* feat(cli): target element_id in show_contents

* feat(cli): target element_id in list_arrays

* feat(cli): add element_id option to modos show

* feat(api): support group ids in show_elements

* fix(deploy): bypass proxy when using htsget with compose minio

* refactor(nginx): use recommended header opts for minio

* docs(deploy): note on aliasing minio host

* docs: release instructions

* docs(deploy): typos

* fix(deploy): forward s3 host header through nginx

* docs(deploy): alt opt for htsget x minio networking

* docs(deploy): section on htsget-minio addressing

* docs(deploy): s3 bucket style in example .env

* refactor(compose): scheme always inside URL env vars

* feat(cli): can omit object_id in modos remove

* feat(cli): allow s3 path in modos stream

* docs(readme): update endpoint options

* docs(cli): drop obsolete example

* feat: code matching client

* feat(remote): register fuzon endpoint in client

* refactor(cli): prompt logic to dedicated prompt module

* refactor(cli): prompt logic to dedicated prompt module

* chore(deps): pyfuzon as extra dep

* chore: update deps

* feat(cli): support code completion in modos add

* perf(codes): limit suggestions to 50 codes

* fix(cli): use labels in recommendations

* refactor(codes): custom Code struct

* chore(deps): bump modos-schema version

* feat(cli): prompt autocompletes text, persists uris

* fix(cli): disable unnecessary autocomplete on modos create

* test(data): use uris when required

* fix(codes): fuzon-http api parameters

* chore(make): document deploy recipe

* feat(compose): add fuzon service

* feat(nginx): register fuzon in reverse proxy

* feat(fuzon): dockerized fuzon-http setup

* fix(compose): add envvar for fuzon service

* fix(compose): fuzon envvars

* fix(nginx): typo

* chore(deps): add prompt-toolkit

* fix(deploy): pin fuzon to tag 0.2.3

* fix(compose): env var typo

Co-authored-by: supermaxiste <supermegaiperste@hotmail.com>

* docs(deploy): describe config variables

* feat(codes): parametrize n top code matches

* fix(codes): update protocol signatures

* fix(codes): default top value in code matcher protocol

* docs(prompt): clearer comments

* fix(deploy): typo in env var

* feat(cli): list remote modos

* fix(server): nest /list values in response

* chore: bump pyfuzon to 0.2.5 for blank node fix and caching support

* feat(cli): add search-codes command

* chore(deploy): bump fuzon server to 0.2.5

* refactor(prompt): allow prompt override in SlotPrompter

* refactor(codes): define protocol attributes in CodeMatcher

* feat(cli): non-interactive code search

---------

Co-authored-by: supermaxiste <supermegaiperste@hotmail.com>

* refactor(cli): only load one matcher in search-codes

* perf(codes): cache code matchers by source file

* fix(codes): create cache dir if missing

* chore(docker): pin python to 3.12 in runtime layer

* chore(deps): modos-schema -> test py313 branch

* chore(deps): pin modos-schema to 0.2.1

* feat: code matching client

* feat(remote): register fuzon endpoint in client

* refactor(cli): prompt logic to dedicated prompt module

* refactor(cli): prompt logic to dedicated prompt module

* chore(deps): pyfuzon as extra dep

* chore: update deps

* feat(cli): support code completion in modos add

* perf(codes): limit suggestions to 50 codes

* fix(cli): use labels in recommendations

* refactor(codes): custom Code struct

* chore(deps): bump modos-schema version

* feat(cli): prompt autocompletes text, persists uris

* fix(cli): disable unnecessary autocomplete on modos create

* test(data): use uris when required

* fix(codes): fuzon-http api parameters

* chore(make): document deploy recipe

* feat(compose): add fuzon service

* feat(nginx): register fuzon in reverse proxy

* feat(fuzon): dockerized fuzon-http setup

* fix(compose): add envvar for fuzon service

* fix(compose): fuzon envvars

* fix(nginx): typo

* chore(deps): add prompt-toolkit

* fix(deploy): pin fuzon to tag 0.2.3

* fix(compose): env var typo

Co-authored-by: supermaxiste <supermegaiperste@hotmail.com>

* docs(deploy): describe config variables

* feat(codes): parametrize n top code matches

* fix(codes): update protocol signatures

* fix(codes): default top value in code matcher protocol

* docs(prompt): clearer comments

* fix(deploy): typo in env var

* chore(deps): pin schema branch + add pyteomics

* feat(mztab): basic extractors [WIP]

* chore: update test modo

* chore: add source data for test modo

* chore: pin schema

* docs(cli): clearer help msg

* feat(io): add branch for mzTab meta. extraction

* refactor(cram): simplify cram extraction logic

* feat(mztab): end-to-end mztab metadata extraction

* fix: pass data instance when extracting metadata

* chore: typos

* feat(cli): add enrich command

* chore(deps): relative -> absolute imports

* test: update reference path

* test: update reference path (bis)

* chore: regen lock

* feat(storage): add open method

* refactor(api): reduce code duplication across methods

* feat: boilerplate for array extraction

* chore: update lock file

* chore(deps): add pandas

* ci: use make recipe for poetry install

* chore(ci): drop python 3.10, test on 3.12

* test(remote): fix pydantic type in endpoint manager doctest

* chore(deps): pin modos-schema to v0.3

* docs: mztab tutorial

* chore: metabolomics init file

* ci(docs): bump python version

* ci(docs): bump python version

---------

Co-authored-by: supermaxiste <supermegaiperste@hotmail.com>