test+ci: add 192 tests across 9 modules, fix dep hygiene, add codecov badge

Add comprehensive unit tests for 9 previously-uncovered modules:
- auth/token_manager.py (56% -> 95.76%, 30 tests)
- database/crud.py (44% -> 98.50%, 53 tests)
- schemas/industry_standards.py + storage.py (0% -> 100%, 12 tests)
- utils/automatic_labeling.py (6% -> 96.22%, 30 tests)
- utils/person_identity.py (18% -> 94.67%, 43 tests)
- pipelines/face_analysis/openface_compatibility.py (0% -> 94.37%, 24 tests)

Also: move pytest/pytest-asyncio from runtime to dev-only deps,
add Codecov badge to README, update JOSS checklist.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: InfantLab

README.md

@@ -6,6 +6,7 @@
 [![uv](https://img.shields.io/badge/uv-package%20manager-FF4B4B?logo=uv&logoColor=white)](https://github.com/astral-sh/uv)
 [![Docker](https://img.shields.io/badge/Docker-GPU%20Ready-2496ED?logo=docker&logoColor=white)](https://docs.docker.com/)
 [![CI](https://github.com/InfantLab/VideoAnnotator/actions/workflows/ci-cd.yml/badge.svg)](https://github.com/InfantLab/VideoAnnotator/actions/workflows/ci-cd.yml)
+[![codecov](https://codecov.io/gh/InfantLab/VideoAnnotator/branch/master/graph/badge.svg)](https://codecov.io/gh/InfantLab/VideoAnnotator)
 [![Ask DeepWiki](https://deepwiki.com/badge.svg)](https://deepwiki.com/InfantLab/VideoAnnotator)
 
 **Automated video analysis toolkit for human interaction research** - Extract comprehensive behavioral annotations from videos using AI pipelines, with an intuitive web interface for visualization and analysis.
@@ -343,7 +344,13 @@ MIT License - Full terms in [LICENSE](LICENSE)
 
 ### **Research Team**
 
-- **Caspar Addyman** (infantologist@gmail.com) - Lead Developer & Research Director
+- **Caspar Addyman** - Stellenbosch University, South Africa [![ORCID](https://img.shields.io/badge/ORCID-0000--0003--0001--9548-green)](https://orcid.org/0000-0003-0001-9548) — Lead Developer & Corresponding Author
+- **Jeremiah Ishaya** - Stellenbosch University, South Africa [![ORCID](https://img.shields.io/badge/ORCID-0000--0002--9014--9372-green)](https://orcid.org/0000-0002-9014-9372)
+- **Irene Uwerikowe** - Stellenbosch University, South Africa [![ORCID](https://img.shields.io/badge/ORCID-0000--0002--1293--7349-green)](https://orcid.org/0000-0002-1293-7349)
+- **Daniel Stamate** - Department of Computing, Goldsmiths, University of London, UK [![ORCID](https://img.shields.io/badge/ORCID-0000--0001--8565--6890-green)](https://orcid.org/0000-0001-8565-6890)
+- **Jamie Lachman** - Department of Social Policy and Intervention, University of Oxford, UK [![ORCID](https://img.shields.io/badge/ORCID-0000--0001--9475--9218-green)](https://orcid.org/0000-0001-9475-9218)
+- **Mark Tomlinson** - Stellenbosch University, South Africa [![ORCID](https://img.shields.io/badge/ORCID-0000--0001--5846--3444-green)](https://orcid.org/0000-0001-5846-3444)
+
 
 ### **Open Source Dependencies**
 

docs/development/joss_testing_ci_polish.md

@@ -21,15 +21,15 @@ Created 2026-02-27 based on coverage analysis of v1.4.1.
 
 ### 1.3 Auth and data layer gaps (44–56% coverage)
 
-- [ ] **`auth/token_manager.py`** — 141 lines, 56% coverage. JWT create/verify/refresh logic. Estimated +40–60 lines covered.
-- [ ] **`database/crud.py`** — 166 lines, 44% coverage. CRUD operations, testable with in-memory SQLite. Estimated +50–80 lines covered.
+- [x] **`auth/token_manager.py`** — 141 lines, 56% -> 95.76%. Tests in `tests/unit/auth/test_token_manager.py` (30 tests). JWT generation/validation tested directly; API key paths tested with mocks.
+- [x] **`database/crud.py`** — 166 lines, 44% -> 98.50%. Tests in `tests/unit/database/test_crud.py` (53 tests). Full CRUD coverage using in-memory SQLite (UserCRUD, APIKeyCRUD, JobCRUD).
 
 ### 1.4 Other notable gaps
 
-- [ ] **`utils/automatic_labeling.py`** — 156 lines, 6% coverage.
-- [ ] **`utils/person_identity.py`** — 163 lines, 18% coverage.
-- [ ] **`pipelines/face_analysis/openface_compatibility.py`** — 69 lines, 0% coverage.
-- [ ] **`schemas/industry_standards.py`** + **`schemas/storage.py`** — 21 lines total, 0% coverage.
+- [x] **`utils/automatic_labeling.py`** — 156 lines, 6% -> 96.22%. Tests in `tests/unit/utils/test_automatic_labeling.py` (30 tests). Size-based, position-based, temporal consistency, and spatial analysis all covered.
+- [x] **`utils/person_identity.py`** — 163 lines, 18% -> 94.67%. Tests in `tests/unit/utils/test_person_identity.py` (35 tests). Full lifecycle: registration, labeling, IoU, face linking, save/load round-trip, label normalization.
+- [x] **`pipelines/face_analysis/openface_compatibility.py`** — 69 lines, 0% -> 94.37%. Tests in `tests/unit/pipelines/test_openface_compatibility.py` (24 tests). All 7 compatibility classes, scipy patching, model paths.
+- [x] **`schemas/industry_standards.py`** + **`schemas/storage.py`** — 21 lines total, 0% -> 100%. Tests in `tests/unit/schemas/test_schemas.py` (12 tests).
 
 ### 1.5 Lower priority (large modules, harder to unit-test)
 
@@ -73,14 +73,14 @@ All actions bumped in ci-cd.yml:
 
 ### 2.5 Dependency hygiene
 
-- [ ] **Move `pytest` and `pytest-asyncio` from `[project.dependencies]` to dev-only** — they are runtime test deps shipped to end users today.
+- [x] **Move `pytest` and `pytest-asyncio` from `[project.dependencies]` to dev-only** — removed from runtime deps, added `pytest>=8.3.2` to `[dependency-groups] dev`.
 
 ---
 
 ## 3. Metadata Fixes
 
 - [x] **Fix `project.urls`** in pyproject.toml — updated to `InfantLab/VideoAnnotator`.
-- [ ] **Add Codecov badge** to README.md.
+- [x] **Add Codecov badge** to README.md.
 
 ---
 
@@ -102,3 +102,7 @@ All actions bumped in ci-cd.yml:
 | 2026-02-27 | Fixed all 82 ruff lint errors (31 autofix + 51 manual) | — |
 | 2026-02-27 | CI: broadened ruff rules, un-gated mypy, un-gated integration tests, added coverage threshold, bumped all action versions | — |
 | 2026-02-27 | Fixed project.urls to point to InfantLab/VideoAnnotator | — |
+| 2026-02-27 | Added tests for token_manager, crud, schemas (3 new test files, 95 new tests) | 51.97% -> ~55% (est.) |
+| 2026-02-27 | Moved pytest/pytest-asyncio from runtime to dev-only deps | — |
+| 2026-02-27 | Added Codecov badge to README.md | — |
+| 2026-02-27 | Added tests for automatic_labeling, person_identity, openface_compatibility (3 new test files, 97 new tests) | ~55% -> ~58% (est.) |

pyproject.toml

@@ -37,7 +37,7 @@ dependencies = [
     "openpyxl",
     "pandas>=2.2.2",
     "Pillow>=10.4.0",
-    "pytest>=8.3.2",
+    # Note: pytest moved to [dependency-groups] dev — not needed at runtime
     "python-dotenv>=1.0.1",
     # Pin NumPy below 2.0 until all binary deps (scipy, matplotlib, pyannote, etc.) ship compatible wheels
     "numpy>=1.24.0,<2.0",
@@ -98,8 +98,7 @@ dependencies = [
     "uvicorn[standard]>=0.30.0",
     "python-multipart>=0.0.9",
     "psutil>=5.9.0",
-    # Async test support (pytest 8 compatible)
-    "pytest-asyncio>=0.23.6",
+    # Note: pytest-asyncio moved to [dependency-groups] dev — not needed at runtime
     # Configuration and utilities
     "pyyaml>=6.0.0",
     "rich>=13.0.0",
@@ -305,8 +304,9 @@ dev = [
     "mypy>=1.5.0",
     "pre-commit>=4.3.0",
     "pydocstyle>=6.3.0",
-    "pytest-cov>=4.0.0",
+    "pytest>=8.3.2",
     "pytest-asyncio>=1.1.0",
+    "pytest-cov>=4.0.0",
     "ruff>=0.14.0",
 ]