))
+* handle accessino pre-reqs for broker endpoints ([ee5c69d](https://github.com/AustralianBioCommons/atol-canopy/commit/ee5c69d1aad1f31432e71354962447dadba0155b))
+* handle accession pre-reqs for broker endpoints ([baa0d1d](https://github.com/AustralianBioCommons/atol-canopy/commit/baa0d1dc248eb9921e5331af81a7b53452372989))
+* implement genome notes with versioning ([b865bac](https://github.com/AustralianBioCommons/atol-canopy/commit/b865bac9cedc8f910d9d895e0acced0a1c002ec6))
+* improve error messaging for bulk-insert endpoints ([c5aca3e](https://github.com/AustralianBioCommons/atol-canopy/commit/c5aca3e7ebbddbb65303d3d30858b88a5fe74853))
+* include assembly_run.id in manifests, and require assembly_run id for for /cancel ([bc1dcac](https://github.com/AustralianBioCommons/atol-canopy/commit/bc1dcace2731251cc94f45ff00beb2f04e16c581))
+* include qc_reads in aggregate endpoint ([dbe44c0](https://github.com/AustralianBioCommons/atol-canopy/commit/dbe44c0637898dfe23a821ca9014aa735e715bdf))
+* make assembly runs unique on github_repo + git_commit, and improve debugging ([83bcca4](https://github.com/AustralianBioCommons/atol-canopy/commit/83bcca4e65e006bb8c9ee9a058526e6e7f8b3627))
+* make assembly runs unique on github_repo + git_commit, and improve debugging ([15ecc50](https://github.com/AustralianBioCommons/atol-canopy/commit/15ecc502c213633a43b30bec5f263123b499589d))
+* make scientific_name optional in schema (this may be changed when we fetch data from NCBI) ([e190dd5](https://github.com/AustralianBioCommons/atol-canopy/commit/e190dd52e7bc46dc24967e3d48d524a98cde0309))
+* new data ([01f0766](https://github.com/AustralianBioCommons/atol-canopy/commit/01f0766aa6cf4012c66d0ed048e15f4ebd461dce))
+* normalise fk references for submissioon objects, denormalise accession fields ([14e5c03](https://github.com/AustralianBioCommons/atol-canopy/commit/14e5c038bc3e0dba68eee490c1f731fdd5915f94))
+* only require attempt_id as path param in /broker/report endpoint ([affb397](https://github.com/AustralianBioCommons/atol-canopy/commit/affb39739fd3e029121fce49751de017041a21af))
+* re-introduce o.scientific_name, populate from ti.ncbi_sci.._name or else o.bpa_sci.._name ([b801470](https://github.com/AustralianBioCommons/atol-canopy/commit/b80147059d009c4214f91ebd71c75bb0c3893449))
+* rebase update to support qc reads ([31b9c02](https://github.com/AustralianBioCommons/atol-canopy/commit/31b9c02900b8cd676d015575e72c05bbc3531620))
+* redesign genome notes and assemblies ([dd7115e](https://github.com/AustralianBioCommons/atol-canopy/commit/dd7115eb6aaf183739f942b9b6df7e32e1e6ce59))
+* refactor migrations ([afaa9bc](https://github.com/AustralianBioCommons/atol-canopy/commit/afaa9bc0ec9cddf9999a6029e85f364847ea2ce9))
+* remove backwards compatibility shim ([8398098](https://github.com/AustralianBioCommons/atol-canopy/commit/83980987bceaa7883c2c29791049dbe5cced1f09))
+* remove external_run_id from stage_runs ([3329e01](https://github.com/AustralianBioCommons/atol-canopy/commit/3329e016be0a36441939b7952157aa207a3142cb))
+* remove file extension validation for pacbio files, since no equivalent check on ont or hi-c ([b2fe161](https://github.com/AustralianBioCommons/atol-canopy/commit/b2fe16188821ef34e230b03af8613092be36034a))
+* remove sample_id param for /intent endpoint - canopy will select optimal sample for tax_id ([dbf32eb](https://github.com/AustralianBioCommons/atol-canopy/commit/dbf32eb1d6f5489815b5e2b5250c975e15713e49))
+* remove study_accession references ([0b4dd81](https://github.com/AustralianBioCommons/atol-canopy/commit/0b4dd812e8ac95cc4b0b51bbc7fa741b4f3de99a))
+* remove unnecessary function, remove repeated db lookup ([78e3ca4](https://github.com/AustralianBioCommons/atol-canopy/commit/78e3ca462f6b5ee62fed6a1ba2f40611fb235613))
+* remove validation_hints from broker endpoint, broker can decide this ([b6aa696](https://github.com/AustralianBioCommons/atol-canopy/commit/b6aa696ea7568ba1ff9ff0676548e007054eeddc))
+* return meaningful error when reporting entities whose accessions already exist in registry ([d988950](https://github.com/AustralianBioCommons/atol-canopy/commit/d988950c06f623e858be1f8c86dadefc77f06ac6))
+* return sample.kind from /broker/claim endpoint ([e9b3b53](https://github.com/AustralianBioCommons/atol-canopy/commit/e9b3b538be8a22f58f0ebead8918739a8cd4f0d1))
+* return scientific_name ([83eca1b](https://github.com/AustralianBioCommons/atol-canopy/commit/83eca1b0d0e79def5bbc2dfc5a3ff219e1bf2afe))
+* returns meaningful error for duplicate reports - same stage and assembly run ([64284e1](https://github.com/AustralianBioCommons/atol-canopy/commit/64284e1803c9e3ffa38523ab1f74f431f9bfb318))
+* seperate broker contract endpoints and add tests ([270657d](https://github.com/AustralianBioCommons/atol-canopy/commit/270657ddefeb7cef36c20a611a70b3d4eeb201c5))
+* set organism_part to WHOLE ORGANISM for specimen samples ([88deee4](https://github.com/AustralianBioCommons/atol-canopy/commit/88deee4d79dd563fc5fb178c1c302922c283f9ce))
+* sync schema with database, update AssemblyStageRun model ([107fe6a](https://github.com/AustralianBioCommons/atol-canopy/commit/107fe6a118e20b1c0057ae0a66f7166e8c9d4dd5))
+* tighten access token expiration time ([7934e7a](https://github.com/AustralianBioCommons/atol-canopy/commit/7934e7a78e29e69f3a596ba5cdf7acf9736d8519))
+* tighten auth and update outdated projects crud endpoints ([4d394f9](https://github.com/AustralianBioCommons/atol-canopy/commit/4d394f93afea4588eed823c51e56434b098080b4))
+* update accession registry references ([efae4c4](https://github.com/AustralianBioCommons/atol-canopy/commit/efae4c44db3d813b779051cc1e6dce474c4ae7d9))
+* update assembly flow from requesting manifest to reporting results ([5db2cc0](https://github.com/AustralianBioCommons/atol-canopy/commit/5db2cc0c8a031a82148dce9a0b71ff7db04317af))
+* update assembly models to meet new requirements ([ee75d58](https://github.com/AustralianBioCommons/atol-canopy/commit/ee75d58835cc9fe84e841662e59d650f5b617b9d))
+* update assembly models to meet new(est) requirements ([f936379](https://github.com/AustralianBioCommons/atol-canopy/commit/f9363790b6a83e10f38686b5e79a302ea434bb04))
+* update broker ([33915eb](https://github.com/AustralianBioCommons/atol-canopy/commit/33915eb28acadd0c74d260bd93b8dcf6c2b0bef9))
+* update broker ([e62cc53](https://github.com/AustralianBioCommons/atol-canopy/commit/e62cc53250a654c65d88bf5adcac3a27ab18ec58))
+* update manifest fields ([3d1ecac](https://github.com/AustralianBioCommons/atol-canopy/commit/3d1ecac46d8170af5532e7111dc24f3345381fa8))
+* update manifest request flow ([49590ed](https://github.com/AustralianBioCommons/atol-canopy/commit/49590ede247c5f309c7e9e518740b9d14850f9e3))
+* update manifest, bpa base url field ([831a48c](https://github.com/AustralianBioCommons/atol-canopy/commit/831a48cd170f4f24c242ba71877788e48ccbb3de))
+* update ncbi information for taxonomy info objects that already exist ([0c19c04](https://github.com/AustralianBioCommons/atol-canopy/commit/0c19c04edac4e7a80ef7e026ce612523e6e1c876))
+* update organism schema and refine assembly versioning ([e016da5](https://github.com/AustralianBioCommons/atol-canopy/commit/e016da5c969f691f28cc8a3b603f4aaa8a4ff669))
+* update organism.scientific_name after importing taxonomy_info ([b6503ef](https://github.com/AustralianBioCommons/atol-canopy/commit/b6503ef592a031b9b9da9eca665b7be50a20ee27))
+* update policies, update naming, add CRUD endpoints for qc_reads ([7fa2c24](https://github.com/AustralianBioCommons/atol-canopy/commit/7fa2c24cbc48bec76ef8e09193dfadf717363467))
+* update qc_read_file fields ([2d317cd](https://github.com/AustralianBioCommons/atol-canopy/commit/2d317cd734610fe3c8aa20fb8be842486dec8c87))
+* update references from submission tables ([56bd98a](https://github.com/AustralianBioCommons/atol-canopy/commit/56bd98a71c41926914e93091ce1b38d68da3ef1a))
+* update reporting process for qc reads and assembly pipelines (rebased) ([bd794d2](https://github.com/AustralianBioCommons/atol-canopy/commit/bd794d22b02bd4f712c48bf98c40b7123b50f43c))
+* update response from broker endpoints ([f50a38a](https://github.com/AustralianBioCommons/atol-canopy/commit/f50a38ac0fcd776f29692d0aa1ce3a27153e295e))
+* update results reporting and assembly manifest generation ([18a4564](https://github.com/AustralianBioCommons/atol-canopy/commit/18a4564d6435a23aaff6136ac782f931d52a040d))
+* update shape of body for bulk-insert specimen samples endpoint to match mapper output ([c38fba2](https://github.com/AustralianBioCommons/atol-canopy/commit/c38fba2eb974af6c8bd60bd73564445cfad56dad))
+* update submission table references ([2f9ba27](https://github.com/AustralianBioCommons/atol-canopy/commit/2f9ba279ad608960732009fe970c0411e800ac69))
+* update taxonomy and organism fields in schemas and models ([b50566f](https://github.com/AustralianBioCommons/atol-canopy/commit/b50566fb098b41eede5dd82b56b5334119e023a2))
+* update taxonomy_info and organism schema, adding taxonomy details from ncbi ([12a8335](https://github.com/AustralianBioCommons/atol-canopy/commit/12a83356e30fbc1a8bfd559a3d0a94be6c7c0850))
+* update versioning strategy, use json for manifests, require specimen_ids for assemblies ([514370c](https://github.com/AustralianBioCommons/atol-canopy/commit/514370c76b3a18d93d5b663611474206f8bb0b60))
+* updates assembly stage run to rmv "status" and rename "stats" to "data" ([0c437db](https://github.com/AustralianBioCommons/atol-canopy/commit/0c437dbee496e61210caa91b78db850edc0f18e3))
+* uplift error handling, tests, auth policy ([9120188](https://github.com/AustralianBioCommons/atol-canopy/commit/912018880affcc57dd6f20604ea9f0f32121becd))
+
+
+### Bug Fixes
+
+* /claim endpoint to accept experiments and read ids ([28d2681](https://github.com/AustralianBioCommons/atol-canopy/commit/28d2681ded2c9be8ff01c97a3234387ebf50ef82))
+* address codepilot review ([9f8253b](https://github.com/AustralianBioCommons/atol-canopy/commit/9f8253b14f45b92be297bf59db787dcbd2324018))
+* allow no request body on endpoint where all request body fields are optional ([95bfdb3](https://github.com/AustralianBioCommons/atol-canopy/commit/95bfdb3e3dbd481728d6a0d920d101f160237c57))
+* catch error thrown from determine_assembly_data_types in assembly/intent endpoint ([81da31a](https://github.com/AustralianBioCommons/atol-canopy/commit/81da31a1360b58052739569bba76b17fe282485c))
+* consolidate auth policy, add centralised error handling module and pagination ([9df3b9f](https://github.com/AustralianBioCommons/atol-canopy/commit/9df3b9f020a25136841a907071ba56a71cdf3b8d))
+* consolidate auth policy, add centralised error handling module and pagination ([1db5e59](https://github.com/AustralianBioCommons/atol-canopy/commit/1db5e5938632f31769b868ccc0c9d09548e7fa74))
+* Dockerfile ([01f1be5](https://github.com/AustralianBioCommons/atol-canopy/commit/01f1be5d597e4655cdf4bd52a82030a0638f011b))
+* enforce 72-byte limit at user create/update ([44b9bbb](https://github.com/AustralianBioCommons/atol-canopy/commit/44b9bbbb44db3f6e771bb2afb3b575f8048e4109))
+* enforce expiry of leased items on before new lease request ([91dbbbc](https://github.com/AustralianBioCommons/atol-canopy/commit/91dbbbc48c24394e9216c7ce680b9aeed517099e))
+* fix db readiness probe ([175f9d2](https://github.com/AustralianBioCommons/atol-canopy/commit/175f9d2bae5075688a005521e360c3f3b885e170))
+* fix migration ([575f060](https://github.com/AustralianBioCommons/atol-canopy/commit/575f0601737edbf70c397577b1e4c444c7e02a5d))
+* fix migration, specimen lookup and add logging ([305b1a5](https://github.com/AustralianBioCommons/atol-canopy/commit/305b1a577cae2a1e5258ea237caf802e683a6ad0))
+* import if an experiment already exists in the db, still add any valid related runs to the db ([b053cee](https://github.com/AustralianBioCommons/atol-canopy/commit/b053ceeeaea245d537fec4b151f5be0660d7acbb))
+* improve error message ([c547d04](https://github.com/AustralianBioCommons/atol-canopy/commit/c547d048c04d5c6ea98e825e62e1dcf148e8764d))
+* improve errors returned from ingestion endpoints ([32161f4](https://github.com/AustralianBioCommons/atol-canopy/commit/32161f4b62ab8ff8da7b013fb2b1f35b26522eee))
+* improve test for the 72 byte password limitation in bcrypt ([974b29d](https://github.com/AustralianBioCommons/atol-canopy/commit/974b29d96d56b68fd8d12901915e6e6b4435510b))
+* linting ([866797d](https://github.com/AustralianBioCommons/atol-canopy/commit/866797d9581c5cc1342130058d978cb20c64f7ea))
+* make references to entity ids and entity submission ids consistent for broker endpoints ([660e132](https://github.com/AustralianBioCommons/atol-canopy/commit/660e13209c2da426e672ac64341fe7ac0e6fe685))
+* make references to entity ids and entity submission ids consistent for broker endpoints ([c931fd0](https://github.com/AustralianBioCommons/atol-canopy/commit/c931fd0c71de2b9fe4f06ab517c1c5fc01a0edcf))
+* remove qc_reads from specimens discovery endpoint ([33f4465](https://github.com/AustralianBioCommons/atol-canopy/commit/33f4465e090b442eebc4f49f5c3f9e25bb973700))
+* remove redundant or outdated taxonomy columns ([1f6e0d2](https://github.com/AustralianBioCommons/atol-canopy/commit/1f6e0d229325f5a2ecf7460bde84f3eb112944b0))
+* rename testing files ([30bb35d](https://github.com/AustralianBioCommons/atol-canopy/commit/30bb35d8b1349abb0427e8723a05d9e1db096d21))
+* resolve passlib + bcrypt incompatibility ([6ad8cd0](https://github.com/AustralianBioCommons/atol-canopy/commit/6ad8cd045da81f6171649973cf16d7c2d9c7fe7e))
+* shorten migration name to meet alembic constraint of 32 chars ([cb875bb](https://github.com/AustralianBioCommons/atol-canopy/commit/cb875bb889b592ad13064b4ec10e446eaee1052d))
+* shorten migration version label ([14bd6b3](https://github.com/AustralianBioCommons/atol-canopy/commit/14bd6b3e3c04a7ef360d8e59b3ba166f94db8432))
+* shorten migration version label ([546fdef](https://github.com/AustralianBioCommons/atol-canopy/commit/546fdefd4b2a1c7cfef3178d23ccf56385048cee))
+* shorten migration version label, linting ([77a58a6](https://github.com/AustralianBioCommons/atol-canopy/commit/77a58a67da9f3fe4005dc6cac7c8be358fa94a1d))
+* some incorrect fields and move default value from db schema to code ([5329976](https://github.com/AustralianBioCommons/atol-canopy/commit/53299769e307625d286e254df27903e87726c14e))
+* update accepted file types for assemblies ([05c44b6](https://github.com/AustralianBioCommons/atol-canopy/commit/05c44b6850bab54b5dae55353e0ad7cfc41e246b))
+* update data types check, update tests, allow same specimen_id for hi-c + long read data ([9f87c13](https://github.com/AustralianBioCommons/atol-canopy/commit/9f87c13e229bac49a25737b6c42aee1d6acde8f0))
+* update data types check, update tests, allow same specimen_id for hi-c + long read data ([e81716d](https://github.com/AustralianBioCommons/atol-canopy/commit/e81716dc85755ac5275fc95ac0988a25d5a0a09e))
+* update read field from "base_url" to "bioplatforms_base_url" to match atol schema ([4034aa2](https://github.com/AustralianBioCommons/atol-canopy/commit/4034aa26338cc535a0834e113e0c19397287084d))
+* update references to organism key, and resolve conflicting status field ([6b3bdc4](https://github.com/AustralianBioCommons/atol-canopy/commit/6b3bdc48a0ca8badf34ff0ed951b86a93143dbbd))
+* update stale CRUD endpoints ([3ce1982](https://github.com/AustralianBioCommons/atol-canopy/commit/3ce1982bdbe4d0d223bb44c05e63511b0da472a4))
+* update tests ([f85fe77](https://github.com/AustralianBioCommons/atol-canopy/commit/f85fe77033b43288a03e42b6dc7dc0a22c09a3cf))
+* uplift testing, tighten auth policies, fix stale CRUD endpoints ([951cb20](https://github.com/AustralianBioCommons/atol-canopy/commit/951cb20d54735e3b69d34e58b2279f857ff42ed0))
+
+
+### Performance Improvements
+
+* parallelize NCBI API calls in bulk taxonomy import ([6ce8f7f](https://github.com/AustralianBioCommons/atol-canopy/commit/6ce8f7fdf3b7af559cf7ae0be6f45441199f3ee1))
+* parallelize parent and organelle lookups within each organism ([11dcbba](https://github.com/AustralianBioCommons/atol-canopy/commit/11dcbbad9e6689884a68ad44e6191e24a249696a))
+
+
+### Documentation
+
+* add PR template for repo ([7a4d695](https://github.com/AustralianBioCommons/atol-canopy/commit/7a4d69595cc622fa860086d630d8e7f0776352db))
+* known_issues ([c344476](https://github.com/AustralianBioCommons/atol-canopy/commit/c3444768f37e7bc4606ff9b1a4dd744fa380957d))
+* known_issues ([30a0fdf](https://github.com/AustralianBioCommons/atol-canopy/commit/30a0fdfa071e8246c56ede99ebed814b4240b626))
+* organism.scientific_name and taxonomy_info.last_synced_at behaviour ([711659a](https://github.com/AustralianBioCommons/atol-canopy/commit/711659ae3f58eb44cdfa1c8f59b84e18474eede0))
+* update docs ([7f89c24](https://github.com/AustralianBioCommons/atol-canopy/commit/7f89c24f9cb152c93319aa59a33df53c675973e1))
+* update docs ([5e5e2b3](https://github.com/AustralianBioCommons/atol-canopy/commit/5e5e2b372c81f1a958a152225546c8869a75ce1d))
+* update docs ([cb6c67c](https://github.com/AustralianBioCommons/atol-canopy/commit/cb6c67cb00a955bb5e8b69622444e249331151b2))
+* update docs ([52bcb18](https://github.com/AustralianBioCommons/atol-canopy/commit/52bcb180e8a693cc6015593f01b977d6cfb9b62a))
+* update handover docs ([58cee85](https://github.com/AustralianBioCommons/atol-canopy/commit/58cee85505034c96286ba8c9b38e6478d5db16bd))
+* update handover docs ([46b5199](https://github.com/AustralianBioCommons/atol-canopy/commit/46b51997140b7e8ba62cf3f2f131c8f4971f2165))
+* update handover docs ([d4f9e98](https://github.com/AustralianBioCommons/atol-canopy/commit/d4f9e98cffd28a11805c873dcb6bc06ca8bd3a90))