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chore: sync Arize skills from arize-skills@6a622b6c962907f54ca3578cb2cabff161d8aae6 and phoenix@30ccbe6b38cc83719038bf30041335f29bae45e9 (#1690)

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Jim Bennett
2026-05-12 19:08:14 -07:00
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skills/phoenix-cli/SKILL.md
+59 -2
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@@ -24,18 +24,28 @@ px trace list
px trace get <trace-id>
px trace annotate <trace-id>
px trace add-note <trace-id>
px trace-annotations delete
px span list
px span annotate <span-id>
px span add-note <span-id>
px span-annotations delete
px session list
px session get <session-id>
px session annotate <session-id>
px session add-note <session-id>
px session-annotations delete
px dataset list
px dataset get <name>
px project list
px project get <name>
px annotation-config list
px auth status
px profile list
px profile show [name]
px profile create <name>
px profile use <name>
px profile edit <name>
px profile delete <name>
```
## Setup
@@ -52,9 +62,13 @@ Always use `--format raw --no-progress` when piping to `jq`.
| Task | Files |
| ---- | ----- |
| Look at sampled traces and write specific notes about what went wrong (no taxonomy yet) | [references/open-coding](references/open-coding.md) |
| Look at sampled traces, spans, or sessions and write specific notes about what went wrong (no taxonomy yet) | [references/open-coding](references/open-coding.md) |
| Group those notes into a structured failure taxonomy and quantify what matters | [references/axial-coding](references/axial-coding.md) |
Both stages tag every artifact with one shared **coding annotation identifier** (descriptive shape, e.g. `coding-run:chatbot-context-loss-2026-05-06`) so the run is queryable, reversible, and viewable as a unit. Pass `--identifier <value>` explicitly on every `px` call — shell inheritance is unreliable across agent harnesses. Open coding writes notes via `px ... add-note` and records a small local JSONL sidecar at `.px/coding/<sanitized-identifier>.jsonl`; axial coding reads that sidecar as the deterministic handoff and records labels in `.px/coding/<sanitized-identifier>-axial.jsonl`. Pick the identifier once per run (see [references/open-coding.md](references/open-coding.md#coding-annotation-identifier-pick-this-first)), then share the Phoenix UI link from the wrap-up section. Revert is opt-in and runs three identifier-bound DELETEs only after explicit user confirmation.
> **Workflow term vs. server annotation name.** The skill prose calls this value the **coding annotation identifier** (shell-variable hint: `CODING_ANNOTATION_IDENTIFIER`). The server-side annotation NAME used for the UI filter is unchanged — `coding_session_id` — for data compatibility with rows already written by previous runs. Don't try to rename the server-side annotation; treat the asymmetry as load-bearing.
## Workflows
**"What do I do after instrumenting?" / "Where do I focus?" / "What's going wrong?"**
@@ -64,7 +78,7 @@ Always use `--format raw --no-progress` when piping to `jq`.
| Prefix | Description |
| ------ | ----------- |
| `references/open-coding` | Free-form notes against sampled traces — reach for it whenever the user wants to make sense of traces but has no failure categories yet |
| `references/open-coding` | Free-form notes against sampled traces, spans, or sessions — reach for it whenever the user wants to make sense of LLM traffic but has no failure categories yet. Includes a unit-of-analysis diagnostic so the workflow runs at the level the failure modes actually live at (trace for stateless single-shot calls, session for multi-turn agents, span for mechanical/in-isolation failures). |
| `references/axial-coding` | Inductive grouping of notes into a MECE taxonomy with counts — reach for it whenever the user has observations and needs categories or eval targets |
## Auth
@@ -72,15 +86,46 @@ Always use `--format raw --no-progress` when piping to `jq`.
```bash
px auth status # check connection and authentication
px auth status --endpoint http://other:6006 # check a specific endpoint
px auth status --profile staging # check a named profile's connection
```
## Profiles
Named profiles let you switch between multiple Phoenix instances (local, staging, cloud) without juggling environment variables. Profiles are stored in `~/.px/settings.json` (or `$XDG_CONFIG_HOME/px/settings.json`).
Configuration priority (highest to lowest): CLI flags > env vars > active profile > built-in defaults.
```bash
px profile list # list all profiles (shows active profile)
px profile show # show the active profile's settings
px profile show staging # show a named profile's settings
px profile create prod --endpoint https://app.phoenix.arize.com --api-key <key> --activate
px profile create local --endpoint http://localhost:6006 --project my-app
px profile use prod # switch the active profile
px profile edit prod # open profile JSON in $EDITOR (validates on save)
px profile delete prod --yes # delete a profile (--yes skips confirmation)
```
Use `--profile <name>` on any command to target a specific profile without changing the active one:
```bash
px trace list --profile staging --limit 10 --format raw --no-progress | jq .
px auth status --profile prod
```
`px profile create` options: `--endpoint <url>`, `--project <name>`, `--api-key <key>`, `--header <key=value>` (repeatable), `--activate`.
## Projects
```bash
px project list # list all projects (table view)
px project list --format raw --no-progress | jq '.[].name' # project names as JSON
px project get my-project --format raw --no-progress # single record by exact name
px project get my-project --format raw --no-progress | jq -r '.id' # extract project id
```
`project get` exits with `ExitCode.FAILURE` (1) on a name miss and writes a `StructuredError` `{error, code: "FAILURE", hint}` to stderr in `--format json|raw`.
## Traces
```bash
@@ -94,9 +139,14 @@ px trace get <trace-id> --format raw | jq '.spans[] | select(.status_code != "OK
px trace get <trace-id> --include-notes --format raw | jq '.notes'
px trace annotate <trace-id> --name reviewer --label pass
px trace annotate <trace-id> --name reviewer --score 0.9 --format raw --no-progress
px trace annotate <trace-id> --name reviewer --label pass --identifier "<coding-annotation-id>" # tag with a coding annotation identifier
px trace add-note <trace-id> --text "needs follow-up"
px trace add-note <trace-id> --text "needs follow-up" --identifier "<coding-annotation-id>" # tag + upsert on identifier
px trace-annotations delete --identifier "<coding-annotation-id>" --all -y # nuke every annotation tied to this coding annotation identifier
```
`px <entity>-annotations delete` requires `--all` or both `--start-time` and `--end-time` and emits `{deleted: true, target, filter}` on success.
### Trace JSON shape
```
@@ -147,7 +197,10 @@ px span list output.json --limit 100 # save to JSON file
px span list --format raw --no-progress | jq '.[] | select(.status_code == "ERROR")'
px span annotate <span-id> --name reviewer --label pass
px span annotate <span-id> --name checker --score 1 --annotator-kind CODE
px span annotate <span-id> --name reviewer --label pass --identifier "<coding-annotation-id>" # tag with a coding annotation identifier
px span add-note <span-id> --text "verified by agent"
px span add-note <span-id> --text "verified by agent" --identifier "<coding-annotation-id>" # tag + upsert on identifier
px span-annotations delete --identifier "<coding-annotation-id>" --all -y # nuke every annotation tied to this coding annotation identifier
```
### Span JSON shape
@@ -183,7 +236,10 @@ px session get <session-id> --include-annotations --format raw | jq '.session.an
px session get <session-id> --include-notes --format raw | jq '.session.notes'
px session annotate <session-id> --name reviewer --label pass
px session annotate <session-id> --name reviewer --score 0.9 --format raw --no-progress
px session annotate <session-id> --name reviewer --label pass --identifier "<coding-annotation-id>" # tag with a coding annotation identifier
px session add-note <session-id> --text "verified by agent"
px session add-note <session-id> --text "verified by agent" --identifier "<coding-annotation-id>" # tag + upsert on identifier
px session-annotations delete --identifier "<coding-annotation-id>" --all -y # nuke every annotation tied to this coding annotation identifier
```
### Session JSON shape
@@ -192,6 +248,7 @@ px session add-note <session-id> --text "verified by agent"
SessionData
id, session_id, project_id
start_time, end_time
token_count_prompt, token_count_completion, token_count_total — cumulative across all LLM spans in the session (int, default 0)
annotations[] (with --include-annotations, excludes note)
name, result { score, label, explanation }
notes[] (with --include-notes)
skills/phoenix-cli/references/axial-coding.md
+110 -70
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@@ -4,17 +4,40 @@ Group open-ended observations into structured failure taxonomies. Axial coding t
**Reach for this whenever** the user has observations and needs structure — e.g., "what categories of failures do we have", "what should I build evals for", "how do I prioritize fixes", "group these notes", "MECE breakdown", or any framing that asks for categories or counts grounded in real traces rather than invented top-down.
## Coding annotation identifier (reuse the open-coding value)
Reuse the **coding annotation identifier** chosen in open coding — every `annotate` call below passes `--identifier "$CODING_ANNOTATION_IDENTIFIER"` explicitly. In a fresh shell or fresh agent invocation, set `CODING_ANNOTATION_IDENTIFIER` to the same value (recoverable from the wrap-up UI URL or by listing `.px/coding/*.jsonl`); don't mint a new id. See [open-coding.md#coding-annotation-identifier-pick-this-first](open-coding.md#coding-annotation-identifier-pick-this-first) for the rationale and the sanitization rule.
> **Workflow term vs. server annotation name.** The skill calls this value the **coding annotation identifier**; the server annotation NAME used for the UI filter stays `coding_session_id` for data compatibility. Don't try to rename the server-side key.
```bash
CODING_ANNOTATION_IDENTIFIER="coding-run:chatbot-context-loss-2026-05-06"
SLUG=$(echo -n "$CODING_ANNOTATION_IDENTIFIER" | sed 's/[^a-zA-Z0-9_-]/-/g')
NOTES_SIDECAR=".px/coding/${SLUG}.jsonl"
AXIAL_SIDECAR=".px/coding/${SLUG}-axial.jsonl"
```
## Choosing the unit
Open-coding notes are usually **trace-level** (see [open-coding.md#choosing-the-unit](open-coding.md#choosing-the-unit)) — examples below lead with `px trace` and fall back to `px span` for span-level notes. **An axial label can live at a different level than the note that informed it** — that's a feature: a trace-level note "answered shipping when asked returns" can produce a span-level annotation on the retrieval span once a pattern reveals retrieval as the consistent culprit. Re-attribution at axial coding time is what axial coding *is*. Session-level rollups go through REST `/v1/projects/{id}/session_annotations` (no CLI write path).
Open coding's diagnostic in [open-coding.md#choosing-the-unit-of-analysis](open-coding.md#choosing-the-unit-of-analysis) commits to a unit (trace, span, or session). Axial coding inherits that unit by default — if open coding ran at the session level, axial labels will too; same for trace and span.
**An axial label can live at a different level than the note that informed it** — that's a feature, and it works in every direction:
- *Trace → span*: a trace-level note "answered shipping when asked about returns" can produce a span-level annotation on the retrieval span once a pattern reveals retrieval as the consistent culprit.
- *Trace → session*: a batch of trace-level notes describing single-turn confusion can produce a session-level annotation once you see the pattern is "the agent doesn't track the user's stated context across turns."
- *Session → trace*: a session-level note about cross-turn drift may, on closer reading, attribute to one specific turn where the agent dropped the thread; a trace-level annotation can name that turn.
Whichever level you write the axial label on, write the matching `coding_session_id` UI-filter annotation on the same entity (see [UI-filter annotation](#ui-filter-annotation) below) so the UI link picks it up.
## Process
1. **Gather** — Collect open-coding notes from the entities you reviewed (trace-level by default)
2. **Pattern** — Group notes with common themes
3. **Name** — Create actionable category names
4. **Attribute** — Decide what level each category lives at; an axial label can move from the note's level to the component the pattern implicates
5. **Quantify** — Count failures per category
1. **Set the coding annotation identifier** — set `CODING_ANNOTATION_IDENTIFIER` to the value used in open coding and re-derive `SLUG`, `NOTES_SIDECAR`, `AXIAL_SIDECAR` (see [Coding annotation identifier](#coding-annotation-identifier-reuse-the-open-coding-value))
2. **Gather** — read open-coding notes from `$NOTES_SIDECAR` (at the unit committed in open coding); no server round-trip
3. **Pattern** — group notes with common themes
4. **Name** — create actionable category names
5. **Attribute** — decide what level each category lives at; an axial label can move up (trace → session) or down (trace → span) from the source note's level to the level the pattern actually implicates
6. **Record** — `px {trace,span,session} annotate ... --name axial_coding_category --label <cat> --identifier "$CODING_ANNOTATION_IDENTIFIER"`, add/update one JSONL sidecar row for the label, then write the matching `coding_session_id` UI-filter annotation
7. **Quantify** — count failures per category from `$AXIAL_SIDECAR`
## Example Taxonomy
@@ -39,97 +62,110 @@ failure_taxonomy:
## Reading
### 1. Gather — extract open-coding notes
### 1. Gather — read this run's open-coding notes from the sidecar
Open-coding notes are stored as annotations with `name="note"` and are only returned when `--include-notes` is passed. Use `--include-annotations` instead and you will get structured annotations but **not** notes — the server excludes notes from the annotations array.
Open-coding wrote one JSONL line per note to `$NOTES_SIDECAR` (`.px/coding/${SLUG}.jsonl`). Read it directly — no server round-trip is needed. Each line has `entity_kind`, `entity_id`, `note`, `identifier`, and `ts`. If the same `(entity_kind, entity_id)` appears more than once, use the newest `ts` as the current note.
```bash
# Trace-level notes (default for open coding)
px trace list --include-notes --format raw --no-progress | jq '
[ .[] | select((.notes // []) | length > 0) ]
| map({ trace_id: .traceId, notes: [ .notes[].result.explanation ] })
'
**Missing-file behavior.** An absent `$NOTES_SIDECAR` means open coding hasn't run for this coding annotation identifier in this CWD — stop and run open coding first, do not silently treat it as zero notes.
# Span-level notes (when open coding dropped to span for mechanical failures)
px span list --include-notes --format raw --no-progress | jq '
[ .[] | select((.notes // []) | length > 0) ]
| map({ span_id: .context.span_id, notes: [ .notes[].result.explanation ] })
'
```
**Malformed lines.** Each line is independently parseable JSON. If `jq` reports a parse error, fix or drop that line manually; do not edit other lines.
**Notes outside this run.** The sidecar only carries notes this CWD wrote. To pull notes another reviewer or earlier run wrote, fetch them via `px {trace,span,session} list --include-notes` (embeds notes into row output) — the workflow's sidecar is intentionally per-CWD-per-coding-identifier.
### 2. Group — synthesize categories
Review the note text collected above. Manually identify recurring themes and draft candidate category names. Aim for MECE coverage: each note should fit exactly one category.
### 3. Record — write axial-coding annotations
### 3. Record — write axial-coding labels
Write one annotation per entity using `px trace annotate` or `px span annotate`. The level can differ from where the source note lives — see the **Recording** section below.
Write one annotation per entity using `px {trace,span,session} annotate`, passing `--identifier "$CODING_ANNOTATION_IDENTIFIER"` explicitly on every call, and record one JSONL row in `$AXIAL_SIDECAR` so [Quantify](#4-quantify--count-per-category-from-the-axial-sidecar) below can count without a server round-trip. The level can differ from where the source note lives — see [Recording](#recording) below.
### 4. Quantify — count per category
### 4. Quantify — count per category from the axial sidecar
After recording, use `--include-annotations` to count how many entities carry each label. Examples below show span-level counts; for trace-level annotations, swap `px span list` for `px trace list` (the `.annotations[]` shape is the same).
Counts come from `$AXIAL_SIDECAR` (populated by [Record](#3-record--write-axial-coding-labels)). No server query, no project-wide history mixed in — the sidecar holds exactly the labels this run wrote. Count the current rows by `axial_label`; if an entity appears more than once, use the newest `ts`.
```bash
px span list --include-annotations --format raw --no-progress | jq '
[ .[] | .annotations[]? | select(.name == "failure_category" and .result.label != null) ]
| group_by(.result.label)
| map({ label: .[0].result.label, count: length })
| sort_by(-.count)
'
```
Filter to a specific annotation name to check coverage:
```bash
px span list --include-annotations --format raw --no-progress | jq '
[ .[] | select((.annotations // []) | any(.name == "failure_category")) ]
| length
'
```
Same missing-file and malformed-line rules as `$NOTES_SIDECAR`: a missing axial sidecar means no labels have been written yet (run [Record](#3-record--write-axial-coding-labels)); malformed lines are line-local — fix or drop, don't edit neighbors.
## Recording
Use the matching annotate command for the level the **label** belongs at — which may differ from where the source note lives (see [Choosing the unit](#choosing-the-unit)):
Use the matching annotate command for the level the **label** belongs at — which may differ from where the source note lives (see [Choosing the unit](#choosing-the-unit)). Every call carries `--identifier "$CODING_ANNOTATION_IDENTIFIER"` and `--format raw --no-progress`, and is paired with a JSONL row in `$AXIAL_SIDECAR`.
**Axial sidecar JSONL line shape (one per `annotate`):**
```json
{"entity_kind":"trace","entity_id":"<trace-id>","annotation_name":"axial_coding_category","axial_label":"<label>","explanation":"<optional explanation>","identifier":"<original identifier value, unsanitized>","ts":"<ISO-8601 UTC>"}
```
Fields:
- `entity_kind` — `"trace"`, `"span"`, or `"session"` (matches the `annotate` subcommand)
- `entity_id` — the entity argument passed to `annotate`
- `annotation_name` — always `"axial_coding_category"` for axial labels (the workflow's reserved annotation name)
- `axial_label` — the `--label` value, verbatim; this is what [Quantify](#4-quantify--count-per-category-from-the-axial-sidecar) groups on
- `explanation` — optional, but include it when the `annotate` call used `--explanation`
- `identifier` — the **original** `$CODING_ANNOTATION_IDENTIFIER` value, unsanitized; the sanitized form lives only in the filename
- `ts` — ISO-8601 UTC timestamp of the local append
If you revise a label for the same entity under the same coding annotation identifier, either replace that row or append a newer row. When duplicate `(entity_kind, entity_id, annotation_name)` rows exist, the newest `ts` is the current label. This matches the server upsert behavior of `annotate --identifier`.
Minimal trace example:
```bash
# Trace-level label (most common — the trace as a whole exhibits the failure)
px trace annotate <trace-id> \
--name failure_category \
--name axial_coding_category \
--label answered_off_topic \
--explanation "asked about returns; answer covered shipping" \
--annotator-kind HUMAN
# Span-level label (when the pattern implicates a specific component)
px span annotate <span-id> \
--name failure_category \
--label retrieval_off_topic \
--explanation "retrieved shipping docs for a returns query" \
--annotator-kind HUMAN
--annotator-kind HUMAN \
--identifier "$CODING_ANNOTATION_IDENTIFIER" \
--format raw --no-progress
```
Accepted flags: `--name`, `--label`, `--score`, `--explanation`, `--annotator-kind` (`HUMAN`, `LLM`, `CODE`). There are no `--identifier` or `--sync` flags on these commands.
Then add a matching JSONL row to `$AXIAL_SIDECAR` using the line shape above. For span or session labels, change `entity_kind`, `entity_id`, and the `px` subcommand accordingly.
### Bulk recording
Accepted flags: `--name`, `--label`, `--score`, `--explanation`, `--annotator-kind` (`HUMAN`, `LLM`, `CODE`), `--identifier`. There is no `--sync` flag — the CLI passes `sync=true` itself.
Axial coding categorizes the entities you took notes on during open coding. Do **not** filter by `--status-code ERROR` — that captures only spans where Python raised, which excludes most failure modes (hallucination, wrong tone, retrieval miss). See [open-coding.md](open-coding.md#inspection) for the full reasoning.
### UI-filter annotation
Write a `coding_session_id` annotation at the same level as the axial label — see [open-coding.md#ui-filter-annotation](open-coding.md#ui-filter-annotation) for why the Phoenix UI filter requires a name-based annotation rather than the bare `--identifier`. If open coding already wrote `coding_session_id` on the same entity, this call upserts (idempotent). The annotation NAME `coding_session_id` is unchanged; only the workflow's spoken term is "coding annotation identifier".
```bash
# Bulk-annotate traces that already have open-coding notes
px trace list --include-notes --format raw --no-progress \
| jq -r '.[] | select((.notes // []) | length > 0) | .traceId' \
| while read tid; do
px trace annotate "$tid" \
--name failure_category \
--label answered_off_topic \
--annotator-kind HUMAN
done
# Same level as the axial label above
px trace annotate <trace-id> \
--name coding_session_id \
--label "$CODING_ANNOTATION_IDENTIFIER" \
--identifier "$CODING_ANNOTATION_IDENTIFIER"
# or px span annotate / px session annotate at matching levels
```
The same pattern works for span-level notes — swap `px trace` for `px span` and `.traceId` for `.context.span_id`.
### Recording discipline
Aside: for Node-based bulk scripts, `@arizeai/phoenix-client` exposes `addSpanAnnotation`, `addSpanNote`, and `addTraceNote`. (No `addTraceAnnotation` is exported today; use the REST endpoint or `px trace annotate` for trace-level annotations.)
Axial coding categorizes the entities you took notes on during open coding. Use `$NOTES_SIDECAR` as the source of candidate entities and write labels only after reading the note text and surrounding trace/span/session context. Do **not** filter by `--status-code ERROR` — that captures only spans where Python raised, which excludes most failure modes (hallucination, wrong tone, retrieval miss). See [open-coding.md](open-coding.md#inspection) for the full reasoning.
Aside: `px api graphql` rejects mutations — it cannot write annotations.
**Fallback paths:** REST `POST /v1/{trace,span,session}_annotations` and `@arizeai/phoenix-client`'s `addSpanAnnotation` / `addSessionAnnotation` (no `addTraceAnnotation` is exported today — use REST or `px trace annotate`). The GraphQL endpoint rejects mutations.
## Wrapping up
After axial coding finishes, share the Phoenix UI link with the user. The link points to the project's traces table filtered by the `coding_session_id` annotation — `annotations['coding_session_id'].label == '<coding-annotation-id>'`. The UI route `/projects/:projectId` expects an encoded GraphQL node ID, not a project name — resolve it via `px project get`:
```bash
project_id=$(px project get "$PHOENIX_PROJECT" --format raw --no-progress | jq -r '.id')
encoded=$(python3 -c 'import urllib.parse, sys; print(urllib.parse.quote(sys.argv[1]))' \
"annotations['coding_session_id'].label == '$CODING_ANNOTATION_IDENTIFIER'")
echo "Phoenix UI: $PHOENIX_HOST/projects/$project_id/traces?filterCondition=$encoded"
```
If the user wants to discard everything this run produced (open-coding notes, axial-coding labels, and `coding_session_id` annotations on the server, plus the local sidecars), three identifier-bound deletes handle the server side and one `rm` handles the local sidecars. **Confirm before running** — destructive. Each `px <entity>-annotations delete` call requires `--all` to authorize the unbounded sweep; `--identifier` only narrows. Set `PHOENIX_CLI_DANGEROUSLY_ENABLE_DELETES=true` first if not already exported:
```bash
for kind in trace span session; do
px "$kind-annotations" delete \
--identifier "$CODING_ANNOTATION_IDENTIFIER" \
--all -y \
--format raw --no-progress
done
rm -f "$NOTES_SIDECAR" "$AXIAL_SIDECAR"
```
Each `px <entity>-annotations delete` call removes notes, axial-coding labels, and `coding_session_id` annotations together because they share the underlying annotation table; the `rm` clears the local sidecars.
## Agent Failure Taxonomy
@@ -173,6 +209,10 @@ A useful category is:
## Principles
- **MECE** - Each failure fits ONE category
- **Actionable** - Categories suggest fixes
- **Bottom-up** - Let categories emerge from data
- **One coding annotation identifier per run** — every `annotate` call and every sidecar line carries `$CODING_ANNOTATION_IDENTIFIER`, the same value open coding used; never mint a new id mid-run.
- **Pass `--identifier` explicitly** — every `px` call gets `--identifier "$CODING_ANNOTATION_IDENTIFIER"`; do not rely on inherited env vars.
- **Sidecar reads, server writes** — Gather and Quantify read `$NOTES_SIDECAR` and `$AXIAL_SIDECAR` locally; Record writes to the server and updates the sidecar. If an entity appears more than once, the newest `ts` wins.
- **MECE** — Each failure fits ONE category.
- **Actionable** — Categories suggest fixes.
- **Bottom-up** — Let categories emerge from data.
- **UI-filter annotation always paired** — never write `axial_coding_category` without writing the matching `coding_session_id` annotation; the UI link depends on it.
skills/phoenix-cli/references/open-coding.md
+167 -40
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@@ -1,33 +1,100 @@
# Open Coding
Free-form note-writing against sampled traces, before any taxonomy exists. After you pick a sample of traces, read each one and write a short, specific observation of what went wrong. These raw notes feed [axial coding](axial-coding.md), where they get grouped into named failure categories — and ultimately into eval targets or fix priorities.
Free-form note-writing against sampled traces, spans, or sessions, before any taxonomy exists. After you pick a sample at the right unit (see [Choosing the unit of analysis](#choosing-the-unit-of-analysis)), read each one and write a short, specific observation of what went wrong. These raw notes feed [axial coding](axial-coding.md), where they get grouped into named failure categories — and ultimately into eval targets or fix priorities.
**Reach for this whenever** the user wants to look at traces or spans without a fixed taxonomy yet — e.g., "what's going wrong with this agent", "I just instrumented my app, where do I start", "review these traces", "what kinds of mistakes is the model making", "help me make sense of these outputs", or any framing that needs grounded observations before categories.
**Reach for this whenever** the user wants to look at LLM traffic without a fixed taxonomy yet — e.g., "what's going wrong with this agent", "I just instrumented my app, where do I start", "review these traces", "the chatbot keeps losing context", "what kinds of mistakes is the model making", "help me make sense of these conversations", or any framing that needs grounded observations before categories.
## Choosing the unit
## Choosing the unit of analysis
Open coding has two scopes that don't have to match:
The right unit — **trace, span, or session** — depends on the question and the system. Pick deliberately before recording; the choice determines whether you call `px trace`, `px span`, or `px session` throughout, and a wrong default is expensive to undo mid-run.
- **Review scope** — the **trace**. Read input → tool calls → retrieved context → output as one story.
- **Recording scope** — **default to the trace**. The honest observation is usually trace-shaped ("asked X, got Y; the answer didn't address the question"), and forcing localization to a span at this stage commits to causal attribution you don't yet have data to support — that's axial coding's job.
The unit is about **where the failure modes you're investigating actually live**:
Drop to a **span** only when one of:
- The span, read in isolation, is still wrong: an exception fired, a tool returned an error response, the output is malformed.
- You already know the domain well enough to attribute the failure on sight without inferring across spans.
- **Trace** — one input → one call graph → one output. Right for classifiers, single-shot summarizers, stateless tool-using agents, single-query RAG. Failure modes that live here: wrong answer, malformed output, missed retrieval, bad tool selection within one request.
- **Span** — one operation inside a trace. Right for in-isolation mechanical failures (an exception fired, a tool returned an error response, an output is malformed) or when you can attribute on sight to a specific component. Reach for span when the trace as a whole is fine but one piece inside it is the unit of interest.
- **Session** — a sequence of traces sharing a `session.id`. Right for multi-turn conversational agents, agents with episodic memory, anything where the failure mode is a *trajectory*: context loss across turns, drift from the user's stated goal, the agent forgetting a stated preference, repeated user clarifications. These failures don't exist on any single trace; they only exist *across* traces.
Session-level findings are axial-coding rollup targets, not open-coding notes — Phoenix has REST `/v1/projects/{id}/session_annotations` but no session `add-note` path.
### Diagnostic — three signals to read
1. **User framing.** *Tilts session*: "conversation", "agent forgot", "drift", "memory", "across turns", "user had to repeat themselves". *Tilts trace*: "this trace", "this call", "the response was wrong", "wrong output". *Tilts span*: "exception", "error response", "malformed", "the retrieval failed".
2. **Data shape.** Probe before the loop. The session id lives at `rootSpan.attributes["session.id"]` (it is *not* a top-level field on the trace JSON), and is `""` for traces that aren't session-wired — filter both:
```bash
px trace list --limit 200 --format raw --no-progress \
| jq '
[ .[] | .rootSpan.attributes["session.id"] // empty | select(. != "") ]
| { with_session: length,
distinct_sessions: (group_by(.) | length),
median_traces_per_session:
(group_by(.) | map(length) | sort | .[length/2|floor] // 0) }
'
```
`with_session: 0` → sessions not wired; trace is the grain. `median_traces_per_session: 1` → single-trace sessions; still trace. `median_traces_per_session: 5+` → sessions are meaningful; session is plausibly right.
3. **System type.** Open one recent trace and inspect the root span's input. A single user message → one turn or one shot. A message *array* (`[{role: user}, {role: assistant}, ...]`) → that's a turn within a longer dialogue; the dialogue lives at the session level.
```bash
px trace get <trace-id> --format raw \
| jq '.rootSpan.attributes["input.value"] | (try fromjson catch .) | (type, length?)'
```
### Commit out loud, then proceed
State the unit explicitly before recording any note:
> "Question: 'the chatbot keeps losing context'. Data: median 7 traces per session, message-array inputs. Recording at the **session** level; will drop to **trace** for single-turn observations, **span** for mechanical failures."
The unit can shift if data demands it — a trace-level investigation that surfaces "the agent never remembers earlier turns" should pivot to session. Record the observation, then refocus the next batch. The unit is a starting hypothesis, not a contract.
## Coding annotation identifier (pick this first)
Every artifact this workflow produces — open-coding notes, axial-coding labels, the local sidecar files, and the UI-filter annotation — is tagged with one **coding annotation identifier** so the run is queryable, revertible, and viewable as a unit. Pick a **descriptive, unique** identifier before recording any notes. Format suggestion:
coding-run:<short-topic>-<YYYY-MM-DD>
Examples: `coding-run:chatbot-context-loss-2026-05-06`, `coding-run:agent-tool-misuse-q2`. Descriptive ids carry meaning for whoever opens the data later — better than an opaque uuid. The `coding-run:` prefix is a visual convention; the value is the workflow's coding annotation identifier, not a `px session` id.
> **Workflow term vs. server annotation name.** The skill calls this value the **coding annotation identifier**. The server-side annotation NAME used for the UI filter is unchanged — `coding_session_id` — for data compatibility with rows already written. Don't try to rename it.
Pass the identifier explicitly on every `px` call. A shell variable for readability is fine, but **do not rely on shell inheritance** — many agent harnesses spawn each command in a fresh subshell, so `CODING_ANNOTATION_IDENTIFIER` may not propagate.
```bash
CODING_ANNOTATION_IDENTIFIER="coding-run:chatbot-context-loss-2026-05-06"
```
The local sidecar lives at `.px/coding/<sanitized-identifier>.jsonl` (CWD-relative, matching the `.px/docs` precedent). Sanitization rule: replace any character not matching `[a-zA-Z0-9_-]` with `-` before using the value in the filename — colons, slashes, and other shell-fragile characters get normalized. For `CODING_ANNOTATION_IDENTIFIER="coding-run:chatbot-context-loss-2026-05-06"` the sidecar path is `.px/coding/coding-run-chatbot-context-loss-2026-05-06.jsonl`.
Verify this run hasn't already started — uniqueness is a **local file check**, not a server query:
```bash
SLUG=$(echo -n "$CODING_ANNOTATION_IDENTIFIER" | sed 's/[^a-zA-Z0-9_-]/-/g')
SIDECAR=".px/coding/${SLUG}.jsonl"
test ! -f "$SIDECAR" || { echo "Sidecar already exists at $SIDECAR — pick a new identifier or delete the file"; exit 1; }
mkdir -p .px/coding
```
If `$SIDECAR` already exists, append a disambiguator (`-v2`, `-dustin`, etc.) to `CODING_ANNOTATION_IDENTIFIER`, re-derive `SLUG`, and re-check. The agent harness can run open coding and axial coding in independent invocations: each step re-derives `SLUG` from `CODING_ANNOTATION_IDENTIFIER` and reads/writes the same file.
## Process
1. **Inspect** — fetch a trace from your sample
2. **Read** — look at input, output, exceptions, tool calls, retrieved context
3. **Note** — write one specific sentence describing what went wrong (or skip if correct)
4. **Record** — attach the note to the trace with `px trace add-note` (default), or to a span with `px span add-note` for in-isolation/mechanical failures
5. **Iterate** — move to the next trace; repeat until the sample is exhausted or saturation hits
1. **Pick a coding annotation identifier** — choose a descriptive value and verify the sidecar file does not yet exist (see [Coding annotation identifier](#coding-annotation-identifier-pick-this-first))
2. **Pick the unit** — work through [Choosing the unit of analysis](#choosing-the-unit-of-analysis) and commit to trace, span, or session
3. **Inspect** — fetch one entity at the chosen unit (trace / span / session)
4. **Read** — input, output, exceptions, tool calls, retrieved context, and (at session level) the trajectory across child traces
5. **Note** — write one specific sentence describing what went wrong (or skip if correct)
6. **Record** — `px {trace,span,session} add-note <id> --text "..." --identifier "$CODING_ANNOTATION_IDENTIFIER" --format raw --no-progress`, add/update one JSONL sidecar row for the note, then write the matching [UI-filter annotation](#ui-filter-annotation)
7. **Iterate** — move to the next entity; repeat until the sample is exhausted or saturation hits
8. **Hand off** — axial coding reads the sidecar directly (no shared shell required); see [Wrapping up](#wrapping-up) for the UI link
## Inspection
Use `px` to read trace and span context before writing a note. Open coding reviews by **trace** — read input → tool calls → retrieved context → output as a unit. Record on the trace by default; drill to a specific span only when the failure is mechanical (exception, error response, malformed output) or you can attribute on sight (see [Choosing the unit](#choosing-the-unit)).
Use `px` to read context at the unit committed in [Choosing the unit](#choosing-the-unit-of-analysis):
- **Trace unit** — read one trace's input → tool calls → retrieved context → output as one story.
- **Span unit** — read one operation's input/output and surrounding spans for context.
- **Session unit** — read the sequence of traces in order; the trajectory (turns, retrievals, tool-call patterns *across* traces) is the data, not any single trace's inputs and outputs.
> **Don't filter the sample by `--status-code ERROR`.** OTel's `status_code` only flips to `ERROR` when an instrumentor catches a raised Python exception (network failure, 5xx, parse error). Hallucinations, wrong tone, retrieval misses, and bad tool selection all complete cleanly and arrive as `OK` or `UNSET`. Sampling for open coding by `--status-code ERROR` excludes the population this workflow exists to surface.
@@ -63,38 +130,65 @@ Always pipe through `jq` with `--format raw --no-progress` when scripting.
## Recording Notes
Default write path is `px trace add-note <trace-id> --text "..."` — most observations are trace-shaped and shouldn't pre-commit to localization. Drop to `px span add-note <span-id>` when the failure is in-isolation wrong (exception, error response, malformed output) or you already know the failure structure on sight.
Use the `add-note` command matching the unit committed in [Choosing the unit](#choosing-the-unit-of-analysis): `px trace add-note`, `px span add-note`, or `px session add-note`. Every call carries an explicit `--identifier "$CODING_ANNOTATION_IDENTIFIER"` and `--format raw --no-progress`.
Passing `--identifier "$CODING_ANNOTATION_IDENTIFIER"` does two things:
- Tags the note row with the coding annotation identifier on the server, so the cleanup `px <entity>-annotations delete --identifier "$CODING_ANNOTATION_IDENTIFIER" --all` sweep removes every artifact this run produced.
- Makes the call **upsert** on `(entity_id, name='note', identifier)` — re-running open coding on the same entity within the same coding annotation identifier overwrites the prior note instead of appending a second row. (Without `--identifier`, the server stamps a unique `px-{kind}-note:<uuid>` and each call appends.)
After every successful `add-note`, record one JSONL line in `$SIDECAR`. The sidecar is what axial coding reads — no server round-trip. It is a content handoff, not code: keep it readable, inspect it directly, and use whatever simple tooling is convenient.
**Sidecar JSONL line shape (one per `add-note`):**
```json
{"entity_kind":"trace","entity_id":"<trace-id>","note":"<text>","identifier":"<original identifier value, unsanitized>","ts":"<ISO-8601 UTC>"}
```
Fields:
- `entity_kind` — `"trace"`, `"span"`, or `"session"` (matches the `add-note` subcommand used)
- `entity_id` — the entity argument passed to `add-note` (trace id, span id, or session id)
- `note` — the `--text` value, verbatim
- `identifier` — the **original** `$CODING_ANNOTATION_IDENTIFIER` value, unsanitized; the sanitized form lives only in the filename
- `ts` — ISO-8601 UTC timestamp (e.g. `2026-05-08T17:14:09Z`) of the local append
If you revise a note for the same entity under the same coding annotation identifier, either replace that row or append a newer row. When duplicate `(entity_kind, entity_id)` rows exist, the newest `ts` is the current note. This matches the server upsert behavior of `add-note --identifier`.
Minimal trace example:
```bash
# Trace-level note (default)
px trace add-note <trace-id> --text "Asked about returns; final answer covered shipping policy instead"
# Span-level note (mechanical or attributable-on-sight failures)
px span add-note <span-id> --text "Tool call returned 500 — vendor API unreachable"
# Interactive loop — walk traces, write a trace-level note per failing trace
px trace list --last-n-minutes 60 --limit 50 --format raw --no-progress \
| jq -r '.[].traceId' \
| while read tid; do
echo "── trace $tid ──"
px trace get "$tid" --format raw | jq '
{input: .rootSpan.attributes["input.value"],
output: .rootSpan.attributes["output.value"],
spans: (.spans | sort_by(.start_time) | map({name, status_code}))}
'
read -p "Note for $tid (blank to skip): " note
[ -z "$note" ] && continue
px trace add-note "$tid" --text "$note"
done
px trace add-note <trace-id> \
--text "Asked about returns; final answer covered shipping policy instead" \
--identifier "$CODING_ANNOTATION_IDENTIFIER" \
--format raw --no-progress
```
Then add a matching JSONL row to `$SIDECAR` using the line shape above. For span or session notes, change `entity_kind`, `entity_id`, and the `px` subcommand accordingly.
Bulk auto-tagging by status code (e.g. `px span list --status-code ERROR | xargs ... add-note "error"`) is **not open coding** — open coding is manual, observation-grounded, and ranges over all failure modes, not just spans where Python raised. Skip the bulk-by-status-code shortcut; it produces fewer, less informative notes than walking traces.
### UI-filter annotation
Every entity that receives an open-coding note (or an axial-coding label later) also needs a UI-filter annotation so the Phoenix UI can filter by coding annotation identifier. Phoenix's UI filter language is name-based, not identifier-based — there is no UI primitive for filtering by `identifier`, so an annotation whose **name** is the constant `coding_session_id` and whose **label** is the coding annotation identifier value is what the wrap-up UI link actually filters on.
The annotation NAME `coding_session_id` is the load-bearing data key on the server and is **unchanged** in this rewrite. The skill's workflow term is "coding annotation identifier"; the server key stays `coding_session_id` for compatibility with rows already written.
Run this once per touched entity, alongside the `add-note` (and again later when axial coding labels a different entity):
```bash
px trace annotate <trace-id> \
--name coding_session_id \
--label "$CODING_ANNOTATION_IDENTIFIER" \
--identifier "$CODING_ANNOTATION_IDENTIFIER"
# or px span annotate / px session annotate at matching levels
```
The annotation's `--identifier` matches `$CODING_ANNOTATION_IDENTIFIER`, so the [wrap-up DELETE](#wrapping-up) cleans it up in the same call as the notes and the axial-coding labels.
**Fallback write paths (one-line asides):**
- `POST /v1/trace_notes` and `POST /v1/span_notes` — accept one `{data: {trace_id|span_id, note}}` per request; use for scripted writes outside the CLI.
- `@arizeai/phoenix-client` `addTraceNote` and `addSpanNote` wrap the same endpoints.
- `px api graphql` rejects mutations with `"Only queries are permitted."` — use `px trace/span add-note` or the REST endpoints instead.
- `POST /v1/trace_notes` and `POST /v1/span_notes` and `POST /v1/session_notes` — accept one `{data: {trace_id|span_id|session_id, note, identifier}}` per request; the optional `identifier` field upserts on `(entity_id, name='note', identifier)` when non-empty.
- `@arizeai/phoenix-client` `addTraceNote`, `addSpanNote`, and `addSessionNote` wrap the same endpoints and accept an optional `identifier` field on the note object.
- The GraphQL endpoint rejects mutations with `"Only queries are permitted."` — write through `px {trace,span,session} add-note` or the REST endpoints above.
## What Makes a Good Note
@@ -118,10 +212,43 @@ Stop writing notes when observations stop being new. Signals:
At saturation, move on to [axial coding](axial-coding.md) to group what you have. Continuing past saturation adds traces but not insight. You do not need to annotate every trace — annotating correct ones dilutes signal.
## Listing what this run produced
The local sidecar is the handoff record for notes written this run. Inspect it directly. Each line is one note record; if the same entity appears more than once, use the newest `ts` as the current note. Missing-file behavior: an absent sidecar means open coding has not yet started for this coding annotation identifier; treat that as zero notes, not an error. Malformed lines are line-local: fix or drop the bad line without editing neighbors.
## Wrapping up
When the run is done, share the Phoenix UI link with the user. The link filters the project's traces page by the `coding_session_id` annotation written alongside each note. The UI route `/projects/:projectId` expects an encoded GraphQL node ID, not a project name — resolve it via `px project get`:
```bash
project_id=$(px project get "$PHOENIX_PROJECT" --format raw --no-progress | jq -r '.id')
encoded=$(python3 -c 'import urllib.parse, sys; print(urllib.parse.quote(sys.argv[1]))' \
"annotations['coding_session_id'].label == '$CODING_ANNOTATION_IDENTIFIER'")
echo "Phoenix UI: $PHOENIX_HOST/projects/$project_id/traces?filterCondition=$encoded"
```
If the user wants to discard everything this run produced, three identifier-bound deletes handle the server side and one `rm` handles the local sidecars. **Confirm with the user before running** — this is destructive. Each call requires `--all` (or both `--start-time` and `--end-time`) to authorize the sweep; `--identifier` filters further but never authorizes on its own. Set `PHOENIX_CLI_DANGEROUSLY_ENABLE_DELETES=true` first if not already exported:
```bash
for kind in trace span session; do
px "$kind-annotations" delete \
--identifier "$CODING_ANNOTATION_IDENTIFIER" \
--all -y \
--format raw --no-progress
done
rm -f "$SIDECAR" ".px/coding/${SLUG}-axial.jsonl"
```
Each `px <entity>-annotations delete` call covers notes, structured annotations, and the `coding_session_id` annotation in one shot because they share the underlying annotation table.
## Principles
- **One coding annotation identifier per run** — every server artifact and every sidecar line carries the same `$CODING_ANNOTATION_IDENTIFIER`; never mint a per-stage id.
- **Pass `--identifier` explicitly** — every `px` call gets `--identifier "$CODING_ANNOTATION_IDENTIFIER"`; do not rely on inherited env vars across harness-spawned subshells.
- **Sidecar is the handoff record for notes** — axial coding reads from the local sidecar, not from the server; if an entity appears more than once, the newest `ts` wins.
- **Free-form over structured** — do not pre-commit to a taxonomy during open coding; categories emerge in axial coding.
- **Specific over general** — quote or paraphrase the observed failure; vague labels ("bad response") carry no signal.
- **Context before labeling** — inspect input, output, and retrieved context before writing any note.
- **Iterate before categorizing** — work through the full sample first; resist grouping while still collecting.
- **Skip is valid** — a correct span needs no note; annotating everything dilutes signal.
- **Revert is opt-in** — the wrap-up DELETE only runs after explicit user confirmation; the default path prints the UI link and stops.