chore(master): release sophios 0.6.0

[github-actions]

🤖 I have created a release beep boop

0.6.0 (2026-09-02)

⚠ BREAKING CHANGES

• library code raises SophiosError instead of calling sys.exit(1). CLI exit codes are unchanged.
• contrib Python import paths move. sophios.api.utils.converter -> sophios.contrib.converter sophios.api.utils.wfb_util -> sophios.contrib.wfb_util sophios.api.utils.ict.* -> sophios.contrib.ict.* sophios.api.rest.api -> sophios.contrib.rest.api REST HTTP behaviour is unchanged; HTTP clients are unaffected. The design document approves this exception explicitly (§3, exception 2).

Features

• add a typed AST and total parser for the .wic syntax layer (e5cd173)
• added Python API (#102) (38fbd19)
• close the opaque type and preserve literal spellings (7b3eb06)
• code to build pdf copy of the docs (0f01875)
• correctly resolve edam format inputs (df66d0a)
• export a JSON Schema derived from the language definition (6d07b99)
• fix wordings on install docs and refactor clt builder api names (8d15a9f)
• further simplify API surface and improve names (4f82bfe)
• give the library a failure type an embedder can catch (38840d6)
• pythonapi: add Pydantic V2 support (#152) (16be637)
• reconcile dev and user RTD docs (0fb3f4f)
• regularize and simplify API surface (1268551)
• resolve the language version by rule, not by accident (ee568c4)
• revamp dev docs and add edge inference to python workflows API (550849e)
• revamp dev docs and add edge inference to python workflows API (9c1b7c1)
• surface the resolved language version everywhere it matters (71a6eea)
• write the .wic AST back out in both surface spellings (7b3528e)

Bug Fixes

• address the review comments about version management (03bde5b)
• API names and client side code (dac8ef6)
• cleanup stale shims and unused future imports (7575f57)
• close the review's open findings on the syntax layer (4e4be8d)
• collecting tests provisions nothing (4313214)
• configuration is a value, parsed once at the boundary (aa8344e)
• dead code removal, stale comment deletion and test streamlining (d6335c1)
• dead code removal, stale comment deletion and test streamlining (9c0208c)
• deduplicate unlabeled Graphviz edges (9984fb4)
• docker: repair the REST image so it can build and run (2cac4db)
• enforce the language's invariants at the parse boundary (750fd86)
• fixed mypy errors (a7e85e2)
• fixed mypy issues (039bd62)
• give the CWL substrate one declared version (1463e85)
• handle empty requirements and loop index shadowing (e1f9beb)
• move away versioning from versioneer and simplify release prep (626919e)
• never specify more than the loader accepts (b462068)
• pythonapi: fix int, float in yaml (#170) (4a0ccb7)
• pythonapi: fix Workflow object (#135) (cfe1495)
• remove complicated API surface of submit and update client code (6ac0e6d)
• remove directory creation before run and fix up run_async surface (2fc6055)
• report failures instead of terminating the caller's process (2e2ef72)
• simplify compute request and lint fix (6a75c36)
• the pins walk survives the recursive trees the loader builds (ccb8063)
• the sidecar case in the cycle contract was not a cycle (9d752c0)
• the unknown-tag rule belongs to one function, not to each position (d995c4d)
• the writer transcribes, recurses, and is total over the union (09a5cc0)

Documentation

• add the approved core refactor design (c071b76)
• added inline comment for cwl-utils (28d9591)
• added type ignore to CWLInputParameter (aaa2710)
• define the .wic language and reconcile both front-ends (fd4cce5)
• identifiers that dereference, claims that live once (fedf8d1)
• name the language Sophios in the renderer and schema (0be6d5d)
• name the language Sophios, and its version tag lang_version (b3b68af)

Code Refactoring

• generate the JSON Schema from the AST, not beside it (11d0faf)
• improved typehints, addressed mypy (54d4c3d)
• modernize types and supporting code (3af39f6)
• modularize core workflow processing (6570369)
• namespace the language layer's shared state (2f64d8a)
• one home for the wic: vocabulary, one home for the generators (07121da)
• pythonapi: remove docker checks (#148) (1724d99)
• refactored Step init (303ad35)
• separate the core and contrib zones (ceef080)

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