Notable changes introduced in modos releases are documented in this file

[0.3.2] - 2025-06-16#

Bug Fixes#

  • (cli) syntax when reading passphrase from file (#140)

  • (storage) transfer metadata (#148)

[0.3.1] - 2025-05-23#

Bug Fixes#

  • (api) sequential encryption (#138)

  • pin typer AND click versions for compatibility

Documentation#

  • add encryption and upload sections (#136)

[0.3.0] - 2025-05-20#

Bug Fixes#

  • (api) update data path (#118)

  • (deps) remove misplaced pyfuzon import

  • (server) api compatibility for /meta and /get (#126)

Documentation#

  • (readme) fix gha badge url (#132)

  • (tuto) document modos enrich subcommand- add file format design notes (#111)

Features#

  • (cli) update prompts for removal of missing config elements (#123)

  • (deploy) setup refget service (#121)- logger (#130)

  • local crypt4gh encryption (#127)

[0.2.3] - 2024-11-29#

Bug Fixes#

  • (deploy) htsget networking (#102)

  • (htsget) minio connection

Documentation#

  • (readme) fix example sparql query

  • (tuto) fix mztab example

Features#

  • (cli) consistent path options (#105)

  • (cli, api) show only target element (#98)- support terminology codes (#106)

  • mztab support (#107)

[0.2.2] - 2024-08-12#

Bug Fixes#

  • (rdf) inject schema:identifier (#99)

Documentation#

  • (tutorial) update remote and genomics (#97)

[0.2.1] - 2024-08-08#

Bug Fixes#

  • (rdf) schema.org prefix (#96)

[0.2.0] - 2024-08-05#

Bug Fixes#

  • (api) add type hints, fix doctests

  • (api) MODO.metadata extracts own attributes

  • (api) update changed values in update_element (#83)

  • (cli) duplicated prompt for id

  • (cli) drop zarr group creation on modo create

  • (compose) network syntax

  • (compose) volume mounts + listening address

  • (compose) env vars to specify buckets and policies

  • (compose) disconnect s3 volume from modo-server (accessed via net)

  • (cram) add slicing logic

  • (cram) coords -> region

  • (deploy) disable body size limit in nginx (#42)

  • (deploy) disable max body size in nginx

  • (docker) missing dep in client dockerfile

  • (introspection) support inheritance in get_slots

  • (io) rm unneeded id_ -> id

  • (minio) add env variables for auth

  • (minio) expose console port locally

  • (nginx) define rewrite rules for s3+htsget

  • (rdf) handle path->uri conversion for data_path

  • (server) pin dependencies

  • (server) safer bucket replacement

  • (server) safer bucket replacement

  • (server) make exact_match match exactly

  • (server) pin htsget version + bump msrv (#49)

  • (server) reload minio filesystem on server queries (#62)- schema syntax

  • drop unused query

  • visit nodes recursively when extracting metadata

  • path handling on modo creation

  • cli display of modo show

  • rm unused linkml-owl helper+undeclared linkml dep

  • add missing –data-file option

  • set filename using metadata when copying into digital object

  • validate types of has_part relationship in MODO.add

  • handle root path when adding data

  • allow flexible number of elements in yaml

  • change path in example config.yaml

  • use schema model to build modo from yaml

  • directly cast schema models

  • add check for list

  • propagate function name change

  • minor fix in example yaml id

  • add check for existing before adding element to modo

  • missing typing import

  • create unique sequence ids from extracted metadata

  • standardize metadata extraction

  • extract reference from list

  • remote metadata streaming

  • add group level to extract_metadata in line with the new structure

  • adapt tests to zarr path as id

  • prevent failing for non existing keys in whitelist

  • define existing paths in test yaml

  • use relative path to enrich metadata

  • rename whitelist, simplify conditions

  • set full id for has_part attributes when build from yaml

  • adapt has_part ids to full id when build from yaml

  • consistent naming

  • include metadata from all modos

  • wildcard use in fstring

  • adapt env var name

  • name mismatch in slice_remote_cram

  • mutable args (#52)

  • auto upload cram index (#64)

  • Add direnv tooling and ignore

  • Add pyright lsp

  • format bug in feature-request.yml

  • consistent ids (#70)

  • client-side region-filter on htsget streams (#71)

Documentation#

  • (cli) shorten command descriptions

  • (compose) mount -> volume for minio

  • (deploy) add deployment instructions and docs

  • (deploy) update readme with nginx setup

  • (deploy) document configuration with .env file

  • (readme) add usage+development guidelines

  • (readme) refresh api description

  • (readme) add credits (#55)

  • (readme) styling + update examples (#80)

  • (readme) fix api example

  • (typo) deploy/README.md

  • (typo) deploy/README.md- add initial README.md

  • add implementation details to README.md

  • add status to readme

  • add license

  • add NOTE in get_slot_range about class-independence

  • mention class-independence in get_slot_range docstring

  • docstring for MODO.update_element

  • sphinx website with API reference (#32)

  • Add some documentation for using nix

  • format markdown documents (#66)

Features#

  • (api) basic metadata extraction

  • (api) update existing elements

  • (api) allow passing zarr archive to MODO constructor

  • (cli) implement create command

  • (cli) add write commands for metadata+data

  • (cli) add support for multi-choice prompt

  • (cli) allow skipping slot prompts

  • (cli) stream command (#87)

  • (cli) update modo from yaml file (#89)

  • (cli, api) remove modo (#76)

  • (cram) region parsing func

  • (cram) slice local files

  • (deploy) add nginx service in compose

  • (deploy) htsget over s3 (#26)

  • (docker) version as build arg + metadata label

  • (helpers) allow enum from model object

  • (introspection) add getter methods, cache schema views

  • (io) helper functions for loading instances

  • (makefile) docker build recipe

  • (meta) add custom rdf converter

  • (nginx) placeholder config

  • (s3) allow virtual-host-style buckets (#75)

  • (server) extend client dockerfile

  • (server) list modos and gather metadata[wip]

  • (server) sort matches by similarity- add draft rdf metadata schema

  • add taxid in schema

  • add pkg skeleton

  • add helper functions to inspect schema

  • add zarr mgmt funcs to modo.storage

  • list samples in archive via API

  • add remove command

  • allow adding reference genomes

  • relevant metadata from cram file

  • first version to build full obj from yaml

  • extend cli create

  • server deployment (#12)

  • update build_modo_from_file for new structure

  • use zarr path as id, check for unique

  • fail early for duplicated id in build_modo_from_file

  • repeat prompt for invalid inputs (non unique ids)

  • copy files into modo when building from yaml

  • request server endpoints

  • Add get?query to modo server

  • enable instantiation of remote modo

  • add a function to handle both cram and vcf/bcf BytesIO buffers.

  • add helper function to determine the file format. needed for generalized save/stream_genomics methods, and possibly for oter methods/functions as well

  • add a function to handle both cram and vcf/bcf BytesIO buffers.

  • add a function to handle both cram and vcf/bcf BytesIO buffers.

  • Add development setup for Nix shell

  • Enable nix development

  • auto update last_update_date attr (#73)

  • htsget client (#78)

  • streamline remote options (#90)