Add files via upload #11

Workflow file for this run

.github/workflows/excel_inbox.yaml at 7ca4380

	# .github/workflows/excel_inbox.yaml
	#
	# Excel Inbox — apply vocabulary changes and validate
	# ====================================================
	# Triggered when a PR to main touches the inbox/ folder.
	#
	# Contributor flow:
	# 1. Download docs/assets/coremeta4cat_vocabulary.xlsx.
	# 2. Edit it (add/modify/delete rows), re-save as coremeta4cat_vocabulary.xlsx.
	# 3. Open a PR that places the file at inbox/coremeta4cat_vocabulary.xlsx.
	# 4. This workflow runs three dependent jobs:
	# a. Job 1 (apply-inbox): Applies the changes to the schema YAML files.
	# Saves the modified schema and apply report as CI artifacts.
	# b. Job 2 (validate-schema, matrix 3.9–3.13): Validates the modified
	# schema on each supported Python version. Appears as five individual
	# check runs in the PR — same visibility as main.yaml tests.
	# c. Job 3 (finish): Runs a round-trip check (inbox Excel vs the updated
	# schema YAMLs), posts a detailed PR comment, then on success commits
	# the schema changes back to the branch and removes the inbox file.
	# 5. The bot-commit in Job 3 triggers main.yaml to run its full test matrix on
	# the updated PR branch (branch-protection required checks are satisfied).
	# Because the inbox file is gone, main.yaml's paths-ignore suppresses any
	# re-run of excel_inbox.yaml — no infinite loop.
	# 6. A maintainer reviews the diff, verifies the bot commit, and merges.
	# 7. After merge, update_excel.yaml regenerates docs/assets/coremeta4cat_vocabulary.xlsx.
	#
	# Security note: uses pull_request_target with two-checkout pattern.
	# Contributor-controlled files (the xlsx) are only opened as data, never
	# executed. All scripts run from main (checked out in _main_branch/).
	# See: https://securitylab.github.com/resources/github-actions-preventing-pwn-requests/
	---
	name: Excel inbox — apply and validate

	on: # yamllint disable-line rule:truthy
	pull_request_target:
	branches:
	- main
	types: [opened, reopened, synchronize]
	paths:
	- "inbox/**"

	env:
	FORCE_COLOR: "1"
	INBOX_FILE: "inbox/coremeta4cat_vocabulary.xlsx"

	concurrency:
	group: ${{ github.workflow }}-${{ github.event.pull_request.number \|\| github.ref }}
	cancel-in-progress: true

	permissions: {}

	jobs:

	# ══════════════════════════════════════════════════════════════════════════════
	# Job 1 — Apply inbox Excel changes to the schema YAMLs
	# ══════════════════════════════════════════════════════════════════════════════
	apply-inbox:
	name: Apply inbox Excel to schema
	if: ${{ !github.event.pull_request.merged }}
	runs-on: ubuntu-latest
	timeout-minutes: 10

	permissions:
	contents: read # reads fork PR branch; write is granted only in the finish job

	outputs:
	inbox_present: ${{ steps.inbox_check.outputs.present }}
	apply_status: ${{ steps.apply.outputs.status }}

	steps:

	# ── Checkout ─────────────────────────────────────────────────────────────

	- name: Check out PR branch (fork-safe)
	uses: actions/checkout@v6.0.3
	with:
	# Contributor's branch — only read here; write-back is in the finish job.
	repository: ${{ github.event.pull_request.head.repo.full_name }}
	ref: ${{ github.event.pull_request.head.ref }}
	fetch-depth: 1
	persist-credentials: false

	- name: Check out main branch into _main_branch/
	# Always run OUR scripts from main — never from the PR.
	# This is the key security boundary for pull_request_target.
	uses: actions/checkout@v6.0.3
	with:
	ref: main
	path: _main_branch
	fetch-depth: 1
	persist-credentials: false

	# ── Tool setup ───────────────────────────────────────────────────────────

	- name: Install uv
	uses: astral-sh/setup-uv@v8.2.0
	with:
	python-version: "3.12"
	enable-cache: true
	cache-dependency-glob: "uv.lock"

	- name: Install project from main branch
	run: uv sync --dev
	working-directory: _main_branch

	# ── Pre-flight ───────────────────────────────────────────────────────────

	- name: Check inbox file exists
	id: inbox_check
	run: \|
	if [ -f "${{ env.INBOX_FILE }}" ]; then
	echo "present=true" >> "$GITHUB_OUTPUT"
	echo "Inbox file found: ${{ env.INBOX_FILE }}"
	else
	echo "present=false" >> "$GITHUB_OUTPUT"
	echo "No inbox file at ${{ env.INBOX_FILE }} — nothing to process."
	fi

	# ── Apply ────────────────────────────────────────────────────────────────

	- name: Apply inbox to schema (inbox_to_schema.py)
	if: steps.inbox_check.outputs.present == 'true'
	id: apply
	run: \|
	# set +e: prevents shell abort on non-zero exit before we save output.
	set +e
	OUTPUT=$(uv run python scripts/inbox_to_schema.py \
	"../${{ env.INBOX_FILE }}" 2>&1)
	EXIT_CODE=$?
	set -e

	echo "$OUTPUT"

	# Save to file for the finish job's PR comment.
	# printf '%s\n' ensures a trailing newline so GITHUB_ENV delimiter
	# parsing in the finish job always finds its closing marker on its own line.
	printf '%s\n' "$OUTPUT" > /tmp/apply_output.md

	case "$EXIT_CODE" in
	0) echo "status=ok" >> "$GITHUB_OUTPUT" ;;
	2) echo "status=warnings" >> "$GITHUB_OUTPUT" ;;
	*) echo "status=errors" >> "$GITHUB_OUTPUT" ;;
	esac

	# Fail this step (continue-on-error keeps the job alive for artifact upload).
	if [ "$EXIT_CODE" -eq 3 ] \|\| [ "$EXIT_CODE" -eq 1 ]; then
	exit 1
	fi
	working-directory: _main_branch
	continue-on-error: true

	# ── Artifact upload ──────────────────────────────────────────────────────

	- name: Upload apply output (for PR comment in finish job)
	if: steps.inbox_check.outputs.present == 'true'
	uses: actions/upload-artifact@v4
	with:
	name: apply-output
	path: /tmp/apply_output.md
	retention-days: 1

	- name: Upload modified schema (for validate-schema and finish jobs)
	if: >
	steps.inbox_check.outputs.present == 'true' &&
	steps.apply.outcome != 'failure'
	uses: actions/upload-artifact@v4
	with:
	name: modified-schema
	path: _main_branch/src/coremeta4cat/schema/
	retention-days: 1

	# ── Gate ────────────────────────────────────────────────────────────────

	- name: Fail job if apply errored (after artifacts are saved)
	if: steps.apply.outcome == 'failure'
	run: \|
	echo "::error::inbox_to_schema.py reported errors — schema was not modified."
	exit 1

	# ══════════════════════════════════════════════════════════════════════════════
	# Job 2 — Validate the modified schema on every supported Python version
	# ══════════════════════════════════════════════════════════════════════════════
	validate-schema:
	name: Validate schema (Python ${{ matrix.python-version }})
	needs: apply-inbox
	if: >
	!github.event.pull_request.merged &&
	needs.apply-inbox.outputs.inbox_present == 'true' &&
	needs.apply-inbox.outputs.apply_status != 'errors'
	runs-on: ubuntu-latest
	timeout-minutes: 20
	permissions: {}

	strategy:
	matrix:
	python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
	fail-fast: false

	steps:

	- name: Check out main branch
	# Run the test suite against the main-branch project with the modified
	# schema injected from the artifact.
	uses: actions/checkout@v6.0.3
	with:
	ref: main
	fetch-depth: 1
	persist-credentials: false

	- name: Download modified schema
	uses: actions/download-artifact@v4
	with:
	name: modified-schema
	path: src/coremeta4cat/schema/

	- name: Install uv
	uses: astral-sh/setup-uv@v8.2.0
	with:
	python-version: ${{ matrix.python-version }}
	enable-cache: true
	cache-dependency-glob: "uv.lock"

	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v6.2.0
	with:
	python-version: ${{ matrix.python-version }}

	- name: Install just
	run: uv tool install rust-just

	- name: Install project
	run: uv sync --dev

	- name: Regenerate Excel vocabulary from schema
	# Mirrors main.yaml: ensures docs/assets/coremeta4cat_vocabulary.xlsx
	# reflects the modified schema before any test that reads it runs.
	run: just schema-to-excel

	- name: Run test suite
	run: just test

	# ══════════════════════════════════════════════════════════════════════════════
	# Job 3 — Round-trip check, post PR comment, commit schema to PR branch
	# ══════════════════════════════════════════════════════════════════════════════
	finish:
	name: Round-trip, comment, and commit
	needs: [apply-inbox, validate-schema]
	# always() so we post the PR comment even when upstream jobs failed/were skipped.
	if: >
	always() &&
	!github.event.pull_request.merged &&
	needs.apply-inbox.outputs.inbox_present == 'true'
	runs-on: ubuntu-latest
	timeout-minutes: 15

	permissions:
	contents: write # to push the bot-commit back to the PR branch
	pull-requests: write # to post/update the PR comment

	steps:

	# ── Checkout ─────────────────────────────────────────────────────────────

	- name: Check out PR branch (fork-safe)
	uses: actions/checkout@v6.0.3
	with:
	repository: ${{ github.event.pull_request.head.repo.full_name }}
	ref: ${{ github.event.pull_request.head.ref }}
	fetch-depth: 0
	persist-credentials: true

	- name: Check out main branch into _main_branch/
	uses: actions/checkout@v6.0.3
	with:
	ref: main
	path: _main_branch
	fetch-depth: 1
	persist-credentials: false

	# ── Tool setup ───────────────────────────────────────────────────────────

	- name: Install uv
	uses: astral-sh/setup-uv@v8.2.0
	with:
	python-version: "3.12"
	enable-cache: true
	cache-dependency-glob: "_main_branch/uv.lock"

	- name: Install project from main branch
	run: uv sync --dev
	working-directory: _main_branch

	# ── Artifact download ─────────────────────────────────────────────────────

	- name: Download apply output
	uses: actions/download-artifact@v4
	with:
	name: apply-output
	path: /tmp/apply-output/

	- name: Download modified schema (for round-trip check and commit)
	if: needs.apply-inbox.outputs.apply_status != 'errors'
	uses: actions/download-artifact@v4
	with:
	name: modified-schema
	path: _main_branch/src/coremeta4cat/schema/
	continue-on-error: true

	- name: Load apply output into environment
	run: \|
	if [ -f /tmp/apply-output/apply_output.md ]; then
	# Use a random delimiter so the content can never accidentally contain it.
	# The explicit leading \n before the delimiter ensures it lands on its own
	# line even when the file was written without a trailing newline.
	DELIM="$(openssl rand -hex 16)"
	{
	printf 'apply_output<<%s\n' "$DELIM"
	cat /tmp/apply-output/apply_output.md
	printf '\n%s\n' "$DELIM"
	} >> "$GITHUB_ENV"
	fi

	# ── Round-trip check ──────────────────────────────────────────────────────

	- name: Round-trip check (inbox Excel vs updated schema)
	# excel_to_schema.py resolves SCHEMA_DIR from its own location on disk, so
	# it reads the modified YAMLs we just restored from the artifact in
	# _main_branch/src/coremeta4cat/schema/ — no separate regen step needed.
	if: needs.apply-inbox.outputs.apply_status != 'errors'
	id: roundtrip
	run: \|
	set +e
	RT_OUTPUT=$(uv run python scripts/excel_to_schema.py \
	"../${{ env.INBOX_FILE }}" 2>&1)
	RT_EXIT=$?
	set -e

	echo "$RT_OUTPUT"

	{
	echo "roundtrip_output<<RT_EOF"
	echo "$RT_OUTPUT"
	echo "RT_EOF"
	} >> "$GITHUB_ENV"

	if [ "$RT_EXIT" -eq 0 ] \
	&& echo "$RT_OUTPUT" \| grep -q "Schema and workbook are fully aligned"; then
	echo "status=ok" >> "$GITHUB_OUTPUT"
	else
	echo "status=diff" >> "$GITHUB_OUTPUT"
	fi
	working-directory: _main_branch
	continue-on-error: true

	# ── PR comment ────────────────────────────────────────────────────────────

	- name: Post PR comment
	uses: actions/github-script@v7
	with:
	github-token: ${{ secrets.GITHUB_TOKEN }}
	script: \|
	const applyStatus = "${{ needs.apply-inbox.outputs.apply_status }}";
	// "success" \| "failure" \| "skipped" \| "cancelled"
	const testResult = "${{ needs.validate-schema.result }}";
	const rtStatus = "${{ steps.roundtrip.outputs.status }}";

	const applyOutput = (process.env.apply_output \|\| "").trim();
	const rtOutput = (process.env.roundtrip_output \|\| "").trim();

	const applyFailed = applyStatus === "errors";
	const testFailed = testResult === "failure";
	const testSkipped = testResult === "skipped" \|\| testResult === "cancelled";
	const rtDiff = rtStatus === "diff";

	const allOk = !applyFailed && !testFailed && !testSkipped && !rtDiff
	&& testResult === "success";

	const sections = [];

	// ── inbox_to_schema.py report ──────────────────────────────────
	if (applyOutput) {
	sections.push(applyOutput, "");
	} else {
	sections.push(
	"## 📋 Inbox vocabulary — processing report", "",
	"(No output from inbox_to_schema.py)", ""
	);
	}

	// ── schema validation ──────────────────────────────────────────
	if (applyFailed) {
	sections.push(
	"### ⏭️ Schema validation — skipped", "",
	"Tests were not run because the inbox processing step failed.", ""
	);
	} else {
	const icon = testResult === "success" ? "✅"
	: testResult === "failure" ? "❌" : "⏭️";
	const msg = testResult === "success"
	? "All LinkML validation checks passed on Python 3.9 – 3.13."
	: testResult === "failure"
	? "LinkML validation failed on one or more Python versions. "
	+ "See the individual Validate schema (Python …) check runs for details."
	: "Schema validation was skipped or cancelled.";
	sections.push(
	`### ${icon} Schema validation (\`just test\`, Python 3.9 – 3.13)`, "",
	msg, ""
	);
	}

	// ── round-trip check ───────────────────────────────────────────
	if (rtStatus) {
	const icon = rtStatus === "ok" ? "✅" : "⚠️";
	const msg = rtStatus === "ok"
	? "The inbox workbook and the updated schema are fully aligned."
	: "Some fields in the inbox workbook differ from the updated schema. "
	+ "This may indicate fields that could not be automatically converted.";
	sections.push(
	`### ${icon} Round-trip check`, "",
	msg, "",
	"<details><summary>Diff output</summary>", "",
	"```", rtOutput.slice(0, 4000), "```",
	"</details>", ""
	);
	}

	// ── summary ────────────────────────────────────────────────────
	sections.push("---", "");
	if (allOk) {
	sections.push(
	"✅ All checks passed. Schema changes have been applied to this "
	+ "branch. A maintainer will review the diff and merge. "
	+ "The vocabulary workbook (`docs/assets/`) will be regenerated "
	+ "automatically by `update_excel.yaml` after merge.", ""
	);
	} else {
	sections.push(
	"❌ Some checks failed. Fix the issues listed above, "
	+ "update the workbook, and push again.", ""
	);
	}

	const body = sections.join("\n");

	// Update existing bot comment or create a new one
	const { data: comments } = await github.rest.issues.listComments({
	owner: context.repo.owner,
	repo: context.repo.repo,
	issue_number: context.issue.number,
	});
	const existing = comments.find(c =>
	c.user.type === "Bot" &&
	(c.body.includes("Inbox vocabulary") \|\| c.body.includes("Excel inbox"))
	);
	if (existing) {
	await github.rest.issues.updateComment({
	owner: context.repo.owner, repo: context.repo.repo,
	comment_id: existing.id, body,
	});
	} else {
	await github.rest.issues.createComment({
	owner: context.repo.owner, repo: context.repo.repo,
	issue_number: context.issue.number, body,
	});
	}

	# ── Gate / commit ─────────────────────────────────────────────────────────

	- name: Fail on errors (after comment posted)
	if: >
	needs.apply-inbox.outputs.apply_status == 'errors' \|\|
	needs.validate-schema.result == 'failure'
	run: \|
	echo "::error::Inbox processing failed. See the PR comment for details."
	exit 1

	- name: Commit schema changes and remove inbox file
	if: >
	needs.apply-inbox.outputs.apply_status != 'errors' &&
	needs.validate-schema.result == 'success'
	run: \|
	git config user.name "github-actions[bot]"
	git config user.email "github-actions[bot]@users.noreply.github.com"

	# Copy modified schema YAMLs from _main_branch/ back to PR branch.
	mkdir -p src/coremeta4cat/schema/
	cp -f _main_branch/src/coremeta4cat/schema/*.yaml \
	src/coremeta4cat/schema/

	# Stage schema YAMLs and remove the inbox file.
	# docs/assets/coremeta4cat_vocabulary.xlsx is NOT committed here —
	# update_excel.yaml is the designated owner of that file and will
	# regenerate it canonically after this PR is merged to main.
	git add src/coremeta4cat/schema/*.yaml
	git rm --force "${{ env.INBOX_FILE }}"

	# No [skip ci]: this commit triggers main.yaml to run its full test
	# matrix on the updated PR branch, satisfying branch-protection checks.
	# main.yaml's paths-ignore suppresses re-running excel_inbox.yaml
	# because the inbox file is now absent from the PR diff.
	git commit -m "ci: apply inbox vocabulary changes"
	git push

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Add files via upload #11

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Add files via upload #11

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Workflow file for this run