combaero 0.2.0__tar.gz

combaero-0.2.0/.agents/workflows/bulk-merge-workflow.md

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+# Bulk Merge Safe Updates Workflow
+
+This workflow automates the consolidation of verified Dependabot updates into the `main` branch. It ensures that only "green" and "safe" (minor/patch/grouped) updates are merged, significantly reducing manual overhead.
+
+## Prerequisites
+- GitHub CLI (`gh`) installed and authenticated.
+- Local `main` branch is clean and synchronized.
+
+## Steps
+
+### 1. Discovery & LLM Review
+The Agent (LLM) must first perform a dry-run to identify candidates and verify their safety.
+```bash
+./scripts/bulk_merge_safe.sh --dry-run
+```
+
+### 2. Safety Audit
+For each PR identified by the script, the Agent must:
+- [ ] Confirm the CI status is truly **SUCCESS**.
+- [ ] For `minor` bumps, quickly check for known breaking changes in project-critical libraries.
+- [ ] Group the candidates into a summary table for the user.
+
+### 3. User Approval
+Present the candidate table to the user. Do **NOT** proceed until the user provides explicit approval (e.g., "Proceed with merge").
+
+### 4. Execution
+Once approved, run the merger:
+```bash
+./scripts/bulk_merge_safe.sh
+```
+
+### 5. Final Sync
+The script handles the final `git pull` from `main`, but the Agent should verify the local state is up-to-date and all checks remain green on `main`.

combaero-0.2.0/.agents/workflows/commit-and-push.md

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+---
+description: Run style checks, units sync validation, commit locally, and push.
+---
+
+// turbo-all
+Follow the complete validation and commit process in [commit-local](file:///Users/thiemo/Projects/combaero/.agents/workflows/commit-local.md), then push.
+
+## Steps
+
+### 1. Follow commit-local workflow
+Execute all steps in the [commit-local](file:///Users/thiemo/Projects/combaero/.agents/workflows/commit-local.md) workflow to ensure linting, unit sync, and local commit are successful.
+
+### 2. Push to current branch
+```bash
+git push
+```

combaero-0.2.0/.agents/workflows/commit-local.md

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+---
+description: Run style checks, units sync validation, commit with message file. Do not push.
+---
+
+// turbo-all
+This workflow automates the commit process with comprehensive checks and message handling.
+
+## Steps
+
+### 1. Check for old commit message files
+```bash
+./scripts/check-commit-msg.sh
+```
+Note: If a `COMMIT_MSG.md` exists, review it and delete if stale, or keep to reuse it.
+
+### 2. Run Python formatting and linting
+```bash
+uv run ruff format python/
+uv run ruff check --fix python/
+```
+
+### 3. Run Frontend formatting and linting (Biome)
+```bash
+cd gui/frontend && npm run format && cd ../..
+```
+
+### 4. Check for units synchronization (Mandatory)
+```bash
+uv run pytest python/tests/test_units_sync.py
+```
+
+### 5. Check for non-ASCII characters in C++ source
+```bash
+./scripts/check-source-style.sh
+```
+
+### 6. Stage and run pre-commit hooks
+```bash
+git add -A
+uv run pre-commit run --all-files
+git add -A
+```
+
+### 7. Create commit message file
+Create a file named `COMMIT_MSG.md` in the project root with your commit message.
+Follow conventional commit format: `type: brief description`.
+
+### 8. Commit and cleanup
+```bash
+git commit -F COMMIT_MSG.md
+rm COMMIT_MSG.md
+```

combaero-0.2.0/.agents/workflows/create-pr.md

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+---
+description: Create a Pull Request and monitor CI status
+---
+
+// turbo-all
+This workflow automates the creation of a Pull Request using the GitHub CLI and tracks CI progress.
+
+## Steps
+
+### 1. Create Pull Request
+```bash
+gh pr create --title "type: brief description" --body-file COMMIT_MSG.md
+```
+Note: Re-use the `COMMIT_MSG.md` if available, or specify a summary.
+
+### 2. Monitor CI Status
+```bash
+gh pr view --json statusCheckRollup --jq '.statusCheckRollup[]'
+```
+
+### 3. Check specific run logs if needed
+```bash
+gh run list --limit 3
+# Then view specific run
+# gh run view <ID> --json jobs --jq '.jobs[] | {name, status, conclusion}'
+```

combaero-0.2.0/.agents/workflows/merge-and-cleanup.md

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+---
+description: Squash merge PR and cleanup branch (default for small tasks)
+---
+
+// turbo-all
+This workflow handles the final merge and cleanup. It uses squash merge by default as preferred for small task branches.
+
+## Merge Logic Selection
+- **Squash Merge (`--squash`)**: Default for small task branches, bugfixes, and feature refinements to keep history clean.
+- **Normal Merge (`--merge`)**: Used for major architectural changes or multi-contributor feature branches where preserving intermediate commit history is vital.
+
+## Steps
+
+### 1. Verification Checklist
+- [ ] All CI checks are green (confirm with `gh pr view`).
+- [ ] Any manual verification/benchmarks are completed.
+
+### 2. Execute Squash Merge (Preferred)
+```bash
+gh pr merge --squash --delete-branch
+```
+
+### 3. Alternative: Normal Merge (Major Work)
+If the work is major according to project conventions, use:
+```bash
+gh pr merge --merge --delete-branch
+```
+
+### 4. Cleanup Local Branch
+```bash
+git checkout main
+git pull
+# Local branch deletion is handled by --delete-branch if remote, but check local:
+# git branch -d <branch_name>
+```

combaero-0.2.0/.biomeignore

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+.venv/**
+build/**
+dist/**
+python/**
+src/**
+include/**
+scripts/**
+tests/**
+thermo_data_generator/**
+benchmarks/**
+cantera_validation_tests/**
+node_modules/**
+**/__pycache__/**
+**/CMakeFiles/**
+**/cmake_install.cmake
+**/CMakeCache.txt

combaero-0.2.0/.clang-tidy

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+Checks: >
+  # Start with nothing, then opt in
+  -*
+  # Core bug-finding
+  clang-diagnostic-*,
+  clang-analyzer-*,
+  bugprone-*,
+  performance-*,
+  portability-*,
+  # Good modernization for C++17
+  modernize-*,
+  # Readability and basic style
+  readability-*,
+  # A subset of C++ Core Guidelines
+  cppcoreguidelines-*,
+  # But disable rules that fight with style or are project-specific
+  -clang-diagnostic-c++17-extensions,
+  -myproject-no-system-algorithm,
+  -llvm-*,
+  -fuchsia-*,
+  -google-*,
+  -hicpp-*,
+  -zircon-*,
+  # If any of these become noisy, turn them off:
+  -cppcoreguidelines-avoid-magic-numbers,
+  -cppcoreguidelines-owning-memory,
+  -cppcoreguidelines-pro-type-reinterpret-cast,
+  -bugprone-easily-swappable-parameters,
+  -performance-avoid-endl
+
+WarningsAsErrors: ''

combaero-0.2.0/.clangd

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+CompileFlags:
+  Add: [-std=c++17]
+
+Diagnostics:
+  UnusedIncludes: None
+  Suppress:
+    - '-Wc++17-extensions'
+
+---
+
+If:
+  PathMatch: python/combaero/_core.cpp
+Diagnostics:
+  Suppress: '*'

combaero-0.2.0/.envrc

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+# direnv config for combaero (root)
+#
+# This single .envrc manages a shared virtual environment at the repository root
+# for all Python-related tasks: building the combaero wheel, running thermo_data_generator
+# scripts, and executing Python tests.
+
+# Re-run this .envrc when key files change
+watch_file .envrc
+watch_file pyproject.toml
+watch_dir python
+watch_dir thermo_data_generator
+
+VENV_DIR="$PWD/.venv"
+PYTHON_BIN="$VENV_DIR/bin/python"
+
+# 1) Create venv if missing (prefer uv, fall back to python -m venv)
+if [ ! -d "$VENV_DIR" ]; then
+  if command -v uv >/dev/null 2>&1; then
+    echo "[combaero] Creating virtualenv with uv at $VENV_DIR"
+    uv venv "$VENV_DIR"
+  else
+    echo "[combaero] uv not found, creating virtualenv with python -m venv at $VENV_DIR"
+    python3 -m venv "$VENV_DIR"
+  fi
+fi
+
+# 2) Activate venv
+export VIRTUAL_ENV="$VENV_DIR"
+export PATH="$VENV_DIR/bin:$PATH"
+
+# 3) Build-related env flags
+export COMBAERO_BUILD_PYTHON=1
+export PIP_DISABLE_PIP_VERSION_CHECK=1
+
+# 4) Auto-install dependencies via uv (once per venv)
+if command -v uv >/dev/null 2>&1; then
+  MARKER="$VENV_DIR/.uv-bootstrap-done"
+  if [ ! -f "$MARKER" ]; then
+    echo "[combaero] Bootstrapping Python dependencies via uv"
+
+    # Install core tooling: pip, build system, and pybind11 for the wheel
+    uv pip install --python "$PYTHON_BIN" pip build scikit-build-core pybind11
+
+    # Install dev dependencies (pytest)
+    uv pip install --python "$PYTHON_BIN" pytest
+
+    # Install thermo_data_generator dependencies
+    uv pip install --python "$PYTHON_BIN" pandas pyyaml
+
+    touch "$MARKER"
+    echo "[combaero] Bootstrap complete. Dependencies installed."
+  fi
+fi

combaero-0.2.0/.gitignore

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+# Build directories
+build/
+cmake-build-*/
+
+# Excluded folders
+humidair_examples/
+cantera_examples/
+temp/
+
+# IDE files
+.idea/
+.vscode/
+*.swp
+*~
+
+# Compiled objects
+*.o
+*.obj
+*.lo
+*.slo
+
+# Precompiled headers
+*.gch
+*.pch
+
+# Libraries
+*.so
+*.dylib
+*.dll
+*.a
+*.lib
+*.la
+*.lai
+
+# Fortran modules
+*.mod
+*.smod
+
+# Executables
+*.exe
+*.out
+*.app
+
+# CMake
+CMakeCache.txt
+CMakeFiles/
+*.cmake
+!CMakeLists.txt
+!.github/workflows/toolchain-mingw.cmake
+
+# macOS
+.DS_Store
+
+# Windows
+Thumbs.db
+Desktop.ini
+$RECYCLE.BIN/
+
+# Linux
+.directory
+
+# Python
+__pycache__/
+*.py[cod]
+*.pyo
+*.pyd
+.pytest_cache/
+.cache/
+dist/
+.venv/
+*.egg-info/
+
+# scikit-build-core
+_skbuild/
+-sdist/
+
+# Generated artifacts
+thermo_data_generator/test_create_cpp_header_output.txt
+thermo_data_generator/thermo_transport_data.h
+
+# Thermo data generator - source data files (not included due to licensing)
+# Users must obtain these themselves from original sources
+thermo_data_generator/*.yaml
+thermo_data_generator/*.txt
+thermo_data_generator/*.json
+!thermo_data_generator/.generator_state.json
+thermo_data_generator/*.csv
+
+# Example output (plots, data)
+examples/*.png
+examples/*.csv
+examples/*.dat
+python/examples/*.png
+python/examples/*.csv
+python/examples/*.dat
+
+# CTest
+Testing/
+tests/Testing/
+
+# Diagnostic output
+diagnostic_plots/
+diagnostic_reports/
+
+TODO.md
+.aider*
+
+# Benchmark run outputs (auto-generated, not for tracking)
+benchmarks/runs/
+benchmarks/network_solver_benchmark_latest.json
+gui/nw_*.json
+gui/tmp/

combaero-0.2.0/.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+      - id: check-merge-conflict
+
+  - repo: local
+    hooks:
+      - id: python-style-check
+        name: Python style checks (ruff + ruff format + optional mypy)
+        entry: bash -c './scripts/check-python-style.sh'
+        language: system
+        pass_filenames: false
+        files: ^(python/|cantera_validation_tests/|thermo_data_generator/)
+        stages: [pre-commit]
+
+      - id: cantera-validation-tests
+        name: Cantera Validation Tests
+        entry: bash -c 'CANTERA_DATA="$PWD/cantera_validation_tests" uv run --project cantera_validation_tests pytest -v --tb=short'
+        language: system
+        pass_filenames: false
+        always_run: false
+        files: ^(src/|include/|python/|cantera_validation_tests/)
+        stages: [pre-commit]
+
+      - id: python-unit-tests
+        name: Python Unit Tests
+        entry: bash -c 'uv run pytest python/tests/ -v'
+        language: system
+        pass_filenames: false
+        always_run: false
+        files: ^(src/|include/|python/)
+        stages: [pre-commit]
+
+      - id: thermo-header-check
+        name: Thermo/Transport Header (generated file check)
+        entry: bash -c './scripts/check-thermo-header.sh'
+        language: system
+        pass_filenames: false
+        files: ^(thermo_data_generator/|include/thermo_transport_data\.h)
+        stages: [pre-commit]
+
+      - id: common-names-check
+        name: Common names completeness check
+        entry: bash -c './scripts/check-common-names.sh'
+        language: system
+        pass_filenames: false
+        files: ^include/(thermo_transport_data|common_names)\.h$
+        stages: [pre-commit]
+
+      - id: math-constants-check
+        name: Math constants portability check (MSVC compatibility)
+        entry: .pre-commit-hooks/check_math_constants.py
+        language: system
+        files: \.(cpp|h|hpp|cc|cxx)$
+        stages: [pre-commit]
+
+  - repo: https://github.com/biomejs/pre-commit
+    rev: v0.6.1
+    hooks:
+      - id: biome-check
+        additional_dependencies: ["@biomejs/biome@2.4.9"]
+        files: ^gui/frontend/

combaero-0.2.0/.pre-commit-hooks/check_math_constants.py

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+#!/usr/bin/env python3
+"""
+Pre-commit hook to ensure M_PI and related constants are used via math_constants.h
+
+MSVC does not define M_PI by default (POSIX extension), so we must use our
+portable math_constants.h header for cross-platform compatibility.
+"""
+
+import re
+import sys
+from pathlib import Path
+
+# Constants that require math_constants.h
+MATH_CONSTANTS = [
+    "M_PI",
+    "M_PI_2",
+    "M_PI_4",
+    "M_SQRT2",
+    "M_LN10",
+]
+
+
+def check_file(filepath: Path) -> list[str]:
+    """Check if file uses math constants without including math_constants.h"""
+    errors = []
+
+    try:
+        content = filepath.read_text(encoding="utf-8")
+    except (UnicodeDecodeError, FileNotFoundError):
+        return errors
+
+    # Check if any math constants are used
+    constants_used = set()
+    for const in MATH_CONSTANTS:
+        # Match constant but not in comments or strings
+        if re.search(rf"\b{const}\b", content):
+            constants_used.add(const)
+
+    if not constants_used:
+        return errors
+
+    # Check if math_constants.h is included (matches both "math_constants.h" and "../include/math_constants.h")
+    has_include = bool(re.search(r'#include\s+[<"].*math_constants\.h[>"]', content))
+
+    if not has_include:
+        errors.append(
+            f"{filepath}: Uses {', '.join(sorted(constants_used))} "
+            f'but missing #include "math_constants.h" (required for MSVC compatibility)'
+        )
+
+    return errors
+
+
+def main():
+    """Check all C++ files passed as arguments"""
+    errors = []
+
+    for arg in sys.argv[1:]:
+        filepath = Path(arg)
+
+        # Only check C++ source/header files
+        if filepath.suffix not in {".cpp", ".h", ".hpp", ".cc", ".cxx"}:
+            continue
+
+        # Skip the math_constants.h file itself
+        if filepath.name == "math_constants.h":
+            continue
+
+        errors.extend(check_file(filepath))
+
+    if errors:
+        print("\n❌ Math constants portability check failed:\n")
+        for error in errors:
+            print(f"  {error}")
+        print(
+            '\nMSVC does not define M_PI by default. Use #include "math_constants.h" for portability.'
+        )
+        return 1
+
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())

combaero-0.2.0/.python-version

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+# Keep this version in sync with ruff.toml target-version and GitHub workflow python-version fields.
+3.12.11

combaero-0.2.0/.windsurf/workflows/biome-fix-changed.md

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+---
+description: Auto-fix issues in changed Frontend files with Biome
+---
+
+# Biome Auto-Fix Changed Files
+
+This workflow automatically fixes linting and formatting issues in all modified Frontend files using Biome.
+
+## Steps
+
+// turbo
+1. Run Biome check with --write on all changed JS/TS/CSS/JSON files
+```bash
+git status --porcelain | grep '^[AMR].*gui/frontend/.*\.\(js\|ts\|tsx\|css\|json\)$' | cut -c4- | xargs -r npx @biomejs/biome check --write --no-errors-on-unmatched --files-max-size=1000000
+```
+
+// turbo
+2. Verify all issues are fixed
+```bash
+git status --porcelain | grep '^[AMR].*gui/frontend/.*\.\(js\|ts\|tsx\|css\|json\)$' | cut -c4- | xargs -r npx @biomejs/biome check --no-errors-on-unmatched
+```
+
+## Usage
+
+Run this workflow before committing to ensure all Frontend files pass Biome checks.
+
+## Notes
+
+- Only fixes files that are Added, Modified, or Renamed (AMR status) within the `gui/frontend` directory.
+- Uses `check --write` to automatically apply formatting and safe lint fixes.
+- The `-r` flag prevents xargs from failing when no files match.
+- All steps are auto-turbo enabled for seamless execution.
+- Always review the changes after auto-fix.

combaero-0.2.0/.windsurf/workflows/commit-and-push.md

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+---
+description: Run style checks, fix issues, commit with message file, and push
+---
+
+This workflow automates the commit and push process with proper style checking and message handling.
+
+## Steps
+
+### 1-8. Complete commit workflow
+Follow all steps from @[/commit-only] workflow (check for old commit messages, stage, pre-commit, fix issues, create message file, commit, cleanup).
+
+// turbo
+### 9. Push to remote
+```bash
+git push
+```
+
+## Usage
+
+This workflow runs the complete @[/commit-only] workflow and then pushes to the remote repository.
+
+When you run this workflow, Cascade will:
+1. Run all commit-only steps (check, stage, pre-commit, fix, create message, commit, cleanup)
+2. Push to remote
+
+This avoids issues with special characters, backticks, and multi-line messages in shell commands.