Release v 1.2

.github/workflows/ci.yml

@@ -1,10 +1,11 @@
+# yaml-language-server: $schema=https://json.schemastore.org/github-workflow.json
 name: CI (Python)
 
 on:
   push:
-    branches: [ "main", "master" ]
+    branches: [ "master" ]
   pull_request:
-    branches: [ "main", "master" ]
+    branches: [ "master" ]
 
 permissions:
   contents: read
@@ -32,17 +33,12 @@ jobs:
           python-version: ${{ matrix.python-version }}
           cache: pip
           cache-dependency-path: |
-            requirements.txt
+            pyproject.toml
 
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          # Core dev tooling
-          pip install pytest pytest-cov ruff flake8
-          # Project deps
-          pip install -r requirements.txt
-          # If your package is installable (optional)
-          if [ -f pyproject.toml ] || [ -f setup.cfg ] || [ -f setup.py ]; then pip install -e .; fi
+          pip install -e ".[dev]"
 
       - name: Lint (ruff)
         run: |
@@ -54,7 +50,6 @@ jobs:
         run: |
           mkdir -p reports
           pytest -q tests \
-            --maxfail=1 \
             --disable-warnings \
             --junitxml=reports/junit.xml \
             --cov=soa_builder \

changelog/biomedical-concept-grouping_60ce0d1.md

@@ -0,0 +1,85 @@
+# Changelog: biomedical-concept-grouping
+
+**Branch:** `biomedical-concept-grouping`  
+**Base commit:** `60ce0d1`
+
+---
+
+## New Feature: Biomedical Concept Groups
+
+Introduces a global grouping mechanism for biomedical concepts. Groups are
+not SoA-specific — once created they can be associated with activities in
+any SoA.
+
+### Database Migrations (`migrate_database.py`)
+
+- `_migrate_add_concept_group_table()` — creates two new tables:
+  - `concept_group` — stores `concept_group_uid`, `name`, `label`,
+    `description`
+  - `concept_group_concept` — stores the many-to-many relationship between
+    a group and its assigned concept codes
+- `_migrate_activity_concept_add_concept_group_uid()` — adds
+  `concept_group_uid` column to `activity_concept`
+- `_migrate_surrogate_add_concept_group_uid()` — adds `concept_group_uid`
+  column to `biomedical_concept_surrogate`
+
+### New Router (`routers/concept_groups.py`)
+
+Full CRUD for concept groups, including:
+- Create, read, update, delete concept groups (API + UI endpoints)
+- Assign / unassign individual concept codes to a group
+- Link a concept group to an activity (applies all group concepts at once)
+
+### New Template (`templates/concept_groups.html`)
+
+Management page for concept groups — create groups, assign concepts, and
+view group membership.
+
+### `app.py`
+
+- Imports and runs the three new migration functions at startup
+- Registers `concept_groups_router` (both API and UI routers)
+- `_get_activity_concepts()` updated to `LEFT JOIN concept_group` and
+  return `concept_group_uid` and `group_name` alongside existing fields
+- New `_get_concept_groups_for_cell()` helper used when rendering the
+  concepts cell partial
+
+### Updated Router: `routers/activities.py`
+
+- `ui_list_activities` query branches updated to `LEFT JOIN concept_group`
+  when the `concept_group_uid` column is present
+- `concept_group_uid` and `group_name` included in the per-activity concept
+  dict
+- `concept_groups` list fetched globally and passed to the template context
+
+### Updated Router: `routers/bc_surrogates.py`
+
+- `_render_concepts_cell` updated to detect the `concept_group_uid` column
+  and include `concept_group_uid` / `group_name` in `selected_list`
+
+### Updated Templates
+
+- `templates/activities.html` — computes `activity_group_uids` (unique
+  group UIDs currently assigned to the activity) for use inside the
+  `concepts_cell.html` include
+- `templates/base.html` — adds **Biomedical Concept Groups** navigation
+  link; reorders BC-related nav items (Concepts → Categories → Groups →
+  SDTM Specializations)
+- `templates/concepts_cell.html` — updated to display assigned concept
+  groups, render group badges, and expose group-assignment controls via
+  HTMX
+
+---
+
+## CI / Tooling
+
+### `pyproject.toml`
+
+- Added `pytest-cov>=4.0.0` to the `[dev]` optional dependencies so
+  coverage reporting works in local and CI environments.
+
+### `.github/workflows/ci.yml`
+
+- Added `# yaml-language-server: $schema=…` modeline to pin the GitHub
+  Actions schema and suppress false-positive CDISC schema diagnostics
+  from the VS Code YAML extension.