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Documentation - update mapping tables#249

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jdecarolis wants to merge 515 commits intomainfrom
doc_mapping
Closed

Documentation - update mapping tables#249
jdecarolis wants to merge 515 commits intomainfrom
doc_mapping

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@jdecarolis jdecarolis commented Jan 12, 2026

This PR updates the tables and descriptions associated with Temoa sets and parameters, which include the mapping between database tables and code elements.

Summary by CodeRabbit

  • New Features

    • Added network graph visualization for energy system models.
    • Introduced new model configuration parameters (time_sequencing, reserve_margin).
    • Added example database schemas for materials, seasonal storage, and survival curve models.
  • Documentation

    • Comprehensive documentation overhaul with quick start guides, mathematical formulation, and computational implementation details.
    • Updated README to v4.0.0a1 with simplified installation and usage instructions.
    • Added unit checking and visualization guides.
  • Build & Configuration

    • Migrated package management from conda to uv-based workflow.
    • Added pre-commit hooks for code quality.
    • Added GitHub Actions CI/CD and nightly deployment pipelines.

✏️ Tip: You can customize this high-level summary in your review settings.

ParticularlyPythonicBS and others added 26 commits December 11, 2025 15:35
Co-authored-by: Jeff-ws <jeff@westernspark.us>
Update preface and quick start guide
Co-authored-by: jdecarolis <jdecarolis@cmu.edu>
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coderabbitai bot commented Jan 12, 2026

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Review failed

The pull request is closed.

Walkthrough

This PR introduces comprehensive project infrastructure and documentation modernization, including new configuration systems (CodeRabbit, pre-commit, ReadTheDocs), GitHub Actions workflows for CI and nightly deployment automation, extensive documentation overhaul with mathematical formulation and visualization guides, multiple database schema examples with SQL initialization, and removal of legacy configuration approaches.

Changes

Cohort / File(s) Summary
GitHub Configuration & CI
.github/workflows/ci.yml, .github/workflows/deploy-nightly.yml, .github/scripts/deploy_nightly_pypi.py
Adds matrix-based CI pipeline (ubuntu/macos/windows, Python 3.12/3.13) with pytest and mypy type-checking; introduces nightly deployment workflow with scheduled triggers and conditional artifact publishing to Cloudflare R2 and GitHub Pages via dumb-pypi index.
GitHub Issue Templates
.github/ISSUE_TEMPLATE/bug_report.md, .github/ISSUE_TEMPLATE/feature_request.md, .github/ISSUE_TEMPLATE/question.md
Adds three structured issue templates with YAML front-matter (labels, assignees, title defaults) and markdown sections to guide users in reporting bugs, requesting features, and asking questions.
Project Configuration
.coderabbit.yaml, .pre-commit-config.yaml, .readthedocs.yaml
Introduces CodeRabbit linting/review settings with nested configurations for reviews, chat, knowledge base, and tool integrations; adds pre-commit hooks (uv-lock, pip-compile, ruff, pyupgrade, standard checks); configures Read the Docs build (ubuntu-24.04, Python 3.13, Sphinx).
Git Configuration
.gitattributes, .gitignore
Enables LF line endings for text files and marks binary types; restructures .gitignore from granular ignores to blanket root ignore with explicit unignore rules for tracked directories/files.
Root Configuration & Metadata
CITATION.cff, .pre-commit-config.yaml.yml (removed)
Adds citation metadata (authors, journal, DOI); removes old pre-commit config block.
Database Schemas
data_files/example_dbs/materials.sql, data_files/example_dbs/seasonal_storage.sql, data_files/example_dbs/survival_curve.sql, data_files/temoa_basics_0.sql, data_files/temoa_basics_1.sql, data_files/temoa_basics_2.sql, data_files/temoa_schema_v3_1.sql, data_files/temoa_schema_v4.sql
Introduces eight comprehensive SQL schema files with transactional DDL, foreign keys, CHECK constraints, and seed data for capacity, costs, demand, efficiency, emissions, limits, operations, and outputs; schemas support multiple modeling approaches (seasonal storage, survival curves, materials).
Configuration Examples
data_files/my_configs/config_sample.toml, data_files/my_configs/materials.toml, data_files/my_configs/seasonal_storage.toml, data_files/my_configs/mga_utopia.toml, data_files/my_configs/monte_carlo_utopia.toml, data_files/my_configs/morris_utopia.toml, data_files/my_configs/stepped_demand.toml
Adds/updates seven TOML configuration examples with run metadata, solver settings, outputs, time sequencing, reserve margin, and mode-specific parameters (MGA, myopic, morris, SVMGA, monte_carlo).
Documentation: Core Files
README.md, docs/README.md, docs/source/index.rst
Overhauls README with version 4.0.0a1, Quick Start (uv-based installation), programmatic usage examples, CLI guidance, database setup, and typical workflow; updates docs/README with detailed build instructions and uv workflows; adds unit_checking to toctree.
Documentation: Technical Guides
docs/source/preface.rst, docs/source/quick_start.rst, docs/source/computational_implementation.rst, docs/source/mathematical_formulation.rst, docs/source/db_model_comparison.rst, docs/source/unit_checking.rst, docs/source/visualization.rst
Adds seven comprehensive documentation files covering project overview, quick start installation, computational implementation (Pyomo, code style guide), detailed mathematical formulation (sets, parameters, constraints), database-to-model mapping, unit checking system, and Graphviz visualization workflows.
Documentation: Reference & Updates
docs/Database Upgrade and Troubleshooting.md, docs/commodity network notes.md, docs/source/conf.py, docs/automake.sh
Updates reference docs with snake_case naming conventions; refines Sphinx config to read metadata from pyproject.toml, support Markdown via myst_parser, and suppress warnings; removes GPL header from automake.sh.
Visualization Assets
docs/source/default/static/graph_script.js, docs/source/default/static/graph_styles.css, docs/source/default/static/Network_Graph_utopia_1990.html, docs/source/images/graphviz_examples/Network_Graph_utopia_1990.html
Adds interactive network graph visualization using Vis.js with sector filtering, regex search, neighborhood focus, primary/secondary view toggling, and CSS styling for config panels, legends, and controls.
Removed Files
definitions.py, main.py, environment.yml, environment_minimal.yml
Eliminates PROJECT_ROOT/OUTPUT_PATH globals and accessors; removes CLI entry point with argparse setup, logging, output folder creation; deletes conda environment specifications in favor of uv/pip workflows.

Estimated code review effort

🎯 4 (Complex) | ⏱️ ~75 minutes

Rationale: Large heterogeneous diff (50\+ files) spanning multiple domains: infrastructure (workflows, configs), extensive SQL schemas (8 files, 5000\+ lines), comprehensive documentation (7 new files, 3500\+ lines), visualization components (JS/CSS/HTML), configuration examples, and legacy file removals. Requires separate reasoning for each cohort to verify consistency (schema constraints, config option alignment, doc accuracy) and validate removal impact (dependency checks on removed definitions.py/main.py). High volume of additions and structural changes demand careful cross-file consistency verification.

Possibly related PRs

Suggested labels

docs, ci, database, configuration, infrastructure, refactor

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Reviewing files that changed from the base of the PR and between 7d78f29 and 9204f31.

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@jdecarolis jdecarolis closed this Jan 12, 2026
@jdecarolis jdecarolis deleted the doc_mapping branch January 12, 2026 13:22
@jdecarolis jdecarolis restored the doc_mapping branch January 12, 2026 13:25
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