refactor: port describe_pandas from scitex-gen misc.py (v0.2.25)

.github/workflows/auto-merge-to-develop.yaml

@@ -0,0 +1,49 @@
+name: auto-merge-to-develop
+# Merge green PRs that TARGET develop, the moment their checks complete.
+# GitHub reads check_suite-triggered workflows from the DEFAULT branch (main),
+# so this file lives on main but acts ONLY on PRs whose base is develop.
+# codecov + readthedocs checks are ignored (advisory). Fail-safe: if a merge
+# is blocked by branch policy the PR simply stays open.
+on:
+  check_suite:
+    types: [completed]
+  workflow_dispatch: {}
+
+permissions:
+  contents: write
+  pull-requests: write
+
+jobs:
+  automerge:
+    if: ${{ github.event_name == 'workflow_dispatch' || github.event.check_suite.conclusion == 'success' }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: merge green PRs targeting develop
+        env:
+          GH_TOKEN: ${{ github.token }}
+          REPO: ${{ github.repository }}
+          HEAD_SHA: ${{ github.event.check_suite.head_sha }}
+        run: |
+          set -uo pipefail
+          if [ -n "${HEAD_SHA:-}" ]; then
+            prs=$(gh api "repos/$REPO/commits/$HEAD_SHA/pulls" --jq '.[] | select(.state=="open") | .number' 2>/dev/null || true)
+          else
+            prs=$(gh pr list --repo "$REPO" --base develop --state open --json number --jq '.[].number' 2>/dev/null || true)
+          fi
+          [ -z "${prs:-}" ] && { echo "no open PRs"; exit 0; }
+          for pr in $prs; do
+            base=$(gh pr view "$pr" --repo "$REPO" --json baseRefName --jq .baseRefName 2>/dev/null || echo "")
+            [ "$base" = "develop" ] || { echo "skip #$pr (base=$base, not develop)"; continue; }
+            draft=$(gh pr view "$pr" --repo "$REPO" --json isDraft --jq .isDraft 2>/dev/null || echo true)
+            [ "$draft" = "true" ] && continue
+            pending=$(gh pr view "$pr" --repo "$REPO" --json statusCheckRollup --jq '
+              [ .statusCheckRollup[]
+                | select(((.name // .context // "") | ascii_downcase | test("codecov|readthedocs")) | not)
+                | (.conclusion // .state // "")
+                | select(. != "SUCCESS" and . != "NEUTRAL" and . != "SKIPPED" and . != "") ] | length' 2>/dev/null || echo 1)
+            if [ "$pending" = "0" ]; then
+              gh pr merge "$pr" --repo "$REPO" --merge --admin --delete-branch && echo "MERGED #$pr -> develop" || echo "blocked #$pr"
+            else
+              echo "PR #$pr not green ($pending) — skip"
+            fi
+          done

.github/workflows/cla.yml

@@ -1,10 +1,26 @@
 name: CLA Assistant
 
+# Two trigger paths:
+#   1. PRs from contributors           → CLAssistant action checks signature.
+#                                         allowlist already short-circuits to
+#                                         success for `bot*` and the repo
+#                                         owner, so owner PRs land instantly.
+#   2. Direct pushes / tag pushes      → owner-bypass job posts a synthetic
+#      by the repo owner                  `CLAssistant=success` status on the
+#                                         SHA so the release pipeline's
+#                                         sync-main step (a direct ref PATCH)
+#                                         doesn't get rejected by main's
+#                                         branch-protection rule that requires
+#                                         CLAssistant. Operator-direct: 2026-06-04.
+
 on:
   issue_comment:
     types: [created]
   pull_request_target:
     types: [opened, closed, synchronize]
+  push:
+    branches: [main, develop]
+    tags: ['v*']
 
 permissions:
   actions: write
@@ -13,14 +29,36 @@ permissions:
   statuses: write
 
 jobs:
+  owner-bypass:
+    # Fires only for direct pushes by the repo owner. PR events keep
+    # going through the full CLAssistant action below.
+    if: github.event_name == 'push' && github.actor == 'ywatanabe1989'
+    runs-on: ubuntu-latest
+    permissions:
+      statuses: write
+    steps:
+      - name: Mark CLAssistant=success on this SHA (owner-allowlisted direct push)
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          REPO: ${{ github.repository }}
+          SHA: ${{ github.sha }}
+        run: |
+          set -euo pipefail
+          gh api "repos/${REPO}/statuses/${SHA}" \
+            -f state=success \
+            -f context=CLAssistant \
+            -f description="Owner-triggered direct push (CLA bypass per repo allowlist)"
+
   CLAssistant:
+    # PR / comment path — unchanged from the pre-2026-06-04 workflow.
+    if: github.event_name != 'push'
     runs-on: ubuntu-latest
     steps:
       - name: CLA Assistant
         uses: contributor-assistant/github-action@v2.6.1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          PERSONAL_ACCESS_TOKEN: ${{ secrets.CLA_PERSONAL_ACCESS_TOKEN }}
+          PERSONAL_ACCESS_TOKEN: ${{ secrets.GH_PERSONAL_ACCESS_TOKEN }}
         with:
           path-to-signatures: "signatures/cla.json"
           path-to-document: "https://github.com/ywatanabe1989/scitex-stats/blob/main/CLA.md"
@@ -30,4 +68,4 @@ jobs:
             Thank you for signing the SciTeX CLA. Your contribution can now be reviewed.
           custom-notsigned-prcomment: |
             Please sign the [SciTeX CLA](https://github.com/ywatanabe1989/scitex-stats/blob/main/CLA.md) before your contribution can be merged.
-            Comment `I have read and agree to the SciTeX CLA.` to sign.
+            Comment `I have read and agree to the SciTeX CLA.` to sign.

CHANGELOG.md

@@ -7,6 +7,40 @@ versions follow [Semantic Versioning](https://semver.org/).
 
 ## [Unreleased]
 
+## [0.2.25] — 2026-06-07
+
+- feat: port `describe_pandas` from `scitex-gen` `misc.py` (Phase B of
+  the scitex-gen full retirement wave). The legacy symbol name was
+  `describe`, but `scitex_stats.descriptive.describe` already exists
+  with a richer torch/numpy signature; to keep both forms available
+  without a silent breakage the pandas variant is exposed here as
+  `describe_pandas` (DataFrame in, `mean_std`/`mean_ci`/`median_iqr`
+  summary dict out).
+
+## [0.2.24] — 2026-06-03
+
+### Added
+- `tests/agreement` category (new) with two inter-rater agreement scalars:
+  - `test_kendalls_w(matrix, use_abs=False)` — Kendall's coefficient of
+    concordance W ∈ [0, 1] (Kendall & Babington Smith 1939). Accepts a
+    2-D `(n_subjects, k_raters)` matrix or a long-format DataFrame with
+    `(subj, rater, score)` triples. Returns `W`, `S`, `n`, `k`, χ² and
+    p-value via the Friedman χ² approximation, plus effect-size
+    interpretation and a publication-ready `formatted` string.
+  - `test_icc(matrix, form="3,k")` — ICC (Shrout & Fleiss 1979).
+    Computes all six classical forms from one variance decomposition
+    (McGraw & Wong 1996) and surfaces the selected form at the top level;
+    F / p / df / CI / effect size / Koo & Li 2016 interpretation in the
+    result dict.
+- Top-level aliases `sts.test_kendalls_w` and `sts.test_icc` via the
+  PEP-562 lazy attribute loader.
+- 27 pytest tests in `tests/scitex_stats/tests/agreement/`.
+
+## [0.2.22]
+
+- feat(schema): publish the `scitex_stats._dataclasses` Stats schema (`_Stats.py`) — previously only on develop, which forced scitex-io's bundle to git-pin scitex-stats. Publishing it lets scitex-io depend on `scitex-stats>=0.2.22` and exercises the `.stats.zip` bundle integration on PyPI.
+- (incorporates the figrecipe-optional R4 changes merged in #43)
+
 ## [0.2.20] — 2026-05-26
 
 ### Changed

docs/sphinx/cli.rst

@@ -26,6 +26,6 @@ MCP Subcommands
 
    scitex-stats mcp start           # Start MCP server
    scitex-stats mcp doctor          # Check MCP dependencies
-   scitex-stats mcp installation    # Show installation instructions
+   scitex-stats mcp install         # Show installation instructions
    scitex-stats mcp list-tools      # List available MCP tools
    scitex-stats mcp list-tools -v   # With signatures

pyproject.toml

@@ -4,8 +4,8 @@ build-backend = "hatchling.build"
 
 [project]
 name = "scitex-stats"
-version = "0.2.21"
-description = "Publication-ready statistical testing framework with 23 tests, effect sizes, power analysis, and MCP server"
+version = "0.2.25"
+description = "Publication-ready statistical testing framework with 25 tests, effect sizes, power analysis, and MCP server"
 readme = "README.md"
 license = "AGPL-3.0-only"
 requires-python = ">=3.10"
@@ -69,6 +69,13 @@ all = [
     "figrecipe>=0.28.0",
     "torch>=2.0",
 ]
+# Stats ↔ SciTeX bundle I/O: test_result_to_stats / save_stats / load_stats
+# in scitex_stats._bundle_io require scitex-io's bundle subpackage. scitex-io
+# imports the Stats schema back from scitex_stats, so it stays an optional
+# extra (no hard/circular dep).
+bundle = [
+    "scitex-io>=0.2.16",
+]
 dev = [
     "pytest>=7.0.0",
     "pytest-cov>=4.0.0",
@@ -81,6 +88,10 @@ dev = [
     "nbconvert>=7.0",     # executes example .ipynb in tests (PS-505)
     "ipykernel>=6.0",     # kernel for nbconvert --execute
     "openpyxl>=3.1",      # pandas to_excel used by _demo_*.py
+    # Optional cross-package integrations whose tests live in the suite,
+    # so a fresh `pip install -e .[dev]` runs the full suite (PS-210).
+    "scitex-io>=0.2.16",  # [bundle] extra: stats↔bundle I/O round-trip tests
+    "figrecipe>=0.28.0",  # [all] extra: stats↔figrecipe annotation tests
     # Note: fastmcp / mcp / scitex-dev / scitex-logging / pingouin come in via [project.dependencies].
 ]
 docs = [

src/scitex_stats/__init__.py

@@ -113,6 +113,16 @@
     "run_test": "_dispatch",
     # JSON
     "to_json_safe": "_utils._serialize",
+    # Stats ↔ SciTeX bundle I/O (optional scitex-io; extra [bundle])
+    "Stats": "_integration",
+    "BUNDLE_AVAILABLE": "_integration",
+    "test_result_to_stats": "_bundle_io",
+    "save_stats": "_bundle_io",
+    "load_stats": "_bundle_io",
+    # Stats ↔ figrecipe annotations (optional figrecipe; extra [figrecipe])
+    "to_figrecipe": "_figrecipe_integration",
+    "annotate": "_figrecipe_integration",
+    "load_and_annotate": "_figrecipe_integration",
     # Auto convenience
     "StatContext": "auto",
     "StatStyle": "auto",
@@ -123,6 +133,7 @@
     "recommend_tests": "auto",
     # Descriptive
     "describe": "descriptive",
+    "describe_pandas": "descriptive",
     # Parametric (6)
     "test_ttest_ind": "tests",
     "test_ttest_rel": "tests",
@@ -151,6 +162,9 @@
     "test_normality": "tests",
     "test_ks_1samp": "tests",
     "test_ks_2samp": "tests",
+    # Agreement (2)
+    "test_kendalls_w": "tests",
+    "test_icc": "tests",
 }
 
 
@@ -203,8 +217,19 @@ def __dir__() -> list[str]:
     "available_tests",
     # Descriptive
     "describe",
+    "describe_pandas",
     # JSON serialization
     "to_json_safe",
+    # Stats ↔ SciTeX bundle I/O (optional scitex-io; extra [bundle])
+    "Stats",
+    "BUNDLE_AVAILABLE",
+    "test_result_to_stats",
+    "save_stats",
+    "load_stats",
+    # Stats ↔ figrecipe annotations (optional figrecipe; extra [figrecipe])
+    "to_figrecipe",
+    "annotate",
+    "load_and_annotate",
     # Auto convenience
     "StatContext",
     "TestRule",
@@ -241,4 +266,7 @@ def __dir__() -> list[str]:
     "test_normality",
     "test_ks_1samp",
     "test_ks_2samp",
+    # Agreement (2)
+    "test_kendalls_w",
+    "test_icc",
 ]