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fix(ci): checkout PhenoObservability as sibling so workspace path-dep resolves#84

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fix(ci): checkout PhenoObservability as sibling so workspace path-dep resolves#84
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fix/ci-checkout-phenoobservability

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@KooshaPari KooshaPari commented Jun 5, 2026

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Problem

Every cargo test --workspace run on main and on PR branches (including the just-opened connector-parser PR #83) fails before any tests execute:

error: failed to load manifest for workspace member `.../crates/focus-always-on`
Caused by: failed to load manifest for dependency `phenotype-observably-macros`
Caused by: failed to read `.../PhenoObservability/crates/phenotype-observably-macros/Cargo.toml`

11 crates in the FocalPoint workspace depend on phenotype-observably-macros via
path = "../../../PhenoObservability/crates/phenotype-observably-macros". From
crates/<name>/ that resolves to a sibling of the FocalPoint checkout. CI only
checks out FocalPoint, so the relative path is missing.

Fix

  • Check out PhenoObservability into $GITHUB_WORKSPACE/PhenoObservability (sibling of $GITHUB_WORKSPACE/FocalPoint).
  • Pin actions/checkout to the same SHA used in the rest of the org.
  • Move subsequent steps under working-directory: FocalPoint so they keep operating on the workspace.

Risk

  • Workflow-only change.
  • No code or path-deps touched.
  • All run: blocks are hardcoded (no untrusted github.event.* inputs).

Test Plan

🤖 Generated with Claude Code


Note

Low Risk
Workflow-only change with pinned third-party actions and no application or dependency manifest edits.

Overview
Fixes CI failing before tests run because workspace crates resolve phenotype-observably-macros via a relative path to a sibling PhenoObservability repo that was never checked out.

The workflow now checks out FocalPoint into FocalPoint/ and KooshaPari/PhenoObservability into PhenoObservability/ under the same workspace root, adds a small guard that fails fast if PhenoObservability is a broken symlink, pins checkout, rust-toolchain, and rust-cache to specific SHAs, scopes rust-cache to FocalPoint, and runs cargo test / cargo clippy with working-directory: FocalPoint.

Reviewed by Cursor Bugbot for commit 4da4eff. Bugbot is set up for automated code reviews on this repo. Configure here.


CodeAnt-AI Description

Make CI check out the sibling workspace so tests can run

What Changed

  • CI now checks out both FocalPoint and PhenoObservability side by side, so workspace dependencies resolve the same way they do on a local machine.
  • The workflow now runs tests and linting from the FocalPoint checkout instead of the repository root.
  • The checkout and Rust setup steps are pinned to fixed versions for consistent CI runs.

Impact

✅ Fewer workspace load failures in CI
✅ Reliable cargo test runs on PRs
✅ Clearer CI results for workspace and lint checks

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… resolves

11 crates in the FocalPoint workspace depend on `phenotype-observably-macros`
via `path = "../../../PhenoObservability/crates/phenotype-observably-macros"`.
From `crates/<name>/` that resolves to a sibling of the FocalPoint checkout,
but CI only checked out FocalPoint, so every `cargo test --workspace` failed
with:

  failed to read `/home/runner/work/FocalPoint/PhenoObservability/...`

Fix:
- Check out PhenoObservability into the runner's `$GITHUB_WORKSPACE` next to
  the FocalPoint checkout (so the relative path resolves identically to a
  local dev setup).
- Pin actions/checkout to the same SHA used elsewhere in the org.
- Use a `working-directory: FocalPoint` step so the rest of the workflow
  continues to operate on the FocalPoint workspace.

This is a CI-only change; no code or path-deps are touched, so any other
branch that needs CI to pass (e.g. connector parser fixes) can rely on
`cargo test --workspace` actually running.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
@gemini-code-assist

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@codeant-ai codeant-ai Bot added the size:M This PR changes 30-99 lines, ignoring generated files label Jun 5, 2026
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@KooshaPari

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Closing as superseded: PR #80 (fix/focalpoint-observably-vendor) is the proper fix — it vendors phenotype-observably-macros into the workspace and switches 11 deps to workspace = true, eliminating the broken ../../../PhenoObservability path-dep at the source. My PR #84 was a CI-only band-aid that added a sibling checkout; with the macro vendored, the path-dep disappears and CI no longer needs the extra checkout step. Land #80 and no follow-up CI changes are needed.

@KooshaPari KooshaPari closed this Jun 5, 2026
KooshaPari added a commit that referenced this pull request Jun 13, 2026
* Add root STATUS.md

* chore: add CITATION.cff for GitHub citation support

Enables "Cite this repository" feature on GitHub and provides
machine-readable metadata for academic/tooling use.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* chore(Planify): add standard bug_report.md issue template

GitHub's new-issue chooser only matches canonical filenames
(bug_report.md / feature_request.md). The existing --bug-report.yaml
files in .github/ISSUE_TEMPLATE/ are silently ignored, so contributors
land on a blank form.

Adds .github/ISSUE_TEMPLATE/bug_report.md so the chooser offers a
structured bug report form.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* Revert "chore(Planify): add standard bug_report.md issue template"

This reverts commit 71ca6dd.

* chore: add OpenSSF Scorecard workflow

Adds .github/scorecard.yml running ossf/scorecard-action weekly and on
main pushes, uploading SARIF to code-scanning for supply-chain security
visibility.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* chore: clean up audit artifacts and deleted files

* chore: clean up audit artifacts and deleted files

* fix(repos): restore corrupted root STATUS.md

The previous root STATUS.md contained a single junk line that was a
mixture of a `wtmp` system log and a relative link:

    wtmp begins Mon Jun 16 08:38:50 MST 2025phenotype-org-governance/SUPERSEDED.md

Replace it with a proper monorepo status index: header, last-updated
date, a 3-bullet summary of recent work, and links into the sub-project
groups (apps, shared libraries, services, tooling, worktrees).

* chore(audit-2026-06-10): V3 DAG and audits

* chore: record l5-91 stash cleanup

* docs(findings): add MERGE_DASHBOARD_2026_06_11.md with batch-merge results

* docs(plans): update 100-task DAG v3 with resume progress + 100+ PR merge results

* merge(2026-06-11): unify focus repo state — all L1-L5 agent branches merged

Sequential --no-ff merges in dependency order (L2-21/22/24/25 → L2-28..35 →
L3-41..45 → L4-61..71 → L5-83..92) of 55 chore/l* branches across 5 focus
repos. Conflicts on shared .editorconfig / .github/* files resolved with
-X theirs (later agents had more complete content).

PhenoCompose: 11 branches were pre-consolidation (the 2026-06-08 commit
1936a4c dropped 3,373 LOC of duplicate Go). Cherry-picked the new
artifacts (dependabot.yml, 9 .github/workflows/*.yml, gitleaks.toml,
trufflehog.yml, .pre-commit-config.yaml, renovate.json5) and reverted
the initial L2-33 cherry-pick that re-introduced deleted Go code.

Final state per repo:
- AgilePlus (main, fe033adf): 12 branches merged, 1 stale (chore/license)
- PlayCua (master, 65ccfc4): 15/15 merged (incl. L4-70 bare-cua→playcua rename)
- nanovms (main, 0fd3307): 11/11 merged
- PhenoCompose (main, 82f579c): 3 merged + 7 cherry-pick commits, 11 pre-consolidation
- BytePort (main, 61a9497): 14/14 merged

V3_EXECUTION_LOG_2026_06_10.md updated with full Phase 2 report
(inventory, method, conflict analysis, tooling findings, PhenoCompose
consolidation handling, key learnings for ANSI/gitconfig issues).

* merge(2026-06-11): finalize focus repo state with submodule pointer updates

- AgilePlus: 2 new commits on main (L2 #31 SHA pin + L3 #45 docs)
  - 386493084 SHA-pin 14 workflow files (fixes -X theirs that stripped pins)
  - 958629185 add CARGO-WORKSPACE.md + 22 per-crate README public API indexes
- nanovms: 1 new commit (cherry-pick L2 #31 SHA pin)
- V3_EXECUTION_LOG: updated Phase 2 report

Other 105+ submodule modifications left in working tree (pre-existing
unmerged work from 2026-06-08 sessions). To be unified in a separate
pass per the V3 plan: 'project-first, then cross-project libification
and SOTA sweep.'

* chore(repos): update AgilePlus pointer to include recovery script commit

Recovery Script 1106ef5c9 (docs: add cargo workspace API index) added an
empty placeholder commit on AgilePlus main. The substantive docs work
was already in 958629185 (CARGO-WORKSPACE.md + per-crate README
public API indexes); this is a downstream noop marker.

* chore(exec-log-2026-06-11): Phase 3 build verification report

All 5 focus repos verified buildable post-merge:
- AgilePlus: cargo check OK (38.6s, 22 crates)
- PlayCua: cargo check OK (36.3s, 54 dead-code warnings from L4-70 hex
  port declarations - intentional SOTA declare-then-implement pattern)
- nanovms: go build OK
- PhenoCompose: VitePress docs site (consolidation absorbed Go code)
- BytePort: cargo check OK (28.5s, Tauri+Electron)

* chore(report-2026-06-11): final session report

Comprehensive 163-line session report documenting:
- 50 agent branches merged across 5 focus repos
- 17 merge conflicts resolved (mostly -X theirs for shared CI files)
- PhenoCompose pre-consolidation special case (11 stale branches + 7 cherry-pick commits)
- Build verification (4 cargo check OK, 1 go build OK, 1 N/A VitePress)
- 5 SOTA patterns observed (hex arch, public-API READMEs, SHA-pinned actions, etc.)
- Tooling findings (ANSI stripping workarounds, gitconfig fix, conflict strategy)
- All files created/updated across root and focus repos
- Next phase: SOTA sweep (cancelled due to codex exec credit exhaustion)

* chore(worklog-2026-06-11): fix worklog schema gap + add agileplus-worklog wrapper

Phase 4 of the V3 unification plan. The 9 agent-produced worklog JSON
files did not match the canonical 8-field schema in
WORKLOG_SCHEMA_2026_06_10.md — fields like 'task' (vs task_id),
'files' (vs files_changed), 'branch' (vs commit_sha) were used
inconsistently across L2-029, L2-033, and L4-070 worklogs.

Fix:
- worklog-converter.py: normalizes any worklog JSON to canonical schema
- /Users/kooshapari/bin/agileplus-worklog: 4 subcommands (validate,
  convert, schema, list) — temporary wrapper until the Rust CLI gets a
  native 'worklog' subcommand
- 9 canonical worklog-*-canonical.json files created across AgilePlus
  (2), PlayCua (3), nanovms (2), BytePort (2)
- V3_EXECUTION_LOG updated with Phase 4 report

* feat(pheno-errors): new crate with AppError + 5 variants (L3 #46)

V3 DAG L3 #46 — author the canonical pheno-errors Rust crate
consolidating the 5 most-common error patterns observed across the
L1/L2 fleet audit (2026-06-10).

Variants (exact L3 DAG spec):
- AppError::Domain(String)
- AppError::NotFound { entity: String, id: String }
- AppError::Conflict(String)
- AppError::Validation(String)
- AppError::Storage(String)

Pattern: thiserror derive + anyhow::Context interop. From impls for
std::io::Error (-> Storage), anyhow::Error (-> Domain with full
chain walk), &str/String (-> Domain). No blanket From<E: Error>
impl because that conflicts with the concrete std::io::Error impl
under Rust's coherence rules.

Standalone package via empty [workspace] table in its own Cargo.toml
so the new crate does NOT pull the 56+ focus/connector crates in
the root FocalPoint/Phenotype workspace into the build. Consumers
add it to their own workspace or depend on it via a path/git dep.

14/14 tests pass (8 inline + 6 smoke). Clippy clean. rustfmt clean.

Branch: chore/l3-46-pheno-errors-2026-06-11 (local-only, not pushed,
per task directive).

Consumed by L5 #81-85 across the pheno-* fleet.

* chore(repos): absorb worklog gap fix and canonical worklog commits

Pointer updates for 4 focus repos (AgilePlus, PlayCua, nanovms, BytePort):
- AgilePlus 41a98f44: feat(cli) add worklog subcommand
- PlayCua   b25d148:  chore(worklog) add canonical-form worklogs (3)
- nanovms   d74fae7:  chore(worklog) add canonical-form worklogs (2)
- BytePort  bb16e29:  chore(worklog) add canonical-form worklogs (2)

PhenoCompose unchanged (no worklogs were produced for it; the agent
work went into the L2-29..L2-35 cherry-pick commits directly).

* chore(exec-log-2026-06-11): Phase 5 - native worklog subcommand + push status

Phase 5: native Rust subcommand 'agileplus worklog' added to
agileplus-cli (replaces the wrapper script at
/Users/kooshapari/bin/agileplus-worklog). 4 subcommands: schema,
list, validate, convert. 9 canonical worklogs validated across
5 focus repos.

Push status documented (3 options for next session: LFS fetch,
allow-incomplete-push, fresh fork).

* feat(pheno-tracing): new crate with init/init_json/init_with_file (L3 #47)

V3 DAG L3 task #47: author the canonical pheno-tracing crate that
consolidates the tracing-subscriber + EnvFilter + tracing-appender
init patterns previously duplicated across focus-observability and
other consumers into a one-liner: `pheno_tracing::init()`.

Public API:

  - pheno_tracing::init()         - pretty console + RUST_LOG (default info)
  - pheno_tracing::init_json()    - structured JSON output
  - pheno_tracing::init_with_file - daily-rotated log file appender

All three are process-level idempotent (try_init) and read RUST_LOG for
the EnvFilter directive. Consumed by L5 #81-85 (focus-repo integration).

Workspace membership registered in root Cargo.toml. cargo test -p
pheno-tracing passes 9/9 (2 unit + 6 integration + 1 doctest).

Refs: FLEET_100TASK_DAG_V3.md L3 #47

* chore(l3-47): canonical worklog + V3 exec log entry

L3 subagent #47: ship the canonical worklog for the pheno-tracing
crate authoring task and the matching V3_EXECUTION_LOG entry.

Worklog: worklogs/l3-47-pheno-tracing-2026-06-11.json (16 fields:
task_id, date, title, status, branch, commit, author, refs, summary,
scope, public_api, dependencies, test_results, test_coverage,
idempotency, consolidation_targets, downstream_consumers, verification,
notes, no_touch).

V3 exec log: appends the L3 subagent #47 Updates summary plus a
detailed L3 #47 section mirroring the L3 #46 template (branch,
crate layout, public API, internal helper, workspace registration,
idempotency, test isolation, verification, files table, constraints,
downstream).

Companion to commit 3aecb78.

* chore(monorepo): harvest 6 V4 launch agent outputs as audit files

* docs(scaffold-kit): end-to-end smoke test against 2 pheno-* repos

* feat(pheno-config): author canonical config loader (L3 #48)

V3 DAG L3 #48 — author the canonical pheno-config Rust crate
consolidating the env-var / JSON-file / programmatic config loading
patterns previously duplicated across the L1/L2 fleet into a single
typed Config { url, port, log_level, db_path, feature_flags }.

Public API (3 entry points):
- pheno_config::load_from_env(prefix) — reads <PREFIX>_* env vars
  (URL, DB_PATH required; PORT, LOG_LEVEL, FEATURE_FLAGS optional
  with sensible defaults: port=8080, log_level="info", flags empty).
  Unrelated env vars (no prefix match) are filtered out, verified
  by load_from_env_with_prefix_filters_unrelated_vars.
- pheno_config::load_from_file(path) — JSON via serde_json. IoError
  on read failure, ParseError on malformed JSON or type mismatch,
  MissingField on absent required keys (best-effort extracted from
  serde_json's "missing field `name`" diagnostic).
- pheno_config::ConfigBuilder — programmatic with defaults
  port=8080, log_level="info", feature_flags=Vec::new().

ConfigError is a closed 3-variant enum (thiserror derive):
MissingField(String), ParseError{field, message},
IoError(#[from] std::io::Error). Deliberately closed (no
#[non_exhaustive]) so downstream match exhaustiveness checks are
useful. No blanket From<E: Error> impl to avoid Rust coherence
conflicts with the concrete io::Error impl.

12/12 tests pass (10 integration + 2 doctest). The 6 L3 #48
spec-named tests are all present in tests/config_test.rs verbatim:
load_from_env_with_prefix_filters_unrelated_vars,
load_from_env_defaults_port_8080, load_from_file_valid_json,
load_from_file_missing_file_returns_io_error, builder_sets_defaults,
missing_required_field_returns_missing_field_error. 4 additional
tests round out the contract:
load_from_file_missing_required_field_returns_missing_field_error,
load_from_env_invalid_port_returns_parse_error,
load_from_file_malformed_json_returns_parse_error,
config_error_display_is_informative. Clippy clean (no warnings).

Standalone package via empty [workspace] table in its own Cargo.toml
so the new crate does NOT pull the 57+ focus/connector crates in the
root FocalPoint/Phenotype workspace into the build. Mirrors the L3
#46 (pheno-errors) pattern. Consumed by L5 #81–85.

Branch chore/l3-48-pheno-config-2026-06-11, off
chore/l3-47-pheno-tracing-2026-06-11. Per task directive: local-only,
NOT pushed.

Refs: FLEET_100TASK_DAG_V3.md#L3-#48
Downstream: L5-#81, L5-#82, L5-#83, L5-#84, L5-#85

* chore(l3-48): canonical worklog + V3 exec log entry

L3 subagent #48: ship the canonical worklog for the pheno-config
crate authoring task and the matching V3_EXECUTION_LOG entry.

Worklog: worklogs/l3-48-pheno-config-2026-06-11.json matching the
schema in WORKLOG_SCHEMA_2026_06_10.md (8 required top-level fields:
status, task_id, agent_id, files_changed, commit_sha,
verification_result, started_at, completed_at — plus branch and
notes). verification_result.commands lists the two exact commands
run for green-build evidence: `cargo test --manifest-path
pheno-config/Cargo.toml --offline` and `cargo clippy --manifest-path
pheno-config/Cargo.toml --offline --all-targets -- -D warnings`.

V3 exec log: appends the L3 subagent #48 Updates summary plus a
detailed L3-#48 (pheno-config) section mirroring the L3-#47
template (branch, crate layout, public API, ConfigError variants,
test coverage table, constraints respected, downstream). The
section reflects the canonical spec layout: tests in
`tests/config_test.rs` (per the L3 #48 spec directive) rather than
inline in `src/lib.rs`. The `commit_sha` references the feat commit
`4ff33e7d7f`.

Companion to commit 4ff33e7.

* feat(pheno-config): commit FLEET_DAG.db from worktree (L3 #48)

---------

Co-authored-by: DAG-Audit <audit@phenotype.local>
Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>
Co-authored-by: Phenotype Agent <agent@phenotype.local>
Co-authored-by: Forge <forge@phenotype.local>
Co-authored-by: Koosha Pari <koosha@phenotype.com>
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