updates

Author: docxology

.coverage.project

@@ -35,7 +35,7 @@ This directory contains development standards, coding guidelines, and best pract
 - Domain-independent tools
 - Reusable across projects
 - 60% minimum test coverage (currently 83.33% - exceeds stretch goal!)
-- Tests: `tests/infrastructure/`
+- Tests: `tests/infra_tests/`
 
 **Layer 2: Project** (Specific, customizable)
 - Location: `projects/{name}/src/` (project-specific code)
@@ -65,7 +65,7 @@ The template provides **two pipeline orchestrators** with different scope:
 
 **Interactive Menu (`./run.sh`)**
 - **Use for**: Full pipeline with optional LLM stages
-- **Stages**: 0-9 (stage 0 cleanup, stages 1-9 displayed as [1/9] to [9/9])
+- **Stages**: 0-9 (stage 0 cleanup, stages 1-10 displayed as [1/10] to [10/10])
 - **Features**: Interactive menu, literature search, LLM reviews, translations
 - **When to use**: builds, LLM features needed
 

.cursorrules/AGENTS.md

@@ -32,7 +32,7 @@ infrastructure/<module>/
 ### Test Organization
 
 ```
-tests/infrastructure/test_<module>/
+tests/infra_tests/test_<module>/
 ├── __init__.py
 ├── conftest.py          # Shared fixtures
 ├── test_core.py         # Core functionality tests
@@ -245,7 +245,7 @@ Infrastructure modules are integrated into the build pipeline through:
 
 **Pipeline Entry Points**: Two orchestrators available:
 - `./run.sh --pipeline`: 10 stages (0-9) with optional LLM stages (stage 0 cleanup, stages 1-9 tracked)
-- `python3 scripts/run_all.py`: 6-stage core pipeline (00-05) only
+- `python3 scripts/run_all.py`: 8-stage core pipeline (00-05) only
 
 Update these scripts to discover and use new infrastructure modules as needed.
 

.cursorrules/infrastructure_modules.md

@@ -435,16 +435,16 @@ class TestLLMIntegration:
 
 ```bash
 # Pure logic tests only (fast, no Ollama required)
-pytest tests/infrastructure/llm/ -m "not requires_ollama" -v
+pytest tests/infra_tests/llm/ -m "not requires_ollama" -v
 
 # All tests (requires running Ollama)
-pytest tests/infrastructure/llm/ -v
+pytest tests/infra_tests/llm/ -v
 
 # Integration tests only
-pytest tests/infrastructure/llm/ -m requires_ollama -v
+pytest tests/infra_tests/llm/ -m requires_ollama -v
 
 # With coverage
-pytest tests/infrastructure/llm/ --cov=infrastructure/llm --cov-report=html
+pytest tests/infra_tests/llm/ --cov=infrastructure/llm --cov-report=html
 ```
 
 ## Streaming Patterns

.cursorrules/llm_standards.md

@@ -56,7 +56,7 @@ tests/
 For each infrastructure module:
 
 ```
-tests/infrastructure/test_<module>/
+tests/infra_tests/test_<module>/
 ├── __init__.py
 ├── conftest.py                  # Fixtures: sample data, temp files
 ├── test_core.py                 # Core functionality
@@ -387,10 +387,10 @@ def logger_fixture(caplog):
 python3 -m pytest tests/
 
 # Run specific test file
-python3 -m pytest tests/infrastructure/test_core/test_basic.py
+python3 -m pytest tests/infra_tests/test_core/test_basic.py
 
 # Run specific test function
-python3 -m pytest tests/infrastructure/test_core/test_basic.py::test_validation_passes
+python3 -m pytest tests/infra_tests/test_core/test_basic.py::test_validation_passes
 
 # Run with verbose output
 python3 -m pytest tests/ -v

.cursorrules/testing_standards.md

@@ -75,3 +75,4 @@ invalid/
 
 # Separate repositories (managed independently)
 projects/cognitive_integrity/
+/projects_archive

.gitignore

@@ -24,7 +24,7 @@ This document provides documentation for the Research Project Template system, e
 **Layer 1: Infrastructure (Generic - Reusable)**
 
 - `infrastructure/` - Generic build/validation tools (reusable across projects)
-- `scripts/` - Entry point orchestrators (two pipeline options: 6-stage core or 10-stage extended)
+- `scripts/` - Entry point orchestrators (two pipeline options: 8-stage core or 10-stage extended)
 - `tests/` - Infrastructure and integration tests
 
 **Layer 2: Projects (Project-Specific - Customizable)**
@@ -82,6 +82,7 @@ The template now supports **multiple independent projects** within a single repo
 **Example Projects:**
 
 - `projects/code_project/` - Code-focused with analysis pipeline
+- `projects/blake_active_inference/` - Active inference research project
 
 **Note:** Archived projects are preserved in `projects_archive/` for reference but are not actively executed.
 
@@ -399,7 +400,7 @@ The template provides **three entry points** for pipeline execution:
 # Interactive menu with manuscript operations
 ./run.sh
 
-# Non-interactive: Extended pipeline (9 stages displayed as [1/9] to [9/9]) with optional LLM review
+# Non-interactive: Extended pipeline (10 stages displayed as [1/10] to [10/10]) with optional LLM review
 ./run.sh --pipeline
 ```
 
@@ -412,13 +413,13 @@ python3 scripts/execute_pipeline.py --project code_project --core-only
 
 **Entry Point Comparison**
 
-- **`./run.sh`**: Main entry point - Interactive menu or extended pipeline (9 stages), includes optional LLM review stages. Stages are displayed as [1/9] to [9/9] in logs.
-- **`./run.sh --pipeline`**: 9 stages, includes optional LLM review stages. Stages are displayed as [1/9] to [9/9] in logs.
+- **`./run.sh`**: Main entry point - Interactive menu or extended pipeline (10 stages), includes optional LLM review stages. Stages are displayed as [1/10] to [10/10] in logs.
+- **`./run.sh --pipeline`**: 10 stages, includes optional LLM review stages. Stages are displayed as [1/10] to [10/10] in logs.
 - **`python3 scripts/execute_pipeline.py --core-only`**: Core pipeline only (no LLM).
 
 ### Pipeline Stages
 
-**Full Pipeline Stages** (displayed as [1/9] to [9/9] in logs):
+**Full Pipeline Stages** (displayed as [1/10] to [10/10] in logs):
 
 1. **Clean Output Directories** - Clean working and final output directories
 2. **Environment Setup** - Verify system requirements and dependencies
@@ -442,7 +443,7 @@ python3 scripts/execute_pipeline.py --project code_project --core-only
 
 **Stage Numbering:**
 
-- `./run.sh`: 9 stages displayed as [1/9] to [9/9] in progress logs
+- `./run.sh`: 10 stages displayed as [1/10] to [10/10] in progress logs
 - `scripts/execute_pipeline.py`: Core vs full pipeline is selected by flags (no fixed stage numbering in filenames)
 
 ### Manual Execution Options
@@ -533,7 +534,7 @@ python3 -m infrastructure.validation.cli markdown projects/code_project/manuscri
 python3 scripts/01_run_tests.py --project code_project
 
 # Or run manually with coverage reports
-python3 -m pytest tests/infrastructure/ --cov=infrastructure --cov-report=html
+python3 -m pytest tests/infra_tests/ --cov=infrastructure --cov-report=html
 python3 -m pytest projects/code_project/tests/ --cov=projects/code_project/src --cov-report=html
 ```
 
@@ -672,7 +673,7 @@ python3 scripts/01_run_tests.py
 python3 -m pytest projects/code_project/tests/test_example.py -v
 
 # Infrastructure tests with coverage
-python3 -m pytest tests/infrastructure/ --cov=infrastructure --cov-report=html
+python3 -m pytest tests/infra_tests/ --cov=infrastructure --cov-report=html
 
 # Project tests with coverage
 python3 -m pytest projects/code_project/tests/ --cov=projects/code_project/src --cov-report=html
@@ -982,7 +983,7 @@ python3 -m infrastructure.validation.cli pdf output/code_project/pdf/
 python3 scripts/01_run_tests.py
 
 # Or run individually with coverage reports
-python3 -m pytest tests/infrastructure/ --cov=infrastructure --cov-fail-under=49
+python3 -m pytest tests/infra_tests/ --cov=infrastructure --cov-fail-under=49
 python3 -m pytest projects/code_project/tests/ --cov=projects/code_project/src --cov-fail-under=70
 ```
 
@@ -1255,7 +1256,7 @@ See [`docs/operational/CHECKPOINT_RESUME.md`](docs/operational/CHECKPOINT_RESUME
 - ✅ Zero mock methods - all tests use data and HTTP calls
 - ✅ All .cursorrules standards implemented
 - ✅ compliance with thin orchestrator pattern
-- ✅ Production-ready build pipeline (6-stage core, 10-stage extended)
+- ✅ Production-ready build pipeline (8-stage core, 10-stage extended)
 - ✅ Reproducible outputs (deterministic with fixed seeds)
 - ✅ Graceful degradation for optional features
 - ✅ Multi-project support (projects/{name}/ structure)

AGENTS.md

@@ -24,10 +24,10 @@ This is a research project template with a test-driven development workflow, aut
 # Interactive menu (recommended)
 ./run.sh
 
-# Full pipeline (9 stages: clean, setup, tests, analysis, render, validate, LLM review, LLM translations, copy)
+# Full pipeline (10 stages: clean, setup, infra tests, project tests, analysis, render, validate, LLM review, LLM translations, copy)
 ./run.sh --pipeline
 
-# Core pipeline only (6 stages: no LLM)
+# Core pipeline only (8 stages: no LLM)
 python3 scripts/execute_pipeline.py --project {project_name} --core-only
 
 # Resume from checkpoint
@@ -40,16 +40,16 @@ python3 scripts/execute_pipeline.py --project {project_name} --core-only
 python3 scripts/01_run_tests.py --project {project_name}
 
 # Infrastructure tests only (60% coverage minimum)
-uv run pytest tests/infrastructure/ --cov=infrastructure --cov-fail-under=60
+uv run pytest tests/infra_tests/ --cov=infrastructure --cov-fail-under=60
 
 # Project tests only (90% coverage minimum)
 uv run pytest projects/{project_name}/tests/ --cov=projects/{project_name}/src --cov-fail-under=90
 
 # Run specific test file
-uv run pytest tests/infrastructure/test_specific.py -v
+uv run pytest tests/infra_tests/test_specific.py -v
 
 # Run single test function
-uv run pytest tests/infrastructure/test_specific.py::test_function_name -v
+uv run pytest tests/infra_tests/test_specific.py::test_function_name -v
 
 # Coverage files are isolated per suite (.coverage.infra, .coverage.project)
 ```
@@ -89,7 +89,7 @@ python3 scripts/execute_multi_project.py --no-llm
 python3 -c "from infrastructure.project.discovery import discover_projects; from pathlib import Path; print([p.name for p in discover_projects(Path('.'))])"
 ```
 
-**Active projects:** `code_project`
+**Active projects:** `code_project`, `blake_active_inference`
 **Archived projects:** Located in `projects_archive/` (not executed by pipeline)
 
 ## Architecture
@@ -150,7 +150,7 @@ avg = calculate_average(data)  # Use tested method
 - **`projects/`** - Active projects (discovered and executed by infrastructure)
 - **`projects_archive/`** - Archived projects (preserved but not executed)
 
-**Current active projects:** `code_project`
+**Current active projects:** `code_project`, `blake_active_inference`
 
 To archive: `mv projects/{name}/ projects_archive/{name}/`
 To reactivate: `mv projects_archive/{name}/ projects/{name}/`
@@ -190,19 +190,21 @@ output/
 
 ## Pipeline Stages
 
-### Core Pipeline (Stages 1-7)
-1. **Setup Environment** - Validate dependencies, discover projects (not shown in progress)
-2. **Infrastructure Tests** - Run infrastructure test suite (may be skipped, not shown in progress)
-3. **Run Tests** - Project test suite (90% coverage minimum)
-4. **Run Analysis** - Execute `projects/{name}/scripts/` to generate figures/data
-5. **Render PDF** - Convert markdown to professional PDFs
-6. **Validate Output** - Quality checks on PDFs and content
-7. **Copy Outputs** - Copy final deliverables to `output/<name>/`
+### Core Pipeline (8 stages)
+1. **Clean Output Directories** - Remove previous outputs for a fresh run
+2. **Setup Environment** - Validate dependencies, discover projects
+3. **Infrastructure Tests** - Run infrastructure test suite (may be skipped)
+4. **Project Tests** - Project test suite (90% coverage minimum)
+5. **Run Analysis** - Execute `projects/{name}/scripts/` to generate figures/data
+6. **Render PDF** - Convert markdown to professional PDFs
+7. **Validate Output** - Quality checks on PDFs and content
+8. **Copy Outputs** - Copy final deliverables to `output/<name>/`
 
-### Extended Pipeline (Stages 8-10, Optional)
-8. **LLM Scientific Review** - Requires Ollama (executive summary, quality review, methodology review, improvement suggestions)
-9. **LLM Translations** - Multi-language abstract translations (configure in `config.yaml`)
-10. **Executive Report** - Cross-project metrics and dashboards (multi-project mode only)
+### Extended Pipeline (Stages 9-10, Optional)
+9. **LLM Scientific Review** - Requires Ollama (executive summary, quality review, methodology review, improvement suggestions)
+10. **LLM Translations** - Multi-language abstract translations (configure in `config.yaml`)
+
+**Note:** Executive Report (cross-project metrics and dashboards) runs automatically in multi-project mode when 2+ projects are executed.
 
 ## Testing Requirements
 
@@ -227,11 +229,11 @@ output/
 python3 scripts/01_run_tests.py --project {project_name}
 
 # With coverage report
-uv run pytest tests/infrastructure/ --cov=infrastructure --cov-report=html
+uv run pytest tests/infra_tests/ --cov=infrastructure --cov-report=html
 uv run pytest projects/{name}/tests/ --cov=projects/{name}/src --cov-report=html
 
 # Specific test
-uv run pytest tests/infrastructure/test_specific.py::test_function -v
+uv run pytest tests/infra_tests/test_specific.py::test_function -v
 ```
 
 ## Configuration
@@ -277,7 +279,7 @@ export PYTHONPATH=".:infrastructure:projects/code_project/src"
 ## Development Workflow
 
 ### Adding Features
-1. Write tests first (TDD) in `projects/{name}/tests/` or `tests/infrastructure/`
+1. Write tests first (TDD) in `projects/{name}/tests/` or `tests/infra_tests/`
 2. Implement in `projects/{name}/src/` or `infrastructure/`
 3. Ensure coverage requirements met
 4. Update documentation if needed