Bump pip from 24.3.1 to 25.2 in /.github/workflows#8
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Bumps [pip](https://github.com/pypa/pip) from 24.3.1 to 25.2. - [Changelog](https://github.com/pypa/pip/blob/main/NEWS.rst) - [Commits](pypa/pip@24.3.1...25.2) --- updated-dependencies: - dependency-name: pip dependency-version: '25.2' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>
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Superseded by #20. |
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October 27, 2025 16:32
cshenry
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Fix #1: Replace kbu.env.config.get() with kbu.env.get_config_value("section.key") throughout all skill files; document get_config(section, key) as deprecated/INI-compat. Verified against shared_env_utils.py:195,216. Fix #2: Replace fabricated KBJobUtils methods (submit, cancel, refresh, get, list, forget, summary, get_logs with real API (run_job, cancel_job, check_job, refresh_active, refresh_all, get_record, list_active, list_all, get_job_logs, cleanup). Verified against kb_job_utils/utils.py. Fix #3: Add undocumented kb_genome_utils.py methods to module-reference.md and api-summary.md: load_kbase_gene_container, object_to_features, get_ftr, ftr_to_aliases, alias_to_ftrs, object_to_proteins, add_annotations_to_object, load_genome_from_local_files, aggregate_taxonomies, create_synthetic_genome, calculate_gc_content, plus PRD-new methods by name: save_genome_object, save_assembly_from_fasta, save_genome_with_assembly, validate_genome, build_genome_from_fasta_gff. Fix #4: Add Injecting SDK Clients in Notebook Contexts subsection to patterns.md documenting kbu.callback.set_callback_client(name, client) injection hook. Fix #5: Add installed_clients/ shipping constraint note near top of kbutillib-expert.md flagging that AssemblyUtilClient/GenomeFileUtilClient require a separate KBase SDK install; calls raise ImportError without it. Fix #6: Add /kbase-genome-expert to Related Skills in kbutillib-expert.md and a See also pointer in patterns.md callback section. Fix #7: Add KBGenomeUtilsImpl delegate note to module-reference.md (source L805, __getattr__ passthrough). Fix #8: Add ## CLI chapter to api-summary.md covering kbu jobs status/list/summary/ refresh/logs/cancel/forget/cleanup/chain submit/list/status/cancel/advance and kbu jobdaemon. All subcommands verified against src/kbutillib/cli/jobs.py, jobdaemon.py, __init__.py. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> EOF )
cshenry
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Jul 6, 2026
Implements shared TOML I/O helpers in manifest.py (read/write for both project and subproject manifests, now_utc_iso, sha256_file, partial-write helpers append_session_ref and append_notebook_entry_or_update). Adds kbu subproject subcommand group with 8-state machine (plan → p-review → build → b-review → run → synthesize → s-review → complete), full precondition validators per PRD round-2 confront table, HTML verdict comment parser, and subcommands: create, list, status, advance, set-status. Registers subproject group in CLI __init__.py; adds tomli-w >=1.0 to dependencies; adds conftest.py fixtures and 66 passing tests. Satisfies PRD kbu-start-v1 ACs #4, #5, #6, #7, #8, #32, #33, #34, #36, #42, #44. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
cshenry
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Jul 6, 2026
Implements the kbutillib.layout module (PRD kbutillib-v2, Implementation
Decisions → Layout module, Specifics folded from confront round 1).
Public API:
- DEFAULT_SHARED_DIRS = ("data", "models", "genomes")
- read_shared_dirs(project_root) — reads [layout.shared_dirs] from
kbu-project.toml via tomllib; falls back to DEFAULT_SHARED_DIRS when
the file, the [layout] table, or the shared_dirs key is absent.
- subproject_subdirs(adopted=bool) — returns the 6-entry canonical
subdir list, with "archive" appended when adopted=True.
- subproject_gitignore_lines() — [".cache/", "nboutput/",
".adoption-notes.md"]
- root_gitignore_lines(shared_dirs) — 3 large-file globs per shared dir.
35 tests in tests/test_layout.py cover AC #1–#8 (each AC has at least
one test. All 35 pass; 0 existing tests regress.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
EOF
)
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Bumps pip from 24.3.1 to 25.2.
Changelog
Sourced from pip's changelog.
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2e05caeBump for releasef249061Update AUTHORS.txt78d15a5Copyedit news entries before 25.2 (again)4fe68d7Merge pull request #13506 from ichard26/3.14775a86fFix broken unit tests & xfail weird failure2773b13Reformat and add --allow-unix-socket to pytest confige384d10Declare Python 3.14 support4117dc7Always remove authority section when cleaning local URL path (#13510)2e21934Fix cleaning of local URLs with VCS schemes (#13509)853a593Improvepath_to_url()tests (#13496)Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting
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